JAL-2795 added duplication check when calculated nodes are bound to seqs

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
index 9166497..f010450 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -90,8 +90,10 @@ public class ArchaeopteryxTreeBuilder
       NodeData nodeData = sequenceNode.getNodeData();
       nodeData.setSequence(seq);
 
-      nodesWithAlignment.put(sequenceNode, sequence);
-      alignmentWithNodes.put(sequence, sequenceNode);
+      ExternalTreeBuilderI.putWithDuplicationCheck(nodesWithAlignment,
+              sequenceNode, sequence);
+      ExternalTreeBuilderI.putWithDuplicationCheck(alignmentWithNodes,
+              sequence, sequenceNode);
       rootNode.addAsChild(sequenceNode);
     }
 
@@ -161,4 +163,6 @@ public class ArchaeopteryxTreeBuilder
       return ttl;
     }
   }
+  
+
 }