Package org.biojava.nbio.alignment.template

Interface PairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>

Type Parameters:

S - each Sequence of the alignment pair is of type S

C - each element of an AlignedSequence is a Compound of type C

All Superinterfaces:

Aligner<S,C>, PairwiseSequenceScorer<S,C>, Scorer

All Known Implementing Classes:

AbstractPairwiseSequenceAligner, AnchoredPairwiseSequenceAligner, GuanUberbacher, NeedlemanWunsch, SmithWaterman

public interface PairwiseSequenceAligner<S extends Sequence<C>,C extends Compound>
extends Aligner<S,C>, PairwiseSequenceScorer<S,C>

Defines an Aligner for a pair of Sequences.

Author:

Mark Chapman

Method Summary

Modifier and Type	Method	Description
SequencePair<S,C>	getPair()	Returns sequence alignment pair.

Methods inherited from interface org.biojava.nbio.alignment.template.Aligner

getComputationTime, getProfile

Methods inherited from interface org.biojava.nbio.alignment.template.PairwiseSequenceScorer

getQuery, getTarget

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

Method Detail

getPair

SequencePair<S,C> getPair()

Returns sequence alignment pair.

Returns:

sequence alignment pair