Spec UnbandedLocalAlignmentEnumerator
Unbanded 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, Unbanded>;

Template Parameters

TScore The Score type.

Member Function Overview

Interface Function Overview

Interface Functions Inherited From LocalAlignmentEnumerator

Detailed Description


Enumerate all alignments into a Align object.

SimpleScore scoringScheme(2, -1, -1, -2);
LocalAlignmentEnumerator<SimpleScore, Unbanded> enumerator(scoringScheme, 5);

Dna5String seqH = "CGAGAGAGACCGAGA";

Align<Dna5String> align;
resize(rows(align), 2);@s
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[, cutoff]);



scheme The Score object to use for the alignment score.
cutoff Alignments with scores < cutoff will be discarded (int, default 0).