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}