/**
   * 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;
  }
 public void textValueChanged(TextEvent e) {
   boolean b = false;
   String s = tf.getText();
   try {
     int value = MesquiteInteger.fromString(s);
     b = (value <= maxValue && value >= minValue && value != currentValue);
   } catch (NumberFormatException ex) {
   }
   enterButton.setEnabled(b && !enterLock);
 }
 public boolean isTextValid() {
   boolean b = false;
   String s = tf.getText();
   try {
     int value = MesquiteInteger.fromString(s);
     b = (value <= maxValue && value >= minValue);
   } catch (NumberFormatException e) {
   }
   return b;
 }
 public void acceptText() {
   String s = tf.getText();
   oldText = null;
   text = s;
   try {
     int value = MesquiteInteger.fromString(s);
     crement(value);
   } catch (NumberFormatException e) {
   }
 }
  /*.................................................................................................................*/
  public void processSingleXMLPreference(String tag, String content) {
    if ("bootStrapReps".equalsIgnoreCase(tag)) bootstrapreps = MesquiteInteger.fromString(content);
    if ("mxram".equalsIgnoreCase(tag)) mxram = MesquiteInteger.fromString(content);
    if ("convertGapsToMissing".equalsIgnoreCase(tag))
      convertGapsToMissing = MesquiteBoolean.fromTrueFalseString(content);
    if ("resamplingAllConsensusTrees".equalsIgnoreCase(tag))
      resamplingAllConsensusTrees = MesquiteBoolean.fromTrueFalseString(content);
    if ("harvestOnlyStrictConsensus".equalsIgnoreCase(tag))
      harvestOnlyStrictConsensus = MesquiteBoolean.fromTrueFalseString(content);
    if ("searchStyle".equalsIgnoreCase(tag)) searchStyle = MesquiteInteger.fromString(content);
    if ("searchArguments".equalsIgnoreCase(tag))
      searchArguments = StringUtil.cleanXMLEscapeCharacters(content);
    if ("bootstrapSearchArguments".equalsIgnoreCase(tag))
      bootstrapSearchArguments = StringUtil.cleanXMLEscapeCharacters(content);
    if ("otherOptions".equalsIgnoreCase(tag))
      otherOptions = StringUtil.cleanXMLEscapeCharacters(content);

    // parallel, etc.
    preferencesSet = true;
  }
 /*.................................................................................................................*/
 public Object doCommand(String commandName, String arguments, CommandChecker checker) {
   if (checker.compare(
       this.getClass(),
       "Sets the number of randomly chosen taxa to exclude",
       "[number]",
       commandName,
       "setNumberExcluded")) {
     int s = MesquiteInteger.fromString(parser.getFirstToken(arguments));
     if (!MesquiteInteger.isCombinable(s)) {
       s =
           MesquiteInteger.queryInteger(
               containerOfModule(),
               "Number of taxa to exclude",
               "Enter the number of randomly chosen taxa to exclude",
               numExcluded);
     }
     if (MesquiteInteger.isCombinable(s)) {
       numExcluded = s;
       parametersChanged();
     }
   } else return super.doCommand(commandName, arguments, checker);
   return null;
 }
  /*.................................................................................................................*/
  public Object doCommand(String commandName, String arguments, CommandChecker checker) {
    Tree trt = treeDisplay.getTree();
    MesquiteTree t = null;
    if (trt instanceof MesquiteTree) t = (MesquiteTree) trt;
    if (checker.compare(
        this.getClass(),
        "Adjust tool has touched branch",
        "[branch number][x coordinate touched][y coordinate touched][modifiers]",
        commandName,
        "touchedPositionAdjust")) {
      if (t == null) return null;
      MesquiteInteger io = new MesquiteInteger(0);
      int node = MesquiteInteger.fromString(arguments, io);
      int x = MesquiteInteger.fromString(arguments, io);
      int y = MesquiteInteger.fromString(arguments, io);
      String mod = ParseUtil.getRemaining(arguments, io);

      Point newOnLine = treeDisplay.getTreeDrawing().projectionOnLine(node, x, y);
      originalX = newOnLine.x;
      originalY = newOnLine.y;
      // lastX= newOnLine.x;
      // lastY = newOnLine.y;
      Graphics g = null;
      if (GraphicsUtil.useXORMode(null, false)) {
        g = treeDisplay.getGraphics();
        g.setXORMode(Color.white);
        g.setColor(Color.red);
      }
      // double bX = treeDisplay.getTreeDrawing().lineBaseX[node];
      // double bY = treeDisplay.getTreeDrawing().lineBaseY[node];
      // Math.sqrt((originalY-bY)*(originalY-bY) + (originalX-bX)*(originalX-bX));
      lastBL = tree.getBranchLength(node);
      double shortestAbove = MesquiteDouble.unassigned;
      for (int daughter = t.firstDaughterOfNode(node);
          t.nodeExists(daughter);
          daughter = t.nextSisterOfNode(daughter))
        shortestAbove = MesquiteDouble.minimum(shortestAbove, tree.getBranchLength(daughter));
      if (shortestAbove == MesquiteDouble.unassigned) upperLimit = MesquiteDouble.infinite;
      else if (MesquiteDouble.isCombinable(lastBL)) upperLimit = shortestAbove + lastBL;
      else upperLimit = shortestAbove + 1.0;
      int ibX = treeDisplay.getTreeDrawing().lineBaseX[node];
      int ibY = treeDisplay.getTreeDrawing().lineBaseY[node];
      lastX = treeDisplay.getTreeDrawing().lineTipX[node];
      lastY = treeDisplay.getTreeDrawing().lineTipY[node];
      if (GraphicsUtil.useXORMode(null, false)) {
        drawThickLine(g, ibX, ibY, lastX, lastY);
        for (int daughter = t.firstDaughterOfNode(node);
            t.nodeExists(daughter);
            daughter = t.nextSisterOfNode(daughter))
          drawThickLine(
              g,
              treeDisplay.getTreeDrawing().lineTipX[daughter],
              treeDisplay.getTreeDrawing().lineTipY[daughter],
              lastX,
              lastY);
        g.fillOval(
            lastX - ovalRadius,
            lastY - ovalRadius,
            ovalRadius + ovalRadius,
            ovalRadius + ovalRadius);
        try {
          g.drawString(MesquiteDouble.toString(lastBL), lastX + 10, lastY);
        } catch (InternalError e) { // workaround for bug on windows java 1.7.
        } catch (Throwable e) {
        }
        lineOn = true;
        g.dispose();
      }
    } else if (checker.compare(
        this.getClass(),
        "Adjust tool has been dropped",
        "[branch number][x coordinate dropped][y coordinate dropped]",
        commandName,
        "droppedPositionAdjust")) {
      if (t == null) return null;
      if (editorOn) return null;
      MesquiteInteger io = new MesquiteInteger(0);
      int node = MesquiteInteger.fromString(arguments, io);
      int x = MesquiteInteger.fromString(arguments, io);
      int y = MesquiteInteger.fromString(arguments, io);
      if (lineOn) {
        Point newOnLine = treeDisplay.getTreeDrawing().projectionOnLine(node, x, y);
        double bX = treeDisplay.getTreeDrawing().lineBaseX[node];
        double bY = treeDisplay.getTreeDrawing().lineBaseY[node];
        double tX = treeDisplay.getTreeDrawing().lineTipX[node];
        double tY = treeDisplay.getTreeDrawing().lineTipY[node];
        double lengthLine =
            Math.sqrt((originalY - bY) * (originalY - bY) + (originalX - bX) * (originalX - bX));
        double bL;
        if (lengthLine != 0) {
          double extension =
              Math.sqrt(
                      (newOnLine.y - bY) * (newOnLine.y - bY)
                          + (newOnLine.x - bX) * (newOnLine.x - bX))
                  / lengthLine;
          if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node)) bL = extension;
          else bL = t.getBranchLength(node) * extension;
        } else bL = 1;

        if (bL > upperLimit) bL = upperLimit;
        else if (bL < lowerLimit) bL = lowerLimit;
        double oldBL = t.getBranchLength(node);
        if (!MesquiteDouble.isCombinable(oldBL)) oldBL = 1.0;
        t.setBranchLength(node, bL, false);
        double difference = oldBL - t.getBranchLength(node);
        for (int daughter = t.firstDaughterOfNode(node);
            t.nodeExists(daughter);
            daughter = t.nextSisterOfNode(daughter))
          if (MesquiteDouble.isCombinable(t.getBranchLength(daughter)))
            t.setBranchLength(daughter, t.getBranchLength(daughter) + difference, false);
        t.notifyListeners(this, new Notification(MesquiteListener.BRANCHLENGTHS_CHANGED));
        Graphics g = treeDisplay.getGraphics();
        g.setPaintMode();
        g.dispose();
        treeDisplay.pleaseUpdate(true);
        lineOn = false;
      }
    } else if (checker.compare(
        this.getClass(),
        "Adjust tool is being dragged",
        "[branch number][x coordinate][y coordinate]",
        commandName,
        "draggedPositionAdjust")) {
      if (t == null) return null;
      if (editorOn) return null;
      MesquiteInteger io = new MesquiteInteger(0);
      int node = MesquiteInteger.fromString(arguments, io);
      int x = MesquiteInteger.fromString(arguments, io);
      int y = MesquiteInteger.fromString(arguments, io);
      if (lineOn) {
        Point newOnLine = treeDisplay.getTreeDrawing().projectionOnLine(node, x, y);
        // WARNING":  This shouldn't result in length increase if simple click and release with no
        // drag; must subtract original X, Y
        Graphics g = null;
        if (GraphicsUtil.useXORMode(null, false)) {
          g = treeDisplay.getGraphics();
          g.setXORMode(Color.white);
          g.setColor(Color.red);
        }
        // g.fillOval(lastX-ovalRadius, lastY-ovalRadius, ovalRadius + ovalRadius, ovalRadius +
        // ovalRadius);
        // g.fillOval(newOnLine.x-ovalRadius, newOnLine.y -ovalRadius, ovalRadius + ovalRadius,
        // ovalRadius + ovalRadius);

        // g.drawLine(originalX, originalY, lastX, lastY);
        // g.drawLine(originalX, originalY, newOnLine.x, newOnLine.y);

        //				if decreasing, & unassigned involved: push unassigned down and assign values to
        // unassigned above; if increasing, push unassigne up
        int ibX = treeDisplay.getTreeDrawing().lineBaseX[node];
        int ibY = treeDisplay.getTreeDrawing().lineBaseY[node];
        int itX = treeDisplay.getTreeDrawing().lineTipX[node];
        int itY = treeDisplay.getTreeDrawing().lineTipY[node];

        double bX = ibX;
        double bY = ibY;
        double tX = itX;
        double tY = itY;
        double lengthLine =
            Math.sqrt((originalY - bY) * (originalY - bY) + (originalX - bX) * (originalX - bX));
        if (lengthLine != 0) {
          if (GraphicsUtil.useXORMode(null, false)) {
            if (MesquiteTrunk.isMacOSX()
                && MesquiteTrunk.getJavaVersionAsDouble() >= 1.5
                && MesquiteTrunk.getJavaVersionAsDouble() < 1.6) // due to a JVM bug
            g.fillRect(lastX, lastY - 20, 100, 20);
            g.drawString(MesquiteDouble.toString(lastBL), lastX + 10, lastY);
            if (MesquiteTrunk.isMacOSX()
                && MesquiteTrunk.getJavaVersionAsDouble() >= 1.5
                && MesquiteTrunk.getJavaVersionAsDouble() < 1.6) // due to a JVM bug
            g.fillRect(lastX, lastY - 20, 100, 20);
          }
          double extension =
              Math.sqrt(
                      (newOnLine.y - bY) * (newOnLine.y - bY)
                          + (newOnLine.x - bX) * (newOnLine.x - bX))
                  / lengthLine;
          double bL;
          if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node)) bL = extension;
          else bL = t.getBranchLength(node) * extension;
          if (bL > upperLimit) {
            bL = upperLimit;
            if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node))
              extension = upperLimit;
            else extension = upperLimit / t.getBranchLength(node);
          } else if (bL < lowerLimit) {
            bL = lowerLimit;
            if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node))
              extension = lowerLimit;
            else extension = lowerLimit / t.getBranchLength(node);
          }
          lastBL = bL;
          if (GraphicsUtil.useXORMode(null, false)) {
            drawThickLine(g, ibX, ibY, lastX, lastY);
            for (int daughter = t.firstDaughterOfNode(node);
                t.nodeExists(daughter);
                daughter = t.nextSisterOfNode(daughter))
              drawThickLine(
                  g,
                  treeDisplay.getTreeDrawing().lineTipX[daughter],
                  treeDisplay.getTreeDrawing().lineTipY[daughter],
                  lastX,
                  lastY);
            g.fillOval(
                lastX - ovalRadius,
                lastY - ovalRadius,
                ovalRadius + ovalRadius,
                ovalRadius + ovalRadius);
          }
          int newX = ibX + (int) (extension * (tX - bX));
          int newY = ibY + (int) (extension * (tY - bY));
          if (GraphicsUtil.useXORMode(null, false)) {
            g.drawString(MesquiteDouble.toString(bL), newX + 10, newY);
            drawThickLine(g, ibX, ibY, newX, newY);
            for (int daughter = t.firstDaughterOfNode(node);
                t.nodeExists(daughter);
                daughter = t.nextSisterOfNode(daughter))
              drawThickLine(
                  g,
                  treeDisplay.getTreeDrawing().lineTipX[daughter],
                  treeDisplay.getTreeDrawing().lineTipY[daughter],
                  newX,
                  newY);
            g.fillOval(
                newX - ovalRadius,
                newY - ovalRadius,
                ovalRadius + ovalRadius,
                ovalRadius + ovalRadius);
          }
          lastX = newX;
          lastY = newY;
        }

        // lastX= newOnLine.x;
        // lastY = newOnLine.y;
      }
    }
    return null;
  }
  /*.................................................................................................................*/
  public void processSingleXMLPreference(String tag, String content) {

    if ("availMemory".equalsIgnoreCase(tag)) availMemory = MesquiteInteger.fromString(content);
    super.processSingleXMLPreference(tag, content);
  }
  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 + ") ***");
    }
  }