/*.................................................................................................................*/
 public void modifyTree(Tree tree, MesquiteTree modified, RandomBetween rng) {
   if (tree == null || modified == null) return;
   if (tree.getTaxa().anySelected()) { // error fixed in 1. 12
     int[] terminals = tree.getTerminalTaxa(tree.getRoot());
     if (terminals == null) return;
     int numTerminals = 0;
     for (int i = 0; i < terminals.length; i++)
       if (tree.getTaxa().getSelected(terminals[i])) numTerminals++;
     if (numTerminals > numExcluded) {
       int[] selTerminals = new int[numTerminals];
       int icount = 0;
       for (int i = 0; i < terminals.length; i++)
         if (tree.getTaxa().getSelected(terminals[i])) {
           selTerminals[icount] = terminals[i];
           icount++;
         }
       terminals = selTerminals;
       for (int it = 0; it < numExcluded; it++) {
         int taxon = -1;
         int count = 0;
         int ntries = 100000;
         while (terminals[taxon = rng.randomIntBetween(0, numTerminals - 1)] < 0
             && count < ntries) {
           count++;
         }
         if (count >= ntries)
           discreetAlert(
               "ERROR: Rarefy tree failed to find taxon to delete in " + ntries + " tries.");
         else {
           int nT = modified.nodeOfTaxonNumber(terminals[taxon]);
           modified.deleteClade(nT, false);
           terminals[taxon] = -1;
         }
       }
     } else
       MesquiteMessage.warnUser(
           "Sorry, the tree could not be rarefied because more taxa are to be excluded than those available");
   } else {
     int numTerminals = tree.numberOfTerminalsInClade(tree.getRoot());
     if (numTerminals > numExcluded) {
       for (int it = 0; it < numExcluded; it++) {
         int taxon = rng.randomIntBetween(0, numTerminals - it - 1);
         int nT = modified.getTerminalNode(modified.getRoot(), taxon);
         modified.deleteClade(nT, false);
       }
     } else
       MesquiteMessage.warnUser(
           "Sorry, the tree could not be rarefied because more taxa are to be excluded than those available");
   }
 }
  /** monitors the run. */
  public boolean monitorAndCleanUpShell() {
    lastModified = null;
    boolean stillGoing = true;
    if (outputFilePaths != null) {
      lastModified = new long[outputFilePaths.length];
      LongArray.deassignArray(lastModified);
    }

    if (!StringUtil.blank(
        runningFilePath)) // is file at runningFilePath; watch for its disappearance
    while (MesquiteFile.fileExists(runningFilePath) && stillGoing) {
        processOutputFiles();
        try {
          Thread.sleep(sleepTime);
        } catch (InterruptedException e) {
          MesquiteMessage.notifyProgrammer(
              "InterruptedException in shell script executed by " + name);
          return false;
        }
        stillGoing = watcher == null || watcher.continueShellProcess(proc);
      }

    if (outputFileProcessor != null)
      outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
    return true;
  }
 /*.................................................................................................................*/
 boolean checkUsernamePassword(boolean tellUserAboutCipres) {
   if (StringUtil.blank(username) || StringUtil.blank(password)) {
     MesquiteBoolean answer = new MesquiteBoolean(false);
     MesquiteString usernameString = new MesquiteString();
     if (username != null) usernameString.setValue(username);
     MesquiteString passwordString = new MesquiteString();
     if (password != null) passwordString.setValue(password);
     String help =
         "You will need an account on the CIPRes REST system to use this service.  To register, go to https://www.phylo.org/restusers/register.action";
     new UserNamePasswordDialog(
         ownerModule.containerOfModule(),
         "Sign in to CIPRes",
         help,
         "",
         "Username",
         "Password",
         answer,
         usernameString,
         passwordString);
     if (answer.getValue()) {
       username = usernameString.getValue();
       password = passwordString.getValue();
     }
     ownerModule.storePreferences();
   }
   boolean success = StringUtil.notEmpty(username) && StringUtil.notEmpty(password);
   if (!success && tellUserAboutCipres) {
     MesquiteMessage.discreetNotifyUser(
         "Use of the CIPRes service requires an account with CIPRes's REST service.  Go to https://www.phylo.org/restusers/register.action to register for an account");
   }
   return success;
 }
  public boolean clipBoardHasString() {

    Clipboard clip = Toolkit.getDefaultToolkit().getSystemClipboard();
    Transferable t = clip.getContents(this);
    try {
      String s = (String) t.getTransferData(DataFlavor.stringFlavor);
      if (s != null) {
        return true;
      }
    } catch (Exception e) {
      MesquiteMessage.printStackTrace(e);
    }
    return false;
  }
  /*.................................................................................................................*/
  public boolean monitorAndCleanUpShell(String jobURL) {
    boolean stillGoing = true;

    if (!checkUsernamePassword(true)) {
      return false;
    }
    lastModified = null;
    if (outputFilePaths != null) {
      lastModified = new long[outputFilePaths.length];
      LongArray.deassignArray(lastModified);
    }
    String status = "";
    while (!jobCompleted(jobURL) && stillGoing) {
      if (StringUtil.blank(status))
        ownerModule.logln(
            "CIPRes Job Status: " + getJobStatus(jobURL) + "  (" + StringUtil.getDateTime() + ")");

      //	if (jobSubmitted(jobURL))
      //		processOutputFiles();
      try {
        Thread.sleep(minPollIntervalSeconds * 1000);
      } catch (InterruptedException e) {
        MesquiteMessage.notifyProgrammer("InterruptedException in CIPRes monitoring");
        return false;
      }

      stillGoing = watcher == null || watcher.continueShellProcess(null);
      String newStatus = getJobStatus(jobURL);
      if (newStatus != null && !newStatus.equalsIgnoreCase(status)) {
        ownerModule.logln(
            "CIPRes Job Status: " + newStatus + "  (" + StringUtil.getDateTime() + ")");
        status = newStatus;
      } else ownerModule.log(".");
      if (newStatus != null && newStatus.equalsIgnoreCase("SUBMITTED")) { // job is running
        processOutputFiles(jobURL);
      }
    }
    ownerModule.logln("CIPRes job completed.");
    if (outputFileProcessor != null) {
      if (rootDir != null) {
        ownerModule.logln("About to download results from CIPRes.");
        if (downloadResults(jobURL, rootDir, false))
          outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
        else return false;
      }
    }

    return true;
  }
  /**
   * executes a shell script at "scriptPath". If runningFilePath is not blank and not null, then
   * Mesquite will create a file there that will serve as a flag to Mesquite that the script is
   * running.
   */
  public boolean executeInShell() {
    proc = null;
    try {
      ShellScriptUtil.setScriptFileToBeExecutable(scriptPath);
      if (!StringUtil.blank(runningFilePath)) {
        if (StringUtil.blank(runningFileMessage))
          MesquiteFile.putFileContents(runningFilePath, "Script running...", true);
        else MesquiteFile.putFileContents(runningFilePath, runningFileMessage, true);
        if (appendRemoveCommand && MesquiteFile.fileExists(runningFilePath))
          MesquiteFile.appendFileContents(
              scriptPath,
              StringUtil.lineEnding() + ShellScriptUtil.getRemoveCommand(runningFilePath),
              true); // append remove command to guarantee that the runningFile is deleted
        // +StringUtil.lineEnding()+ShellScriptUtil.getExitCommand()
      }
      proc = ShellScriptUtil.executeScript(scriptPath, visibleTerminal);

    } catch (IOException e) {
      MesquiteMessage.warnProgrammer("IOException in shell script executed by " + name);
      return false;
    }
    return true;
  }