org.biojava3.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
 SequencePair<S,C> getPair()
          Returns sequence alignment pair.
 
Methods inherited from interface org.biojava3.alignment.template.Aligner
getComputationTime, getProfile
 
Methods inherited from interface org.biojava3.alignment.template.PairwiseSequenceScorer
getQuery, getTarget
 
Methods inherited from interface org.biojava3.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