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}