bioseqalign 0.0.1

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@@ -0,0 +1,48 @@
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+ #include "FitAlign.hpp"
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+
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+ FitAlign::FitAlign() {}
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+
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+ FitAlign::FitAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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+
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+ // unable to figure out how to properly overload constructor using RICE
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+ //FitAlign::FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS) : PairwiseAlign(s1, s2, matchS, mismatchS, indelS) {}
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+
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+ //std::string FitAlign::getAlignment() {
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+ Rice::Array FitAlign::getAlignment() {
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+ TSequence tseq1 = seq1;
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+ TSequence tseq2 = seq2;
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+
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+ TStringSet sequences;
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+ appendValue(sequences,tseq1);
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+ appendValue(sequences,tseq2);
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+
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+ TAlignGraph alignG(sequences);
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+
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+ // don't penalize gaps on begin/end of seq2
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+ globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
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+
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+ /*
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+ std::stringstream ss;
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+ ss<<alignG;
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+ return ss.str();
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+ */
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+ std::string mat;
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+ convertAlignment(alignG, mat);
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+ return getArrayFromAlignStr(mat);
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+ }
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+
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+
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+ void FitAlign::run() {
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+ TSequence tseq1 = seq1;
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+ TSequence tseq2 = seq2;
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+
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+ TStringSet sequences;
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+ appendValue(sequences,tseq1);
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+ appendValue(sequences,tseq2);
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+
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+ TAlignGraph alignG(sequences);
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+
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+ // don't penalize gaps on begin/end of seq2
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+ score = globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
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+
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+ }
@@ -0,0 +1,42 @@
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+ #include "FitAlign.hpp"
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+
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+ FitAlign::FitAlign() {}
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+
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+ FitAlign::FitAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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+
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+ // unable to figure out how to properly overload constructor using RICE
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+ //FitAlign::FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS) : PairwiseAlign(s1, s2, matchS, mismatchS, indelS) {}
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+
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+ std::string FitAlign::getAlignment() {
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+ TSequence tseq1 = seq1;
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+ TSequence tseq2 = seq2;
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+
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+ TStringSet sequences;
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+ appendValue(sequences,tseq1);
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+ appendValue(sequences,tseq2);
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+
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+ TAlignGraph alignG(sequences);
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+
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+ // don't penalize gaps on begin/end of seq2
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+ globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
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+
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+ std::stringstream ss;
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+ ss<<alignG;
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+ return ss.str();
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+ }
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+
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+
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+ void FitAlign::run() {
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+ TSequence tseq1 = seq1;
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+ TSequence tseq2 = seq2;
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+
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+ TStringSet sequences;
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+ appendValue(sequences,tseq1);
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+ appendValue(sequences,tseq2);
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+
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+ TAlignGraph alignG(sequences);
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+
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+ // don't penalize gaps on begin/end of seq2
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+ score = globalAlignment(alignG, Score<int,Simple>(matchScore,mismatchScore,indelScore), AlignConfig<true, false, false, true>(), NeedlemanWunsch());
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+
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+ }
@@ -0,0 +1,22 @@
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+
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+ #include <iostream>
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+ #include <string>
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+ #include <seqan/align.h>
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+
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+ #include "PairwiseAlign.hpp"
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+
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+ using namespace seqan;
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+
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+ class FitAlign : public PairwiseAlign {
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+ public:
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+ FitAlign();
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+ FitAlign(std::string s1, std::string s2);
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+ //FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS);
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+ virtual ~FitAlign() {}
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+
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+ virtual void run();
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+ //virtual std::string getAlignment();
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+ virtual Rice::Array getAlignment();
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+
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+ };
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+
@@ -0,0 +1,20 @@
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+ #include <iostream>
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+ #include <string>
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+ #include <seqan/align.h>
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+
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+ #include "PairwiseAlign.hpp"
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+
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+ using namespace seqan;
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+
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+ class FitAlign : public PairwiseAlign {
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+ public:
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+ FitAlign();
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+ FitAlign(std::string s1, std::string s2);
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+ //FitAlign(std::string s1, std::string s2, int matchS, int mismatchS, int indelS);
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+ virtual ~FitAlign() {}
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+
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+ virtual void run();
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+ virtual std::string getAlignment();
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+
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+ };
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+
@@ -0,0 +1,45 @@
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+ // global alignment
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+
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+ #include "GlobalAlign.hpp"
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+
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+ GlobalAlign::GlobalAlign() {}
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+
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+ GlobalAlign::GlobalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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+
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+ Rice::Array GlobalAlign::getAlignment() {
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+ TAlign ali;
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+ resize(rows(ali), 2);
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+ assignSource(row(ali, 0), seq1);
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+ assignSource(row(ali, 1), seq2);
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+
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+ globalAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore));
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+
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+ typedef Iterator<TRow>::Type TRowIterator;
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+ TRowIterator it = begin(row(ali, 0));
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+ TRowIterator itEnd = end(row(ali, 0));
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+ std::string s_row1 = "";
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+ for(; it != itEnd; ++it) {
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+ if(isGap(it)) s_row1 += "-";
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+ else s_row1 += (*it);
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+ }
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+ TRowIterator it2 = begin(row(ali, 1));
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+ TRowIterator itEnd2 = end(row(ali, 1));
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+ std::string s_row2 = "";
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+ for(; it2 != itEnd2; ++it2) {
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+ if(isGap(it2)) s_row2 += "-";
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+ else s_row2 += (*it2);
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+ }
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+
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+ return getArrayFromAlignStr(s_row1+s_row2);
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+ }
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+
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+
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+ void GlobalAlign::run() {
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+ TAlign ali;
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+ resize(rows(ali), 2);
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+ assignSource(row(ali, 0), seq1);
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+ assignSource(row(ali, 1), seq2);
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+
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+ score = globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore));
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+ }
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+
@@ -0,0 +1,53 @@
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+ // global alignment
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+
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+ #include "GlobalAlign.hpp"
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+
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+ GlobalAlign::GlobalAlign() {}
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+
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+ GlobalAlign::GlobalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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+
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+ Rice::Array GlobalAlign::getAlignment() {
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+ TAlign ali;
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+ resize(rows(ali), 2);
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+ assignSource(row(ali, 0), seq1);
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+ assignSource(row(ali, 1), seq2);
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+
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+ //globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+ globalAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+
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+ //std::cout<<row(ali, 0)<<std::endl;
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+ //std::cout<<row(ali, 1)<<std::endl;
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+
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+ typedef Iterator<TRow>::Type TRowIterator;
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+ TRowIterator it = begin(row(ali, 0));
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+ TRowIterator itEnd = end(row(ali, 0));
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+ std::string s_row1 = "";
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+ for(; it != itEnd; ++it) {
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+ if(isGap(it)) s_row1 += "-";
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+ else s_row1 += (*it);
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+ }
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+ TRowIterator it2 = begin(row(ali, 1));
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+ TRowIterator itEnd2 = end(row(ali, 1));
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+ std::string s_row2 = "";
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+ for(; it2 != itEnd2; ++it2) {
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+ if(isGap(it2)) s_row2 += "-";
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+ else s_row2 += (*it2);
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+ }
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+
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+ // std::cout<<s_row1<<std::endl;
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+ // std::cout<<s_row2<<std::endl;
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+ // std::cout<<ali<<std::endl;
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+
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+ return getArrayFromAlignStr(s_row1+s_row2);
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+ }
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+
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+
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+ void GlobalAlign::run() {
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+ TAlign ali;
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+ resize(rows(ali), 2);
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+ assignSource(row(ali, 0), seq1);
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+ assignSource(row(ali, 1), seq2);
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+
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+ score = globalAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+ }
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+
@@ -0,0 +1,20 @@
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+ // global alignment
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+
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+ #include <iostream>
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+ #include <string>
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+ #include <seqan/align.h>
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+
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+ #include "PairwiseAlign.hpp"
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+
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+ using namespace seqan;
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+
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+ class GlobalAlign : public PairwiseAlign {
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+ public:
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+ GlobalAlign();
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+ GlobalAlign(std::string s1, std::string s2);
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+ virtual ~GlobalAlign() {}
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+
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+ virtual void run();
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+ virtual Rice::Array getAlignment();
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+
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+ };
@@ -0,0 +1,53 @@
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+ // local alignment
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+
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+ #include "LocalAlign.hpp"
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+
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+ LocalAlign::LocalAlign() {}
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+
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+ LocalAlign::LocalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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+
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+ Rice::Array LocalAlign::getAlignment() {
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+ TAlign ali;
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+ resize(rows(ali), 2);
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+ assignSource(row(ali, 0), seq1);
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+ assignSource(row(ali, 1), seq2);
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+
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+ //localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+ localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+
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+ //std::cout<<row(ali, 0)<<std::endl;
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+ //std::cout<<row(ali, 1)<<std::endl;
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+
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+ typedef Iterator<TRow>::Type TRowIterator;
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+ TRowIterator it = begin(row(ali, 0));
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+ TRowIterator itEnd = end(row(ali, 0));
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+ std::string s_row1 = "";
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+ for(; it != itEnd; ++it) {
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+ if(isGap(it)) s_row1 += "-";
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+ else s_row1 += (*it);
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+ }
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+ TRowIterator it2 = begin(row(ali, 1));
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+ TRowIterator itEnd2 = end(row(ali, 1));
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+ std::string s_row2 = "";
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+ for(; it2 != itEnd2; ++it2) {
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+ if(isGap(it2)) s_row2 += "-";
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+ else s_row2 += (*it2);
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+ }
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+
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+ // std::cout<<s_row1<<std::endl;
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+ // std::cout<<s_row2<<std::endl;
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+ // std::cout<<ali<<std::endl;
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+
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+ return getArrayFromAlignStr(s_row1+s_row2);
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+ }
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+
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+
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+ void LocalAlign::run() {
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+ TAlign ali;
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+ resize(rows(ali), 2);
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+ assignSource(row(ali, 0), seq1);
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+ assignSource(row(ali, 1), seq2);
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+
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+ score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+ }
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+
@@ -0,0 +1,53 @@
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+ // local alignment
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+
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+ #include "LocalAlign.hpp"
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+
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+ LocalAlign::LocalAlign() {}
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+
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+ LocalAlign::LocalAlign(std::string s1, std::string s2) : PairwiseAlign(s1, s2) { }
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+
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+ Rice::Array LocalAlign::getAlignment() {
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+ TAlign ali;
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+ resize(rows(ali), 2);
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+ assignSource(row(ali, 0), seq1);
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+ assignSource(row(ali, 1), seq2);
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+
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+ //localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+ localAlignment(ali, Score<int>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+
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+ //std::cout<<row(ali, 0)<<std::endl;
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+ //std::cout<<row(ali, 1)<<std::endl;
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+
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+ typedef Iterator<TRow>::Type TRowIterator;
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+ TRowIterator it = begin(row(ali, 0));
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+ TRowIterator itEnd = end(row(ali, 0));
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+ std::string s_row1 = "";
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+ for(; it != itEnd; ++it) {
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+ if(isGap(it)) s_row1 += "-";
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+ else s_row1 += (*it);
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+ }
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+ TRowIterator it2 = begin(row(ali, 1));
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+ TRowIterator itEnd2 = end(row(ali, 1));
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+ std::string s_row2 = "";
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+ for(; it2 != itEnd2; ++it2) {
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+ if(isGap(it2)) s_row2 += "-";
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+ else s_row2 += (*it2);
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+ }
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+
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+ // std::cout<<s_row1<<std::endl;
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+ // std::cout<<s_row2<<std::endl;
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+ // std::cout<<ali<<std::endl;
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+
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+ return getArrayFromAlignStr(s_row1+s_row2);
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+ }
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+
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+
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+ void LocalAlign::run() {
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+ TAlign ali;
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+ resize(rows(ali), 2);
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+ assignSource(row(ali, 0), seq1);
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+ assignSource(row(ali, 1), seq2);
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+
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+ score = localAlignment(ali, Score<int,Simple>(matchScore,mismatchScore,indelScore), SmithWaterman());
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+ }
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+
@@ -0,0 +1 @@
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+ // local alignment
@@ -0,0 +1,21 @@
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+ // local alignment
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+
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+ #include <iostream>
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+ #include <string>
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+ #include <seqan/align.h>
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+
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+ #include "PairwiseAlign.hpp"
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+
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+ using namespace seqan;
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+
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+ class LocalAlign : public PairwiseAlign {
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+ public:
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+ LocalAlign();
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+ LocalAlign(std::string s1, std::string s2);
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+ virtual ~LocalAlign() {}
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+
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+ virtual void run();
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+ virtual Rice::Array getAlignment();
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+
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+ };
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+
@@ -0,0 +1 @@
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+ // local alignment
@@ -0,0 +1,251 @@
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+
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+ SHELL = /bin/sh
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+
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+ # V=0 quiet, V=1 verbose. other values don't work.
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+ V = 0
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+ Q1 = $(V:1=)
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+ Q = $(Q1:0=@)
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+ n=$(NULLCMD)
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+ ECHO1 = $(V:1=@$n)
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+ ECHO = $(ECHO1:0=@echo)
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+
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+ #### Start of system configuration section. ####
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+
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+ srcdir = .
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+ topdir = /usr/include/ruby-1.9.1
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+ hdrdir = /usr/include/ruby-1.9.1
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+ arch_hdrdir = /usr/include/ruby-1.9.1/$(arch)
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+ VPATH = $(srcdir):$(arch_hdrdir)/ruby:$(hdrdir)/ruby
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+
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+ prefix = $(DESTDIR)/usr
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+
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+ rubylibprefix = $(libdir)/$(RUBY_BASE_NAME)
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+
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+ exec_prefix = $(prefix)
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+
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+ vendorhdrdir = $(rubyhdrdir)/vendor_ruby
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+
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+ sitehdrdir = $(rubyhdrdir)/site_ruby
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+
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+ rubyhdrdir = $(includedir)/$(RUBY_BASE_NAME)-$(ruby_version)
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+
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+ vendordir = $(DESTDIR)/usr/lib/ruby/vendor_ruby
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+
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+ sitedir = $(DESTDIR)/usr/local/lib/site_ruby
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+
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+ ridir = $(datarootdir)/$(RI_BASE_NAME)
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+
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+ mandir = $(prefix)/share/man
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+
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+ localedir = $(datarootdir)/locale
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+
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+ libdir = $(exec_prefix)/lib
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+
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+ psdir = $(docdir)
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+
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+ pdfdir = $(docdir)
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+
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+ dvidir = $(docdir)
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+
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+ htmldir = $(docdir)
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+
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+ infodir = $(prefix)/share/info
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+
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+ docdir = $(datarootdir)/doc/$(PACKAGE)
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+
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+ oldincludedir = $(DESTDIR)/usr/include
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+
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+ includedir = $(prefix)/include
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+
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+ localstatedir = $(DESTDIR)/var
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+
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+ sharedstatedir = $(prefix)/com
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+
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+ sysconfdir = $(DESTDIR)/etc
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+
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+ datadir = $(datarootdir)
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+
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+ datarootdir = $(prefix)/share
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+
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+ libexecdir = $(prefix)/lib/ruby1.9.1
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+
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+ sbindir = $(exec_prefix)/sbin
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+
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+ bindir = $(exec_prefix)/bin
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+
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+ rubylibdir = $(rubylibprefix)/$(ruby_version)
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+
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+ archdir = $(rubylibdir)/$(arch)
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+
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+ sitelibdir = $(sitedir)/$(ruby_version)
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+
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+ sitearchdir = $(sitelibdir)/$(sitearch)
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+
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+ vendorlibdir = $(vendordir)/$(ruby_version)
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+
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+ vendorarchdir = $(vendorlibdir)/$(sitearch)
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+
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+
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+ NULLCMD = :
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+
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+ CC = gcc
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+ CXX = g++
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+ LIBRUBY = $(LIBRUBY_SO)
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+ LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
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+ LIBRUBYARG_SHARED = -l$(RUBY_SO_NAME)
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+ LIBRUBYARG_STATIC = -lruby-1.9.1-static
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+ OUTFLAG = -o
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+ COUTFLAG = -o
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+
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+ RUBY_EXTCONF_H =
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+ cflags = $(optflags) $(debugflags) $(warnflags)
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+ optflags = -O3
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+ debugflags = -ggdb
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+ warnflags = -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wimplicit-function-declaration
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+ CFLAGS = -fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fno-strict-aliasing -fPIC $(ARCH_FLAG)
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+ INCFLAGS = -I. -I$(arch_hdrdir) -I$(hdrdir)/ruby/backward -I$(hdrdir) -I$(srcdir)
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+ DEFS =
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+ CPPFLAGS = -D_FORTIFY_SOURCE=2 $(DEFS) $(cppflags) -I/home/stef/ruby_gems/gems/rice-1.6.2/ruby/lib/include
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+ CXXFLAGS = $(CFLAGS) -Wall -g
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+ ldflags = -L. -Wl,-Bsymbolic-functions -Wl,-z,relro -rdynamic -Wl,-export-dynamic -L/home/stef/ruby_gems/gems/rice-1.6.2/ruby/lib/lib -lrice
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+ dldflags =
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+ ARCH_FLAG =
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+ DLDFLAGS = $(ldflags) $(dldflags) $(ARCH_FLAG)
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+ LDSHARED = g++ -shared
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+ LDSHAREDXX = $(CXX) -shared
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+ AR = ar
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+ EXEEXT =
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+
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+ RUBY_BASE_NAME = ruby
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+ RUBY_INSTALL_NAME = ruby1.9.1
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+ RUBY_SO_NAME = ruby-1.9.1
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+ arch = x86_64-linux
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+ sitearch = $(arch)
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+ ruby_version = 1.9.1
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+ ruby = /usr/bin/ruby1.9.1
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+ RUBY = $(ruby)
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+ RM = rm -f
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+ RM_RF = $(RUBY) -run -e rm -- -rf
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+ RMDIRS = rmdir --ignore-fail-on-non-empty -p
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+ MAKEDIRS = /bin/mkdir -p
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+ INSTALL = /usr/bin/install -c
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+ INSTALL_PROG = $(INSTALL) -m 0755
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+ INSTALL_DATA = $(INSTALL) -m 644
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+ COPY = cp
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+
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+ #### End of system configuration section. ####
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+
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+ preload =
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+
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+
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+ CXX = g++
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+
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+ libpath = . $(libdir)
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+ LIBPATH = -L. -L$(libdir)
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+ DEFFILE =
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+
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+ CLEANFILES = mkmf.log
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+ DISTCLEANFILES =
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+ DISTCLEANDIRS =
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+
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+ extout =
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+ extout_prefix =
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+ target_prefix =
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+ LOCAL_LIBS =
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+ LIBS = -lruby-1.9.1 -lpthread -lrt -ldl -lcrypt -lm -lc
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+ SRCS = PrefixSuffixAlign.cpp PairwiseAlign.cpp LocalAlign.cpp fitalgntest.cpp GlobalAlign.cpp FitAlign.cpp
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+ OBJS = PrefixSuffixAlign.o PairwiseAlign.o LocalAlign.o fitalgntest.o GlobalAlign.o FitAlign.o
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+ TARGET = SeqAlign
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+ DLLIB = $(TARGET).so
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+ EXTSTATIC =
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+ STATIC_LIB =
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+
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+ BINDIR = $(bindir)
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+ RUBYCOMMONDIR = $(sitedir)$(target_prefix)
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+ RUBYLIBDIR = $(sitelibdir)$(target_prefix)
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+ RUBYARCHDIR = $(sitearchdir)$(target_prefix)
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+ HDRDIR = $(rubyhdrdir)/ruby$(target_prefix)
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+ ARCHHDRDIR = $(rubyhdrdir)/$(arch)/ruby$(target_prefix)
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+
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+ TARGET_SO = $(DLLIB)
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+ CLEANLIBS = $(TARGET).so
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+ CLEANOBJS = *.o *.bak
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+
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+ all: $(DLLIB)
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+ static: $(STATIC_LIB)
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+ .PHONY: all install static install-so install-rb
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+ .PHONY: clean clean-so clean-rb
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+
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+ clean-rb-default::
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+ clean-rb::
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+ clean-so::
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+ clean: clean-so clean-rb-default clean-rb
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+ @-$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES)
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+
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+ distclean-rb-default::
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+ distclean-rb::
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+ distclean-so::
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+ distclean: clean distclean-so distclean-rb-default distclean-rb
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+ @-$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
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+ @-$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
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+ @-$(RMDIRS) $(DISTCLEANDIRS) 2> /dev/null || true
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+
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+ realclean: distclean
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+ install: install-so install-rb
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+
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+ install-so: $(RUBYARCHDIR)
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+ install-so: $(RUBYARCHDIR)/$(DLLIB)
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+ $(RUBYARCHDIR)/$(DLLIB): $(DLLIB)
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+ @-$(MAKEDIRS) $(@D)
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+ $(INSTALL_PROG) $(DLLIB) $(@D)
201
+ install-rb: pre-install-rb install-rb-default
202
+ install-rb-default: pre-install-rb-default
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+ pre-install-rb: Makefile
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+ pre-install-rb-default: Makefile
205
+ pre-install-rb-default:
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+ $(ECHO) installing default SeqAlign libraries
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+ $(RUBYARCHDIR):
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+ $(Q) $(MAKEDIRS) $@
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+
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+ site-install: site-install-so site-install-rb
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+ site-install-so: install-so
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+ site-install-rb: install-rb
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+
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+ .SUFFIXES: .c .m .cc .mm .cxx .cpp .C .o
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+
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+ .cc.o:
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+ $(ECHO) compiling $(<)
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+ $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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+
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+ .mm.o:
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+ $(ECHO) compiling $(<)
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+ $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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+
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+ .cxx.o:
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+ $(ECHO) compiling $(<)
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+ $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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+
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+ .cpp.o:
229
+ $(ECHO) compiling $(<)
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+ $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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+
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+ .C.o:
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+ $(ECHO) compiling $(<)
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+ $(Q) $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(COUTFLAG)$@ -c $<
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+
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+ .c.o:
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+ $(ECHO) compiling $(<)
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+ $(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
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+
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+ .m.o:
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+ $(ECHO) compiling $(<)
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+ $(Q) $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) $(COUTFLAG)$@ -c $<
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+
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+ $(DLLIB): $(OBJS) Makefile
245
+ $(ECHO) linking shared-object $(DLLIB)
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+ @-$(RM) $(@)
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+ $(Q) $(LDSHAREDXX) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
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+
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+
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+
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+ $(OBJS): $(hdrdir)/ruby.h $(hdrdir)/ruby/defines.h $(arch_hdrdir)/ruby/config.h