/**
* increments the number of occurrences for all conditional clades
*
* @param tree - the tree to be added
*/
public void addTree(Tree tree, HashMap<String, Integer> taxonMap) {
samples++;
List<Clade> clades = new ArrayList<Clade>();
List<Clade> parentClades = new ArrayList<Clade>();
// get clades contained in the tree
getClades(tree, tree.getRoot(), parentClades, clades, taxonMap);
// add the clade containing all taxa as well so that it get counted
clades.add(parentClades.get(parentClades.size() - 1));
parentClades.add(clades.get(clades.size() - 1));
int size = clades.size();
// for every clade multiply its conditional clade probability to the
// tree probability
for (int i = 0; i < size; i++) {
Clade c = clades.get(i);
// get the bits of the clade
Clade parent = parentClades.get(i);
HashMap<BitSet, Clade> coFreqs;
// increment the clade occurrences
if (cladeProbabilities.containsKey(c.getBits())) {
Clade tmp = cladeProbabilities.get(c.getBits());
// tmp.addSample();
tmp.addHeight(c.getHeight());
// add the amount to the current occurences
// frequency += cladeProbabilities.get(c);
} else {
// just to set the first value of the height value list
// c.addSample();
c.addHeight(c.getHeight());
cladeProbabilities.put(c.getBits(), c);
}
// increment the conditional clade occurrences
if (!parent.equals(c)) {
if (cladeCoProbabilities.containsKey(parent.getBits())) {
coFreqs = cladeCoProbabilities.get(parent.getBits());
} else {
// if it's the first time we observe the parent then we need
// a new list for its conditional clades
coFreqs = new HashMap<BitSet, Clade>();
cladeCoProbabilities.put(parent.getBits(), coFreqs);
}
// add the previous observed occurrences for this conditional
// clade
if (coFreqs.containsKey(c.getBits())) {
Clade tmp = coFreqs.get(c.getBits());
tmp.addHeight(c.getHeight());
// coFrequency += coFreqs.get(c.getBits());
} else {
// TODO check this code, especially if the cloning is needed
// and not just the clade could be added
Clade tmp = new Clade((BitSet) c.getBits().clone(), c.getHeight());
tmp.addHeight(c.getHeight());
coFreqs.put(c.getBits(), tmp);
}
}
}
}
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);
}