Example #1
0
  /*.................................................................................................................*/
  public Tree retrieveTreeBlock(TreeVector treeList, MesquiteDouble finalScore) {
    logln("Preparing to receive TNT trees.");
    boolean success = false;
    taxa = treeList.getTaxa();
    // TODO		finalScore.setValue(finalValue);

    suppressProjectPanelReset();
    CommandRecord oldCR = MesquiteThread.getCurrentCommandRecord();
    CommandRecord scr = new CommandRecord(true);
    MesquiteThread.setCurrentCommandRecord(scr);

    // define file paths and set tree files as needed.
    setFileNames();
    String[] outputFilePaths = externalProcRunner.getOutputFilePaths();

    String treeFilePath = outputFilePaths[OUT_TREEFILE];
    taxonNumberTranslation = getTaxonNumberTranslation(taxa);
    namer.setNumberTranslationTable(taxonNumberTranslation);

    runFilesAvailable();

    // read in the tree files
    success = false;
    Tree t = null;

    MesquiteBoolean readSuccess = new MesquiteBoolean(false);
    // TreeVector tv = new TreeVector(taxa);
    if (bootstrapOrJackknife()) {
      if (resamplingAllConsensusTrees)
        t =
            ZephyrUtil.readTNTTreeFile(
                this,
                treeList,
                taxa,
                treeFilePath,
                "TNT " + getResamplingKindName() + " Rep",
                0,
                readSuccess,
                false,
                false,
                null,
                namer); // set first tree number as 0 as will remove the first one later.
      else
        t =
            ZephyrUtil.readTNTTreeFile(
                this,
                treeList,
                taxa,
                treeFilePath,
                "TNT " + getResamplingKindName() + " Majority Rule Tree",
                1,
                readSuccess,
                false,
                false,
                freqRef,
                namer);
    } else
      t =
          ZephyrUtil.readTNTTreeFile(
              this,
              treeList,
              taxa,
              treeFilePath,
              "TNTTree",
              1,
              readSuccess,
              false,
              harvestOnlyStrictConsensus,
              null,
              namer);
    success = t != null;
    if (success && bootstrapOrJackknife() && resamplingAllConsensusTrees) {
      t = t.cloneTree();
      treeList.removeElementAt(0, false); // get rid of first one as this is the bootstrap tree
    }

    MesquiteThread.setCurrentCommandRecord(oldCR);
    success = readSuccess.getValue();
    if (!success) {
      logln("Execution of TNT unsuccessful [2]");
      if (!beanWritten) postBean("unsuccessful [2]", false);
      beanWritten = true;
    } else {
      if (!beanWritten) postBean("successful", false);
      beanWritten = true;
    }

    desuppressProjectPanelReset();
    if (data != null) data.decrementEditInhibition();
    //	manager.deleteElement(tv);  // get rid of temporary tree block
    externalProcRunner.finalCleanup();
    if (success) return t;
    return null;
  }
  /*................................................................................................*/
  private TreeVector fillBlock(Taxa taxa) { // TODO: fill in
    TreeVector filledVector = new TreeVector(taxa);
    int vectorTreeCount = 0;
    for (int fillers = 0; fillers < fillerTasks.size(); fillers++) {
      if (fillerTasks.get(fillers) instanceof SampleOneTreeFromFile) {
        ((SampleOneTreeFromFile) fillerTasks.get(fillers))
            .resetTreesToSample(); // One unnecessary resetting of bits on first call
        TreeVector tempTreeVector = new TreeVector(taxa);
        ((TreeBlockFiller) fillerTasks.get(fillers)).fillTreeBlock(tempTreeVector, 1);
        if (tempTreeVector.getNumberOfTrees() < 1) {
          logln(
              "Not enough trees were supplied by "
                  + ((TreeBlockFiller) fillerTasks.get(fillers)).getName()
                  + "; "
                  + tempTreeVector.getNumberOfTrees()
                  + " provided, one requested.");
          ;
        }
        if (tempTreeVector.getNumberOfTrees() > 0) {
          int treeCount = 0;
          while (treeCount < 1
              && treeCount
                  < tempTreeVector
                      .getNumberOfTrees()) { // Check so we don't ask for more trees that are there.
            filledVector.addElement(tempTreeVector.getTree(treeCount), false);
            if (filledVector != null && tempTreeVector != null) {
              if (filledVector.getTree(vectorTreeCount) != null
                  && tempTreeVector.getName() != null) {
                if (filledVector.getTree(vectorTreeCount).getName() != null)
                  logln(
                      filledVector.getTree(vectorTreeCount).getName()
                          + " added from "
                          + tempTreeVector.getName());
              }
            }
            treeCount++;
            vectorTreeCount++;
          }
        }
        tempTreeVector.dispose(); // disposed to reduce memory demands

        //				(fillerTask.get(fillers)).
      }
    }
    return filledVector;
  }