public String getOperatorName() {
return TreeNodeSlideParser.TREE_NODE_REHEIGHT
+ "("
+ multree.getId()
+ ","
+ species.getId()
+ ")";
}
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();
}