*
* used when the alignment associated to a tree has changed.
*
- * @param alignment
- * Vector
+ * @param list
+ * Sequence set to be associated with tree nodes
*/
- public void UpdatePlaceHolders(Vector alignment)
+ public void UpdatePlaceHolders(List<SequenceI> list)
{
Vector leaves = new Vector();
findLeaves(top, leaves);
{
SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
- if (alignment.contains(leaf.element()))
+ if (list.contains(leaf.element()))
{
leaf.setPlaceholder(false);
}
if (seqmatcher == null)
{
// Only create this the first time we need it
- SequenceI[] seqs = new SequenceI[alignment.size()];
+ SequenceI[] seqs = new SequenceI[list.size()];
for (int j = 0; j < seqs.length; j++)
{
- seqs[j] = (SequenceI) alignment.elementAt(j);
+ seqs[j] = (SequenceI) list.get(j);
}
seqmatcher = new SequenceIdMatcher(seqs);