in progress...

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

diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java
index d760297..6fd94f6 100644 (file)
--- a/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedCombinableDomains.java
@@ -30,19 +30,22 @@ 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 ) );
+            binary_combinations.add( AdjactantDirectedBinaryDomainCombination.obtainInstance( getKeyDomain(), domain ) );
         }
         return binary_combinations;
     }