in progress

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

diff --git a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
index a33527d..feda0bc 100644 (file)
--- a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.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
@@ -17,13 +17,13 @@
 // 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;
 
@@ -31,16 +31,17 @@ import java.util.List;
 
 public class CombinationsBasedPairwiseDomainSimilarityCalculator 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 List<DomainId> d1 = domains_1.getCombinableDomains();
-        final List<DomainId> d2 = domains_2.getCombinableDomains();
+        final List<String> d1 = domains_1.getCombinableDomains();
+        final List<String> d2 = domains_2.getCombinableDomains();
         int same = 0;
         int different = 0;
-        for( final DomainId domain : d1 ) {
+        for( final String domain : d1 ) {
             if ( d2.contains( domain ) ) {
                 same++;
             }
@@ -48,7 +49,7 @@ public class CombinationsBasedPairwiseDomainSimilarityCalculator implements Pair
                 different++;
             }
         }
-        for( final DomainId domain : d2 ) {
+        for( final String domain : d2 ) {
             if ( !( d1.contains( domain ) ) ) {
                 different++;
             }