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align.cpp
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#include "seqanpy.h"
#include <seqan/align.h>
using namespace seqan;
// Functions
int align_global(std::string seq1, std::string seq2, std::string* ali1, std::string* ali2, int band,
int score_match, int score_mismatch, int score_gapext, int score_gapopen) {
typedef String<char> TSequence; // sequence type
typedef Align<TSequence,ArrayGaps> TAlign; // align type
typedef Row<TAlign>::Type TRow; // gapped sequence type
std::stringstream rowstream;
int score;
// Build alignment object
TAlign ali;
resize(rows(ali), 2);
assignSource(row(ali, 0), seq1);
assignSource(row(ali, 1), seq2);
// Align
if(band >= 0)
score = globalAlignment(ali,
Score<int,Simple>(score_match, score_mismatch,
score_gapext, score_gapopen),
-band, band);
else
score = globalAlignment(ali,
Score<int,Simple>(score_match, score_mismatch,
score_gapext, score_gapopen));
// Set the output
TRow row1 = row(ali,0);
rowstream.str("");
rowstream << row1;
(*ali1) = rowstream.str();
TRow row2 = row(ali,1);
rowstream.str("");
rowstream << row2;
(*ali2) = rowstream.str();
return score;
}
int align_overlap(std::string seq1, std::string seq2, std::string* ali1, std::string* ali2, int band,
int score_match, int score_mismatch, int score_gapext, int score_gapopen, int cut_flanks) {
typedef String<char> TSequence; // sequence type
typedef Align<TSequence,ArrayGaps> TAlign; // align type
typedef Row<TAlign>::Type TRow; // gapped sequence type
std::stringstream rowstream;
int score;
// Build alignment object
TAlign ali;
resize(rows(ali), 2);
assignSource(row(ali, 0), seq1);
assignSource(row(ali, 1), seq2);
// Align
if(band >= 0)
score = globalAlignment(ali,
Score<int,Simple>(score_match, score_mismatch,
score_gapext, score_gapopen),
AlignConfig<true, false, false, true>(),
-band, band);
else
score = globalAlignment(ali,
Score<int,Simple>(score_match, score_mismatch,
score_gapext, score_gapopen),
AlignConfig<true, false, false, true>());
// Set the output
TRow row1 = row(ali,0);
rowstream.str("");
rowstream << row1;
(*ali1) = rowstream.str();
TRow row2 = row(ali,1);
rowstream.str("");
rowstream << row2;
(*ali2) = rowstream.str();
return score;
}
int align_ladder(std::string seq1, std::string seq2, std::string* ali1, std::string* ali2, int band,
int score_match, int score_mismatch, int score_gapext, int score_gapopen) {
typedef String<char> TSequence; // sequence type
typedef Align<TSequence,ArrayGaps> TAlign; // align type
typedef Row<TAlign>::Type TRow; // gapped sequence type
std::stringstream rowstream;
int score;
// Build alignment object
TAlign ali;
resize(rows(ali), 2);
assignSource(row(ali, 0), seq1);
assignSource(row(ali, 1), seq2);
// Align
if(band >= 0)
score = globalAlignment(ali,
Score<int,Simple>(score_match, score_mismatch,
score_gapext, score_gapopen),
AlignConfig<true, false, true, false>(),
-band, band);
else
score = globalAlignment(ali,
Score<int,Simple>(score_match, score_mismatch,
score_gapext, score_gapopen),
AlignConfig<true, false, true, false>());
// Set the output
TRow row1 = row(ali,0);
rowstream.str("");
rowstream << row1;
(*ali1) = rowstream.str();
TRow row2 = row(ali,1);
rowstream.str("");
rowstream << row2;
(*ali2) = rowstream.str();
return score;
}
int align_local(std::string seq1, std::string seq2, std::string* ali1, std::string* ali2,
int score_match, int score_mismatch, int score_gapext, int score_gapopen) {
typedef String<char> TSequence; // sequence type
typedef Align<TSequence,ArrayGaps> TAlign; // align type
typedef Row<TAlign>::Type TRow; // gapped sequence type
std::stringstream rowstream;
int score;
// Build alignment object
TAlign ali;
resize(rows(ali), 2);
assignSource(row(ali, 0), seq1);
assignSource(row(ali, 1), seq2);
// Align (best alignment only)
score = localAlignment(ali,
Score<int,Simple>(score_match, score_mismatch,
score_gapext, score_gapopen));
// Set the output
TRow row1 = row(ali,0);
rowstream.str("");
rowstream << row1;
(*ali1) = rowstream.str();
TRow row2 = row(ali,1);
rowstream.str("");
rowstream << row2;
(*ali2) = rowstream.str();
return score;
}