X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FCombinationsBasedPairwiseDomainSimilarityCalculator.java;h=feda0bc6b5d04036df0d57e4d4aea3a9429a6c93;hb=0898ccf757a9e1b3c10f0a8ad51829eb809d3062;hp=27327b6b73cdac95075ea24421aa11d0bc965f3d;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
index 27327b6..feda0bc 100644
--- a/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
+++ b/forester/java/src/org/forester/surfacing/CombinationsBasedPairwiseDomainSimilarityCalculator.java
@@ -29,8 +29,6 @@ package org.forester.surfacing;
 
 import java.util.List;
 
-import org.forester.protein.DomainId;
-
 public class CombinationsBasedPairwiseDomainSimilarityCalculator implements PairwiseDomainSimilarityCalculator {
 
     @Override
@@ -39,11 +37,11 @@ public class CombinationsBasedPairwiseDomainSimilarityCalculator implements Pair
         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++;
             }
@@ -51,7 +49,7 @@ public class CombinationsBasedPairwiseDomainSimilarityCalculator implements Pair
                 different++;
             }
         }
-        for( final DomainId domain : d2 ) {
+        for( final String domain : d2 ) {
             if ( !( d1.contains( domain ) ) ) {
                 different++;
             }