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.util.Comparator;
026
027
028/** a comparator to sort AlternativeAlignments based on their number of equivalent residues
029 * and RMSD.
030 *
031 * @author Andreas Prlic
032 *
033 */
034public class AltAligComparator implements Comparator<AlternativeAlignment> {
035
036
037        public AltAligComparator() {
038                super();
039
040        }
041
042        @Override
043        public int compare(AlternativeAlignment a, AlternativeAlignment b) {
044
045                int s1 = a.getIdx1().length;
046                int s2 = b.getIdx1().length;
047
048                if ( s1 > s2)
049                        return 1;
050                if ( s1 < s2)
051                        return -1;
052
053                // seem to have the same length
054
055                double rms1 = a.getRmsd();
056                double rms2 = b.getRmsd();
057
058                if ( rms1 < rms2)
059                        return 1;
060                if ( rms1 < rms2)
061                        return -1;
062
063                return 0;
064        }
065
066
067}