/**
* Initialise a CTMain before usage with a first tree, going through and setting up the hash table
* etc.
*
* @param root Root of the initial tree to initialise with
* @param noOfSamples Current number of samples taken
*/
public void initialize(TreeNode root, int noOfSamples) {
// Parameter initialisation
this.noOfSamples = noOfSamples;
noOfTrees = 0;
// TaxaMap initialisation
List<TreeNode> leaves = root.getLeaves();
noOfTaxa = leaves.size();
// Hash initialisation
hashUtils = new HashUtils();
hashUtils.initialize(noOfTaxa, noOfSamples, C, seed);
hashTable = new HashTable(hashUtils.m1);
// Taxamap initialisation
taxa = new TaxaMap(noOfTaxa);
for (int i = 0; i < leaves.size(); i++) {
taxa.put(leaves.get(i).name, i);
}
leafEdgeLengths = new double[noOfTaxa];
// Adds a single star partition, once and for all.
BitSet star = new BitSet(noOfTaxa);
star.flip(0, noOfTaxa);
HashEntry entry = new HashEntry(-1, star, 0.0d);
entry.count = noOfSamples + 1;
partitions.add(entry);
// Majority threshold initialisation
updateInterestThreshold();
}
