org.biojava3.alignment.template
Interface PartitionRefiner<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>, ProfileProfileScorer<S,C>, Scorer

public interface PartitionRefiner<S extends Sequence<C>,C extends 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
 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.ProfileProfileScorer
getQuery, getTarget
 
Methods inherited from interface org.biojava3.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