JAL-2844 work started on moving the graphical partitioning code to Aptx

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

diff --git a/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java b/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
index 2103d26..35f73f8 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/DirectedCombinableDomains.java
@@ -6,7 +6,7 @@
 // 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
@@ -16,32 +16,35 @@
 // 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;
 
 import java.util.ArrayList;
 import java.util.List;
 
+import org.forester.protein.BinaryDomainCombination;
+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;
     }