PairwiseSequenceScorer (biojava 5.2.0 API)

Type Parameters:

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

C - each element of a Sequence is a Compound of type C

All Superinterfaces:

Scorer

All Known Subinterfaces:

PairInProfileScorer<S,C>, PairwiseSequenceAligner<S,C>

All Known Implementing Classes:

AbstractPairwiseSequenceAligner, AnchoredPairwiseSequenceAligner, FractionalIdentityInProfileScorer, FractionalIdentityScorer, FractionalSimilarityInProfileScorer, FractionalSimilarityScorer, GuanUberbacher, NeedlemanWunsch, SmithWaterman, SubstitutionMatrixScorer
```
public interface PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound>
extends Scorer
```
Defines an algorithm which computes a score for a pair of sequences.

Author:

Mark Chapman

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`S`	`getQuery()`	Returns the first sequence of the pair.
`S`	`getTarget()`	Returns the second sequence of the pair.

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

- Method Detail
  - getQuery
```
S getQuery()
```
    Returns the first sequence of the pair.
    
    Returns:
    
    the first sequence of the pair
  - getTarget
```
S getTarget()
```
    Returns the second sequence of the pair.
    
    Returns:
    
    the second sequence of the pair