/*................................................................................................*/
 public void setPreferredTaxa(Taxa taxa) { // Copied from SampleTreesMultSources
   if (taxa != currentTaxa) {
     if (currentTaxa != null) currentTaxa.removeListener(this);
     currentTaxa = taxa;
     currentTaxa.addListener(this);
   }
 }
 /*.................................................................................................................*/
 public void setTaxonTranslation(Taxa taxa) {
   int countTaxa = 0;
   for (int it = 0; it < data.getNumTaxa(); it++)
     if ((!selectedTaxaOnly || taxa.getSelected(it)) && (data.hasDataForTaxon(it, false))) {
       setTaxonNumberInTree(taxa, it, countTaxa);
       countTaxa++;
     } else setTaxonNumberInTree(taxa, it, -1);
 }
 /*.................................................................................................................*/
 public int[] getTaxonNumberTranslation(Taxa taxa) {
   int max = -1;
   for (int it = 0; it < taxa.getNumTaxa(); it++) {
     long translateNumber = getTaxonNumberInTree(taxa, it);
     if (MesquiteLong.isCombinable(translateNumber) && translateNumber > max) {
       max = (int) translateNumber;
     }
   }
   int[] translate = new int[max + 1];
   for (int it = 0; it < data.getNumTaxa(); it++) {
     long translateNumber = getTaxonNumberInTree(taxa, it);
     if (MesquiteLong.isCombinable(translateNumber) && translateNumber >= 0) {
       translate[(int) translateNumber] = it;
     }
   }
   return translate;
 }
  /*.................................................................................................................*/
  public Tree getTrees(
      TreeVector trees,
      Taxa taxa,
      MCharactersDistribution matrix,
      long seed,
      MesquiteDouble finalScore) {
    if (!initializeGetTrees(CategoricalData.class, taxa, matrix)) return null;
    setTNTSeed(seed);
    isProtein = data instanceof ProteinData;

    // David: if isDoomed() then module is closing down; abort somehow

    // write data file
    String tempDir =
        MesquiteFileUtil.createDirectoryForFiles(
            this, MesquiteFileUtil.IN_SUPPORT_DIR, "TNT", "-Run.");
    if (tempDir == null) return null;
    String dataFileName = "data.ss"; // replace this with actual file name?
    String dataFilePath = tempDir + dataFileName;

    FileInterpreterI exporter = ZephyrUtil.getFileInterpreter(this, "#InterpretTNT");
    if (exporter == null) return null;
    boolean fileSaved = false;
    String translationTable = namer.getTranslationTable(taxa);
    ((InterpretHennig86Base) exporter).setTaxonNamer(namer);

    fileSaved = ZephyrUtil.saveExportFile(this, exporter, dataFilePath, data, selectedTaxaOnly);
    if (!fileSaved) return null;

    String translationFileName = IOUtil.translationTableFileName;
    setTaxonTranslation(taxa);
    taxonNumberTranslation = getTaxonNumberTranslation(taxa);
    namer.setNumberTranslationTable(taxonNumberTranslation);

    setFileNames();

    TaxaSelectionSet outgroupSet =
        (TaxaSelectionSet) taxa.getSpecsSet(outgroupTaxSetString, TaxaSelectionSet.class);
    int firstOutgroup = MesquiteInteger.unassigned;
    if (outgroupSet != null) firstOutgroup = outgroupSet.firstBitOn();
    formCommandFile(dataFileName, firstOutgroup);
    logln("\n\nCommands given to TNT:");
    logln(commands);
    logln("");

    MesquiteString arguments = new MesquiteString();
    arguments.setValue(" proc " + commandsFileName);

    String programCommand = externalProcRunner.getExecutableCommand();

    int numInputFiles = 3;
    String[] fileContents = new String[numInputFiles];
    String[] fileNames = new String[numInputFiles];
    for (int i = 0; i < numInputFiles; i++) {
      fileContents[i] = "";
      fileNames[i] = "";
    }
    fileContents[0] = MesquiteFile.getFileContentsAsString(dataFilePath);
    fileNames[0] = dataFileName;
    fileContents[1] = commands;
    fileNames[1] = commandsFileName;
    fileContents[2] = translationTable;
    fileNames[2] = translationFileName;

    // ----------//
    boolean success =
        runProgramOnExternalProcess(
            programCommand, arguments, fileContents, fileNames, ownerModule.getName());

    if (!isDoomed()) {
      if (success) {
        desuppressProjectPanelReset();
        return retrieveTreeBlock(trees, finalScore); // here's where we actually process everything.
      } else {
        if (!beanWritten) postBean("unsuccessful [1]", false);
        beanWritten = true;
      }
    }
    desuppressProjectPanelReset();
    if (data == null) data.decrementEditInhibition();
    externalProcRunner.finalCleanup();
    return null;
  }