Пример #1
0
  /*................................................................................................*/
  private boolean hireFillers(String directoryPath) {
    String[] files = directory.list();
    String treePath;
    for (int i = 0; i < files.length; i++) {
      if (files[i] != null) {
        String fileLowerCase = files[i].toLowerCase();
        if (fileLowerCase.endsWith(".nex") || fileLowerCase.endsWith(".nexus")) {
          treePath = directoryPath + MesquiteFile.fileSeparator + files[i];
          File treeFile = new File(treePath);
          String treeFileName = treeFile.getName();
          if (StringUtil.blank(treeFileName)) {
            return false;
          }
          TreeBlockFiller newFiller;
          newFiller =
              (TreeBlockFiller)
                  hireNamedEmployee(TreeBlockFiller.class, "#SampleOneTreeFromFile"); // treePath);
          if (newFiller != null) {
            if (((SampleOneTreeFromFile) newFiller).setFilePath(treePath)
                && ((SampleOneTreeFromFile) newFiller).processFile()) {
              fillerTasks.addElement(newFiller);
            } else
              Debugg.println(
                  "Filler "
                      + i
                      + " processFile = "
                      + ((SampleOneTreeFromFile) newFiller).processFile());
          }
        }
      }
    }

    return true;
  }
Пример #2
0
  /*................................................................................................*/
  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;
  }
 /*.................................................................................................................*/
 public TreeDisplayExtra createTreeDisplayExtra(TreeDisplay treeDisplay) {
   PAdjustToolExtra newPj = new PAdjustToolExtra(this, treeDisplay);
   extras.addElement(newPj);
   return newPj;
 }