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//![main]
#include <iostream>
#include <seqan/align.h>
using namespace seqan2;
int main()
{
//![main]
//![typedef]
typedef String<Dna> TSequence;
typedef StringSet<TSequence> TStringSet;
typedef StringSet<TSequence, Dependent<> > TDepStringSet;
typedef Graph<Alignment<TDepStringSet> > TAlignGraph;
typedef typename VertexDescriptor<TAlignGraph>::Type TVertexDescriptor;
//![typedef]
std::cout << "//![output_init]" << std::endl;
//![init]
TSequence seq1 = "TTGT";
TSequence seq2 = "TTAGT";
TStringSet strings;
appendValue(strings, seq1);
appendValue(strings, seq2);
TAlignGraph alignG(strings);
std::cout << alignG << std::endl;
//![init]
std::cout << "//![output_init]" << std::endl;
std::cout << "//![output_construct]" << std::endl;
//![construct]
TVertexDescriptor u,v;
// TT
u = addVertex(alignG, positionToId(stringSet(alignG), 0), 0, 2);
v = addVertex(alignG, positionToId(stringSet(alignG), 1), 0, 2);
addEdge(alignG, u, v);
// A
addVertex(alignG, positionToId(stringSet(alignG), 1), 2, 1);
// GT
addVertex(alignG, positionToId(stringSet(alignG), 0), 2, 2);
addVertex(alignG, positionToId(stringSet(alignG), 1), 3, 2);
u = findVertex(alignG, positionToId(stringSet(alignG), 0), 2);
v = findVertex(alignG, positionToId(stringSet(alignG), 1), 3);
addEdge(alignG, u, v);
std::cout << alignG << std::endl;
//![construct]
std::cout << "//![output_construct]" << std::endl;
//![construct]
return 0;
}
//![construct]
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