/**
* FOR TESTING ONLY Add a single split to the hash table
*
* @param partition BitSet split to add
*/
public void addTestSplit(BitSet partition) {
long tableKey2 = 0;
long bucketKey2 = 0;
// always calculate the split directly
for (int k = 0; k < noOfTaxa; k++) {
if (partition.get(k) == true) {
tableKey2 += hashUtils.a1[k];
bucketKey2 += hashUtils.a2[k];
}
}
hashTable.put(
partition,
1,
(int) (tableKey2 % hashUtils.m1),
(int) (bucketKey2 % hashUtils.m2),
interestThreshold,
partitions);
}
/**
* Create partitions from an input tree - recursive so will be called by many nodes, beginning
* with root but with calculations actually beginning on leaves.
*
* @param node Node in tree with above split to add to the hash table
*/
private BitSet createPartitions(TreeNode node) {
if (node.isLeaf()) { // Leaf node.
int index = taxa.get(node.name);
// leaf simply has it's keys stored in the hash utilities
node.addProperty("tableHashKey", hashUtils.a1[index]);
node.addProperty("bucketHashKey", hashUtils.a2[index]);
// Updates the edge length array.
leafEdgeLengths[index] += node.edgeLength;
// Create a new partition from scratch to represent it
BitSet partition = new BitSet(noOfTaxa);
partition.set(index);
assert partition.cardinality() == 1 : "There should be exactly a single bit set.";
return partition;
} else { // An internal node: Traverses the tree in post order.
BitSet partition = new BitSet(noOfTaxa);
// Get the node's partition representation from its children
List<TreeNode> children = node.children;
for (TreeNode child : children) {
partition.or(createPartitions(child));
}
// if this node is NOT to the right side of the root then add it... (Avoid adding splits twice
// for CNetworks)
if (node.parent != root || root.getRight() != node) {
noOfPartitions++;
long tableKey = 0;
long bucketKey = 0;
long tableKey2 = 0;
long bucketKey2 = 0;
// Calculate the hash keys for this partition
for (TreeNode child : children) {
tableKey += child.getIntProperty("tableHashKey");
bucketKey += child.getIntProperty("bucketHashKey");
}
// if first is one then we need to store the flipped version so we store each split in one
// representation only.
if (partition.get(0) == true) {
// copy to a new partition that is the flipped version
BitSet partitionF = new BitSet(noOfTaxa);
for (int l = 0; l < noOfTaxa; l++) {
if (partition.get(l) == false) partitionF.set(l);
}
// calculate the hash keys for the flipped partition...
for (int k = 0; k < noOfTaxa; k++) {
if (partitionF.get(k) == true) {
tableKey2 += hashUtils.a1[k];
bucketKey2 += hashUtils.a2[k];
}
}
// store the properties in the node
node.addProperty("tableHashKey", (int) (tableKey2 % hashUtils.m1));
node.addProperty("bucketHashKey", (int) (bucketKey2 % hashUtils.m2));
if (noOfPartitions < noOfTaxa - 2) { // Avoids the addition of the star partition
hashTable.put(
partitionF,
node.edgeLength,
node.getIntProperty("tableHashKey"),
node.getIntProperty("bucketHashKey"),
interestThreshold,
partitions);
}
// remember to still return the original partition with its appropriate keys...
node.addProperty("tableHashKey", (int) (tableKey % hashUtils.m1));
node.addProperty("bucketHashKey", (int) (bucketKey % hashUtils.m2));
return partition;
}
// if first is zero then simply add the partition, recursively calculating the hash
else {
node.addProperty("tableHashKey", (int) (tableKey % hashUtils.m1));
node.addProperty("bucketHashKey", (int) (bucketKey % hashUtils.m2));
if (noOfPartitions < noOfTaxa - 2) { // Avoids the addition of the star partition
hashTable.put(
partition,
node.edgeLength,
node.getIntProperty("tableHashKey"),
node.getIntProperty("bucketHashKey"),
interestThreshold,
partitions);
}
return partition;
}
}
// still return the partition even if node was not added as was right of root...
return partition;
}
}