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

diff --git a/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java b/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java
index c04333c..02a8278 100644 (file)
--- a/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/BasicCombinableDomains.java
@@ -40,11 +40,11 @@ import org.forester.util.ForesterUtil;
 
 public class BasicCombinableDomains implements CombinableDomains {
 
+    final private TreeMap<String, Integer> _combining_domains;
     final private String                   _key_domain;
     private int                            _key_domain_count;
-    final private Species                  _species;
-    final private TreeMap<String, Integer> _combining_domains;
     final private Set<String>              _proteins_with_key_domain;
+    final private Species                  _species;
 
     public BasicCombinableDomains( final String key_domain, final Species species ) {
         _key_domain = key_domain;
@@ -117,10 +117,6 @@ public class BasicCombinableDomains implements CombinableDomains {
         return sb;
     }
 
-    protected TreeMap<String, Integer> getCombiningDomains() {
-        return _combining_domains;
-    }
-
     @Override
     public String getKeyDomain() {
         return _key_domain;
@@ -132,6 +128,11 @@ public class BasicCombinableDomains implements CombinableDomains {
     }
 
     @Override
+    public Set<String> getKeyDomainProteins() {
+        return _proteins_with_key_domain;
+    }
+
+    @Override
     public int getKeyDomainProteinsCount() {
         return getKeyDomainProteins().size();
     }
@@ -170,7 +171,8 @@ public class BasicCombinableDomains implements CombinableDomains {
     public List<BinaryDomainCombination> toBinaryDomainCombinations() {
         final List<BinaryDomainCombination> binary_combinations = new ArrayList<BinaryDomainCombination>( getNumberOfCombinableDomains() );
         for( final String domain : getCombiningDomains().keySet() ) {
-            binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
+            // binary_combinations.add( new BasicBinaryDomainCombination( getKeyDomain(), domain ) );
+            binary_combinations.add( BasicBinaryDomainCombination.obtainInstance( getKeyDomain(), domain ) );
         }
         return binary_combinations;
     }
@@ -190,8 +192,7 @@ public class BasicCombinableDomains implements CombinableDomains {
         return sb.toString();
     }
 
-    @Override
-    public Set<String> getKeyDomainProteins() {
-        return _proteins_with_key_domain;
+    protected TreeMap<String, Integer> getCombiningDomains() {
+        return _combining_domains;
     }
 }