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 24, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.alignment;
025
026import org.biojava.nbio.core.alignment.SimpleSequencePair;
027import org.biojava.nbio.alignment.template.AbstractPairwiseSequenceAligner;
028import org.biojava.nbio.core.alignment.template.AlignedSequence;
029import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
030import org.biojava.nbio.alignment.template.GapPenalty;
031import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
032import org.biojava.nbio.core.sequence.template.Compound;
033import org.biojava.nbio.core.sequence.template.Sequence;
034
035import java.util.List;
036
037/**
038 * Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each
039 * {@link Sequence}).  This class performs such local sequence comparisons efficiently by dynamic programming.
040 *
041 * @author Mark Chapman
042 * @param <S> each {@link Sequence} of the alignment pair is of type S
043 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
044 */
045public class SmithWaterman<S extends Sequence<C>, C extends Compound> extends AbstractPairwiseSequenceAligner<S, C> {
046
047        /**
048         * Before running a pairwise local sequence alignment, data must be sent in via calls to
049         * {@link #setQuery(Sequence)}, {@link #setTarget(Sequence)}, {@link #setGapPenalty(GapPenalty)}, and
050         * {@link #setSubstitutionMatrix(SubstitutionMatrix)}.
051         */
052        public SmithWaterman() {
053                super(null, null, null, null, true);
054        }
055
056        /**
057         * Prepares for a pairwise local sequence alignment.
058         *
059         * @param query the first {@link Sequence} of the pair to align
060         * @param target the second {@link Sequence} of the pair to align
061         * @param gapPenalty the gap penalties used during alignment
062         * @param subMatrix the set of substitution scores used during alignment
063         */
064        public SmithWaterman(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) {
065                super(query, target, gapPenalty, subMatrix, true);
066        }
067
068        // method for AbstractMatrixAligner
069
070        @Override
071        protected void setProfile(List<Step> sx, List<Step> sy) {
072                profile = pair = new SimpleSequencePair<S, C>(getQuery(), getTarget(), sx, xyStart[0],
073                                getQuery().getLength() - xyMax[0], sy, xyStart[1], getTarget().getLength() - xyMax[1]);
074        }
075
076}