org.biojava.nbio.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

Modifier and Type	Method and 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