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//![main]
#include <iostream>
#include <seqan/align.h>
using namespace seqan;
int main()
{
typedef String<AminoAcid> TSequence; // sequence type
typedef Align<TSequence, ArrayGaps> TAlign; // align type
//![main]
//![init]
TSequence seq1 = "TELKDD";
TSequence seq2 = "LKTEL";
int gapExtend = -2;
int gapOpen = -10;
TAlign alignAffine;
resize(rows(alignAffine), 2);
assignSource(row(alignAffine, 0), seq1);
assignSource(row(alignAffine, 1), seq2);
TAlign alignDynamic;
resize(rows(alignDynamic), 2);
assignSource(row(alignDynamic, 0), seq1);
assignSource(row(alignDynamic, 1), seq2);
//![init]
//![alignment]
int scoreAffine = globalAlignment(alignAffine, Blosum62(gapExtend, gapOpen), AffineGaps());
std::cout << "ScoreAffine: " << scoreAffine << std::endl;
std::cout << alignAffine << std::endl;
int scoreDynamic = globalAlignment(alignDynamic, Blosum62(gapExtend, gapOpen), DynamicGaps());
std::cout << "ScoreDynamic: " << scoreDynamic << std::endl;
std::cout << alignDynamic << std::endl;
return 0;
}
//![alignment]
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