- Type Parameters:
S
- each element of the alignmentinvalid reference
Profile
C
- each element of aninvalid reference
AlignedSequence
Compound
of type C
- All Known Implementing Classes:
StandardRescoreRefiner
Defines an algorithm which computes a new alignment
by rescoring all pairs in an alignment and
realigning.
invalid reference
Profile
- Author:
- Mark Chapman
-
Method Summary
Modifier and TypeMethodDescriptionReturns class type of pairwise scoring subroutine.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
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Method Details
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getPairInProfileScorer
Alignments.PairInProfileScorerType getPairInProfileScorer()Returns class type of pairwise scoring subroutine.- Returns:
- class type of pairwise scoring subroutine
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getProfileProfileAligner
Alignments.ProfileProfileAlignerType getProfileProfileAligner()Returns class type of profile-profile alignment subroutine.- Returns:
- class type of profile-profile alignment subroutine
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