1 #include <iostream>
2 #include <seqan/align.h>
3 #include <seqan/graph_align.h>
4
5 using namespace seqan;
6
main()7 int main()
8 {
9 typedef String<Dna> TSequence;
10 TSequence seq1 = "atcgaatgcgga";
11 TSequence seq2 = "actcgttgca";
12 Score<int> score(0, -1, -1, -2);
13 Align<TSequence, ArrayGaps> align;
14 resize(rows(align), 2);
15 assignSource(row(align, 0), seq1);
16 assignSource(row(align, 1), seq2);
17
18 ::std::cout << "Score = " << globalAlignment(align, score) << ::std::endl;
19 ::std::cout << align << ::std::endl;
20 ::std::cout << "Score = " << globalAlignment(align, score, MyersHirschberg()) << ::std::endl;
21 ::std::cout << align << ::std::endl;
22 typedef StringSet<TSequence, Dependent<> > TStringSet;
23 typedef Graph<Alignment<TStringSet, void> > TAlignmentGraph;
24
25 TStringSet string_set;
26 appendValue(string_set, seq1);
27 appendValue(string_set, seq2);
28 TAlignmentGraph alignment_graph(string_set);
29
30 ::std::cout << "Score = " << globalAlignment(alignment_graph, score, Gotoh()) << ::std::endl;
31 ::std::cout << alignment_graph << ::std::endl;
32 return 0;
33 }
34