Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[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..5ea97fb 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);
@@ -416,11 +415,12 @@ public class Tree extends DatastoreItem
             }
             else
             {
-              System.err.println("WARNING: Unassociated treeNode "
-                      + tnode.element().toString() + " "
-                      + ((tnode.getName() != null)
-                              ? " label " + tnode.getName()
-                              : ""));
+              jalview.bin.Console
+                      .errPrintln("WARNING: Unassociated treeNode "
+                              + tnode.element().toString() + " "
+                              + ((tnode.getName() != null)
+                                      ? " label " + tnode.getName()
+                                      : ""));
             }
           }
         }
@@ -467,7 +467,7 @@ public class Tree extends DatastoreItem
       occurence = Integer.valueOf(oval).intValue();
     } catch (Exception e)
     {
-      System.err.println("Invalid nodespec '" + nodespec + "'");
+      jalview.bin.Console.errPrintln("Invalid nodespec '" + nodespec + "'");
       return null;
     }
     jalview.datamodel.BinaryNode bn = null;