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 SC
- 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
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