Revert "c++11"

This reverts commit a4991cf.

Makefile

@@ -4,7 +4,7 @@
 #  and documentation
 # make coverage-report to check coverage of the python scripts by the tests
 
-CPPSOURCES=$(wildcard lib/*.cc lib/*.hh khmer/_khmermodule.cc) setup.py
+CPPSOURCES=$(wildcard lib/*.cc lib/*.hh khmer/_khmermodule.cc)
 PYSOURCES=$(wildcard khmer/*.py scripts/*.py)
 SOURCES=$(PYSOURCES) $(CPPSOURCES) setup.py
 DEVPKGS=sphinxcontrib-autoprogram pep8==1.5 diff_cover \
@@ -24,8 +24,7 @@ khmer/_khmermodule.so: $(CPPSOURCES)
 	./setup.py build_ext --inplace
 
 coverage-debug: $(CPPSOURCES)
-	export CFLAGS="-pg -fprofile-arcs -ftest-coverage -O0 \
-		-D_GLIBCXX_DEBUG_PEDANTIC -D_GLIBCXX_DEBUG"; ./setup.py \
+	export CFLAGS="-pg -fprofile-arcs -ftest-coverage -O0"; ./setup.py \
 		build_ext --debug --inplace --libraries gcov
 	touch coverage-debug
 
@@ -47,8 +46,8 @@ clean: FORCE
 	rm -Rf .coverage || true
 
 debug: FORCE
-	export CFLAGS="-pg -fprofile-arcs -D_GLIBCXX_DEBUG_PEDANTIC \
-		-D_GLIBCXX_DEBUG"; python setup.py build_ext --debug --inplace
+	export CFLAGS="-pg -fprofile-arcs"; python setup.py build_ext --debug \
+		--inplace
 
 doc: build/sphinx/html/index.html
 
@@ -69,13 +68,13 @@ build/sphinx/latex/khmer.pdf: $(SOURCES) doc/conf.py $(wildcard doc/*.txt)
 cppcheck-result.xml: $(CPPSOURCES)
 	ls lib/*.cc khmer/_khmermodule.cc | grep -v test | cppcheck -DNDEBUG \
 		-DVERSION=0.0.cppcheck -UNO_UNIQUE_RC --enable=all \
-		--file-list=- -j8 --platform=unix64 --std=c++11 --xml \
+		--file-list=- -j8 --platform=unix64 --std=posix --xml \
 		--xml-version=2 2> cppcheck-result.xml
 
 cppcheck: $(CPPSOURCES)
 	ls lib/*.cc khmer/_khmermodule.cc | grep -v test | cppcheck -DNDEBUG \
 		-DVERSION=0.0.cppcheck -UNO_UNIQUE_RC --enable=all \
-		--file-list=- -j8 --platform=unix64 --std=c++11 --quiet
+		--file-list=- -j8 --platform=unix64 --std=posix --quiet
 
 pep8: $(PYSOURCES) $(wildcard tests/*.py)
 	pep8 --exclude=_version.py setup.py khmer/ scripts/ tests/ || true

lib/counting.cc

@@ -228,12 +228,12 @@ void CountingHash::fasta_dump_kmers_by_abundance(
             for (unsigned int i = 0; i < seq.length() - _ksize + 1; i++) {
                 string kmer = seq.substr(i, i + _ksize);
                 BoundedCounterType n = get_count(kmer.c_str());
-                char * ss = new char[_ksize + 1];
+                char ss[_ksize + 1];
                 strncpy(ss, kmer.c_str(), _ksize);
                 ss[_ksize] = 0;
 
                 if (n == limit_by_count) {
-                    cout << &ss << endl;
+                    cout << ss << endl;
                 }
             }
         }

lib/counting.hh

@@ -271,7 +271,7 @@ class CountingHashGzFileWriter : public CountingHashFile
 public:
     CountingHashGzFileWriter(const std::string &outfilename, const CountingHash &ht);
 };
-}
+};
 
 #endif // COUNTING_HH
 

lib/hashbits.hh

@@ -229,7 +229,7 @@ public:
         return 1;
     }
 };
-}
+};
 
 #include "counting.hh"
 #include "labelhash.hh"

lib/hashtable.hh

@@ -559,7 +559,7 @@ public:
         return kmer_degree(kmer_f, kmer_r);
     }
 };
-}
+};
 
 
 

lib/kmer_hash.cc

@@ -94,4 +94,4 @@ std::string _revhash(HashIntoType hash, WordLength k)
 }
 
 
-}
+};

lib/kmer_hash.hh

@@ -73,6 +73,6 @@ HashIntoType _hash(const char * kmer, const WordLength k,
 HashIntoType _hash_forward(const char * kmer, WordLength k);
 
 std::string _revhash(HashIntoType hash, WordLength k);
-}
+};
 
 #endif // KMER_HASH_HH

lib/labelhash.hh

@@ -147,7 +147,7 @@ public:
                                      LabelPtrSet& found_labels);
 
 };
-}
+};
 
 #define ACQUIRE_TAG_COLORS_SPIN_LOCK \
   while(!__sync_bool_compare_and_swap( &_tag_labels_spin_lock, 0, 1));

lib/read_parsers.cc

@@ -8,7 +8,6 @@
 #include <cstdlib>
 #include <cstring>
 #include <cstdio>
-#include <stdexcept>
 
 #include <sys/types.h>
 #include <sys/stat.h>
@@ -1593,15 +1592,10 @@ _parse_read( ParserState &state, Read &the_read )
     );
 #endif
     the_read.bytes_consumed += (line.length( ) + 1);
-    try {
-        if ('>' != line.at(0))
-            throw InvalidFASTAFileFormat(
-                "invalid sequence name indicator", line.c_str( )
-            );
-    }
-    catch (std::out_of_range oor) {
-        throw InvalidFASTAFileFormat("invalid sequence name identifiter", line.c_str( ) );
-    }
+    if ('>' != line[ 0 ])
+        throw InvalidFASTAFileFormat(
+            "invalid sequence name indicator", line.c_str( )
+        );
     the_read.name = line.substr( 1 );
 
     // Grab sequence lines until exit conditions are met.
@@ -1616,11 +1610,8 @@ _parse_read( ParserState &state, Read &the_read )
 #endif
 
         // If a new record is detected, then existing one is complete.
-        try {
-            if ('>' == line.at(0)) {
-                break;
-            }
-        } catch (std::out_of_range oor) {
+        if ('>' == line[ 0 ]) {
+            break;
         }
 
         // TODO? Uppercase and validate entire sequence here.
@@ -1670,15 +1661,10 @@ _parse_read( ParserState &state, Read &the_read )
     );
 #endif
     the_read.bytes_consumed += (line.length( ) + 1);
-    try {
-        if ('@' != line.at(0))
-            throw InvalidFASTQFileFormat(
-                "invalid sequence name indicator", line.c_str( )
-            );
-    } catch (std::out_of_range oor) {
-        throw InvalidFASTQFileFormat("invalid sequence name indicator",
-                                     line.c_str() );
-    }
+    if ('@' != line[ 0 ])
+        throw InvalidFASTQFileFormat(
+            "invalid sequence name indicator", line.c_str( )
+        );
     the_read.name = line.substr( 1 );
 
     // Grab sequence lines until exit conditions are met.

lib/subset.cc

@@ -1623,12 +1623,12 @@ unsigned long long SubsetPartition::repartition_largest_partition(
 
     // find biggest.
     PartitionCountDistribution::const_iterator di = d.end();
-    if (di == d.begin()) {
+    --di;
+
+    if (d.empty()) {
         throw khmer_exception();
     }
 
-    --di;
-
     for (PartitionCountMap::const_iterator cmi = cm.begin(); cmi != cm.end();
             ++cmi) {
         if (cmi->second == di->first) {
@@ -1641,13 +1641,14 @@ unsigned long long SubsetPartition::repartition_largest_partition(
 
 #if VERBOSE_REPARTITION
     std::cout << "biggest partition: " << di->first << "\n";
+#endif // 0
+    --di;
+
+#if VERBOSE_REPARTITION
     std::cout << "biggest partition ID: " << biggest_p << "\n";
 #endif // 0
 
-    if (di != d.begin()) {
-        --di;
-        next_largest = di->first;
-    }
+    next_largest = di->first;
 
 #if VERBOSE_REPARTITION
     std::cout << "next biggest partition: " << di->first << "\n";

setup.py

@@ -57,7 +57,7 @@
     "read_parsers", "kmer_hash", "hashtable", "hashbits", "labelhash",
     "counting", "subset", "read_aligner"])
 
-EXTRA_COMPILE_ARGS = ['-O3', '-std=c++0x', '-pedantic' ]
+EXTRA_COMPILE_ARGS = ['-O3']
 
 if sys.platform == 'darwin':
     EXTRA_COMPILE_ARGS.extend(['-arch', 'x86_64'])  # force 64bit only builds