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 7, 2010
021 * Author: Mark Chapman
022 */
023
024package org.biojava.nbio.alignment.template;
025
026import org.biojava.nbio.core.sequence.template.Compound;
027import org.biojava.nbio.core.sequence.template.Sequence;
028
029/**
030 * Defines an {@link Aligner} which builds a score matrix during computation.
031 *
032 * @author Mark Chapman
033 * @param <S> each element of the alignment {@link Profile} is of type S
034 * @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
035 */
036public interface MatrixAligner<S extends Sequence<C>, C extends Compound> extends Aligner<S, C> {
037
038        /**
039         * Returns the entire score matrix built during alignment.  The first dimension has the length of the first (query)
040         * sequence + 1; the second has the length of the second (target) sequence + 1; the third has length equal to the
041         * number of scores stored per pairing of an element from each {@link Sequence}.
042         *
043         * @return the score matrix
044         */
045        int[][][] getScoreMatrix();
046
047        /**
048         * Returns a depiction of the score matrix as a {@link String}.  This may include additional description such as
049         * labels for each dimension: element from query sequence, element from target sequence, and meaning of each score.
050         *
051         * @return the score matrix as a character sequence
052         */
053        String getScoreMatrixAsString();
054
055}