001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 * Created on June 7, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.alignment.template;
025
026import org.biojava.nbio.alignment.Alignments.PairInProfileScorerType;
027import org.biojava.nbio.alignment.Alignments.ProfileProfileAlignerType;
028import org.biojava.nbio.core.sequence.template.Compound;
029import org.biojava.nbio.core.sequence.template.Sequence;
030
031/**
032 * Defines an algorithm which computes a new alignment {@link Profile} by rescoring all pairs in an alignment and
033 * realigning.
034 *
035 * @author Mark Chapman
036 * @param <S> each element of the alignment {@link Profile} is of type S
037 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
038 */
039public interface RescoreRefiner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C> {
040
041        /**
042         * Returns class type of pairwise scoring subroutine.
043         *
044         * @return class type of pairwise scoring subroutine
045         */
046        PairInProfileScorerType getPairInProfileScorer();
047
048        /**
049         * Returns class type of profile-profile alignment subroutine.
050         *
051         * @return class type of profile-profile alignment subroutine
052         */
053        ProfileProfileAlignerType getProfileProfileAligner();
054
055}