public void forwardIBD() {
int numNodes = treeModel.getNodeCount();
int stateCount = substitutionModel.getStateCount();
getDiagonalRates(diag);
for (int nodeId = 0; nodeId < numNodes; ++nodeId) {
NodeRef node = treeModel.getNode(nodeId);
NodeRef parent = treeModel.getParent(node);
if (parent == null) { // handle the root
} else if (treeModel.isExternal(node)) { // Handle the tip
double branchTime =
branchRateModel.getBranchRate(treeModel, node)
* (treeModel.getNodeHeight(parent) - treeModel.getNodeHeight(node));
for (int state = 0; state < stateCount; ++state) {
ibdForward[nodeId][state] = Math.exp(-diag[state] * branchTime);
}
} else { // Handle internal node
double branchTime =
branchRateModel.getBranchRate(treeModel, node)
* (treeModel.getNodeHeight(parent) - treeModel.getNodeHeight(node));
int childCount = treeModel.getChildCount(node);
for (int state = 0; state < stateCount; ++state) {
ibdForward[nodeId][state] = 0;
for (int child = 0; child < childCount; ++child) {
int childNodeId = treeModel.getChild(node, child).getNumber();
ibdForward[nodeId][state] += ibdForward[childNodeId][state];
}
ibdForward[nodeId][state] *= Math.exp(-diag[state] * branchTime);
}
}
}
}
public void backwardIBD(NodeRef node) {
int stateCount = substitutionModel.getStateCount();
if (node == null) {
node = treeModel.getRoot();
int nodeId = node.getNumber();
for (int state = 0; state < stateCount; ++state) {
ibdBackward[nodeId][state] = 0;
}
}
getDiagonalRates(diag);
int childCount = treeModel.getChildCount(node);
int nodeId = node.getNumber();
for (int child = 0; child < childCount; ++child) {
NodeRef childNode = treeModel.getChild(node, child);
int childNodeId = childNode.getNumber();
double branchTime =
branchRateModel.getBranchRate(treeModel, childNode)
* (treeModel.getNodeHeight(node) - treeModel.getNodeHeight(childNode));
for (int state = 0; state < stateCount; ++state) {
ibdBackward[childNodeId][state] = ibdBackward[nodeId][state];
for (int sibling = 0; sibling < childCount; ++sibling) {
if (sibling != child) {
int siblingId = treeModel.getChild(node, sibling).getNumber();
ibdBackward[childNodeId][state] += ibdForward[siblingId][state];
}
}
ibdBackward[childNodeId][state] *= Math.exp(-diag[state] * branchTime);
}
}
for (int child = 0; child < childCount; ++child) {
NodeRef childNode = treeModel.getChild(node, child);
backwardIBD(childNode);
}
}
public static void checkTree(TreeModel treeModel) {
// todo Should only be run if there exists a zero-length interval
// TreeModel treeModel = (TreeModel) tree;
for (int i = 0; i < treeModel.getInternalNodeCount(); i++) {
NodeRef node = treeModel.getInternalNode(i);
if (node != treeModel.getRoot()) {
double parentHeight = treeModel.getNodeHeight(treeModel.getParent(node));
double childHeight0 = treeModel.getNodeHeight(treeModel.getChild(node, 0));
double childHeight1 = treeModel.getNodeHeight(treeModel.getChild(node, 1));
double maxChild = childHeight0;
if (childHeight1 > maxChild) maxChild = childHeight1;
double newHeight = maxChild + MathUtils.nextDouble() * (parentHeight - maxChild);
treeModel.setNodeHeight(node, newHeight);
}
}
treeModel.pushTreeChangedEvent();
}
private void setup() {
DataType dataType = baseSubstitutionModel.getDataType();
FrequencyModel freqModel = baseSubstitutionModel.getFrequencyModel();
Parameter kappaParameter = new Parameter.Default("kappa", 1, baseSubstitutionModel.getKappa());
substitutionModels = new LinkedList<SubstitutionModel>();
branchAssignmentMap = new LinkedHashMap<NodeRef, Integer>();
int branchClass = 0;
for (NodeRef node : treeModel.getNodes()) {
if (!treeModel.isRoot(node)) {
double nodeHeight = treeModel.getNodeHeight(node);
double parentHeight = treeModel.getNodeHeight(treeModel.getParent(node));
double time = 0.5 * (parentHeight + nodeHeight);
double baseOmega = baseSubstitutionModel.getOmega();
double fixed = baseOmega * time;
double epsilon =
(Math.log(1 - random.nextDouble())
/ (-rate)); // Math.exp((random.nextGaussian() * stdev + mean));
double value = fixed + epsilon;
Parameter omegaParameter = new Parameter.Default("omega", 1, value);
GY94CodonModel gy94 =
new GY94CodonModel((Codons) dataType, omegaParameter, kappaParameter, freqModel);
substitutionModels.add(gy94);
branchAssignmentMap.put(node, branchClass);
branchClass++;
} // END: root check
} // END: nodes loop
} // END: setup
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();
}
}