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#include <iostream>
#include <seqan/basic.h>
#include <seqan/stream.h>
#include <seqan/align.h>
#include <seqan/graph_align.h>
using namespace seqan;
int main()
{
typedef StringSet<DnaString, Dependent<> > TStringSet;
typedef Graph<Alignment<TStringSet, void> > TAlignmentGraph;
// Define scorings scheme.
//
// In this case, affine gap costs with match = 0, mismatch = -1,
// gapextend = -1 and gapopen = -2.
Score<int> scoringScheme(0, -1, -1, -2);
// Define the two sequence to be allocated.
DnaString seq1 = "atcgaatgcgga";
DnaString seq2 = "actcgttgca";
// Create StringSet with these two sequences and construct an
// AlignmentGraph for them.
TStringSet stringSet;
appendValue(stringSet, seq1);
appendValue(stringSet, seq2);
TAlignmentGraph alignmentGraph(stringSet);
// Compute global alignment of seq1 and seq1 using Gotoh's algorithm and
// print score and alignment graph.
int score = globalAlignment(alignmentGraph, scoringScheme, Gotoh());
std::cout << "Score = " << score << "\n"
<< alignmentGraph << std::endl;
return 0;
}
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