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;
}
/** constructor taking a dimension */
public DistanceMatrix(TaxonList taxa) {
super();
this.taxa = taxa;
dimension = taxa.getTaxonCount();
distances = new double[dimension][dimension];
distancesKnown = true;
}
private boolean isUnique(TaxonList taxonList, Tree tree, NodeRef node) {
Set<String> taxa = Tree.Utils.getDescendantLeaves(tree, node);
int count = 0;
for (String taxon : taxa) {
count += (taxonList.getTaxonIndex(taxon) >= 0 ? 1 : 0);
// System.out.print(taxon + "\t");
}
boolean unique = (count == 0) || (count == taxa.size());
// System.out.println(count + "\t" + unique);
return unique;
}
public boolean contained(TaxonList taxons, TaxonList taxons1) {
return sizeOfIntersection(taxons, taxons1) == taxons.getTaxonCount();
}