RescoreRefiner (biojava 5.2.0 API)

Type Parameters:

S - each element of the alignment Profile is of type S

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

All Superinterfaces:

Aligner<S,C>, Scorer

All Known Implementing Classes:

StandardRescoreRefiner
```
public interface RescoreRefiner<S extends Sequence<C>,C extends Compound>
extends Aligner<S,C>
```
Defines an algorithm which computes a new alignment Profile by rescoring all pairs in an alignment and realigning.

Author:

Mark Chapman

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`Alignments.PairInProfileScorerType`	`getPairInProfileScorer()`	Returns class type of pairwise scoring subroutine.
`Alignments.ProfileProfileAlignerType`	`getProfileProfileAligner()`	Returns class type of profile-profile alignment subroutine.

Methods inherited from interface org.biojava.nbio.alignment.template.Aligner
getComputationTime, getProfile

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

- Method Detail
  - getPairInProfileScorer
```
Alignments.PairInProfileScorerType getPairInProfileScorer()
```
    Returns class type of pairwise scoring subroutine.
    
    Returns:
    
    class type of pairwise scoring subroutine
  - getProfileProfileAligner
```
Alignments.ProfileProfileAlignerType getProfileProfileAligner()
```
    Returns class type of profile-profile alignment subroutine.
    
    Returns:
    
    class type of profile-profile alignment subroutine