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.core.alignment.template.ProfilePair;
027import org.biojava.nbio.core.sequence.template.Compound;
028import org.biojava.nbio.core.sequence.template.Sequence;
029
030/**
031 * Defines an {@link Aligner} for a pair of {@link Profile}s.
032 *
033 * @author Mark Chapman
034 * @param <S> each {@link Sequence} in the pair of alignment {@link Profile}s is of type S
035 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
036 */
037public interface ProfileProfileAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C>,
038                ProfileProfileScorer<S, C> {
039
040        /**
041         * Returns alignment profile pair.
042         *
043         * @return alignment profile pair
044         */
045        ProfilePair<S, C> getPair();
046
047}