X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FAdjactantDirectedCombinableDomains.java;h=eb4f9f1f6f286b62412feb5d2941f2847e31edb6;hb=e0d3ddb03137a2f01528e995186c657d5067e673;hp=adfd02cc8f0eecfe8e67fbb176d6caa413b2cfc1;hpb=48f7a89be9d34f1930a1f863e608235cc27184c5;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java
index adfd02c..eb4f9f1 100644
--- a/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.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
@@ -17,7 +17,7 @@
 // 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
@@ -30,16 +30,19 @@ package org.forester.surfacing;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.species.Species;
+
 public class AdjactantDirectedCombinableDomains extends BasicCombinableDomains {
 
-    public AdjactantDirectedCombinableDomains( final DomainId n_terminal_key_domain, final Species species ) {
+    public AdjactantDirectedCombinableDomains( final String n_terminal_key_domain, final Species species ) {
         super( n_terminal_key_domain, species );
     }
 
     @Override
     public List<BinaryDomainCombination> toBinaryDomainCombinations() {
         final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
-        for( final DomainId domain : getCombiningDomains().keySet() ) {
+        for( final String domain : getCombiningDomains().keySet() ) {
             // Precondition (!): key domain is most upstream domain.
             //TODO ensure this is true.
             binary_combinations.add( new AdjactantDirectedBinaryDomainCombination( getKeyDomain(), domain ) );