Example #1
0
 /** constructor taking a dimension */
 public DistanceMatrix(TaxonList taxa) {
   super();
   this.taxa = taxa;
   dimension = taxa.getTaxonCount();
   distances = new double[dimension][dimension];
   distancesKnown = true;
 }
Example #2
0
 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;
 }
Example #3
0
 public boolean contained(TaxonList taxons, TaxonList taxons1) {
   return sizeOfIntersection(taxons, taxons1) == taxons.getTaxonCount();
 }