public static Transform[] parseListOfTransforms(XMLObject xo, int maxDim)
throws XMLParseException {
Transform[] transforms = null;
boolean anyTransforms = false;
for (int i = 0; i < xo.getChildCount(); ++i) {
if (xo.getChild(i) instanceof Transform.ParsedTransform) {
Transform.ParsedTransform t = (Transform.ParsedTransform) xo.getChild(i);
if (transforms == null) {
transforms = Transform.Util.getListOfNoTransforms(maxDim);
}
t.end = Math.max(t.end, maxDim);
if (t.start < 0 || t.end < 0 || t.start > t.end) {
throw new XMLParseException("Invalid bounds for transform in " + xo.getId());
}
for (int j = t.start; j < t.end; j += t.every) {
transforms[j] = t.transform;
anyTransforms = true;
}
}
}
if (anyTransforms) {
StringBuilder sb =
new StringBuilder("Using distributional transforms in " + xo.getId() + "\n");
for (int i = 0; i < transforms.length; ++i) {
if (transforms[i] != Transform.NONE) {
sb.append("\t")
.append(transforms[i].getTransformName())
.append(" on index ")
.append(i + 1)
.append("\n");
}
}
sb.append("Please cite:\n").append(Citable.Utils.getCitationString(Transform.LOG));
Logger.getLogger("dr.utils.Transform").info(sb.toString());
}
return transforms;
}
public void proposeTree() throws OperatorFailedException {
TreeModel tree = c2cLikelihood.getTreeModel();
BranchMapModel branchMap = c2cLikelihood.getBranchMap();
NodeRef i;
double oldMinAge, newMinAge, newRange, oldRange, newAge, q;
// choose a random node avoiding root, and nodes that are ineligible for this move because they
// have nowhere to
// go
final int nodeCount = tree.getNodeCount();
do {
i = tree.getNode(MathUtils.nextInt(nodeCount));
} while (tree.getRoot() == i || !eligibleForMove(i, tree, branchMap));
final NodeRef iP = tree.getParent(i);
// this one can go anywhere
NodeRef j = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
NodeRef k = tree.getParent(j);
while ((k != null && tree.getNodeHeight(k) <= tree.getNodeHeight(i)) || (i == j)) {
j = tree.getNode(MathUtils.nextInt(tree.getNodeCount()));
k = tree.getParent(j);
}
if (iP == tree.getRoot() || j == tree.getRoot()) {
throw new OperatorFailedException("Root changes not allowed!");
}
if (k == iP || j == iP || k == i) throw new OperatorFailedException("move failed");
final NodeRef CiP = getOtherChild(tree, iP, i);
NodeRef PiP = tree.getParent(iP);
newMinAge = Math.max(tree.getNodeHeight(i), tree.getNodeHeight(j));
newRange = tree.getNodeHeight(k) - newMinAge;
newAge = newMinAge + (MathUtils.nextDouble() * newRange);
oldMinAge = Math.max(tree.getNodeHeight(i), tree.getNodeHeight(CiP));
oldRange = tree.getNodeHeight(PiP) - oldMinAge;
q = newRange / Math.abs(oldRange);
// need to account for the random repainting of iP
if (branchMap.get(PiP.getNumber()) != branchMap.get(CiP.getNumber())) {
q *= 0.5;
}
if (branchMap.get(k.getNumber()) != branchMap.get(j.getNumber())) {
q *= 2;
}
tree.beginTreeEdit();
if (j == tree.getRoot()) {
// 1. remove edges <iP, CiP>
tree.removeChild(iP, CiP);
tree.removeChild(PiP, iP);
// 2. add edges <k, iP>, <iP, j>, <PiP, CiP>
tree.addChild(iP, j);
tree.addChild(PiP, CiP);
// iP is the new root
tree.setRoot(iP);
} else if (iP == tree.getRoot()) {
// 1. remove edges <k, j>, <iP, CiP>, <PiP, iP>
tree.removeChild(k, j);
tree.removeChild(iP, CiP);
// 2. add edges <k, iP>, <iP, j>, <PiP, CiP>
tree.addChild(iP, j);
tree.addChild(k, iP);
// CiP is the new root
tree.setRoot(CiP);
} else {
// 1. remove edges <k, j>, <iP, CiP>, <PiP, iP>
tree.removeChild(k, j);
tree.removeChild(iP, CiP);
tree.removeChild(PiP, iP);
// 2. add edges <k, iP>, <iP, j>, <PiP, CiP>
tree.addChild(iP, j);
tree.addChild(k, iP);
tree.addChild(PiP, CiP);
}
tree.setNodeHeight(iP, newAge);
tree.endTreeEdit();
//
logq = Math.log(q);
// repaint the parent to match either its new parent or its new child (50% chance of each).
if (MathUtils.nextInt(2) == 0) {
branchMap.set(iP.getNumber(), branchMap.get(k.getNumber()), true);
} else {
branchMap.set(iP.getNumber(), branchMap.get(j.getNumber()), true);
}
if (DEBUG) {
c2cLikelihood.checkPartitions();
}
}