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;
}
int main()
{
// Create an alignment between subject and query.
seqan::Peptide subject =
"MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE"
"DLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKH"
"PGDFGADAQGAMNKALELFRKDMASNYK";
seqan::Peptide query =
"MSLTKTERTIIVSMWAKISTQADTIGTETLERLFLSHPQTKTYFPHFDLHPGSA"
"QLRAHGSKVVAAVGDAVKSIDDIGGALSKLSELHAYILRVDPVNFKLLSHCLLVTLAARF"
"PADFTAEAHAAWDKFLSVTEKYR";
seqan::Align<seqan::Peptide> align;
resize(rows(align), 2);
setSource(row(align, 0), subject);
setSource(row(align, 1), query);
seqan::Blosum62 scoringScheme(-1, -12);
globalAlignment(align, scoringScheme);
// Compute the statistics of the alignment.
seqan::AlignmentStats stats;
int scoreVal = computeAlignmentStats(stats, align, scoringScheme);
SEQAN_ASSERT_EQ(scoreVal, stats.alignmentScore);
std::cout << align
<< "gap opens: " << stats.numGapOpens << "\n"
<< "gap extensions: " << stats.numGapExtensions << "\n"
<< "num matches: " << stats.numMatches << "\n"
<< "num mismatches: " << stats.numMismatches << "\n"
<< "num positive scores: " << stats.numPositiveScores << "\n"
<< "num negative scores: " << stats.numNegativeScores << "\n\n\n";
// Clip alignment rows and compute score of this view.
setClippedEndPosition(row(align, 0), 100);
setClippedEndPosition(row(align, 1), 100);
setClippedBeginPosition(row(align, 0), 5);
setClippedBeginPosition(row(align, 1), 5);
scoreVal = computeAlignmentStats(stats, align, scoringScheme);
SEQAN_ASSERT_EQ(scoreVal, stats.alignmentScore);
std::cout << "Clipping alignment to (5, 100)\n"
<< align
<< "gap opens: " << stats.numGapOpens << "\n"
<< "gap extensions: " << stats.numGapExtensions << "\n"
<< "num matches: " << stats.numMatches << "\n"
<< "num mismatches: " << stats.numMismatches << "\n"
<< "num positive scores: " << stats.numPositiveScores << "\n"
<< "num negative scores: " << stats.numNegativeScores << "\n";
return 0;
}
PairwiseAlignment _pairwise_global(const std::string& ref, const std::string& qry,
const int match_score, const int mismatch_score,
const int gap_open, const int gap_extend)
{
typedef String<char> TSequence;
typedef Align<TSequence,ArrayGaps> TAlign;
typedef Row<TAlign>::Type TRow;
typedef Iterator<TRow>::Type TRowIterator;
TAlign align;
resize(rows(align), 2);
assignSource(row(align, 0), ref);
assignSource(row(align, 1), qry);
Score<int,Simple> score_scheme(match_score, mismatch_score, gap_extend, gap_open);
AlignConfig<false,QGAP,false,QGAP> a_config;
PairwiseAlignment result;
result.score = globalAlignment(align, score_scheme, a_config);
result.aligned_ref = aligned_string(row(align, 0));
result.aligned_qry = aligned_string(row(align, 1));
return result;
}
