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}