Ejemplo n.º 1
0
  /*................................................................................................*/
  public boolean startJob(String arguments, Object condition, boolean hiredByName) {
    addMenuItem("Directory for Sample Trees From Directory...", makeCommand("setDirPath", this));
    fillerTasks = new Vector();
    if (!MesquiteThread
        .isScripting()) { // enclosed in conditional to avoid hiring query when opening file; should
      // be handled by snapshot/doCommand when file is opened.
      String directoryPath =
          MesquiteFile.chooseDirectory(
              "Choose directory containing tree files:",
              previousDirectory); // MesquiteFile.saveFileAsDialog("Base name for files (files will
      // be named <name>1.nex, <name>2.nex, etc.)", baseName);

      if (StringUtil.blank(directoryPath)) { // TODO: clean this up?
        return false;
      } else {
        directory = new File(directoryPath);
        previousDirectory = directory.getParent();
        if (directory.exists() && directory.isDirectory()) {
          return hireFillers(directoryPath);
        }
      }
    }
    return true; // Add something to make sure directory paths are set up correctly, when not
    // scripting...
  }
Ejemplo n.º 2
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;
  }
 /*.................................................................................................................*/
 public void processOutputFiles(String jobURL) {
   if (rootDir != null) {
     downloadWorkingResults(jobURL, rootDir, true);
     if (outputFileProcessor != null && outputFilePaths != null && lastModified != null) {
       String[] paths = outputFileProcessor.modifyOutputPaths(outputFilePaths);
       for (int i = 0; i < paths.length && i < lastModified.length; i++) {
         File file = new File(paths[i]);
         long lastMod = file.lastModified();
         if (!MesquiteLong.isCombinable(lastModified[i]) || lastMod > lastModified[i]) {
           outputFileProcessor.processOutputFile(paths, i);
           lastModified[i] = lastMod;
         }
       }
     }
   }
 }