private static int mauCanonicalSub(
Tree tree, NodeRef node, int loc, NodeRef[] order, boolean[] wasSwaped) {
if (tree.isExternal(node)) {
order[loc] = node;
assert (loc & 0x1) == 0;
return loc + 1;
}
final boolean swap = MathUtils.nextBoolean();
// wasSwaped[(loc-1)/2] = swap;
int l = mauCanonicalSub(tree, tree.getChild(node, swap ? 1 : 0), loc, order, wasSwaped);
order[l] = node;
assert (l & 0x1) == 1;
wasSwaped[(l - 1) / 2] = swap;
l = mauCanonicalSub(tree, tree.getChild(node, swap ? 0 : 1), l + 1, order, wasSwaped);
return l;
}
public double splitClade(Clade parent, Clade[] children) {
// the number of all possible clades is 2^n with n the number of tips
// reduced by 2 because we wont consider the clades with all or no tips
// contained
// divide this number by 2 because every clade has a matching clade to
// form the split
// #splits = 2^(n-1) - 1
final double splits = Math.pow(2, parent.getSize() - 1) - 1;
double prob = 0;
if (cladeCoProbabilities.containsKey(parent.getBits())) {
HashMap<BitSet, Clade> childClades = cladeCoProbabilities.get(parent.getBits());
double noChildClades = 0.0;
double sum = 0.0;
Set<BitSet> keys = childClades.keySet();
for (BitSet child : keys) {
Clade tmp = childClades.get(child);
if (parent.getSize() > tmp.getSize() + 1) {
sum += (tmp.getSampleCount() + EPSILON) / 2.0;
noChildClades += 0.5;
} else {
sum += (tmp.getSampleCount() + EPSILON);
noChildClades += 1.0;
}
}
// add epsilon for each not observed clade
sum += EPSILON * (splits - noChildClades);
// roulette wheel
double randomNumber = Math.random() * sum;
for (BitSet child : keys) {
Clade tmp = childClades.get(child);
if (parent.getSize() > tmp.getSize() + 1) {
randomNumber -= (tmp.getSampleCount() + EPSILON) / 2.0;
} else {
randomNumber -= (tmp.getSampleCount() + EPSILON);
}
if (randomNumber < 0) {
children[0] = tmp;
prob = (tmp.getSampleCount() + EPSILON) / sum;
break;
}
}
if (randomNumber >= 0) {
// randomNumber /= EPSILON;
prob = EPSILON / sum;
BitSet newChild;
BitSet inverseBits;
do {
do {
newChild = (BitSet) parent.getBits().clone();
int index = -1;
do {
index = newChild.nextSetBit(index + 1);
if (index > -1 && MathUtils.nextBoolean()) {
newChild.clear(index);
}
} while (index > -1);
} while (newChild.cardinality() == 0 || newChild.cardinality() == parent.getSize());
inverseBits = (BitSet) newChild.clone();
inverseBits.xor(parent.getBits());
} while (childClades.containsKey(newChild) || childClades.containsKey(inverseBits));
Clade randomClade = new Clade(newChild, 0.9999 * parent.getHeight());
children[0] = randomClade;
BitSet secondChild = (BitSet) children[0].getBits().clone();
secondChild.xor(parent.getBits());
children[1] = new Clade(secondChild, 0.9999 * parent.getHeight());
} else {
BitSet secondChild = (BitSet) children[0].getBits().clone();
secondChild.xor(parent.getBits());
children[1] = childClades.get(secondChild);
if (children[1] == null) {
children[1] = new Clade(secondChild, 0.9999 * parent.getHeight());
}
}
} else {
prob = 1.0 / splits;
BitSet newChild;
do {
newChild = (BitSet) parent.getBits().clone();
int index = -1;
do {
index = newChild.nextSetBit(index + 1);
if (index > -1 && MathUtils.nextBoolean()) {
newChild.clear(index);
}
} while (index > -1);
} while (newChild.cardinality() == 0 || newChild.cardinality() == parent.getSize());
Clade randomClade = new Clade(newChild, 0.9999 * parent.getHeight());
// randomClade.addSample();
randomClade.addHeight(0.9999 * parent.getHeight());
children[0] = randomClade;
BitSet secondChild = (BitSet) children[0].getBits().clone();
secondChild.xor(parent.getBits());
children[1] = new Clade(secondChild, 0.9999 * parent.getHeight());
// children[1].addSample();
randomClade.addHeight(0.9999 * parent.getHeight());
}
return Math.log(prob);
}
