Пример #1
0
  private JMenu createExtrasMenu() {

    List<JComponent> menuItems = new ArrayList<JComponent>();

    MenuAction menuAction = null;

    final JCheckBoxMenuItem exomeModeItem = new JCheckBoxMenuItem("Exome mode");
    exomeModeItem.setSelected(FrameManager.isExomeMode());
    exomeModeItem.addActionListener(
        new ActionListener() {
          @Override
          public void actionPerformed(ActionEvent actionEvent) {
            FrameManager.setExomeMode(exomeModeItem.isSelected(), true);
            igv.resetFrames();
          }
        });
    menuItems.add(exomeModeItem);
    menuItems.add(new JSeparator());

    // Preferences reset
    menuAction = new ResetPreferencesAction("Reset Preferences", IGV.getInstance());
    menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));

    menuItems.add(new JSeparator());

    menuAction =
        new MenuAction("Variant list ...  *EXPERIMENTAL*") {
          @Override
          public void actionPerformed(ActionEvent e) {
            VariantListManager.openNavigator(IGV.getMainFrame());
          }
        };
    menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));

    menuItems.add(new JSeparator());

    // Set frame dimensions
    menuAction =
        new MenuAction("Set window dimensions", null, KeyEvent.VK_C) {

          @Override
          public void actionPerformed(ActionEvent e) {
            String value = JOptionPane.showInputDialog("Enter dimensions, e.g. 800x400");
            if (value != null) {
              String[] vals = value.split("x");
              if (vals.length == 2) {
                int w = Integer.parseInt(vals[0]);
                int h = Integer.parseInt(vals[1]);
                IGV.getMainFrame().setSize(w, h);
              }
            }
          }
        };
    menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));

    // Save entire window
    menuAction =
        new MenuAction("Save Screenshot ...", null, KeyEvent.VK_A) {

          @Override
          public void actionPerformed(ActionEvent e) {
            IGV.getInstance().saveImage(IGV.getInstance().getContentPane());
          }
        };

    menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));

    menuAction = new ExportTrackNamesMenuAction("Export track names...", IGV.getInstance());
    menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));

    menuAction =
        new MenuAction("Scatter Plot ...") {
          @Override
          public void actionPerformed(ActionEvent e) {
            final ReferenceFrame defaultFrame = FrameManager.getDefaultFrame();
            String chr = defaultFrame.getChrName();
            int start = (int) defaultFrame.getOrigin();
            int end = (int) defaultFrame.getEnd();
            int zoom = defaultFrame.getZoom();
            ScatterPlotUtils.openPlot(chr, start, end, zoom);
          }
        };
    menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));

    MenuAction extrasMenuAction = new MenuAction("Extras");
    JMenu menu = MenuAndToolbarUtils.createMenu(menuItems, extrasMenuAction);

    //
    JMenu lfMenu = new JMenu("L&F");
    LookAndFeel lf = UIManager.getLookAndFeel();
    for (UIManager.LookAndFeelInfo info : UIManager.getInstalledLookAndFeels()) {

      final String lfName = info.getName();
      JMenuItem cb = new JMenuItem(lfName);
      // cb.setSelected(info.getClassName().equals(lf.getClass().getName());
      cb.addActionListener(
          new AbstractAction() {

            public void actionPerformed(ActionEvent actionEvent) {
              for (UIManager.LookAndFeelInfo info : UIManager.getInstalledLookAndFeels()) {

                if (lfName.equals(info.getName())) {
                  try {
                    UIManager.setLookAndFeel(info.getClassName());
                  } catch (Exception e) {
                    e.printStackTrace();
                  }
                  break;
                }
              }
            }
          });
      lfMenu.add(cb);
    }
    menu.add(lfMenu);

    menu.setVisible(false);

    return menu;
  }
Пример #2
0
  /**
   * Generate the "tools" menu. This is imperative, it is written to field {@code toolsMenu}. Reason
   * being, when we add (TODO remove) a new tool, we need to refresh just this menu
   */
  void refreshToolsMenu() {
    List<JComponent> menuItems = new ArrayList<JComponent>(10);

    // batch script
    MenuAction menuAction = new RunScriptMenuAction("Run Batch Script...", KeyEvent.VK_X, igv);
    menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));

    // igvtools
    // menuItems.add(new JSeparator());
    menuAction =
        new SortTracksMenuAction("Run igvtools...", KeyEvent.VK_T, igv) {
          @Override
          public void actionPerformed(ActionEvent e) {
            IgvToolsGui.launch(false, igv.getGenomeManager().getGenomeId());
          }
        };
    menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));

    List<JComponent> otherToolMenus = igv.getOtherToolMenus();
    if (otherToolMenus.size() > 0) {
      for (JComponent entry : otherToolMenus) {
        menuItems.add(entry);
      }
    }
    // menuItems.add(new JSeparator());

    // -------------------------------------//
    // "Add tool" option, for loading cli_plugin from someplace else
    JMenuItem addTool = new JMenuItem("Add Tool...");
    addTool.addActionListener(
        new ActionListener() {
          @Override
          public void actionPerformed(ActionEvent e) {
            File pluginFi = FileDialogUtils.chooseFile("Select cli_plugin .xml spec");
            if (pluginFi == null) return;

            try {
              PluginSpecReader.addCustomPlugin(pluginFi.getAbsolutePath());
              refreshToolsMenu();
            } catch (IOException e1) {
              MessageUtils.showErrorMessage("Error loading custom cli_plugin", e1);
            }
          }
        });
    // menuItems.add(addTool);
    // menuItems.add(new JSeparator());

    // -------------------------------------//

    for (final PluginSpecReader pluginSpecReader : PluginSpecReader.getPlugins()) {
      for (final PluginSpecReader.Tool tool : pluginSpecReader.getTools()) {
        final String toolName = tool.name;
        boolean toolVisible = tool.visible;
        JMenuItem toolMenu;

        if (toolVisible) {

          final String toolPath = pluginSpecReader.getToolPath(tool);
          final String tool_url = tool.toolUrl;
          boolean isValid = PluginSpecReader.isToolPathValid(toolPath);

          ActionListener invalidActionListener =
              new ActionListener() {
                @Override
                public void actionPerformed(ActionEvent e) {
                  String msg = String.format("%s executable not found at %s", toolName, toolPath);
                  if (tool_url != null) {
                    msg += "<br/>See " + tool_url + " to install";
                  }
                  MessageUtils.showMessage(msg);
                }
              };

          toolMenu = new JMenu(toolName);
          // Kind of overlaps with the side-pull menu, doesn't look great
          // toolMenu.setToolTipText(tool.getAttribute("description"));
          for (final PluginSpecReader.Command command : tool.commandList) {
            final String cmdName = command.name;
            JMenuItem cmdItem = new JMenuItem(cmdName);
            toolMenu.add(cmdItem);
            if (isValid || toolPath == null) {
              cmdItem.addActionListener(
                  new ActionListener() {
                    @Override
                    public void actionPerformed(ActionEvent e) {
                      RunPlugin runPlugin = null;
                      try {
                        runPlugin =
                            new RunPlugin(IGV.getMainFrame(), pluginSpecReader, tool, command);
                      } catch (IllegalStateException e1) {
                        MessageUtils.showErrorMessage(e1.getMessage(), e1);
                        return;
                      }
                      runPlugin.setVisible(true);
                    }
                  });
              cmdItem.setEnabled(true);
            } else {
              cmdItem.setEnabled(false);
            }
          }
          // Hack so we can have a tool which is just general command line stuff
          // Don't let the user change the path in that case
          if (tool.defaultPath != null) {
            JMenuItem setPathItem = new JMenuItem(String.format("Set path to %s...", toolName));
            setPathItem.addActionListener(
                new ActionListener() {
                  @Override
                  public void actionPerformed(ActionEvent e) {
                    (new SetPluginPathDialog(IGV.getMainFrame(), pluginSpecReader, tool))
                        .setVisible(true);
                    refreshToolsMenu();
                  }
                });
            toolMenu.add(setPathItem);
          }
          menuItems.add(toolMenu);
        }
      }
    }
    // -------------------------------------//

    // -----------SQL DB Tools--------------//
    boolean showDBEditor = Globals.isDevelopment();
    if (showDBEditor) {
      JMenu sqlDBProfileEditor = new JMenu("SQL DB Profile Editor");
      JMenuItem createNewProfile = new JMenuItem("Create New Profile");
      createNewProfile.addActionListener(
          new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e) {
              File file =
                  FileDialogUtils.chooseFile(
                      "Save DB Profile", DirectoryManager.getUserDirectory(), FileDialogUtils.SAVE);
              if (file != null) {
                DBProfileEditor editor =
                    new DBProfileEditor(IGV.getMainFrame(), file.getAbsolutePath());
                editor.setVisible(true);
              }
            }
          });
      JMenuItem editExistingProfile = new JMenuItem("Edit Existing Profile");
      editExistingProfile.addActionListener(
          new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e) {
              File file = FileDialogUtils.chooseFile("Select .dbxml database profile");
              if (file != null) {
                if (!file.exists()) {}

                DBProfileEditor editor =
                    new DBProfileEditor(IGV.getMainFrame(), file.getAbsolutePath());
                editor.setVisible(true);
              }
            }
          });
      sqlDBProfileEditor.add(createNewProfile);
      sqlDBProfileEditor.add(editExistingProfile);
      menuItems.add(sqlDBProfileEditor);
    }

    // -------------------------------------//

    // DataTrack Math------------------------//
    if (Globals.isDevelopment()) {
      JMenuItem combineDataItem = new JMenuItem("Combine Data Tracks");
      combineDataItem.addActionListener(
          new ActionListener() {
            @Override
            public void actionPerformed(ActionEvent e) {
              CombinedDataSourceDialog dialog = new CombinedDataSourceDialog(IGV.getMainFrame());
              dialog.setVisible(true);
            }
          });
      menuItems.add(combineDataItem);
    }

    // -------------------------------------//

    MenuAction toolsMenuAction = new MenuAction("Tools", null);
    if (toolsMenu == null) {
      toolsMenu = MenuAndToolbarUtils.createMenu(menuItems, toolsMenuAction);
      toolsMenu.setName("Tools");
    } else {
      toolsMenu.removeAll();
      for (JComponent item : menuItems) {
        toolsMenu.add(item);
      }
    }
  }