SemiGlobalAlignerInterface
in
Interface SemiGlobalAlignerInterface - aligns two sequences without penalizing gaps at either end of either sequence, so a short sequence fully contained in a longer one (a primer inside a vector, an overlap between two fragments to assemble) scores as if the longer sequence's untouched flanks were never there.
The result is the best overlap holding one aligned column at least, never the empty one : two sequences with nothing in common still get their best (possibly negative) overlap, where an ends-free alignment in the strict sense would score the empty overlap 0. A caller screening for a real overlap tests the score (> 0) rather than taking any result as one.
Tags
Table of Contents
Methods
Methods
align()
public
align(AbstractMolecularSequence $oFirst, AbstractMolecularSequence $oSecond, SubstitutionScoringInterface $oScoring, int $iGapPenalty) : PairwiseAlignmentResult
Parameters
- $oFirst : AbstractMolecularSequence
- $oSecond : AbstractMolecularSequence
- $oScoring : SubstitutionScoringInterface
- $iGapPenalty : int
-
Strictly negative