org.biojava3.alignment.template
Interface RescoreRefiner<S extends Sequence<C>,C extends Compound>

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
 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.biojava3.alignment.template.Aligner
getComputationTime, getProfile
 
Methods inherited from interface org.biojava3.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