JAL-4134 - brutal hack to build a tree clustering columns of PAE Matrix

[jalview.git] / src / jalview / io / vamsas / Tree.java

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index 260894d..c0d1774 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -322,7 +322,7 @@ public class Tree extends DatastoreItem
       Console.warn("Not updating SequenceTreeMap for " + tree.getVorbaId());
       return;
     }
-    Vector<SequenceNode> leaves = tp.getTree()
+    Vector<BinaryNode> leaves = tp.getTree()
             .findLeaves(tp.getTree().getTopNode());
     Treenode[] tn = tree.getTreenode(); // todo: select nodes for this
     // particular tree
@@ -381,7 +381,7 @@ public class Tree extends DatastoreItem
    */
   public Treenode[] makeTreeNodes(TreeModel treeModel, Newick newick)
   {
-    Vector<SequenceNode> leaves = treeModel
+    Vector<BinaryNode> leaves = treeModel
             .findLeaves(treeModel.getTopNode());
     Vector tnv = new Vector();
     Enumeration l = leaves.elements();