// only the values in the lower triangle are used.
// !matrix values will be changed!
private final void reset(final BasicSymmetricalDistanceMatrix distances) {
_n = distances.getSize();
_d = distances;
_r = new double[_n];
_mappings = new int[_n];
_d_values = _d.getValues();
initExternalNodes();
}
private final void initExternalNodes() {
_external_nodes = new PhylogenyNode[_n];
String id;
for (int i = 0; i < _n; ++i) {
_external_nodes[i] = new PhylogenyNode();
id = _d.getIdentifier(i);
if (id != null) {
_external_nodes[i].setName(id);
} else {
_external_nodes[i].setName(Integer.toString(i));
}
_mappings[i] = i;
}
}