Spec
BandedLocalAlignmentEnumeratorBanded enumeration of local alignments using the Waterman-Eggert algorithm.
Banded enumeration of local alignments using the Waterman-Eggert algorithm.
Extends | LocalAlignmentEnumerator |
---|---|
All Extended | LocalAlignmentEnumerator |
Defined in | <seqan/align.h> |
Signature |
template <typename TScore>
class LocalAlignmentEnumerator<TScore, Banded>;
|
Member Function Overview
Interface Function Overview
Interface Functions Inherited From LocalAlignmentEnumerator
Detailed Description
Examples
Enumerate all alignments in the band between -3 and 0 into an Align object.
SimpleScore scoringScheme(2, -1, -1, -2);
LocalAlignmentEnumerator<SimpleScore, Banded> enumerator(scoringScheme, -3, 0, 5);
Dna5String seqH = "CGAGAGAGACCGAGA";
Dna5String seqV = "TTCTGAGATCCGTTTTT";
Align<Dna5String> align;
resize(rows(align), 2);
assignSource(row(align), 0, seqH);
assignSource(row(align), 1, seqV);
int i = 0;
while (nextLocalAlignment(align, enumerator))
{
std::cout << i << "-th alignment:\n";
std::cout << align << "\n\n";
std::cout << "score == " << getScore(enumerator) << "\n";
}
Member Functions Detail
LocalAlignmentEnumerator::LocalAlignmentEnumerator(scheme, upperDiag, lowerDiag[, cutoff]);
Constructor.
Parameters
scheme
|
The Score object to use for the alignment score. |
---|---|
upperDiag
|
An int with the upper diagonal. |
lowerDiag
|
An int with the lower diagonal. |
cutoff
|
Alignments with scores < cutoff will be discarded (int, default 0). |
Data Races
Thread safety unknown!