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
}
if (jvseq instanceof SequenceI)
{
- leaf.setElement(jvseq);
+ leaf.setElement((SequenceI) jvseq);
leaf.setPlaceholder(false);
}
else
*/
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();
{
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);
}
else
{
- System.err.println("WARNING: Unassociated treeNode "
+ jalview.bin.Console.errPrintln("WARNING: Unassociated treeNode "
+ tnode.element().toString() + " "
+ ((tnode.getName() != null)
? " label " + tnode.getName()
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;