@Test
public void testOperator2() throws Exception {
Tree tree;
int taxaSize = 3;
// make a caterpillar
Node left = new ZeroBranchSANode();
left.setNr(0);
left.setHeight(0.0);
for (int i = 1; i < taxaSize; i++) {
Node right = new ZeroBranchSANode();
right.setNr(i);
right.setHeight(i);
Node parent = new ZeroBranchSANode();
parent.setNr(taxaSize + i - 1);
parent.setHeight(i);
left.setParent(parent);
parent.setLeft(left);
right.setParent(parent);
parent.setRight(right);
left = parent;
}
left.setHeight(left.getRight().getHeight() + 2);
tree = new Tree(left);
System.out.println("Tree was = " + tree.getRoot().toShortNewick(false));
TreeDimensionJump operator = new TreeDimensionJump();
operator.initByName("tree", tree);
double logHastingsRatio = operator.proposal();
System.out.println("Proposed tree = " + tree.getRoot().toShortNewick(false));
System.out.println("Log Hastings ratio = " + logHastingsRatio);
}
/**
* Set up node's parent as the new root with a height of destTime, with oldRoot as node's new
* sister.
*
* @param node
* @param oldRoot
* @param destTime
*/
public void connectBranchToRoot(Node node, Node oldRoot, double destTime) {
// Check argument validity:
if (node.isRoot() || !oldRoot.isRoot())
throw new IllegalArgumentException("Illegal argument " + "to connectBranchToRoot().");
// Obtain existing parent of node and set new time:
Node newRoot = node.getParent();
newRoot.setHeight(destTime);
// Implement topology changes:
newRoot.setParent(null);
if (newRoot.getLeft() == node) newRoot.setRight(oldRoot);
else if (newRoot.getRight() == node) newRoot.setLeft(oldRoot);
oldRoot.setParent(newRoot);
// Ensure BEAST knows to recalculate affected likelihood:
newRoot.makeDirty(Tree.IS_FILTHY);
oldRoot.makeDirty(Tree.IS_FILTHY);
node.makeDirty(Tree.IS_FILTHY);
}
/**
* 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);
}
/**
* Creates a new branch between node and a new node at time destTime between destBranchBase and
* its parent. Colour changes are divided between the two new branches created by the split.
*
* @param node
* @param destBranchBase
* @param destTime
*/
public void connectBranch(Node node, Node destBranchBase, double destTime) {
// Check argument validity:
if (node.isRoot() || destBranchBase.isRoot())
throw new IllegalArgumentException("Illegal argument to " + "connectBranch().");
// Obtain existing parent of node and set new time:
Node parent = node.getParent();
parent.setHeight(destTime);
MultiTypeNode mtParent = (MultiTypeNode) parent;
MultiTypeNode mtDestBranchBase = (MultiTypeNode) destBranchBase;
// Determine where the split comes in the list of colour changes
// attached to destBranchBase:
int split;
for (split = 0; split < mtDestBranchBase.getChangeCount(); split++)
if (mtDestBranchBase.getChangeTime(split) > destTime) break;
// Divide colour changes between new branches:
mtParent.clearChanges();
for (int idx = split; idx < mtDestBranchBase.getChangeCount(); idx++)
mtParent.addChange(mtDestBranchBase.getChangeType(idx), mtDestBranchBase.getChangeTime(idx));
mtDestBranchBase.truncateChanges(split);
// Set colour at split:
mtParent.setNodeType(mtDestBranchBase.getFinalType());
// Implement topology changes:
replace(destBranchBase.getParent(), destBranchBase, parent);
destBranchBase.setParent(parent);
if (parent.getLeft() == node) parent.setRight(destBranchBase);
else if (parent.getRight() == node) parent.setLeft(destBranchBase);
// Ensure BEAST knows to update affected likelihoods:
node.makeDirty(Tree.IS_FILTHY);
parent.makeDirty(Tree.IS_FILTHY);
destBranchBase.makeDirty(Tree.IS_FILTHY);
}