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 11, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.alignment;
025
026import org.biojava.nbio.alignment.routines.AnchoredPairwiseSequenceAligner;
027import org.biojava.nbio.core.alignment.template.AlignedSequence;
028import org.biojava.nbio.alignment.template.GapPenalty;
029import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
030import org.biojava.nbio.core.sequence.template.Compound;
031import org.biojava.nbio.core.sequence.template.Sequence;
032
033/**
034 * Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last
035 * {@link Compound} of each {@link Sequence}).  This class performs such global sequence comparisons efficiently by
036 * dynamic programming.
037 *
038 * @author Mark Chapman
039 * @param <S> each {@link Sequence} of the alignment pair is of type S
040 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
041 */
042public class NeedlemanWunsch<S extends Sequence<C>, C extends Compound> extends AnchoredPairwiseSequenceAligner<S, C> {
043
044        /**
045         * Before running a pairwise global sequence alignment, data must be sent in via calls to
046         * {@link #setQuery(Sequence)}, {@link #setTarget(Sequence)}, {@link #setGapPenalty(GapPenalty)}, and
047         * {@link #setSubstitutionMatrix(SubstitutionMatrix)}.
048         */
049        public NeedlemanWunsch() {
050        }
051
052        /**
053         * Prepares for a pairwise global sequence alignment.
054         *
055         * @param query the first {@link Sequence} of the pair to align
056         * @param target the second {@link Sequence} of the pair to align
057         * @param gapPenalty the gap penalties used during alignment
058         * @param subMatrix the set of substitution scores used during alignment
059         */
060        public NeedlemanWunsch(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) {
061                super(query, target, gapPenalty, subMatrix);
062        }
063}