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;
}
}
