int main()
{
typedef seqan::Seed<seqan::Simple> TSeed;
typedef seqan::SeedSet<seqan::Simple> TSeedSet;
seqan::Dna5String seqH;
seqan::Dna5String seqV;
seqan::Score<int, seqan::Simple> scoringScheme(1, -1, -1);
seqan::String<TSeed> seeds;
appendValue(seeds, TSeed(0, 0, 2));
appendValue(seeds, TSeed(3, 5, 2));
appendValue(seeds, TSeed(4, 2, 3));
appendValue(seeds, TSeed(9, 9, 2));
TSeedSet seedSet;
for (unsigned i = 0; i < length(seeds); ++i)
{
if (!addSeed(seedSet, seeds[i], 2, 2, scoringScheme,
seqH, seqV, seqan::Chaos()))
addSeed(seedSet, seeds[i], seqan::Single());
}
std::cout << "Resulting seeds.\n";
typedef seqan::Iterator<TSeedSet>::Type TIter;
for (TIter it = begin(seedSet, seqan::Standard());
it != end(seedSet, seqan::Standard()); ++it)
std::cout << "(" << beginPositionH(*it) << ", " << endPositionH(*it)
<< ", " << beginPositionV(*it) << ", " << endPositionV(*it)
<< ", " << lowerDiagonal(*it) << ", " << upperDiagonal(*it)
<< ")\n";
return 0;
}
int main()
{
// FRAGMENT(example)
// The horizontal and vertical sequence (database and query).
seqan::CharString seqH = "The quick BROWN fox jumped again!";
seqan::CharString seqV = "thick BROWN boxes of brownies!";
// ^^^
// Create seed and print the seeed sequence.
seqan::Seed<seqan::Simple> seed(11, 7, 14, 10);
// Perform match extension.
seqan::Score<int, seqan::Simple> scoringScheme(1, -1, -1);
extendSeed(seed, seqH, seqV, seqan::EXTEND_BOTH, scoringScheme, 3,
seqan::UnGappedXDrop());
// Perform a banded alignment.
seqan::Align<seqan::CharString> align;
resize(rows(align), 2);
assignSource(row(align, 0), infix(seqH, beginPositionH(seed),
endPositionH(seed)));
assignSource(row(align, 1), infix(seqV, beginPositionV(seed),
endPositionV(seed)));
// TODO(holtgrew): Use seed diagonals as bands.
globalAlignment(align, scoringScheme);
std::cerr << "Resulting alignment\n" << align << "\n";
// FRAGMENT(footer)
return 0;
}
size_t GetSeedNumBases(const TSeed seed)
{
return endPositionV(seed) - beginPositionV(seed);
}
bool operator()(const TSeed& seed1, const TSeed& seed2)
{
return beginPositionV(seed1) < beginPositionV(seed2);
}