Ejemplo n.º 1
0
  /*.................................................................................................................*/
  public void calculateNumber(
      Tree tree1, Tree tree2, MesquiteNumber result, MesquiteString resultString) {
    if (result == null) return;
    clearResultAndLastResult(result);
    if (tree1 == null) return;
    if (tree2 == null) return;

    int numTaxa = tree1.getTaxa().getNumTaxa();

    double[][] patristic1 = null;
    patristic1 =
        p1.calculatePatristic(
            tree1,
            numTaxa,
            patristic1); // for this tree calculate patristic distances (number of nodes separating
                         // terminals; no branch lengths)
    double[][] patristic2 = null;
    patristic2 =
        p2.calculatePatristic(
            tree2,
            numTaxa,
            patristic2); // for this tree calculate patristic distances (number of nodes separating
                         // terminals; no branch lengths)

    double correl = offDiagonalPMCorrelationFILTERED(patristic1, patristic2);
    if (isDistance && (MesquiteDouble.isCombinable(correl)))
      correl = -correl + 1.0; // shifting 1 to -1 to be 0 to 2 to act as distance
    result.setValue(correl);
    if (resultString != null) {
      if (isDistance)
        resultString.setValue(
            "Patristic correlation (converted to distance): " + result.toString());
      else resultString.setValue("Patristic correlation: " + result.toString());
    }
    saveLastResult(result);
    saveLastResultString(resultString);
  }
 public void calculateNumber(Taxon taxon, MesquiteNumber result, MesquiteString resultString) {
   if (result == null) return;
   clearResultAndLastResult(result);
   Taxa taxa = taxon.getTaxa();
   int it = taxa.whichTaxonNumber(taxon);
   if (taxa != currentTaxa || observedStates == null) {
     observedStates = matrixSourceTask.getCurrentMatrix(taxa);
     currentTaxa = taxa;
   }
   if (observedStates == null || !(observedStates.getParentData() instanceof DNAData)) return;
   DNAData data = (DNAData) observedStates.getParentData();
   int count = data.getAminoAcidNumbers(it, ProteinData.TER, countEvenIfOthers.getValue());
   if (result != null) result.setValue(count);
   if (resultString != null)
     resultString.setValue(
         "Number of stop codons in taxon " + observedStates.getName() + ": " + count);
   saveLastResult(result);
   saveLastResultString(resultString);
 }