X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FProteinCountsBasedPairwiseDomainSimilarityCalculator.java;h=8c42787c106dcf59cca739dd24cf1e36744c9a0a;hb=b528989f688291ba7615867e5322090ec42096d8;hp=d61252c9490ace32f2ad9aa36d0031e932836112;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.java
index d61252c..8c42787 100644
--- a/forester/java/src/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/ProteinCountsBasedPairwiseDomainSimilarityCalculator.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 +17,31 @@
 // 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 ProteinCountsBasedPairwiseDomainSimilarityCalculator 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 pc1 = domains_1.getKeyDomainProteinsCount();
-        final int pc2 = domains_2.getKeyDomainProteinsCount();
-        return new CountsBasedPairwiseDomainSimilarity( pc1 - pc2, pc1 + pc2 );
+        if ( ( domains_1.getKeyDomainProteinsCount() > Short.MAX_VALUE )
+                || ( domains_2.getKeyDomainProteinsCount() > Short.MAX_VALUE )
+                || ( ( domains_1.getKeyDomainProteinsCount() + domains_2.getKeyDomainCount() ) > Short.MAX_VALUE ) ) {
+            throw new IllegalArgumentException( "too large for short!" );
+        }
+        final short pc1 = ( short ) domains_1.getKeyDomainProteinsCount();
+        final short pc2 = ( short ) domains_2.getKeyDomainProteinsCount();
+        return new CountsBasedPairwiseDomainSimilarity( ( short ) ( pc1 - pc2 ), ( short ) ( pc1 + pc2 ) );
     }
 }