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//![main]
#include <iostream>
#include <seqan/align.h>
using namespace seqan2;
int main()
{
// Define the types we need.
typedef String<char> TSequence;
typedef StringSet<TSequence> TStringSet;
typedef StringSet<TSequence, Dependent<> > TDepStringSet;
typedef Graph<Alignment<TDepStringSet> > TAlignGraph;
typedef typename VertexDescriptor<TAlignGraph>::Type TVertexDescriptor;
// Initializing the sequences and the string set.
TSequence seq1 = "GARFIELDTHECAT";
TSequence seq2 = "GARFIELDTHEBIGCAT";
TSequence seq3 = "THEBIGCAT";
TStringSet strings;
appendValue(strings, seq1);
appendValue(strings, seq2);
appendValue(strings, seq3);
// Load the string set into the Alignment Graph.
TAlignGraph alignG(strings);
TVertexDescriptor u,v;
// Add two vertices covering "GARFIELD" in the first and the second sequence and connect them with an edge.
u = addVertex(alignG, positionToId(stringSet(alignG), 0), 0, 8);
v = addVertex(alignG, positionToId(stringSet(alignG), 1), 0, 8);
addEdge(alignG, u, v);
// Add two vertices covering "THE" in the first and the second sequence and connect them with an edge.
u = addVertex(alignG, positionToId(stringSet(alignG), 0), 8, 3);
v = addVertex(alignG, positionToId(stringSet(alignG), 1), 8, 3);
addEdge(alignG, u, v);
// Find the vertex covering "THE" in the first sequence and add the vertex covering "THE" in the third sequence and connect them with an edge.
u = findVertex(alignG, positionToId(stringSet(alignG), 0), 8);
v = addVertex(alignG, positionToId(stringSet(alignG), 2), 0, 3);
addEdge(alignG, u, v);
// Find the vertices covering "THE" in the second and the third sequence and connect them with an edge.
u = findVertex(alignG, positionToId(stringSet(alignG), 1), 8);
v = findVertex(alignG, positionToId(stringSet(alignG), 2), 0);
addEdge(alignG, u, v);
// Add two vertices covering "FAT" in the second and the third sequence and connect them with an edge.
u = addVertex(alignG, positionToId(stringSet(alignG), 1), 11, 3);
v = addVertex(alignG, positionToId(stringSet(alignG), 2), 3, 3);
addEdge(alignG, u, v);
// Add two vertices covering "CAT" in the first and the second sequence and connect them with an edge.
u = addVertex(alignG, positionToId(stringSet(alignG), 0), 11, 3);
v = addVertex(alignG, positionToId(stringSet(alignG), 1), 14, 3);
addEdge(alignG, u, v);
// Find the vertex covering "CAT" in the first sequence and add the vertex covering "CAT" in the third sequence and connect them with an edge.
u = findVertex(alignG, positionToId(stringSet(alignG), 0), 11);
v = addVertex(alignG, positionToId(stringSet(alignG), 2), 6, 3);
addEdge(alignG, u, v);
// Find the vertices covering "CAT" in the second and the third sequence and connect them with an edge.
u = findVertex(alignG, positionToId(stringSet(alignG), 1), 14);
v = findVertex(alignG, positionToId(stringSet(alignG), 2), 6);
addEdge(alignG, u, v);
std::cout << alignG << std::endl;
return 0;
}
//![main]
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