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 May 27, 2006
021 *
022 */
023package org.biojava.nbio.structure.align.pairwise;
024
025import java.io.Serializable;
026import java.util.Comparator;
027
028
029/**
030 * A comparator to sort AlternativeAlignments based on their number of equivalent residues
031 * and RMSD.
032 *
033 * @author Andreas Prlic
034 *
035 */
036public class AltAligComparator implements Comparator<AlternativeAlignment> {
037
038        @Override
039        public int compare(AlternativeAlignment a, AlternativeAlignment b) {
040
041                int s1 = a.getIdx1().length;
042                int s2 = b.getIdx1().length;
043
044                if ( s1 > s2)
045                        return 1;
046                else if ( s1 < s2)
047                        return -1;
048                else {
049                        // seem to have the same length
050                        double rms1 = a.getRmsd();
051                        double rms2 = b.getRmsd();
052                        return Double.compare(rms1, rms2);
053                }
054
055        }
056
057
058}