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 */
021
022
023package org.biojava.bio.dp;
024
025import org.biojava.bio.dist.Distribution;
026import org.biojava.bio.symbol.Alphabet;
027
028/**
029 * A log odds weight matrix.
030 * <p>
031 * The weight matrix uses computer-coordinates. Thus, a 10 column weight matrix
032 * has columns (0 - 9). I guess that if you try to access columns outside the
033 * logical range, the implementation may throw an IndexOutOfBoundsException.
034 *
035 * @author Matthew Pocock
036 */
037public interface WeightMatrix {
038  /**
039   * The alphabet for the sequences that this weight matrix models.
040   *
041   * @return  the Alphabet
042   */
043  Alphabet getAlphabet();
044  
045  /**
046   * The number of columns modeled by the weight matrix.
047   *
048   * @return the number of columns
049   */
050  int columns();
051  
052  /**
053   * Retrieve a column as an EmissionState.
054   * <p>
055   * To find the emission probability for Symbol sym at column col use:
056   * <code>wm.getColumn(col).getWeight(sym)</code>.
057   *
058   * @param column  the weight matrix column to retrieve
059   * @throws IndexOutOfBoundsException if column is not between 0 and
060   *         columns()-1
061   * @return the EmissionState that represents the individual column
062   */
063  Distribution getColumn(int column) throws IndexOutOfBoundsException;
064}