/** constructor taking a dimension */
public DistanceMatrix(TaxonList taxa) {
super();
this.taxa = taxa;
dimension = taxa.getTaxonCount();
distances = new double[dimension][dimension];
distancesKnown = true;
}
public int sizeOfIntersection(TaxonList tl1, TaxonList tl2) {
int nIn = 0;
for (int j = 0; j < tl1.getTaxonCount(); ++j) {
if (tl2.getTaxonIndex(tl1.getTaxon(j)) >= 0) {
++nIn;
}
}
return nIn;
}
public boolean contained(TaxonList taxons, TaxonList taxons1) {
return sizeOfIntersection(taxons, taxons1) == taxons.getTaxonCount();
}