protected void init(DistanceMatrix distanceMatrix) {
numClusters = distanceMatrix.getTaxonCount();
clusters = new SimpleNode[numClusters];
distance = new double[numClusters][numClusters];
for (int i = 0; i < numClusters; i++) {
for (int j = 0; j < numClusters; j++) {
distance[i][j] = distanceMatrix.getElement(i, j);
}
}
for (int i = 0; i < numClusters; i++) {
clusters[i] = new SimpleNode();
clusters[i].setTaxon(distanceMatrix.getTaxon(i));
}
alias = new int[numClusters];
tipCount = new int[numClusters];
for (int i = 0; i < numClusters; i++) {
alias[i] = i;
tipCount[i] = 1;
}
}
/**
* constructor ClusteringTree
*
* @param distanceMatrix distance matrix
*/
public ClusteringTree(DistanceMatrix distanceMatrix, int minimumTaxa) {
this.distanceMatrix = distanceMatrix;
if (distanceMatrix.getTaxonCount() < minimumTaxa) {
throw new IllegalArgumentException("less than " + minimumTaxa + " taxa in distance matrix");
}
init(distanceMatrix);
while (true) {
findNextPair();
if (numClusters < minimumTaxa) break;
newCluster();
}
finish();
}