in progress (special coloring is still true)

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

diff --git a/forester/java/src/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.java
index d902e75..904b642 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/DomainCountsBasedPairwiseSimilarityCalculator.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
@@ -17,25 +17,30 @@
 // 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 DomainCountsBasedPairwiseSimilarityCalculator implements PairwiseDomainSimilarityCalculator {
 
+    @Override
     public PairwiseDomainSimilarity calculateSimilarity( final CombinableDomains domains_1,
                                                          final CombinableDomains domains_2 ) {
         if ( !domains_1.getKeyDomain().equals( domains_2.getKeyDomain() ) ) {
             throw new IllegalArgumentException( "attempt to calculate similarity between domain collection with different keys" );
         }
-        final int dc1 = domains_1.getKeyDomainCount();
-        final int dc2 = domains_2.getKeyDomainCount();
-        return new CountsBasedPairwiseDomainSimilarity( dc1 - dc2, dc1 + dc2 );
+        if ( ( domains_1.getKeyDomainCount() > Short.MAX_VALUE ) || ( domains_2.getKeyDomainCount() > Short.MAX_VALUE )
+                || ( ( domains_1.getKeyDomainCount() + domains_2.getKeyDomainCount() ) > Short.MAX_VALUE ) ) {
+            throw new IllegalArgumentException( "too large for short!" );
+        }
+        final short dc1 = ( short ) domains_1.getKeyDomainCount();
+        final short dc2 = ( short ) domains_2.getKeyDomainCount();
+        return new CountsBasedPairwiseDomainSimilarity( ( short ) ( dc1 - dc2 ), ( short ) ( dc1 + dc2 ) );
     }
 }