if (tp.getTree() == null)
{
- Console.warn(
- "Not updating SequenceTreeMap for " + tree.getVorbaId());
+ 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
*/
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);
{
if (tp.getEntry(pe).getInputCount() > 1)
{
- Console.warn(
- "Ignoring additional input spec in provenance entry "
- + tp.getEntry(pe).toString());
+ Console.warn("Ignoring additional input spec in provenance entry "
+ + tp.getEntry(pe).toString());
}
// LATER: deal sensibly with multiple inputs
Input vInput = tp.getEntry(pe).getInput(0);