Package org.biojava.nbio.alignment.template

Interface PartitionRefiner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.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>, ProfileProfileScorer<S,C>, Scorer

public interface PartitionRefiner<S extends org.biojava.nbio.core.sequence.template.Sequence<C>,C extends org.biojava.nbio.core.sequence.template.Compound>
extends Aligner<S,C>, ProfileProfileScorer<S,C>

Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.

Author:

Mark Chapman

Method Summary

Modifier and Type	Method	Description
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.ProfileProfileScorer

getQuery, getTarget

Methods inherited from interface org.biojava.nbio.alignment.template.Scorer

getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity

Method Detail

getProfileProfileAligner

Alignments.ProfileProfileAlignerType getProfileProfileAligner()

Returns class type of profile-profile alignment subroutine.

Returns:

class type of profile-profile alignment subroutine