Exemplo n.º 1
0
  /*.................................................................................................................*/
  public void actionPerformed(ActionEvent e) {
    if (e.getActionCommand().equalsIgnoreCase("setToDefaults")) {
      setDefaultTNTCommandsSearchOptions();
      searchField.setText(searchArguments);
      bootstrapSearchField.setText(bootstrapSearchArguments);
      harvestOnlyStrictConsensusBox.setState(harvestOnlyStrictConsensus);
      resamplingAllConsensusTreesBox.setState(!resamplingAllConsensusTrees);
      bootStrapRepsField.setValue(bootstrapreps);

    } else if (e.getActionCommand().equalsIgnoreCase("setToDefaultsOtherOptions")) {
      setDefaultTNTCommandsOtherOptions();
      otherOptionsField.setText(otherOptions);
      convertGapsBox.setState(convertGapsToMissing);
    } else if (e.getActionCommand().equalsIgnoreCase("browseSearchScript")
        && searchScriptPathField != null) {
      MesquiteString directoryName = new MesquiteString();
      MesquiteString fileName = new MesquiteString();
      String path =
          MesquiteFile.openFileDialog("Choose Search Script File", directoryName, fileName);
      if (StringUtil.notEmpty(path)) searchScriptPathField.setText(path);
    } else if (e.getActionCommand().equalsIgnoreCase("browseBootSearchScript")
        && bootSearchScriptPathField != null) {

      MesquiteString directoryName = new MesquiteString();
      MesquiteString fileName = new MesquiteString();
      String path =
          MesquiteFile.openFileDialog(
              "Choose Resampling Search Script File", directoryName, fileName);
      if (StringUtil.notEmpty(path)) bootSearchScriptPathField.setText(path);
    }
  }
Exemplo n.º 2
0
 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);
   }
 }
Exemplo n.º 3
0
 private static void appendHTML(JEditorPane editor, String html) {
   try {
     html = StringUtil.replaceAll(html, "\t", "    ");
     html = StringUtil.replaceAll(html, "\r\n", "\n");
     html = StringUtil.replaceAll(html, "\r", "");
     Vector vt = StringUtil.toStringVector(html, "\n");
     HTMLEditorKit kit = (HTMLEditorKit) editor.getEditorKit();
     HTMLDocument doc = (HTMLDocument) editor.getDocument();
     for (int iIndex = 0; iIndex < vt.size(); iIndex++)
       kit.insertHTML(doc, doc.getLength(), (String) vt.elementAt(iIndex), 0, 0, null);
   } catch (Exception e) {
     e.printStackTrace();
   }
 }
 public boolean isVerified() {
   boolean enable = !StringUtil.isEmpty(getProjectName());
   try {
     enable = (new Float(getProjectVersion()) > 0);
   } catch (NumberFormatException e) {
     enable = false;
   } // end of try-catch
   return enable;
 }
Exemplo n.º 5
0
  /*.................................................................................................................*/
  public String preparePreferencesForXML() {
    StringBuffer buffer = new StringBuffer(200);
    StringUtil.appendXMLTag(buffer, 2, "mxram", mxram);
    StringUtil.appendXMLTag(buffer, 2, "bootStrapReps", bootstrapreps);
    StringUtil.appendXMLTag(buffer, 2, "convertGapsToMissing", convertGapsToMissing);
    StringUtil.appendXMLTag(buffer, 2, "resamplingAllConsensusTrees", resamplingAllConsensusTrees);
    StringUtil.appendXMLTag(buffer, 2, "harvestOnlyStrictConsensus", harvestOnlyStrictConsensus);
    StringUtil.appendXMLTag(buffer, 2, "searchArguments", searchArguments);
    StringUtil.appendXMLTag(buffer, 2, "bootstrapSearchArguments", bootstrapSearchArguments);
    StringUtil.appendXMLTag(buffer, 2, "searchStyle", searchStyle);
    StringUtil.appendXMLTag(buffer, 2, "otherOptions", otherOptions);

    preferencesSet = true;
    return buffer.toString();
  }
Exemplo n.º 6
0
  /*.................................................................................................................*/
  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;
  }
Exemplo n.º 7
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;
  }
Exemplo n.º 8
0
  public void setNoteName(String noteName) {
    int idx = 0;
    int i = 0;
    for (int c = _lstFile.getElementCount() - 1; i < c; i++) {
      ListElement le = (ListElement) _lstFile.getElement(i);
      if (StringUtil.equalsIgnoreCase(le.getName(), noteName)) idx = i;
    }

    _lstFile.setSelectedIndex(idx);
    super.btnOk.setEnabled(idx != -1);
  }
 void fetchUserDetails() {
   try {
     UserDetails d = plugin.getUserDetails(getMyLoginId(), contactListEntry.getText());
     String s =
         getMyLoginId()
             + " reports: user details for "
             + contactListEntry.getText()
             + " are:\r\n  nick="
             + StringUtil.toPrintableString(d.getNick())
             + ",\r\n  real name="
             + StringUtil.toPrintableString(d.getRealName())
             + ",\r\n  email="
             + StringUtil.toPrintableString(d.getEmail())
             + ".";
     CAT.info(s);
     log(s);
   } catch (Exception ex) {
     printException(ex);
   }
 }
Exemplo n.º 10
0
  public final String readCommand(byte[] b)
      throws IOException, InterruptedException, MessagingNetworkException {
    InputStream is = getInputStream();
    synchronized (is) {
      long abortTime =
          System.currentTimeMillis() + 1000 * MSNMessagingNetwork.REQPARAM_SOCKET_TIMEOUT_SECONDS;
      int ofs = 0;
      boolean d = false;
      for (; ; ) {
        if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
        int by = is.read();
        if (by == -1) throw new IOException("unexpected EOF");
        if (by == 10 && d) break;
        d = (by == 13);
        if (ofs < b.length) {
          b[ofs++] = (byte) by;
        }
        if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
        /*
        if (len >= buffer.length)
        {
          ...
          return ...;
        }
        int pos = findCRLF();
        if (pos != -1) break;
        fill(is, abortTime);
        */
      }
      if (b[ofs - 1] == 13) --ofs;

      String line = new String(b, 0, ofs, "ASCII");

      if (StringUtil.startsWith(line, "MSG")) {
        StringTokenizer st = new StringTokenizer(line);
        String len_s = null;
        while (st.hasMoreTokens()) {
          len_s = st.nextToken();
        }
        if (len_s == null) throw new AssertException("len_s is null");
        int len;
        try {
          len = Integer.parseInt(len_s);
        } catch (NumberFormatException ex) {
          ServerConnection.throwProtocolViolated("MSG length must be int");
          len = 0;
        }
        String msg = readMSG(len);
        line = line + "\r\n" + msg;
      }
      if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("S: " + line);
      return line;
    }
  }
 /*.................................................................................................................*/
 public void appendAdditionalSearchDetails() {
   appendToSearchDetails("CIPRes Analysis, " + StringUtil.getDateTime() + "\n");
   appendToSearchDetails("Search details: \n");
   if (bootstrapOrJackknife()) {
     appendToSearchDetails("   Bootstrap analysis\n");
     appendToSearchDetails("   " + bootstrapreps + " bootstrap replicates");
   } else {
     appendToSearchDetails("   Search for maximum-likelihood tree\n");
     appendToSearchDetails("   " + numRuns + " search replicate");
     if (numRuns > 1) appendToSearchDetails("s");
   }
 }
Exemplo n.º 12
0
 /*.................................................................................................................*/
 public void fromString(String description, MesquiteInteger stringPos, int format) {
   hasDefaultValues = false;
   ParseUtil.getToken(description, stringPos); // RMatrix
   ParseUtil.getToken(description, stringPos); // =
   ParseUtil.getToken(description, stringPos); // (
   for (int i = 0; i < getNumStates(); i++) {
     String s = ParseUtil.getToken(description, stringPos);
     if (s.equalsIgnoreCase(")") || StringUtil.blank(s)) return;
     setStateFreq(i, MesquiteDouble.fromString(s));
   }
   checkNormality(getStateFrequencies());
 }
Exemplo n.º 13
0
 public String toString() {
   if (StringUtil.isEmptyString(alias)) return name;
   if (isShowFileName()) {
     StringBuffer sb = new StringBuffer();
     sb.append(alias);
     sb.append("(");
     sb.append(name);
     sb.append(")");
     return sb.toString();
   } else {
     return alias;
   }
 }
Exemplo n.º 14
0
 void insertMatchButton_actionPerformed(ActionEvent e) {
   String key = (String) matchComboBox.getSelectedItem();
   String format = (String) matchesKeys.get(key);
   if (key.equals(STRING_LITERAL)) {
     format =
         escapeReservedChars(
             (String)
                 JOptionPane.showInputDialog(
                     this,
                     "Enter the string you wish to match",
                     "String Literal Input",
                     JOptionPane.OK_CANCEL_OPTION));
     if (StringUtil.isNullString(format)) {
       return;
     }
   }
   if (selectedPane == 0) {
     insertText(format, PLAIN_ATTR, editorPane.getSelectionStart());
   } else {
     // add the combobox data value to the edit box
     int pos = formatTextArea.getCaretPosition();
     formatTextArea.insert(format, pos);
   }
 }
Exemplo n.º 15
0
 private void jbInit() throws Exception {
   ////////////////////////////////////////////////////////
   // Init LAF
   ////////////////////////////////////////////////////////
   ButtonGroup grpLAF = new ButtonGroup();
   ActionListener lsnLAF =
       new ActionListener() {
         public void actionPerformed(ActionEvent evt) {
           int iIndex = mvtLAFItem.indexOf(evt.getSource());
           if (iIndex >= 0) changeLAF(iIndex);
         }
       };
   ////////////////////////////////////////////////////////
   UIManager.LookAndFeelInfo laf =
       new UIManager.LookAndFeelInfo(
           "Kunststoff", "com.incors.plaf.kunststoff.KunststoffLookAndFeel");
   marrLaf = UIManager.getInstalledLookAndFeels();
   int iIndex = 0;
   while (iIndex < marrLaf.length && !marrLaf[iIndex].getName().equals(laf.getName())) iIndex++;
   if (iIndex >= marrLaf.length) {
     UIManager.installLookAndFeel(laf);
     marrLaf = UIManager.getInstalledLookAndFeels();
   }
   for (iIndex = 0; iIndex < marrLaf.length; iIndex++) {
     JMenuItem mnu = new JRadioButtonMenuItem(marrLaf[iIndex].getName());
     mnu.addActionListener(lsnLAF);
     mvtLAFItem.addElement(mnu);
     mnuUI.add(mnu);
     grpLAF.add(mnu);
   }
   mnuUI.addSeparator();
   ////////////////////////////////////////////////////////
   // Init language
   ////////////////////////////////////////////////////////
   ButtonGroup grpLanguage = new ButtonGroup();
   ActionListener lsnLanguage =
       new ActionListener() {
         public void actionPerformed(ActionEvent e) {
           int iIndex = mvtLanguageItem.indexOf(e.getSource());
           if (iIndex >= 0) changeDictionary((String) mvtLanguage.elementAt(iIndex));
         }
       };
   ////////////////////////////////////////////////////////
   String[] str = MonitorDictionary.getSupportedLanguage();
   for (iIndex = 0; iIndex < str.length; iIndex++) {
     JMenuItem mnu =
         new JRadioButtonMenuItem(MonitorDictionary.getDictionary(str[iIndex]).getLanguage());
     mnu.addActionListener(lsnLanguage);
     mvtLanguage.addElement(str[iIndex]);
     mvtLanguageItem.addElement(mnu);
     mnuUI.add(mnu);
     grpLanguage.add(mnu);
   }
   ////////////////////////////////////////////////////////
   // Add to main menu
   ////////////////////////////////////////////////////////
   mnuMain.removeAll();
   mnuMain.add(mnuSystem);
   mnuSystem.add(mnuSystem_Login);
   mnuSystem.add(mnuSystem_ChangePassword);
   mnuSystem.addSeparator();
   mnuSystem.add(mnuSystem_StopServer);
   mnuSystem.add(mnuSystem_EnableThreads);
   mnuMain.add(mnuUI);
   mnuMain.add(mnuHelp);
   mnuHelp.add(mnuHelp_About);
   ////////////////////////////////////////////////////////
   mnuMain.add(chkVietnamese);
   mnuMain.add(lblStatus);
   ////////////////////////////////////////////////////////
   pnlThread.setTabPlacement(JTabbedPane.LEFT);
   pnlThread.setTabLayoutPolicy(JTabbedPane.SCROLL_TAB_LAYOUT);
   ////////////////////////////////////////////////////////
   tblUser.addColumn("", 1, false);
   tblUser.addColumn("", 2, false, Global.FORMAT_DATE_TIME);
   tblUser.addColumn("", 3, false);
   ////////////////////////////////////////////////////////
   JPanel pnlMessage = new JPanel();
   pnlMessage.setLayout(new GridBagLayout());
   pnlMessage.add(
       new JScrollPane(txtBoard),
       new GridBagConstraints(
           0,
           0,
           2,
           1,
           1.0,
           1.0,
           GridBagConstraints.CENTER,
           GridBagConstraints.BOTH,
           new Insets(2, 2, 2, 2),
           0,
           0));
   pnlMessage.add(
       txtMessage,
       new GridBagConstraints(
           0,
           1,
           1,
           1,
           1.0,
           0.0,
           GridBagConstraints.CENTER,
           GridBagConstraints.BOTH,
           new Insets(2, 2, 2, 2),
           0,
           0));
   pnlMessage.add(
       btnSend,
       new GridBagConstraints(
           1,
           1,
           1,
           1,
           0.0,
           0.0,
           GridBagConstraints.CENTER,
           GridBagConstraints.NONE,
           new Insets(2, 2, 2, 2),
           0,
           0));
   txtBoard.setEditable(false);
   txtBoard.setAutoscrolls(true);
   txtBoard.setContentType("text/html");
   clearAll(txtBoard);
   ////////////////////////////////////////////////////////
   JPanel pnlUserButton = new JPanel(new GridLayout(1, 2, 4, 4));
   pnlUserButton.add(btnKick);
   pnlUserButton.add(btnRefresh);
   ////////////////////////////////////////////////////////
   JPanel pnlManager = new JPanel(new GridBagLayout());
   pnlManager.add(
       new JScrollPane(tblUser),
       new GridBagConstraints(
           0,
           0,
           1,
           1,
           1.0,
           1.0,
           GridBagConstraints.CENTER,
           GridBagConstraints.BOTH,
           new Insets(2, 2, 2, 2),
           0,
           0));
   pnlManager.add(
       pnlUserButton,
       new GridBagConstraints(
           0,
           1,
           1,
           1,
           0.0,
           0.0,
           GridBagConstraints.CENTER,
           GridBagConstraints.NONE,
           new Insets(4, 2, 4, 2),
           0,
           0));
   ////////////////////////////////////////////////////////
   pnlUser.setDividerLocation(320);
   pnlUser.setLeftComponent(pnlManager);
   pnlUser.setRightComponent(pnlMessage);
   pnlUser.setOneTouchExpandable(true);
   ////////////////////////////////////////////////////////
   setOrientation(JSplitPane.VERTICAL_SPLIT);
   setOneTouchExpandable(true);
   pnlThread.setVisible(false);
   pnlUser.setVisible(false);
   setTopComponent(pnlThread);
   setBottomComponent(pnlUser);
   ////////////////////////////////////////////////////////
   pmn.add(mnuSelectAll);
   pmn.addSeparator();
   pmn.add(mnuClearSelected);
   pmn.add(mnuClearAll);
   ////////////////////////////////////////////////////////
   setBorder(BorderFactory.createEmptyBorder());
   pnlUser.setBorder(BorderFactory.createEmptyBorder());
   pnlManager.setBorder(
       BorderFactory.createBevelBorder(
           javax.swing.border.BevelBorder.RAISED,
           Color.white,
           UIManager.getColor("Panel.background"),
           UIManager.getColor("Panel.background"),
           UIManager.getColor("Panel.background")));
   pnlMessage.setBorder(
       BorderFactory.createBevelBorder(
           javax.swing.border.BevelBorder.RAISED,
           Color.white,
           UIManager.getColor("Panel.background"),
           UIManager.getColor("Panel.background"),
           UIManager.getColor("Panel.background")));
   ////////////////////////////////////////////////////////
   Skin.applySkin(mnuMain);
   Skin.applySkin(tblUser);
   Skin.applySkin(pmn);
   Skin.applySkin(this);
   ////////////////////////////////////////////////////////
   // Default setting
   ////////////////////////////////////////////////////////
   Hashtable prt = null;
   try {
     prt = Global.loadHashtable(Global.FILE_CONFIG);
   } catch (Exception e) {
     prt = new Hashtable();
   }
   changeLAF(Integer.parseInt(StringUtil.nvl(prt.get("LAF"), "0")));
   changeDictionary(StringUtil.nvl(prt.get("Language"), "VN"));
   Skin.LANGUAGE_CHANGE_LISTENER = this;
   MonitorProcessor.setRootObject(this);
   updateKeyboardUI();
   ////////////////////////////////////////////////////////
   // Event handler
   ////////////////////////////////////////////////////////
   tblUser.addMouseListener(
       new MouseAdapter() {
         public void mouseClicked(MouseEvent e) {
           if (e.getClickCount() > 1) btnKick.doClick();
         }
       });
   ////////////////////////////////////////////////////////
   btnRefresh.addActionListener(
       new java.awt.event.ActionListener() {
         public void actionPerformed(ActionEvent evt) {
           try {
             DDTP request = new DDTP();
             request.setRequestID(String.valueOf(System.currentTimeMillis()));
             DDTP response = channel.sendRequest("ThreadProcessor", "queryUserList", request);
             if (response != null) {
               tblUser.setData((Vector) response.getReturn());
               if (mstrChannel != null) removeUser(mstrChannel);
             }
           } catch (Exception e) {
             e.printStackTrace();
             MessageBox.showMessageDialog(pnlThread, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
           }
         }
       });
   ////////////////////////////////////////////////////////
   btnKick.addActionListener(
       new java.awt.event.ActionListener() {
         public void actionPerformed(ActionEvent evt) {
           int iSelected = tblUser.getSelectedRow();
           if (iSelected < 0) return;
           int iResult =
               MessageBox.showConfirmDialog(
                   pnlThread,
                   mdic.getString("ConfirmKick"),
                   Global.APP_NAME,
                   MessageBox.YES_NO_OPTION);
           if (iResult == MessageBox.NO_OPTION) return;
           try {
             String strChannel = (String) tblUser.getRow(iSelected).elementAt(0);
             DDTP request = new DDTP();
             request.setRequestID(String.valueOf(System.currentTimeMillis()));
             request.setString("strChannel", strChannel);
             DDTP response = channel.sendRequest("ThreadProcessor", "kickUser", request);
           } catch (Exception e) {
             e.printStackTrace();
             MessageBox.showMessageDialog(pnlThread, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
           }
         }
       });
   ////////////////////////////////////////////////////////
   txtMessage.addActionListener(
       new java.awt.event.ActionListener() {
         public void actionPerformed(ActionEvent evt) {
           btnSend.doClick();
         }
       });
   ////////////////////////////////////////////////////////
   btnSend.addActionListener(
       new java.awt.event.ActionListener() {
         public void actionPerformed(ActionEvent evt) {
           if (txtMessage.getText().length() == 0) return;
           try {
             DDTP request = new DDTP();
             request.setString("strMessage", txtMessage.getText());
             channel.sendRequest("ThreadProcessor", "sendMessage", request);
             txtMessage.setText("");
           } catch (Exception e) {
             e.printStackTrace();
             MessageBox.showMessageDialog(pnlThread, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);
           }
         }
       });
   ////////////////////////////////////////////////////////
   mnuClearAll.addActionListener(
       new java.awt.event.ActionListener() {
         public void actionPerformed(ActionEvent e) {
           clearAll(txtBoard);
         }
       });
   ////////////////////////////////////////////////////////
   mnuClearSelected.addActionListener(
       new java.awt.event.ActionListener() {
         public void actionPerformed(ActionEvent e) {
           txtBoard.setEditable(true);
           txtBoard.replaceSelection("");
           txtBoard.setEditable(false);
         }
       });
   ////////////////////////////////////////////////////////
   mnuSelectAll.addActionListener(
       new java.awt.event.ActionListener() {
         public void actionPerformed(ActionEvent e) {
           txtBoard.requestFocus();
           txtBoard.selectAll();
         }
       });
   ////////////////////////////////////////////////////////
   txtBoard.addMouseListener(
       new MouseAdapter() {
         public void mouseClicked(MouseEvent e) {
           if (e.getButton() == e.BUTTON3) pmn.show(txtBoard, e.getX(), e.getY());
         }
       });
   ////////////////////////////////////////////////////////
   mnuSystem_Login.addActionListener(
       new ActionListener() {
         public void actionPerformed(ActionEvent e) {
           login();
         }
       });
   ////////////////////////////////////////////////////////
   mnuSystem_ChangePassword.addActionListener(
       new ActionListener() {
         public void actionPerformed(ActionEvent e) {
           changePassword();
         }
       });
   ////////////////////////////////////////////////////////
   mnuSystem_StopServer.addActionListener(
       new ActionListener() {
         public void actionPerformed(ActionEvent e) {
           stopServer();
         }
       });
   ////////////////////////////////////////////////////////
   mnuSystem_EnableThreads.addActionListener(
       new ActionListener() {
         public void actionPerformed(ActionEvent e) {
           manageThreads();
         }
       });
   ////////////////////////////////////////////////////////
   mnuHelp_About.addActionListener(
       new ActionListener() {
         public void actionPerformed(ActionEvent e) {
           WindowManager.centeredWindow(new DialogAbout(PanelThreadManager.this));
         }
       });
   ////////////////////////////////////////////////////////
   chkVietnamese.addActionListener(
       new java.awt.event.ActionListener() {
         public void actionPerformed(ActionEvent e) {
           switchKeyboard();
         }
       });
 }
Exemplo n.º 16
0
 public String getAppVersion() {
   return StringUtil.nvl(mstrAppVersion, "Unknown version");
 }
Exemplo n.º 17
0
 public String getAppName() {
   return StringUtil.nvl(mstrAppName, "Unknown application");
 }
  /*.................................................................................................................*/
  void getArguments(
      MultipartEntityBuilder builder,
      StringBuffer sb,
      String fileName,
      String LOCproteinModel,
      String LOCdnaModel,
      String LOCotherOptions,
      int LOCbootstrapreps,
      int LOCbootstrapSeed,
      int LOCnumRuns,
      String LOCoutgroupTaxSetString,
      String LOCMultipleModelFile,
      boolean preflight) {
    if (builder == null) return;
    /*
    if (preflight)
    	arguments += " -n preflight.out ";
    else
    	arguments += " -s " + fileName + " -n file.out ";
    */

    if (isProtein) {
      if (StringUtil.blank(LOCproteinModel))
        addArgument(builder, sb, "vparam.protein_opts_", "PROTGAMMAJTT");
      else addArgument(builder, sb, "vparam.protein_opts_", LOCproteinModel);
    } else if (StringUtil.blank(LOCdnaModel))
      addArgument(builder, sb, "vparam.dna_gtrcat_", "GTRGAMMA");
    else addArgument(builder, sb, "vparam.dna_gtrcat_", "GTRGAMMA");
    //	builder.addTextBody("vparam.dna_gtrcat_",LOCdnaModel);

    /*
    		if (StringUtil.notEmpty(LOCMultipleModelFile))
    			arguments += " -q " + ShellScriptUtil.protectForShellScript(LOCMultipleModelFile);

    		if (!StringUtil.blank(LOCotherOptions))
    			arguments += " " + LOCotherOptions;

    */

    addArgument(builder, sb, "vparam.provide_parsimony_seed_", "1");
    addArgument(builder, sb, "vparam.parsimony_seed_val_", "" + randomIntSeed);

    if (bootstrapOrJackknife()) {
      if (LOCbootstrapreps > 0) {
        addArgument(builder, sb, "vparam.choose_bootstrap_", "b");
        addArgument(builder, sb, "vparam.bootstrap_value_", "" + LOCbootstrapreps);
        addArgument(builder, sb, "vparam.seed_value_", "" + LOCbootstrapSeed);
        //	addArgument(builder, sb, "vparam.bootstrap_",""+LOCbootstrapreps);
        //	addArgument(builder, sb, "vparam.mulparambootstrap_seed_",""+LOCbootstrapSeed);
      } else Debugg.println("TOO FEW BOOTSTRAP REPS");

    } else {
      addArgument(builder, sb, "vparam.specify_runs_", "1");
      addArgument(builder, sb, "vparam.altrun_number_", "" + LOCnumRuns);
      //	if (RAxML814orLater)
      // addArgument(builder, sb, "vparam.mesquite_output_","1");
    }

    TaxaSelectionSet outgroupSet = null;
    if (!StringUtil.blank(LOCoutgroupTaxSetString)) {
      outgroupSet =
          (TaxaSelectionSet) taxa.getSpecsSet(LOCoutgroupTaxSetString, TaxaSelectionSet.class);
      if (outgroupSet != null)
        addArgument(builder, sb, "vparam.outgroup_", outgroupSet.getStringList(",", true));
      arguments += " -o " + outgroupSet.getStringList(",", true);
    }
  }
Exemplo n.º 19
0
  public void login() {
    mbAutoLogIn = false;
    while (!mbAutoLogIn) {
      try {
        // Confirm logout
        if (isOpen()) {
          if (MessageBox.showConfirmDialog(
                  this,
                  MonitorDictionary.getString("Confirm.Exit"),
                  Global.APP_NAME,
                  MessageBox.YES_NO_OPTION)
              == MessageBox.NO_OPTION) return;

          // Disconnect from server
          disconnect();
        }

        // Login
        DialogLogin dlgLogin = new DialogLogin(this);
        WindowManager.centeredWindow(dlgLogin);

        if (dlgLogin.miReturn == JOptionPane.OK_OPTION) {
          // Update UI
          SwingUtilities.updateComponentTreeUI(pnlUser);
          SwingUtilities.updateComponentTreeUI(pnlThread);

          // Request to connect
          Socket sck = new Socket(dlgLogin.mstrHost, Integer.parseInt(dlgLogin.mstrPort));
          sck.setSoLinger(true, 0);

          // Start up a channel thread that reads messages from the server
          channel =
              new SocketTransmitter(sck) {
                public void close() {
                  if (msckMain != null) {
                    super.close();
                    closeAll();
                    if (mbAutoLogIn) login();
                  }
                }
              };
          channel.setUserName(dlgLogin.mstrUserName);
          channel.setPackage("com.fss.thread.");
          channel.start();

          // Request to Server
          DDTP request = new DDTP();
          request.setRequestID(String.valueOf(System.currentTimeMillis()));
          request.setString("UserName", dlgLogin.mstrUserName);
          request.setString("Password", dlgLogin.mstrPassword);

          // Response from Server
          DDTP response = channel.sendRequest("ThreadProcessor", "login", request);
          mstrThreadAppName = response.getString("strThreadAppName");
          mstrThreadAppVersion = response.getString("strThreadAppVersion");
          mstrAppName = response.getString("strAppName");
          mstrAppVersion = response.getString("strAppVersion");
          if (response != null) {
            if (response.getString("PasswordExpired") != null) {
              DialogChangePassword frm = new DialogChangePassword(this, channel);
              WindowManager.centeredWindow(frm);
              if (frm.miReturnValue != JOptionPane.OK_OPTION) throw new AppException("FSS-10003");
            }
            String strLog = StringUtil.nvl(response.getString("strLog"), "");
            showResult(txtBoard, strLog);
            Vector vtThread = response.getVector("vtThread");
            updateTabBar(vtThread);

            mstrChannel = response.getString("strChannel");
            if (mstrChannel != null) removeUser(mstrChannel);
          }
          btnRefresh.doClick();
          pnlThread.setVisible(true);
          pnlUser.setVisible(true);
          setResizeWeight(1);
          setDividerLocation((int) (getSize().getHeight() - 160));
        }
        mbAutoLogIn = true;
        updateLanguage();
      } catch (Exception e) {
        e.printStackTrace();
        MessageBox.showMessageDialog(this, e, Global.APP_NAME, MessageBox.ERROR_MESSAGE);

        // Disconnect from server
        mstrChannel = null;
        disconnect();
      }
    }
  }
Exemplo n.º 20
0
  private boolean recalcPositions(Graphics g) {
    Font f = g.getFont();
    if (f != oldFont || !(StringUtil.stringsEqual(oldText, text))) {
      FontMetrics fm = g.getFontMetrics(f);
      sw = MesquiteInteger.maximum(fm.stringWidth("888"), fm.stringWidth(tf.getText()));
      sh = fm.getMaxAscent() + fm.getMaxDescent();
    }
    oldText = text;
    oldFont = f;
    if (oldTextBoxWidth < sw + MesquiteModule.textEdgeCompensationWidth - 1
        || oldTextBoxHeight < sh + MesquiteModule.textEdgeCompensationHeight - 1) {
      textBoxWidth = sw + MesquiteModule.textEdgeCompensationWidth; // 34
      textBoxHeight = sh + MesquiteModule.textEdgeCompensationHeight; // 18
      oldTextBoxWidth = textBoxWidth;
      oldTextBoxHeight = textBoxHeight;
      if (horizontal) {
        if (stacked) {
          totalWidth = textBoxWidth + EnterButton.MIN_DIMENSION + 2;
          totalHeight = textBoxHeight + 20;
          setSize(totalWidth, totalHeight);
          tf.setSize(textBoxWidth, textBoxHeight);
          tf.setLocation(0, 0);
          decrementButton.setLocation(2, textBoxHeight + 4);
          incrementButton.setLocation(totalWidth - 20, textBoxHeight + 4);
        } else {
          totalWidth = textBoxWidth + 36 + EnterButton.MIN_DIMENSION + 2;
          totalHeight = textBoxHeight + 4;
          setSize(totalWidth, totalHeight);
          tf.setSize(textBoxWidth, textBoxHeight);
          decrementButton.setLocation(0, 2);
          tf.setLocation(
              decrementButton.getBounds().x + decrementButton.getBounds().width + 1,
              0); // 1 added to x
          incrementButton.setLocation(
              tf.getBounds().x + tf.getBounds().width + EnterButton.MIN_DIMENSION + 2,
              2); // 1 added to x
        }
        enterButton.setLocation(tf.getBounds().x + tf.getBounds().width + 1, 2);
      } else {
        if (stacked) {
          totalWidth = textBoxWidth + EnterButton.MIN_DIMENSION + 2;
          totalHeight = textBoxHeight + 20;
          setSize(totalWidth, totalHeight);
          tf.setSize(textBoxWidth, textBoxHeight);
          tf.setLocation(0, 0);
          decrementButton.setLocation(2, textBoxHeight + 4);
          incrementButton.setLocation(totalWidth - 22, textBoxHeight + 4);
          enterButton.setLocation(tf.getBounds().x + tf.getBounds().width + 1, 2);
        } else {
          totalWidth = textBoxWidth; // should be 0
          totalHeight = textBoxHeight + 36 + EnterButton.MIN_DIMENSION + 2;

          setSize(totalWidth, totalHeight);
          tf.setSize(textBoxWidth, textBoxHeight);
          incrementButton.setLocation(1, 2);
          tf.setLocation(0, incrementButton.getBounds().height + 3);
          decrementButton.setLocation(
              1, tf.getBounds().y + tf.getBounds().height + EnterButton.MIN_DIMENSION + 2);
          enterButton.setLocation(1, tf.getBounds().y + tf.getBounds().height + 1);
        }
      }
      incrementButton.repaint();
      decrementButton.repaint();
      enterButton.repaint();
      repaint();
      getParent().repaint();
      return true;
    }
    if (checkBackground()) {
      repaint();
      return true;
    }
    /*	if (!getBackground().equals(getParent().getBackground())) {
    	bg =getParent().getBackground();
    	setBackground(bg);
    	//setBackground(Color.green);
    	tf.setBackground(bg);
    	decrementButton.setBackground(bg);
    	incrementButton.setBackground(bg);
    	enterButton.setBackground(bg);
    	repaint();
    	return true;
    }*/
    return false;
  }
Exemplo n.º 21
0
  void insertButton_actionPerformed(ActionEvent e) {
    Object selected = paramComboBox.getSelectedItem();
    ConfigParamDescr descr;
    String key;
    int type = 0;
    String format = "";
    if (selected instanceof ConfigParamDescr) {
      descr = (ConfigParamDescr) selected;
      key = descr.getKey();
      type = descr.getType();
      switch (type) {
        case ConfigParamDescr.TYPE_STRING:
        case ConfigParamDescr.TYPE_URL:
        case ConfigParamDescr.TYPE_BOOLEAN:
          format = "%s";
          break;
        case ConfigParamDescr.TYPE_INT:
        case ConfigParamDescr.TYPE_LONG:
        case ConfigParamDescr.TYPE_POS_INT:
          NumericPaddingDialog dialog = new NumericPaddingDialog();
          Point pos = this.getLocationOnScreen();
          dialog.setLocation(pos.x, pos.y);
          dialog.pack();
          dialog.setVisible(true);
          StringBuilder fbuf = new StringBuilder("%");
          int width = dialog.getPaddingSize();
          boolean is_zero = dialog.useZero();
          if (width > 0) {
            fbuf.append(".");
            if (is_zero) {
              fbuf.append(0);
            }
            fbuf.append(width);
          }
          if (type == ConfigParamDescr.TYPE_LONG) {
            fbuf.append("ld");
          } else {
            fbuf.append("d");
          }
          format = fbuf.toString();
          break;
        case ConfigParamDescr.TYPE_YEAR:
          if (key.startsWith(DefinableArchivalUnit.PREFIX_AU_SHORT_YEAR)) {
            format = "%02d";
          } else {
            format = "%d";
          }
          break;
        case ConfigParamDescr.TYPE_RANGE:
        case ConfigParamDescr.TYPE_NUM_RANGE:
        case ConfigParamDescr.TYPE_SET:
          format = "%s";
          break;
      }
      if (selectedPane == 0) {
        insertParameter(descr, format, editorPane.getSelectionStart());
      } else if (selectedPane == 1) {
        // add the combobox data value to the edit box
        int pos = formatTextArea.getCaretPosition();
        formatTextArea.insert(format, pos);

        pos = parameterTextArea.getCaretPosition();
        parameterTextArea.insert(", " + key, pos);
      }
    } else {
      key = selected.toString();
      format =
          escapePrintfChars(
              (String)
                  JOptionPane.showInputDialog(
                      this,
                      "Enter the string you wish to input",
                      "String Literal Input",
                      JOptionPane.OK_CANCEL_OPTION));
      if (StringUtil.isNullString(format)) {
        return;
      }
      if (selectedPane == 0) {
        insertText(format, PLAIN_ATTR, editorPane.getSelectionStart());
      } else if (selectedPane == 1) {
        // add the combobox data value to the edit box
        formatTextArea.insert(format, formatTextArea.getCaretPosition());
      }
    }
  }
Exemplo n.º 22
0
  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 + ") ***");
    }
  }
Exemplo n.º 23
0
 /*.................................................................................................................*/
 String getComDelim() {
   if (externalProcRunner.isWindows()) return ";" + StringUtil.lineEnding();
   else return ";" + StringUtil.lineEnding();
 }
Exemplo n.º 24
0
 /*.................................................................................................................*/
 public String preparePreferencesForXML() {
   StringBuffer buffer = new StringBuffer(200);
   StringUtil.appendXMLTag(buffer, 2, "availMemory", availMemory);
   buffer.append(super.preparePreferencesForXML());
   return buffer.toString();
 }
Exemplo n.º 25
0
 public String getThreadAppName() {
   return StringUtil.nvl(mstrThreadAppName, "Unknown platform");
 }
Exemplo n.º 26
0
  /*.................................................................................................................*/
  void formCommandFile(String dataFileName, int firstOutgroup) {
    if (parallel) {
      commands = "";
    }
    commands += getTNTCommand("mxram " + mxram);

    commands += getTNTCommand("report+0/1/0");
    commands += getTNTCommand("log " + logFileName);
    commands += getTNTCommand("p " + dataFileName);
    commands += getTNTCommand("vversion");
    if (MesquiteInteger.isCombinable(firstOutgroup) && firstOutgroup >= 0)
      commands += getTNTCommand("outgroup " + firstOutgroup);
    if (bootstrapOrJackknife()) {
      if (parallel) {
        commands += indentTNTCommand("ptnt begin parallelRun " + numSlaves + "/ram x 2 = ");
      }
      if (StringUtil.notEmpty(bootSearchScriptPath)) {
        String script = MesquiteFile.getFileContentsAsString(bootSearchScriptPath);
        if (StringUtil.notEmpty(script)) commands += script;
      } else
        commands += StringUtil.lineEnding() + bootstrapSearchArguments + StringUtil.lineEnding();
      String saveTreesString = "";
      if (resamplingAllConsensusTrees) saveTreesString = " savetrees ";
      String bootSearchString = " [xmult; bb]";
      bootSearchString = "";

      if (parallel) {
        int numRepsPerSlave = bootstrapreps / numSlaves;
        if (numRepsPerSlave * numSlaves < bootstrapreps) numRepsPerSlave++;
        if (searchStyle == BOOTSTRAPSEARCH)
          commands +=
              getTNTCommand(
                  "resample boot cut 50 "
                      + saveTreesString
                      + " replications "
                      + numRepsPerSlave
                      + " [xmult; bb] savetrees"); // + getComDelim();
        else if (searchStyle == JACKKNIFESEARCH)
          commands +=
              getTNTCommand(
                  "resample jak cut 50 "
                      + saveTreesString
                      + " replications "
                      + numRepsPerSlave
                      + " [xmult; bb] savetrees"); // + getComDelim();
        else if (searchStyle == SYMSEARCH)
          commands +=
              getTNTCommand(
                  "resample sym cut 50 "
                      + saveTreesString
                      + " replications "
                      + numRepsPerSlave
                      + " [xmult; bb] savetrees"); // + getComDelim();
        else if (searchStyle == POISSONSEARCH)
          commands +=
              getTNTCommand(
                  "resample poisson cut 50 "
                      + saveTreesString
                      + " replications "
                      + numRepsPerSlave
                      + " [xmult; bb] savetrees"); // + getComDelim();
        commands += getTNTCommand("return");
        commands += getTNTCommand("ptnt wait parallelRun");
        commands += getTNTCommand("ptnt get parallelRun");
      } else {
        if (!resamplingAllConsensusTrees) {
          commands += getTNTCommand("macro=");
          commands += getTNTCommand("ttags =");
        }
        commands += getTNTCommand("tsave *" + treeFileName);
        if (bootstrapAllowed) {
          if (searchStyle == BOOTSTRAPSEARCH)
            commands +=
                getTNTCommand(
                    "resample boot "
                        + saveTreesString
                        + " replications "
                        + bootstrapreps
                        + bootSearchString); // + getComDelim();
          else if (searchStyle == JACKKNIFESEARCH)
            commands +=
                getTNTCommand(
                    "resample jak cut 50 "
                        + saveTreesString
                        + " replications "
                        + bootstrapreps
                        + bootSearchString); // + getComDelim();
          else if (searchStyle == SYMSEARCH)
            commands +=
                getTNTCommand(
                    "resample sym cut 50 "
                        + saveTreesString
                        + " replications "
                        + bootstrapreps
                        + bootSearchString); // + getComDelim();
          else if (searchStyle == POISSONSEARCH)
            commands +=
                getTNTCommand(
                    "resample poisson cut 50 "
                        + saveTreesString
                        + " replications "
                        + bootstrapreps
                        + bootSearchString); // + getComDelim();
        }
        if (!resamplingAllConsensusTrees) commands += getTNTCommand("save *");
        else commands += getTNTCommand("save");
        commands += getTNTCommand("tsave/");
        if (!resamplingAllConsensusTrees) {
          commands += getTNTCommand("ttags -/");
          commands += getTNTCommand("macro-");
        }
      }

      // commands += getTNTCommand("proc/") ;

      commands += getTNTCommand("log/");

      //	if (!parallel)
      commands += getTNTCommand("quit");
    } else {
      // commands += getTNTCommand("tsave !5 " + treeFileName) ;   // if showing intermediate trees
      commands += getTNTCommand("tsave *" + treeFileName);
      if (StringUtil.notEmpty(searchScriptPath)) {
        String script = MesquiteFile.getFileContentsAsString(searchScriptPath);
        if (StringUtil.notEmpty(script)) commands += script;
      } else commands += searchArguments;
      commands += otherOptions;
      if (harvestOnlyStrictConsensus) commands += getTNTCommand("nelsen *");
      commands += getTNTCommand("save");
      commands += getTNTCommand("log/");

      commands += getTNTCommand("tsave/");
      commands += getTNTCommand("quit");
    }
  }