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/** a comparator to sort AlternativeAlignments based on their number of equivalent residues
030 * and RMSD.
031 *
032 * @author Andreas Prlic
033 *
034 */
035public class AltAligComparator implements Comparator<AlternativeAlignment>, Serializable {
036    private static final long serialVersionUID = 1;
037
038        public AltAligComparator() {
039                super();
040
041        }
042
043        @Override
044        public int compare(AlternativeAlignment a, AlternativeAlignment b) {
045
046                int s1 = a.getIdx1().length;
047                int s2 = b.getIdx1().length;
048
049                if ( s1 > s2)
050                        return 1;
051                if ( s1 < s2)
052                        return -1;
053
054                // seem to have the same length
055
056                double rms1 = a.getRmsd();
057                double rms2 = b.getRmsd();
058
059                if ( rms1 < rms2)
060                        return 1;
061                if ( rms1 < rms2)
062                        return -1;
063
064                return 0;
065        }
066
067
068}