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 */
021package org.biojava.bio.program.blast2html;
022
023
024/**
025 * <p>
026 * Interface for specifying whether a particular pair
027 * of residues/bases should be coloured.
028 * </p>
029 *
030 * <p>
031 * This can be independent of the method that
032 * chooses which colour.
033 * </p>
034 *
035 * <p>
036 * Example usage: highlight mismatches only.
037 * </p>
038 *
039 * <p><pre>
040 * Primary author -
041 *                 Colin Hardman      (CAT)
042 * Other authors  -
043 *                 Tim Dilks          (CAT)
044 *                 Simon Brocklehurst (CAT)
045 *                 Stuart Johnston    (CAT)
046 *                 Lawerence Bower    (CAT)
047 *                 Derek Crockford    (CAT)
048 *                 Neil Benn          (CAT)
049 *
050 * Copyright 2001 Cambridge Antibody Technology Group plc.
051 * </pre></p>
052 *
053 * <p>
054 * This code released to the biojava project, May 2001
055 * under the LGPL license.
056 * </p>
057 *
058 * @author Cambridge Antibody Technology Group plc
059 * @version 1.0
060 *
061 */
062public interface ColourCommand {
063
064    /**
065     * Returns true if the alignment pair should be coloured
066     * else false.
067     *
068     * @param poFirst  - the first character
069     * @param poSecond - the second character.
070     * @return boolean - true if colour, else false.
071     */
072    public boolean isColoured( String poFirst, String poSecond );
073}