PairwiseSequenceAligner

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 Details
- getPair
  
  SequencePair<S,C> getPair()
  
  Returns sequence alignment pair.
  
  Returns:
  
  sequence alignment pair