public double[][] simulateLocations() {
NodeRef root = m_tree.getRoot();
// assume uniform
double[][] latLongs = new double[m_tree.getNodeCount()][2];
double rootLat = MathUtils.nextDouble() * (maxLat - minLat) + minLat;
double rootLong = MathUtils.nextDouble() * (maxLong - minLong) + minLong;
int rootNum = root.getNumber();
latLongs[rootNum][LATITUDE_INDEX] = rootLat;
latLongs[rootNum][LONGITUDE_INDEX] = rootLong;
traverse(root, latLongs[rootNum], latLongs);
return latLongs;
}
@Override
public double doOperation() throws OperatorFailedException {
apspnet.beginNetworkEdit();
double b = (1.0 - scalingFactor) * (1.0 - scalingFactor) / scalingFactor;
double c = scalingFactor / (1.0 - scalingFactor);
double y = MathUtils.nextDouble();
double s = b * (y + c) * (y + c);
int i = MathUtils.nextInt(apspnet.getNumberOfTetraTrees());
apspnet.setOneHybPopValue(i, s * apspnet.getOneHybPopValue(i));
apspnet.endNetworkEdit();
return 0.0; // this way of scaling, with proposal proportional to x^-(1/2) has hastings ratio 1
}
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();
}
/** change the parameter and return the hastings ratio. */
public final double doOperation() throws OperatorFailedException {
final double scale =
(scaleFactor + (MathUtils.nextDouble() * ((1.0 / scaleFactor) - scaleFactor)));
int goingUp = 0, goingDown = 0;
if (upParameter != null) {
for (Scalable.Default up : upParameter) {
goingUp += up.scaleAllAndNotify(scale, -1);
}
}
if (downParameter != null) {
for (Scalable.Default dn : downParameter) {
goingDown += dn.scaleAllAndNotify(1.0 / scale, -1);
}
}
return (goingUp - goingDown - 2) * Math.log(scale);
}
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();
}
}
public void operateOneNode(final double factor) throws OperatorFailedException {
// #print "operate: tree", ut.treerep(t)
// if( verbose) System.out.println(" Mau at start: " + tree.getSimpleTree());
final int count = multree.getExternalNodeCount();
assert count == species.nSpSeqs();
NodeRef[] order = new NodeRef[2 * count - 1];
boolean[] swapped = new boolean[count - 1];
mauCanonical(multree, order, swapped);
// internal node to change
// count-1 - number of internal nodes
int which = MathUtils.nextInt(count - 1);
FixedBitSet left = new FixedBitSet(count);
FixedBitSet right = new FixedBitSet(count);
for (int k = 0; k < 2 * which + 1; k += 2) {
left.set(multree.speciesIndex(order[k]));
}
for (int k = 2 * (which + 1); k < 2 * count; k += 2) {
right.set(multree.speciesIndex(order[k]));
}
double newHeight;
if (factor > 0) {
newHeight = multree.getNodeHeight(order[2 * which + 1]) * factor;
} else {
final double limit = species.speciationUpperBound(left, right);
newHeight = MathUtils.nextDouble() * limit;
}
multree.beginTreeEdit();
multree.setPreorderIndices(preOrderIndexBefore);
final NodeRef node = order[2 * which + 1];
multree.setNodeHeight(node, newHeight);
mauReconstruct(multree, order, swapped);
// restore pre-order of pops -
{
multree.setPreorderIndices(preOrderIndexAfter);
double[] splitPopValues = null;
for (int k = 0; k < preOrderIndexBefore.length; ++k) {
final int b = preOrderIndexBefore[k];
if (b >= 0) {
final int a = preOrderIndexAfter[k];
if (a != b) {
// if( verbose) System.out.println("pops: " + a + " <- " + b);
final Parameter p1 = multree.sppSplitPopulations;
if (splitPopValues == null) {
splitPopValues = p1.getParameterValues();
}
if (multree.constPopulation()) {
p1.setParameterValue(count + a, splitPopValues[count + b]);
} else {
for (int i = 0; i < 2; ++i) {
p1.setParameterValue(count + 2 * a + i, splitPopValues[count + 2 * b + i]);
}
}
}
}
}
}
multree.endTreeEdit();
}