/**
* Number any nodes in a clade which were not explicitly numbered by the parsed string.
*
* @param node clade parent
*/
private void numberUnnumberedNodes(Node node) {
if (node.isLeaf()) return;
for (Node child : node.getChildren()) {
numberUnnumberedNodes(child);
}
if (node.getNr() < 0) node.setNr(numberedNodeCount);
numberedNodeCount += 1;
}
/**
* Disconnect node from root, discarding all colouring on <node,root> and <node's sister,root>.
*
* @param node
*/
public void disconnectBranchFromRoot(Node node) {
// Check argument validity:
if (node.isRoot() || !node.getParent().isRoot())
throw new IllegalArgumentException("Illegal argument to" + " disconnectBranchFromRoot().");
// Implement topology change:
Node parent = node.getParent();
Node sister = getOtherChild(parent, node);
sister.setParent(null);
parent.getChildren().remove(sister);
// Clear colour changes on new root:
((MultiTypeNode) sister).clearChanges();
// Ensure BEAST knows to update affected likelihoods:
parent.makeDirty(Tree.IS_FILTHY);
sister.makeDirty(Tree.IS_FILTHY);
node.makeDirty(Tree.IS_FILTHY);
}