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
022package org.biojava.bio.chromatogram.graphic;
023
024import org.biojava.bio.chromatogram.Chromatogram;
025
026/**
027 * Provides the mechanism whereby a ChromatogramGraphic can display
028 * a Chromatogram with a non-linear horizontal scale.
029 *
030 * @author Rhett Sutphin (<a href="http://genome.uiowa.edu/">UI CBCB</a>)
031 * @author Matthew Pocock
032 * @since 1.3
033 */
034public interface ChromatogramNonlinearScaler {
035    /**
036     * Returns the remapped coordinate for the provided trace sample index of the
037     * given chromatogram.
038     *
039     * @param c  the Chromatogram
040     * @param sampleIndex the sample index
041     * @return the new coordinagte
042     */
043    public float scale(Chromatogram c, int sampleIndex) 
044        throws IndexOutOfBoundsException;
045
046    /**
047     * The default scaler that displays the chromatogram 1:1.
048     */
049    public static class Identity implements ChromatogramNonlinearScaler {
050        private static Identity INSTANCE;
051
052      /**
053       * Retrieve the singleton instance of this class.
054       *
055       * @return the Identity instance
056       */
057        public static Identity getInstance() {
058            if (INSTANCE == null)
059                INSTANCE = new Identity();
060            return INSTANCE;
061        }
062
063        private Identity() { }
064
065        public float scale(Chromatogram c, int sampleIndex) {
066            return sampleIndex;
067        }
068    }
069}