@Override
protected Double modifyARG()
throws InvalidParameterValueException, IllegalModificationException,
ModificationImpossibleException {
List<ARGNode> internalNodes = arg.getInternalNodes();
int nodeNum = RandomSource.getNextIntFromTo(0, internalNodes.size() - 1);
ARGNode node = internalNodes.get(nodeNum);
if (internalNodes.size() == 1) // Must be two tips, no recomb nodes
throw new ModificationImpossibleException("No internal nodes to modify");
// Pick a node that is not the root
while (node.getParent(0) == null) {
node = internalNodes.get(RandomSource.getNextIntFromTo(0, internalNodes.size() - 1));
}
double hr;
if (node instanceof CoalNode) {
hr = swapCoalNode((CoalNode) node);
} else {
hr = swapRecombNode((RecombNode) node);
}
return hr;
}
protected double swapCoalNode(CoalNode node)
throws ModificationImpossibleException, IllegalModificationException {
List<ARGNode> branches = arg.getBranchesCrossingTime(node.getHeight());
ARGNode newChild =
branches.get(
RandomSource.getNextIntFromTo(
0, branches.size() - 1)); // This will be new child of coal node
ARGNode newParent = findDisplaceableParent(newChild, node.getHeight()); // New parent of node
int oldChildIndex = RandomSource.getNextIntFromTo(0, 1);
ARGNode oldChild =
node.getOffspring(oldChildIndex); // Child that will be attached to node's parent
ARGNode oldParent = node.getParent();
// Attach the old child we are leaving to the old parent
int pIndex = whichChild(node, oldParent);
oldChild.proposeParent(whichParent(oldChild, node), oldParent);
oldParent.proposeOffspring(pIndex, oldChild);
// Insert the new node between newChild and newParent
int cIndex = whichParent(newChild, newParent);
int cpIndex = whichChild(newChild, newParent);
node.proposeParent(newParent);
newParent.proposeOffspring(cpIndex, node);
newChild.proposeParent(cIndex, node);
node.proposeOffspring(oldChildIndex, newChild);
propogateRangeProposals(oldChild);
propogateRangeProposals(node);
if (verbose)
System.out.println(
"Swapping coal node "
+ node
+ " to branch connecting parent "
+ newParent
+ " to offspring "
+ newChild);
return 1.0;
}