@Override
public Node visitTree(@NotNull NewickParser.TreeContext ctx) {
Node root = visit(ctx.node());
// Ensure tree is properly sorted in terms of node numbers.
root.sort();
// Replace lengths read from Newick with heights.
convertLengthToHeight(root);
// Make sure internal nodes are numbered correctly
numberUnnumberedNodes(root);
// Check for duplicate taxa
BitSet nodeNrSeen = new BitSet();
for (Node leaf : root.getAllLeafNodes()) {
if (leaf.getNr() < 0) continue; // Skip unnumbered leaves
if (nodeNrSeen.get(leaf.getNr()))
throw new ParseCancellationException(
"Duplicate taxon found: " + labels.get(leaf.getNr()));
else nodeNrSeen.set(leaf.getNr());
}
return root;
}
