X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FDirectedCombinableDomains.java;h=35f73f8ac30ceddf636bb578845ee7d28e67b8f9;hb=612e51e63eb66025a04439fc380384a945a4a30f;hp=1f2a6745fececf9673bfb3f52e4a799c726b6b1e;hpb=73c5b11c1a00e539afb246e345ebf3f042dded78;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java b/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
index 1f2a674..35f73f8 100644
--- a/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
@@ -22,7 +22,7 @@
 // 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;
 
@@ -30,22 +30,21 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.forester.protein.BinaryDomainCombination;
-import org.forester.protein.DomainId;
 import org.forester.species.Species;
 
 public class DirectedCombinableDomains extends BasicCombinableDomains {
 
-    public DirectedCombinableDomains( final DomainId n_terminal_key_domain, final Species species ) {
+    public DirectedCombinableDomains( 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 DirectedBinaryDomainCombination( getKeyDomain(), domain ) );
+            binary_combinations.add( DirectedBinaryDomainCombination.obtainInstance( getKeyDomain(), domain ) );
         }
         return binary_combinations;
     }