Class LocalAlignmentEnumerator
Enumeration of local alignments.

All Subcl's BandedLocalAlignmentEnumerator, UnbandedLocalAlignmentEnumerator
Defined in <seqan/align.h>
Signature template <typename TScore, typename TSpec> class LocalAlignmentEnumerator;

Template Parameters

TScore The type of the Score to use for the local alignment.
TSpec The tag to use for specializing the enumerator.

Interface Function Overview

Detailed Description

See the documentation of the specializations for examples.


  • Waterman MS, Eggert M: A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J Mol Biol 1987, 197(4):723-728.

Interface Functions Detail

TScoreVal getScore(enumerator);

Get current alignment score.


enumerator The LocalAlignmentEnumerator to query.


TScoreVal The current alignment score (Value of TScore).

bool nextLocalAlignment(align, enumerator); bool nextLocalAlignment(gapsH, gapsV, enumerator);

Compute next suboptimal local alignment.


align Align object to use for the alignment representation.
gapsH Gaps object to use for the first/horizontal sequence in the alignment matrix.
gapsV Gaps object to use for the second/vertical sequence in the alignment matrix.
enumerator The LocalAlignmentEnumerator to advance.


bool true if another suboptimal alignment above the given threshold was found and false otherwise.