RescoreRefiner

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

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 Details
- 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