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 August 11, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.alignment.routines;
025
026import org.biojava.nbio.core.alignment.template.AlignedSequence;
027import org.biojava.nbio.alignment.template.GapPenalty;
028import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
029import org.biojava.nbio.core.sequence.template.Compound;
030import org.biojava.nbio.core.sequence.template.Sequence;
031
032/**
033 * Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last
034 * {@link Compound} of each {@link Sequence}).  This class performs such global sequence comparisons efficiently by
035 * dynamic programming with a space requirement reduced from quadratic (a multiple of query sequence length times
036 * target sequence length) to only linear (a multiple of query sequence length).  The counterpoint to this reduction in
037 * space complexity is a modest (a multiple < 2) increase in time.
038 *
039 * @author Mark Chapman
040 * @param <S> each {@link Sequence} of the alignment pair is of type S
041 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
042 */
043public class GuanUberbacher<S extends Sequence<C>, C extends Compound> extends AnchoredPairwiseSequenceAligner<S, C> {
044
045        private static int defaultCutsPerSection = 10;
046
047        /**
048         * Sets the default number of cuts added to each section during each pass.
049         * @param defaultCutsPerSection the default number of cuts added to each section during each pass
050         */
051        public static void setDefaultCutsPerSection(int defaultCutsPerSection) {
052                defaultCutsPerSection = Math.max(1, defaultCutsPerSection);
053        }
054
055        /**
056         * Before running a pairwise global sequence alignment, data must be sent in via calls to
057         * {@link #setQuery(Sequence)}, {@link #setTarget(Sequence)}, {@link #setGapPenalty(GapPenalty)}, and
058         * {@link #setSubstitutionMatrix(SubstitutionMatrix)}.
059         */
060        public GuanUberbacher() {
061                setDefaultCutsPerSection(defaultCutsPerSection);
062        }
063
064        /**
065         * Prepares for a pairwise global sequence alignment.
066         *
067         * @param query the first {@link Sequence} of the pair to align
068         * @param target the second {@link Sequence} of the pair to align
069         * @param gapPenalty the gap penalties used during alignment
070         * @param subMatrix the set of substitution scores used during alignment
071         */
072        public GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) {
073                super(query, target, gapPenalty, subMatrix);
074                setDefaultCutsPerSection(defaultCutsPerSection);
075        }
076
077        /**
078         * Prepares for a pairwise global sequence alignment.
079         *
080         * @param query the first {@link Sequence} of the pair to align
081         * @param target the second {@link Sequence} of the pair to align
082         * @param gapPenalty the gap penalties used during alignment
083         * @param subMatrix the set of substitution scores used during alignment
084         * @param cutsPerSection the number of cuts added to each section during each pass
085         */
086        public GuanUberbacher(S query, S target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix,
087                        int cutsPerSection) {
088                super(query, target, gapPenalty, subMatrix);
089                setCutsPerSection(cutsPerSection);
090        }
091
092        /**
093         * Returns the number of cuts added to each section during each pass.
094         *
095         * @return the number of cuts added to each section during each pass
096         */
097        public int getCutsPerSection() {
098                return cutsPerSection;
099        }
100
101        /**
102         * Sets the number of cuts added to each section during each pass.
103         *
104         * @param cutsPerSection the number of cuts added to each section during each pass
105         */
106        public void setCutsPerSection(int cutsPerSection) {
107                this.cutsPerSection = Math.max(1, cutsPerSection);
108        }
109}