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.Profile;
027import org.biojava.nbio.core.sequence.template.Compound;
028import org.biojava.nbio.core.sequence.template.Sequence;
029
030/**
031 * Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment {@link Profile}.
032 *
033 * @author Mark Chapman
034 * @param <S> each {@link Sequence} of the alignment pair is of type S
035 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
036 */
037public interface PairInProfileScorer<S extends Sequence<C>, C extends Compound> extends PairwiseSequenceScorer<S, C> {
038
039        /**
040         * Returns the {@link Profile} from which the aligned pair originated.
041         * @return the original profile
042         */
043        Profile<S, C> getProfile();
044
045}