org.biojava.nbio.alignment.template.PartitionRefiner Maven / Gradle / Ivy
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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on June 7, 2010
* Author: Mark Chapman
*/
package org.biojava.nbio.alignment.template;
import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType;
import org.biojava.nbio.core.sequence.template.Compound;
import org.biojava.nbio.core.sequence.template.Sequence;
/**
* Defines an algorithm which computes a new alignment {@link Profile} by splitting a current alignment and realigning.
*
* @author Mark Chapman
* @param each element of the alignment {@link Profile} is of type S
* @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
*/
public interface PartitionRefiner, C extends Compound> extends Aligner,
ProfileProfileScorer {
/**
* Returns class type of profile-profile alignment subroutine.
*
* @return class type of profile-profile alignment subroutine
*/
ProfileProfileAlignerType getProfileProfileAligner();
}