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 July 12, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.alignment;
025
026import org.biojava.nbio.core.alignment.SimpleSequencePair;
027import org.biojava.nbio.core.alignment.template.AlignedSequence;
028import org.biojava.nbio.alignment.template.PairInProfileScorer;
029import org.biojava.nbio.core.alignment.template.Profile;
030import org.biojava.nbio.core.sequence.template.Compound;
031import org.biojava.nbio.core.sequence.template.Sequence;
032
033/**
034 * Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment
035 * {@link Profile}.  The reported score is the number of alignment columns which have identical {@link Compound}s.
036 *
037 * @author Mark Chapman
038 * @param <S> each {@link Sequence} of the alignment pair is of type S
039 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
040 */
041public class FractionalIdentityInProfileScorer<S extends Sequence<C>, C extends Compound>
042                extends FractionalIdentityScorer<S, C> implements PairInProfileScorer<S, C> {
043
044        private Profile<S, C> profile;
045
046        /**
047         * Creates a fractional identity scorer for an aligned pair of sequences in the given alignment profile.
048         *
049         * @param profile alignment profile containing pair of sequences
050         * @param query index in the profile of the first sequence of the pair
051         * @param target index in the profile of the second sequence of the pair
052         */
053        public FractionalIdentityInProfileScorer(Profile<S, C> profile, int query, int target) {
054                super(new SimpleSequencePair<S, C>(profile.getAlignedSequence(query), profile.getAlignedSequence(target)));
055                this.profile = profile;
056        }
057
058        @Override
059        public Profile<S, C> getProfile() {
060                return profile;
061        }
062
063}