PairwiseSequenceAligner (biojava-alignment 5.2.0 API)

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 org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>
extends Aligner<S,C>, PairwiseSequenceScorer<S,C>
```
Defines an Aligner for a pair of Sequences.

Author:

Mark Chapman

- Method Summary
  
  All Methods Instance Methods Abstract Methods
  Modifier and Type Method Description
  
  org.biojava.nbio.core.alignment.template.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
```
org.biojava.nbio.core.alignment.template.SequencePair<S,C> getPair()
```
    Returns sequence alignment pair.
    
    Returns:
    
    sequence alignment pair