Changes to enable CMake compilation

bioinfologics · Mar 9, 2016 · 04ca14b · 04ca14b
1 parent f0e3c78
commit 04ca14b
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Showing 37 changed files with 98 additions and 97 deletions.
diff --git a/analysis/AlignProbability.cc b/analysis/AlignProbability.cc
@@ -3,8 +3,8 @@
 #define NDEBUG
 #endif
 
-#include "analysis/AlignProbability.h"
-#include "analysis/DNAVector.h"
+#include "AlignProbability.h"
+#include "DNAVector.h"
 
 #include <math.h>
 

diff --git a/analysis/Blosum.h b/analysis/Blosum.h
@@ -1,7 +1,7 @@
 #ifndef BLOSUM_H
 #define BLOSUM_H
 
-#include "analysis/DNAVector.h"
+#include "DNAVector.h"
 
 const int blosum_table[] = 
 {

diff --git a/analysis/ChainMatches.cc b/analysis/ChainMatches.cc
@@ -6,9 +6,9 @@
 
 #include <string>
 
-#include "base/CommandLineParser.h"
-#include "analysis/MatchDynProg.h"
-#include "analysis/SequenceMatch.h"
+#include "../base/CommandLineParser.h"
+#include "MatchDynProg.h"
+#include "SequenceMatch.h"
 
 //================================================================
 //================================================================

diff --git a/analysis/CodonTranslate.cc b/analysis/CodonTranslate.cc
@@ -1,4 +1,4 @@
-#include "analysis/CodonTranslate.h"
+#include "CodonTranslate.h"
 
 void CodonTranslator::SetFullMatrix()
 {

diff --git a/analysis/CrossCorr.cc b/analysis/CrossCorr.cc
@@ -5,11 +5,11 @@
 
 
 
-#include "analysis/CrossCorr.h"
-#include "analysis/DNAVector.h"
-#include "analysis/CodonTranslate.h"
-#include "extern/RealFFT/FFTReal.hpp"
-#include "analysis/Blosum.h"
+#include "CrossCorr.h"
+#include "DNAVector.h"
+#include "CodonTranslate.h"
+#include "../extern/RealFFT/FFTReal.hpp"
+#include "Blosum.h"
 #include <math.h>
 
 

diff --git a/analysis/CrossCorr.h b/analysis/CrossCorr.h
@@ -1,8 +1,8 @@
 #ifndef _CROSSCORR_H_
 #define _CROSSCORR_H_
 
-#include "extern/RealFFT/FFTReal.h"
-#include "analysis/DNAVector.h"
+#include "../extern/RealFFT/FFTReal.h"
+#include "DNAVector.h"
 
 
 

diff --git a/analysis/DNAMatrix.h b/analysis/DNAMatrix.h
@@ -1,7 +1,7 @@
 #ifndef DNAMATRIX_H
 #define DNAMATRIX_H
 
-#include "analysis/DNAVector.h"
+#include "DNAVector.h"
 
 
 

diff --git a/analysis/DNAVector.cc b/analysis/DNAVector.cc
@@ -2,10 +2,10 @@
 //#define NDEBUG
 //#endif
 
-#include "analysis/DNAVector.h"
-#include "base/FileParser.h"
-#include "util/mutil.h"
-#include "analysis/Coordinate.h"
+#include "DNAVector.h"
+#include "../base/FileParser.h"
+#include "../util/mutil.h"
+#include "Coordinate.h"
 
 
 #define ONE_THIRD 1./3.

diff --git a/analysis/GridSearch.cc b/analysis/GridSearch.cc
@@ -3,7 +3,7 @@
 #endif
 
 
-#include "analysis/GridSearch.h"
+#include "GridSearch.h"
 
 
 

diff --git a/analysis/GridSearch.h b/analysis/GridSearch.h
@@ -2,8 +2,8 @@
 #define GRIDSEARCH_H_
 
 
-#include "analysis/SeqChunk.h"
-#include "analysis/SequenceMatch.h"
+#include "SeqChunk.h"
+#include "SequenceMatch.h"
 
 
 class GridSequence

diff --git a/analysis/HomologyByXCorrSlave.cc b/analysis/HomologyByXCorrSlave.cc
@@ -2,18 +2,18 @@
 #define NDEBUG
 #endif
 
-#include "analysis/DNAVector.h"
+#include "DNAVector.h"
 #include <string>
 #include <unistd.h>
-#include "base/CommandLineParser.h"
-#include "analysis/CrossCorr.h"
-#include "analysis/SequenceMatch.h"
-#include "analysis/SeqChunk.h"
-#include "analysis/AlignProbability.h"
-#include "analysis/MatchDynProg.h"
-#include "analysis/WorkQueue.h"
-#include "analysis/ProbTable.h"
-#include "util/mutil.h"
+#include "../base/CommandLineParser.h"
+#include "CrossCorr.h"
+#include "SequenceMatch.h"
+#include "SeqChunk.h"
+#include "AlignProbability.h"
+#include "MatchDynProg.h"
+#include "WorkQueue.h"
+#include "ProbTable.h"
+#include "../util/mutil.h"
 #include <queue>
 #include <thread>
 #include <mutex>

diff --git a/analysis/MatchDynProg.cc b/analysis/MatchDynProg.cc
@@ -7,9 +7,9 @@
 #include <string>
 #include <math.h>
 #include <vector>
-#include "base/CommandLineParser.h"
-#include "analysis/SequenceMatch.h"
-#include "analysis/MatchDynProg.h"
+#include "../base/CommandLineParser.h"
+#include "SequenceMatch.h"
+#include "MatchDynProg.h"
 
 
 

diff --git a/analysis/MatchDynProg.h b/analysis/MatchDynProg.h
@@ -1,7 +1,7 @@
 #ifndef MATCHDYNPROG_H_
 #define MATCHDYNPROG_H_
 
-#include "analysis/SequenceMatch.h"
+#include "SequenceMatch.h"
 
 
 bool RunMatchDynProg(MultiMatches & out, const MultiMatches & in);

diff --git a/analysis/MergeXCorrMatches.cc b/analysis/MergeXCorrMatches.cc
@@ -3,15 +3,15 @@
 //#endif
 
 
-#include "analysis/DNAVector.h"
+#include "DNAVector.h"
 
 
 #include <string.h>
 
-#include "base/CommandLineParser.h"
-#include "analysis/CrossCorr.h"
-#include "analysis/SequenceMatch.h"
-#include "analysis/XCorrDynProg.h"
+#include "../base/CommandLineParser.h"
+//#include "CrossCorr.h"
+#include "SequenceMatch.h"
+#include "XCorrDynProg.h"
 
 
 //--------------------------------------------------------------------------------

diff --git a/analysis/MultiProtein.h b/analysis/MultiProtein.h
@@ -1,7 +1,7 @@
 #ifndef MULTIPROTEIN
 #define MULTIPROTEIN
 
-#include "analysis/DNAVector.h"
+#include "DNAVector.h"
 
 class CMReadFileStream;
 class CMWriteFileStream;

diff --git a/analysis/ProbTable.cc b/analysis/ProbTable.cc
@@ -1,4 +1,4 @@
-#include "analysis/ProbTable.h"
+#include "ProbTable.h"
 
 ProbTable::ProbTable() {
   m_size = 100000;

diff --git a/analysis/ProbTable.h b/analysis/ProbTable.h
@@ -5,7 +5,7 @@
 #endif
 
 #include <math.h>
-#include "analysis/DNAVector.h"
+#include "DNAVector.h"
 
 class ProbTable
 {

diff --git a/analysis/SatsumaSynteny2.cc b/analysis/SatsumaSynteny2.cc
@@ -7,16 +7,17 @@
 
 #include <string.h>
 #include <unistd.h>
-#include "base/CommandLineParser.h"
-#include "analysis/SequenceMatch.h"
-#include "analysis/GridSearch.h"
-#include "analysis/SeqChunk.h"
-#include "analysis/MatchDynProg.h"
-#include "util/SysTime.h"
+#include "../base/CommandLineParser.h"
+#include "SequenceMatch.h"
+#include "GridSearch.h"
+#include "SeqChunk.h"
+#include "MatchDynProg.h"
+#include "../util/SysTime.h"
 #include <math.h>
 #include <netinet/in.h> 
 #include <sys/socket.h>
-#include "analysis/WorkQueue.h"
+#include "WorkQueue.h"
+#include "DNAVector.h"
 #define POSITION_CHR_CNST 10000000000L
 
 class SyntenyInterpolator
@@ -463,12 +464,12 @@ int main( int argc, char** argv )
     matches.Collapse();
   }
   else {
-  cout << "SATSUMA: Processing  KMATCH results, date and time: " << GetTimeStatic() << endl;
-  unsigned long int new_matches_count;
-  wq.collect_new_matches(matches); //matches.Read(seedFile);
-  matches.Sort();
-  matches.Collapse();
-  matches.LengthFilter(min_seed_length);//XXX:hardcoded lenght filter-->terrible!!!
+    cout << "SATSUMA: Processing  KMATCH results, date and time: " << GetTimeStatic() << endl;
+    unsigned long int new_matches_count;
+    wq.collect_new_matches(matches); //matches.Read(seedFile);
+    matches.Sort();
+    matches.Collapse();
+    matches.LengthFilter(min_seed_length);//XXX:hardcoded lenght filter-->terrible!!!
   }
   //=============================================================
 

diff --git a/analysis/SeqChunk.cc b/analysis/SeqChunk.cc
@@ -2,8 +2,8 @@
 #define NDEBUG
 #endif
 
-#include "analysis/SeqChunk.h"
-#include "util/mutil.h"
+#include "SeqChunk.h"
+#include "../util/mutil.h"
 
 
 void SeqChunkSelect::Read(const string & file)

diff --git a/analysis/SeqChunk.h b/analysis/SeqChunk.h
@@ -1,7 +1,7 @@
 #ifndef SEQCHUNK_H_
 #define SEQCHUNK_H_
 
-#include "analysis/DNAVector.h"
+#include "DNAVector.h"
 
 
 

diff --git a/analysis/SequenceMatch.cc b/analysis/SequenceMatch.cc
@@ -1,7 +1,7 @@
-#include "analysis/SequenceMatch.h"
-#include "util/mutil.h"
+#include "SequenceMatch.h"
+#include "../util/mutil.h"
 
-#include "base/FileParser.h"
+#include "../base/FileParser.h"
 
 
 

diff --git a/analysis/WorkQueue.cc b/analysis/WorkQueue.cc
@@ -3,7 +3,7 @@
 #endif
 
 
-#include "analysis/WorkQueue.h"
+#include "WorkQueue.h"
 
 
 WorkQueue::WorkQueue(int _minLen, string _sQuery, int _queryChunk, string _sTarget, int _targetChunk, double _minProb, double _sigCutoff, bool _probtable, int _slave_count, int _threads){

diff --git a/analysis/WorkQueue.h b/analysis/WorkQueue.h
@@ -4,9 +4,9 @@
 #include <string.h>
 #include <unistd.h>
 #include <fcntl.h>
-#include "analysis/SequenceMatch.h"
-#include "analysis/SeqChunk.h"
-#include "util/SysTime.h"
+#include "SequenceMatch.h"
+#include "SeqChunk.h"
+#include "../util/SysTime.h"
 #include <math.h>
 #include <thread>
 #include <mutex>

diff --git a/analysis/XCorrDynProg.cc b/analysis/XCorrDynProg.cc
@@ -2,10 +2,10 @@
 //#define NDEBUG
 //#endif
 
-#include "analysis/XCorrDynProg.h"
+#include "XCorrDynProg.h"
 #include <math.h>
-#include "analysis/Blosum.h"
-#include "analysis/MultiProtein.h"
+#include "Blosum.h"
+#include "MultiProtein.h"
 
 MatchDynProg::MatchDynProg(int targetStart, int targetLen) 
 {

diff --git a/analysis/XCorrDynProg.h b/analysis/XCorrDynProg.h
@@ -2,8 +2,8 @@
 #define XCORRDYNPROG_H
 
 
-#include "analysis/SequenceMatch.h"
-#include "analysis/DNAVector.h"
+#include "SequenceMatch.h"
+#include "DNAVector.h"
 #include <math.h>
 #include <algorithm>
 

diff --git a/base/CommandLineParser.h b/base/CommandLineParser.h
@@ -8,8 +8,8 @@
 #include <set>
 #include <stdlib.h>
 
-#include "base/StringUtil.h"
-#include "base/FileParser.h"
+#include "StringUtil.h"
+#include "FileParser.h"
 
 using namespace std;
 

diff --git a/base/FileParser.cc b/base/FileParser.cc
@@ -1,5 +1,5 @@
 
-#include "base/FileParser.h"
+#include "../base/FileParser.h"
 #include <stdlib.h>
 
 

diff --git a/base/FileParser.h b/base/FileParser.h
@@ -4,7 +4,7 @@
 #define FILEPARSER_H_
 
 
-#include "util/mutil.h"
+#include "../util/mutil.h"
 #include <string>
 #include <vector>
 #include <iostream>

diff --git a/base/StringUtil.cc b/base/StringUtil.cc
@@ -1,5 +1,5 @@
 
-#include "base/StringUtil.h"
+#include "../base/StringUtil.h"
 
 int PositionAfter(string& in, string& to_find, int startSearchAt)
 {

diff --git a/extern/RealFFT/DynArray.h b/extern/RealFFT/DynArray.h
@@ -89,7 +89,7 @@ class DynArray
 
 
 
-#include	"extern/RealFFT/DynArray.hpp"
+#include	"DynArray.hpp"
 
 
 

diff --git a/extern/RealFFT/FFTReal.h b/extern/RealFFT/FFTReal.h
@@ -35,9 +35,9 @@ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
 /*\\\ INCLUDE FILES \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\*/
 
-#include	"extern/RealFFT/def.h"
-#include	"extern/RealFFT/DynArray.h"
-#include	"extern/RealFFT/OscSinCos.h"
+#include	"def.h"
+#include	"DynArray.h"
+#include	"OscSinCos.h"
 
 
 
@@ -131,7 +131,7 @@ class FFTReal
 
 
 
-#include	"extern/RealFFT/FFTReal.hpp"
+#include	"FFTReal.hpp"