/** Called to alter data in all cells */
 public boolean operateOnData(CharacterData data) {
   if (!(data instanceof ContinuousData)) return false;
   ContinuousData cData = (ContinuousData) data;
   int numItems = cData.getNumItems();
   String[] items = new String[numItems];
   for (int i = 0; i < items.length; i++) {
     if (StringUtil.blank(cData.getItemName(i))) items[i] = "(unnamed)";
     else items[i] = cData.getItemName(i);
   }
   int d =
       ListDialog.queryList(
           containerOfModule(),
           "Rename item",
           "Rename item:",
           MesquiteString.helpString,
           items,
           0);
   if (!MesquiteInteger.isCombinable(d) || d < 0 || d >= numItems) return false;
   else {
     String s =
         MesquiteString.queryString(
             containerOfModule(), "Rename Item", "New name for " + items[d], items[d]);
     if (StringUtil.blank(s)) return false;
     cData.setItemReference(d, NameReference.getNameReference(s));
     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;
 }
 /** This method simply lists the tools available */
 public void listTools(HttpClient httpclient) {
   Document cipresResponseDoc = cipresQuery(httpclient, baseURL + "/tool", "tools");
   if (cipresResponseDoc != null) {
     String elementName = "tool";
     List tools = cipresResponseDoc.getRootElement().elements(elementName);
     int count = 0;
     for (Iterator iter = tools.iterator();
         iter.hasNext(); ) { // let's get a count as to how many tools there are.
       Element nextTool = (Element) iter.next();
       count++;
     }
     String[] toolName = new String[count];
     count = 0;
     for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
       Element nextTool = (Element) iter.next();
       String name = nextTool.elementText("toolId");
       if (!StringUtil.blank(name) && count < toolName.length) {
         ownerModule.logln(name);
       }
       name = nextTool.elementText("toolName");
       if (!StringUtil.blank(name) && count < toolName.length) {
         ownerModule.logln("   " + name);
       }
       count++;
     }
   }
 }
  /**
   * Gets background color for cell for row ic. Override it if you want to change the color from the
   * default.
   */
  public Color getBackgroundColorOfCell(int it, boolean selected) {
    if (observedStates == null) {
      doCalcs();
      if (observedStates == null) return null;
    }
    if (observedStates.getParentData() != null) {
      captureCharacterDataFromObservedStates();

      Associable tInfo = data.getTaxaInfo(false);
      NameReference genBankColor = NameReference.getNameReference("genbankcolor");
      Object obj = tInfo.getAssociatedObject(genBankColor, it); // not saved to file
      if (obj instanceof Color) return (Color) obj;
    }
    if (bits == null || it < 0 || it > bits.getSize()) return null;
    String note = getNote(it);
    if (selected) {
      if (bits.isBitOn(it)) return ColorDistribution.darkGreen;
      else return ColorDistribution.darkRed;
    } else if (bits.isBitOn(it)) {
      if (StringUtil.blank(note)) return ColorDistribution.veryLightGreen;
      if (!(note.equalsIgnoreCase("x"))) return ColorDistribution.lightGreenYellowish;
      return ColorDistribution.lightGreenYellow;
    } else {
      if (StringUtil.blank(note)) return ColorDistribution.brown;
      if (!(note.equalsIgnoreCase("x"))) {
        return Color.red;
      }
      return ColorDistribution.lightRed;
    }
  }
 public void processCompletedOutputFiles(String[] outputFilePaths) {
   if (outputFilePaths.length > 1 && !StringUtil.blank(outputFilePaths[1])) {
     ZephyrUtil.copyLogFile(this, "TNT", outputFilePaths[1]);
   }
   if (outputFilePaths.length > 2 && !StringUtil.blank(outputFilePaths[2])) {
     ZephyrUtil.copyOutputText(this, outputFilePaths[2], commands);
   }
 }
  /** 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;
  }
  /*................................................................................................*/
  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 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...
  }
 public String[] getJobURLs(Document cipresResponseDoc) {
   String elementName = "jobstatus";
   Element jobs = cipresResponseDoc.getRootElement().element("jobs");
   if (jobs == null) return null;
   List tools = jobs.elements("jobstatus");
   int count = 0;
   for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
     Element nextTool = (Element) iter.next();
     count++;
   }
   String[] url = new String[count];
   count = 0;
   for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
     Element nextJob = (Element) iter.next();
     if (nextJob != null) {
       Element selfUriElement = nextJob.element("selfUri");
       if (selfUriElement != null) {
         String jobURL = selfUriElement.elementText("url");
         if (!StringUtil.blank(jobURL) && count < url.length) {
           url[count] = jobURL;
         }
       }
       count++;
     }
   }
   return url;
 }
 /*.................................................................................................................*/
 public boolean downloadWorkingResults(
     HttpClient httpclient,
     String jobURL,
     String rootDir,
     String fileName,
     boolean onlyNewOrModified) {
   if (StringUtil.blank(fileName)) return false;
   String workingUri = getWorkingDirectory(jobURL);
   if (StringUtil.notEmpty(workingUri)) {
     Document cipresResponseDoc = cipresQuery(httpclient, workingUri, "workingdir");
     if (cipresResponseDoc != null) {
       CipresJobFile[] cipresJobFiles = processFilesDocument(cipresResponseDoc);
       if (cipresJobFiles == null || cipresJobFiles.length == 0) {
         return false;
       }
       for (int job = 0; job < cipresJobFiles.length; job++) {
         if (fileName.equalsIgnoreCase(cipresJobFiles[job].getFileName())
             && (!onlyNewOrModified
                 || fileNewOrModified(previousCipresJobFiles, cipresJobFiles, job)))
           cipresDownload(
               httpclient,
               cipresJobFiles[job].getDownloadURL(),
               rootDir + cipresJobFiles[job].getFileName());
       }
       previousCipresJobFiles = cipresJobFiles.clone();
       return true;
     }
   }
   return false;
 }
 /**
  * this is the primary method that sends a query to the CIPRes REST service. It expects to receive
  * an XML file, which it returns in Document if the root tag matc hes xmlRootTag
  */
 public Document cipresQuery(HttpClient httpclient, String URL, String xmlRootTag) {
   if (StringUtil.blank(URL)) return null;
   try {
     HttpGet httpget = new HttpGet(URL);
     httpget.addHeader("cipres-appkey", CIPRESkey);
     try {
       HttpResponse response = httpclient.execute(httpget);
       HttpEntity responseEntity = response.getEntity();
       InputStream instream = responseEntity.getContent();
       BufferedReader br = new BufferedReader(new InputStreamReader(instream));
       String line = "";
       StringBuffer sb = new StringBuffer();
       while ((line = br.readLine()) != null) {
         sb.append(line + StringUtil.lineEnding());
       }
       Document cipresResponseDoc = loadXMLFile(xmlRootTag, sb.toString());
       if (cipresResponseDoc != null && verbose) {
         ownerModule.logln(sb.toString());
       }
       if (cipresResponseDoc == null) {
         Document errorDoc = loadXMLFile(sb.toString());
         if (errorDoc != null) reportError(errorDoc, "Error in communicating with CIPRes", true);
       }
       EntityUtils.consume(response.getEntity());
       return cipresResponseDoc;
     } catch (IOException e) {
       Debugg.printStackTrace(e);
     } catch (Exception e) {
       Debugg.printStackTrace(e);
     }
   } catch (Exception e) {
     Debugg.printStackTrace(e);
   }
   return null;
 }
 /**
  * This method returns a Document from the contents of the XML file as contained in the String
  * xmlFile, with no restriction as to the root element.
  */
 public Document loadXMLFile(String xmlFile) {
   if (!StringUtil.blank(xmlFile)) {
     Document CipresDoc = XMLUtil.getDocumentFromString(xmlFile);
     return CipresDoc;
   }
   return null;
 }
  /**
   * This processes information about the files contained in either the results or working directory
   * of a job.
   */
  public CipresJobFile[] processFilesDocument(Document cipresResponseDoc) {
    Element jobfiles = cipresResponseDoc.getRootElement().element("jobfiles");
    if (jobfiles == null) return null;
    List tools = jobfiles.elements("jobfile");
    int count = 0;
    for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
      Element nextTool = (Element) iter.next();
      count++;
    }
    if (count == 0) return null;
    CipresJobFile[] cipresJobFile = new CipresJobFile[count];
    count = 0;
    for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
      Element nextJob = (Element) iter.next();
      if (nextJob != null) {
        if (cipresJobFile[count] == null) cipresJobFile[count] = new CipresJobFile();
        Element jobFileElement = nextJob.element("downloadUri");
        String fileInfo = null;
        if (jobFileElement != null) {
          fileInfo = jobFileElement.elementText("url");
          if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
            cipresJobFile[count].setDownloadURL(fileInfo);
          }
          fileInfo = jobFileElement.elementText("title");
          if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
            cipresJobFile[count].setDownloadTitle(fileInfo);
          }
        }
        fileInfo = nextJob.elementText("dateModified");
        if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
          cipresJobFile[count].setLastModified(fileInfo);
        }
        fileInfo = nextJob.elementText("filename");
        if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
          cipresJobFile[count].setFileName(fileInfo);
        }
        fileInfo = nextJob.elementText("length");
        if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
          cipresJobFile[count].setLength(MesquiteLong.fromString(fileInfo));
        }

        count++;
      }
    }
    return cipresJobFile;
  }
 /*..........................................MContinuousStates................*/
 public int userQueryItem(String message, MesquiteModule module) {
   int numItems = getNumItems();
   String[] items = new String[numItems];
   for (int i = 0; i < items.length; i++) {
     if (StringUtil.blank(getItemName(i))) items[i] = "(unnamed)";
     else items[i] = getItemName(i);
   }
   return ListDialog.queryList(
       module.containerOfModule(), "Select item", message, MesquiteString.helpString, items, 0);
 }
Beispiel #15
0
  /**
   * A request for the MesquiteModule to perform a command. It is passed two strings, the name of
   * the command and the arguments. This should be overridden by any module that wants to respond to
   * a command.
   */
  public Object doCommand(String commandName, String arguments, CommandChecker checker) {
    if (checker.compare(MesquiteModule.class, null, null, commandName, "paint")) {
      MesquiteInteger io = new MesquiteInteger(0);
      int column = MesquiteInteger.fromString(arguments, io);
      int row = MesquiteInteger.fromString(arguments, io);
      if (MesquiteInteger.isCombinable(row)) {
        if (!MesquiteLong.isCombinable(currentColor)) removeColor(row, true);
        else setColor(row, (int) currentColor);
      }
    } else if (checker.compare(
        this.getClass(),
        "Sets the color to be used to paint cells",
        "[name of color]",
        commandName,
        "setColor")) {
      int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
      if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
        removeColor.setValue(false);
        currentColor = bc;
        savedColor = bc;
        colorString = "Color " + ColorDistribution.standardColorNames.getValue(bc);
      }
    } else if (checker.compare(
        this.getClass(),
        "Sets the color of selected taxa",
        "[name of color]",
        commandName,
        "setColorSelected")) {
      int bc = ColorDistribution.standardColorNames.indexOf(parser.getFirstToken(arguments));
      if (bc >= 0 && MesquiteLong.isCombinable(bc)) {
        for (int it = 0; it < taxa.getNumTaxa(); it++) if (taxa.getSelected(it)) setColor(it, bc);
      }
    } else if (checker.compare(
        this.getClass(), "Removes color from all the cells", null, commandName, "removeAllColor")) {
      removeAllColor(true);
    } else if (checker.compare(
        this.getClass(),
        "Sets the paint brush so that it removes colors from any cells touched",
        null,
        commandName,
        "removeColor")) {
      if (StringUtil.blank(arguments)) removeColor.setValue(!removeColor.getValue());
      else removeColor.toggleValue(parser.getFirstToken(arguments));

      if (removeColor.getValue()) {
        colorString = "Remove color";
        currentColor = MesquiteLong.unassigned;
      } else {
        colorString = "Color " + ColorDistribution.standardColorNames.getValue((int) currentColor);
        currentColor = savedColor;
      }
    } else return super.doCommand(commandName, arguments, checker);
    return null;
  }
  /**
   * 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;
  }
  /*.................................................................................................................*/
  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;
  }
  public ShellScriptRunner(
      String scriptPath,
      String runningFilePath,
      String runningFileMessage,
      boolean appendRemoveCommand,
      String name,
      String[] outputFilePaths,
      OutputFileProcessor outputFileProcessor,
      ShellScriptWatcher watcher,
      boolean visibleTerminal) {
    this.scriptPath = scriptPath;
    this.runningFilePath = runningFilePath;
    if (runningFilePath == null && !StringUtil.blank(scriptPath))
      this.runningFilePath = ShellScriptUtil.getDefaultRunningFilePath();

    this.runningFileMessage = runningFileMessage;
    this.appendRemoveCommand = appendRemoveCommand;
    this.name = name;
    this.outputFilePaths = outputFilePaths;
    this.outputFileProcessor = outputFileProcessor;
    this.watcher = watcher;
    this.visibleTerminal = visibleTerminal;
  }
  boolean showOptions() {

    MesquiteInteger buttonPressed = new MesquiteInteger(1);
    ExtensibleDialog queryDialog =
        new ExtensibleDialog(containerOfModule(), "Reinterpret Node Labels", buttonPressed);
    queryDialog.addLargeOrSmallTextLabel(
        "Some programs write information as node labels; e.g. MrBayes writes posterior probabilities as if they were the names of clades (= node labels)."
            + "\nHere you can reintepret such information.");
    // name for information (e.g., "posteriorProbability", "bootstrapFrequency")
    queryDialog.addLabel(
        "Name for information? (e.g., \"posteriorProbability\", \"bootstrapFrequency\")",
        Label.LEFT);
    TextField nameField = queryDialog.addTextField(name, 30);

    queryDialog.addHorizontalLine(2);

    // where to attach
    queryDialog.addLabel("Applies to branch or node?", Label.LEFT);
    String[] where =
        new String[] {
          "Information applies to branch (e.g., posterior probability, bootstrap frequency)",
          "Information applies to node (e.g., clade name)"
        };
    RadioButtons whereButtons = queryDialog.addRadioButtons(where, 0);
    queryDialog.addLabel(
        "(This determines how the information will behave when the tree is rerooted.)", Label.LEFT);
    queryDialog.addHorizontalLine(2);

    // how to treat
    queryDialog.addLabel("Number or text?", Label.LEFT);
    String[] what =
        new String[] {
          "Treat as number (e.g., posterior probability)", "Treat as text (e.g., clade name)"
        };
    RadioButtons whatButtons = queryDialog.addRadioButtons(what, 0);
    queryDialog.addHorizontalLine(2);

    // delete internal node labels after reinterpreting?
    Checkbox delete =
        queryDialog.addCheckBox("Delete internal node labels after reinterpreting?", deleteAfter);
    queryDialog.addHorizontalLine(2);

    queryDialog.completeAndShowDialog(true);

    boolean ok = (queryDialog.query() == 0);

    if (ok) {
      if (StringUtil.blank(nameField.getText())) {
        ok = false;
        alert("A name must be entered for the information");
      } else {
        name = nameField.getText();
        nameRef = NameReference.getNameReference(name);
        appliesToBranch = whereButtons.getValue() == 0;
        isNumber = whatButtons.getValue() == 0;
        deleteAfter = delete.getState();
      }
    }

    queryDialog.dispose();
    return ok;
  }
  public void runFilesAvailable(int fileNum) {
    String[] logFileNames = getLogFileNames();
    if ((progIndicator != null && progIndicator.isAborted()) || logFileNames == null) return;
    String[] outputFilePaths = new String[logFileNames.length];
    outputFilePaths[fileNum] = externalProcRunner.getOutputFilePath(logFileNames[fileNum]);
    String filePath = outputFilePaths[fileNum];

    if (fileNum == 0
        && outputFilePaths.length > 0
        && !StringUtil.blank(outputFilePaths[0])
        && !bootstrapOrJackknife()) { // tree file
      if (ownerModule instanceof NewTreeProcessor) {
        String treeFilePath = filePath;
        if (taxa != null) {
          TaxaSelectionSet outgroupSet =
              (TaxaSelectionSet) taxa.getSpecsSet(outgroupTaxSetString, TaxaSelectionSet.class);
          ((NewTreeProcessor) ownerModule).newTreeAvailable(treeFilePath, outgroupSet);

        } else ((NewTreeProcessor) ownerModule).newTreeAvailable(treeFilePath, null);
      }
    } else if (fileNum == 1
        && outputFilePaths.length > 1
        && !StringUtil.blank(outputFilePaths[1])
        && !bootstrapOrJackknife()) { // log file
      if (MesquiteFile.fileExists(filePath)) {
        String s = MesquiteFile.getFileLastContents(filePath);
        if (!StringUtil.blank(s))
          if (progIndicator != null) {
            parser.setString(s);
            String rep = parser.getFirstToken(); // generation number
            logln("");
            if (MesquiteInteger.isNumber(rep)) {
              int numReps = MesquiteInteger.fromString(rep) + 1;
              progIndicator.setText(
                  "Replicate: " + numReps); // + ", ln L = " + parser.getNextToken());
              if (bootstrapOrJackknife()) {
                logln("Replicate " + numReps + " of " + bootstrapreps);
              }
              logln("Replicate " + numReps + " of " + totalNumHits);

              progIndicator.spin();
              double timePerRep = 0;
              if (MesquiteInteger.isCombinable(numReps) && numReps > 0) {
                timePerRep = timer.timeSinceVeryStartInSeconds() / numReps; // this is time per rep
              }
              int timeLeft = 0;
              if (bootstrapOrJackknife()) {
                timeLeft = (int) ((bootstrapreps - numReps) * timePerRep);
              } else {
                String token = parser.getNextToken(); // algorithm
                token = parser.getNextToken(); // Tree
                token = parser.getNextToken(); // Score
                String best = parser.getNextToken(); // Best
                logln("  Score " + token + "; best found so far " + best);
                timeLeft = (int) ((totalNumHits - numReps) * timePerRep);
              }

              logln(
                  "  Running time so far "
                      + StringUtil.secondsToHHMMSS((int) timer.timeSinceVeryStartInSeconds())
                      + ", approximate time remaining "
                      + StringUtil.secondsToHHMMSS(timeLeft));
            }
          }
        count++;
      } else if (MesquiteTrunk.debugMode) logln("*** File does not exist (" + filePath + ") ***");
    }
  }
  /** for those permitting editing, indicates user has edited to incoming string. */
  public void setString(int row, String s) {

    if (StringUtil.blank(s)) setNote(row, null);
    else if (s.equalsIgnoreCase("Yes") || s.equalsIgnoreCase("No Data")) return;
    else setNote(row, s);
  }
  /*.................................................................................................................*/
  public Object doCommand(String commandName, String arguments, CommandChecker checker) {
    if (checker.compare(
        this.getClass(), "Returns the matrix source", null, commandName, "getMatrixSource")) {
      return matrixSourceTask;
    } else if (checker.compare(
        this.getClass(), "Copies the data for selected taxon", null, commandName, "copyData")) {
      if (observedStates == null) return null;
      CharacterData data = observedStates.getParentData();
      if (data == null) return null;
      int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
      if (MesquiteInteger.isCombinable(it)) {
        StringBuffer sb = new StringBuffer();
        data.copyDataFromRowIntoBuffer(it, sb);
        if (StringUtil.notEmpty(sb.toString())) {
          localCopyDataClipboard = sb.toString();
          localCopyData = data;
          localCopyDataTaxon = data.getTaxa().getTaxonName(it);
        } else {
          localCopyDataClipboard = null;
          localCopyData = null;
          localCopyDataTaxon = null;
        }
      }
      return null;
    } else if (checker.compare(
        this.getClass(), "Pastes the data for selected taxon", null, commandName, "pasteData")) {
      if (observedStates == null) return null;
      CharacterData data = observedStates.getParentData();
      if (data == null) return null;
      int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
      if (MesquiteInteger.isCombinable(it) && StringUtil.notEmpty(localCopyDataClipboard)) {
        data.pasteDataFromStringIntoTaxon(it, localCopyDataClipboard);
      }
      return null;
    } else if (checker.compare(
        this.getClass(),
        "Pastes the data for selected taxon",
        null,
        commandName,
        "deleteDataTouched")) {
      if (observedStates == null) return null;
      CharacterData data = observedStates.getParentData();
      if (data == null) return null;
      int it = MesquiteInteger.fromString(parser.getFirstToken(arguments));
      Debugg.println("prepare to delete row: " + it);
      if (MesquiteInteger.isCombinable(it)) {
        if (!AlertDialog.query(
            containerOfModule(),
            "Delete Data?",
            "Are you sure you want to delete the data for taxon "
                + data.getTaxa().getTaxonName(it)
                + " in the matrix \""
                + data.getName()
                + "\"",
            "No",
            "Yes")) {
          zapData(data, it);
        }
      }
      return null;
    } else if (checker.compare(
        this.getClass(), "Deletes the data for selected taxa", null, commandName, "deleteData")) {
      if (observedStates == null) return null;
      captureCharacterDataFromObservedStates();
      if (data == null) return null;
      if (!AlertDialog.query(
          containerOfModule(),
          "Delete Data?",
          "Are you sure you want to delete the data for these taxa in the matrix \""
              + data.getName()
              + "\"",
          "No",
          "Yes")) zapData(data);
      return null;
    } else if (checker.compare(
        this.getClass(),
        "deleteds () and anything between",
        null,
        commandName,
        "deletePrepended")) {
      if (observedStates == null || taxa == null) return null;
      boolean anySelected = taxa.anySelected();
      int myColumn = -1;
      if (getEmployer() instanceof ListModule) {

        myColumn = ((ListModule) getEmployer()).getMyColumn(this);
        if (table != null)
          anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
      }

      for (int it = 0; it < taxa.getNumTaxa(); it++) {
        if ((!anySelected || selected(taxa, it, myColumn))) {
          String note = getNote(it);
          while (!StringUtil.blank(note) && note.indexOf("(") >= 0) {
            int start = note.indexOf("(");
            int end = note.indexOf(")");
            String firstBit = "";
            if (start > 0) firstBit = note.substring(0, start);
            note = firstBit + note.substring(end + 1, note.length());
          }
          setNote(it, note);
        }
      }
      outputInvalid();
      parametersChanged();
      return null;
    } else if (checker.compare(this.getClass(), "deletes *", null, commandName, "deleteStar")) {
      if (observedStates == null || taxa == null) return null;
      boolean anySelected = taxa.anySelected();
      int myColumn = -1;
      if (getEmployer() instanceof ListModule) {

        myColumn = ((ListModule) getEmployer()).getMyColumn(this);
        if (table != null)
          anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
      }
      for (int it = 0; it < taxa.getNumTaxa(); it++) {
        if ((!anySelected || selected(taxa, it, myColumn))) {
          String note = getNote(it);
          while (!StringUtil.blank(note) && note.indexOf("*") >= 0) {
            int start = note.indexOf("*");
            String firstBit = "";
            if (start > 0) firstBit = note.substring(0, start);
            note = firstBit + note.substring(start + 1, note.length());
          }
          setNote(it, note);
        }
      }
      outputInvalid();
      parametersChanged();
      return null;
    } else if (checker.compare(
        this.getClass(),
        "Prepends to the note the sequence length (including N\'s and ?\'s) for the selected taxa",
        null,
        commandName,
        "prependLength")) {
      if (observedStates == null || taxa == null) return null;
      boolean anySelected = taxa.anySelected();
      int myColumn = -1;
      if (getEmployer() instanceof ListModule) {

        myColumn = ((ListModule) getEmployer()).getMyColumn(this);
        if (table != null)
          anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
      }
      for (int it = 0; it < taxa.getNumTaxa(); it++) {
        if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
          String note = getNote(it);
          if (StringUtil.blank(note)) note = "(" + sequenceLength(it) + ")";
          else note = "(" + sequenceLength(it) + ") " + note;
          setNote(it, note);
        }
      }
      outputInvalid();
      parametersChanged();
      return null;
    } else if (checker.compare(
        this.getClass(),
        "Prepends to the note the number of non-missing sites (not including N\'s and ?\'s) for the selected taxa",
        null,
        commandName,
        "prependNumSites")) {
      if (observedStates == null || taxa == null) return null;
      boolean anySelected = taxa.anySelected();
      int myColumn = -1;
      if (getEmployer() instanceof ListModule) {

        myColumn = ((ListModule) getEmployer()).getMyColumn(this);
        if (table != null)
          anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
      }
      for (int it = 0; it < taxa.getNumTaxa(); it++) {
        if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
          String note = getNote(it);
          if (StringUtil.blank(note)) note = "(" + numSites(it) + ")";
          else note = "(" + numSites(it) + ") " + note;
          setNote(it, note);
        }
      }
      outputInvalid();
      parametersChanged();
      return null;
    } else if (checker.compare(
        this.getClass(),
        "Deletes the notes for the selected taxa",
        null,
        commandName,
        "deleteAnnotation")) {
      if (observedStates == null || taxa == null) return null;
      boolean anySelected = taxa.anySelected();
      int myColumn = -1;
      if (getEmployer() instanceof ListModule) {

        myColumn = ((ListModule) getEmployer()).getMyColumn(this);
        if (table != null)
          anySelected = anySelected || table.anyCellSelectedInColumnAnyWay(myColumn);
      }
      for (int it = 0; it < taxa.getNumTaxa(); it++) {
        if (hasData(it) && (!anySelected || selected(taxa, it, myColumn))) {
          setNote(it, null);
        }
      }
      outputInvalid();
      parametersChanged();
      return null;
    } else return super.doCommand(commandName, arguments, checker);
  }