Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups

[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 e8f6f6b..f6d17d4 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
@@ -358,7 +358,7 @@ public class Tree extends DatastoreItem
         }
         if (jvseq instanceof SequenceI)
         {
-          leaf.setElement(jvseq);
+          leaf.setElement((SequenceI) jvseq);
           leaf.setPlaceholder(false);
         }
         else
@@ -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();
@@ -394,8 +394,7 @@ public class Tree extends DatastoreItem
       {
         if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
         {
-          Object assocseq = ((jalview.datamodel.SequenceNode) tnode)
-                  .element();
+          Object assocseq = ((BinaryNode) tnode).element();
           if (assocseq instanceof SequenceI)
           {
             Vobject vobj = this.getjv2vObj(assocseq);