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//![header]
#include <seqan/sequence.h>
#include <seqan/align.h>
#include <seqan/score.h>
#include <seqan/seeds.h>
using namespace seqan;
int main()
{
//![header]
//![example]
typedef Seed<Simple> TSeed;
Dna5String sequenceH = "CGAATCCATCCCACACA";
Dna5String sequenceV = "GGCGATNNNCATGGCACA";
String<TSeed> seedChain;
appendValue(seedChain, TSeed(0, 2, 5, 6));
appendValue(seedChain, TSeed(6, 9, 9, 12));
appendValue(seedChain, TSeed(11, 14, 17, 16));
Align<Dna5String, ArrayGaps> alignment;
resize(rows(alignment), 2);
assignSource(row(alignment, 0), sequenceH);
assignSource(row(alignment, 1), sequenceV);
Score<int, Simple> scoringScheme(2, -1, -2);
int result = bandedChainAlignment(alignment, seedChain, scoringScheme, 2);
std::cout << "Score: " << result << std::endl;
std::cout << alignment << std::endl;
//![example]
//![footer]
return 0;
}
//![footer]
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