JAL-1953 JAL-2852 added public "paintFile" method

[jalview.git] / forester / java / src / org / forester / surfacing / CombinationsBasedPairwiseDomainSimilarity.java

diff --git a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java
index b3035c5..a98298d 100644 (file)
--- a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java
+++ b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarity.java
@@ -7,7 +7,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -17,21 +17,21 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.surfacing;
 
 public class CombinationsBasedPairwiseDomainSimilarity implements PairwiseDomainSimilarity {
 
-    private final int    _same_domains;
-    private final int    _different_domains;
     private final int    _difference_in_counts;
+    private final int    _different_domains;
+    private final int    _same_domains;
     private final double _score;
 
     public CombinationsBasedPairwiseDomainSimilarity( final int same_domains,
@@ -64,6 +64,7 @@ public class CombinationsBasedPairwiseDomainSimilarity implements PairwiseDomain
         return _same_domains;
     }
 
+    @Override
     public double getSimilarityScore() {
         return _score;
     }