/*
 *                  BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on May 27, 2006
 *
 */
package org.biojava.nbio.structure.align.pairwise;

import java.io.Serializable;
import java.util.Comparator;


/** a comparator to sort AlternativeAlignments based on their number of equivalent residues
 * and RMSD.
 *
 * @author Andreas Prlic
 *
 */
public class AltAligComparator implements Comparator<AlternativeAlignment>, Serializable {
	private static final long serialVersionUID = 1;

	public AltAligComparator() {
		super();

	}

	@Override
	public int compare(AlternativeAlignment a, AlternativeAlignment b) {

		int s1 = a.getIdx1().length;
		int s2 = b.getIdx1().length;

		if ( s1 > s2)
			return 1;
		if ( s1 < s2)
			return -1;

		// seem to have the same length

		double rms1 = a.getRmsd();
		double rms2 = b.getRmsd();

		if ( rms1 < rms2)
			return 1;
		if ( rms1 < rms2)
			return -1;

		return 0;
	}


}

@@ -1231,24 +1231,29 @@
 return 1;%0A%09%09
+else 
 if ( s1 %3C s2
@@ -1268,17 +1268,26 @@
 urn -1;%0A
-%0A
+%09%09else %7B%0A%09
 %09%09// see
@@ -1312,19 +1312,19 @@
  length%0A
-%0A
 %09%09
+%09
 double r
@@ -1344,16 +1344,17 @@
 sd();%0A%09%09
+%09
 double r
@@ -1376,88 +1376,50 @@
 ();%0A
-%0A%09%09if ( rms1 %3C rms2)%0A%09%09%09return 1;%0A%09%09if ( 
+%09%09%09return Double.compare(
 rms1
- %3C
+,
  rms2)
-%0A%09%09%09return -1;%0A%0A%09%09return 0;
+;%0A%09%09%7D%0A
 %0A%09%7D%0A

Fix issue 864