X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGDesktop.java;h=290c4a4f0a2f8e92f2603acf52aceb22c3807d76;hb=cf64def09a8b741483854ddd8c034d0aefff15b4;hp=5505e692f0586fddadd1e867dcf6ead0d6a92135;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 5505e69..290c4a4 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -1,307 +1,666 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.jbgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class GDesktop extends JFrame
-{
-    protected static JMenu windowMenu = new JMenu();
-    JMenuBar DesktopMenubar = new JMenuBar();
-    JMenu FileMenu = new JMenu();
-    JMenu HelpMenu = new JMenu();
-    JMenuItem inputLocalFileMenuItem = new JMenuItem();
-    JMenuItem inputURLMenuItem = new JMenuItem();
-    JMenuItem inputTextboxMenuItem = new JMenuItem();
-    JMenuItem quit = new JMenuItem();
-    JMenuItem aboutMenuItem = new JMenuItem();
-    JMenuItem documentationMenuItem = new JMenuItem();
-    FlowLayout flowLayout1 = new FlowLayout();
-    JMenu toolsMenu = new JMenu();
-    JMenuItem preferences = new JMenuItem();
-    JMenuItem saveState = new JMenuItem();
-    JMenuItem loadState = new JMenuItem();
-    JMenu jMenu1 = new JMenu();
-  JMenuItem vamsasLoad = new JMenuItem();
-  JMenuItem inputSequence = new JMenuItem();
-
-  /**
-     * Creates a new GDesktop object.
-     */
-    public GDesktop()
-    {
-        try
-        {
-            jbInit();
-            this.setJMenuBar(DesktopMenubar);
-        }
-        catch (Exception e)
-        {
-            e.printStackTrace();
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @throws Exception DOCUMENT ME!
-     */
-    private void jbInit() throws Exception
-    {
-        FileMenu.setMnemonic('F');
-        FileMenu.setText("File");
-        HelpMenu.setText("Help");
-        inputLocalFileMenuItem.setMnemonic('L');
-        inputLocalFileMenuItem.setText("from File");
-        inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    inputLocalFileMenuItem_actionPerformed(e);
-                }
-            });
-        inputURLMenuItem.setMnemonic('U');
-        inputURLMenuItem.setText("from URL");
-        inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    inputURLMenuItem_actionPerformed(e);
-                }
-            });
-        inputTextboxMenuItem.setMnemonic('C');
-        inputTextboxMenuItem.setText("from Textbox");
-        inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    inputTextboxMenuItem_actionPerformed(e);
-                }
-            });
-        quit.setMnemonic('Q');
-        quit.setText("Quit");
-        quit.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    quit();
-                }
-            });
-        aboutMenuItem.setText("About");
-        aboutMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    aboutMenuItem_actionPerformed(e);
-                }
-            });
-        documentationMenuItem.setText("Documentation");
-        documentationMenuItem.addActionListener(new java.awt.event.ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    documentationMenuItem_actionPerformed(e);
-                }
-            });
-        this.getContentPane().setLayout(flowLayout1);
-        windowMenu.setText("Window");
-        preferences.setText("Preferences...");
-        preferences.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    preferences_actionPerformed(e);
-                }
-            });
-        toolsMenu.setText("Tools");
-        saveState.setMnemonic('S');
-        saveState.setText("Save Project");
-        saveState.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    saveState_actionPerformed(e);
-                }
-            });
-        loadState.setMnemonic('L');
-        loadState.setText("Load Project");
-        loadState.addActionListener(new ActionListener()
-            {
-                public void actionPerformed(ActionEvent e)
-                {
-                    loadState_actionPerformed(e);
-                }
-            });
-        jMenu1.setMnemonic('I');
-        jMenu1.setText("Input Alignment");
-    vamsasLoad.setText("Vamsas");
-    vamsasLoad.setVisible(false);
-    vamsasLoad.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        vamsasLoad_actionPerformed(e);
-      }
-    });
-    inputSequence.setText("Fetch Sequence...");
-    inputSequence.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        inputSequence_actionPerformed(e);
-      }
-    });
-    DesktopMenubar.add(FileMenu);
-        DesktopMenubar.add(toolsMenu);
-        DesktopMenubar.add(HelpMenu);
-        DesktopMenubar.add(windowMenu);
-        FileMenu.addSeparator();
-        FileMenu.add(jMenu1);
-    FileMenu.add(inputSequence);
-    FileMenu.addSeparator();
-        FileMenu.add(saveState);
-        FileMenu.add(loadState);
-        FileMenu.addSeparator();
-        FileMenu.add(quit);
-        HelpMenu.add(aboutMenuItem);
-        HelpMenu.add(documentationMenuItem);
-        toolsMenu.add(preferences);
-        jMenu1.add(inputLocalFileMenuItem);
-        jMenu1.add(inputURLMenuItem);
-        jMenu1.add(inputTextboxMenuItem);
-    jMenu1.add(vamsasLoad);
-  }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void inputLocalFileMenuItem_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void inputURLMenuItem_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void inputTextboxMenuItem_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    protected void quit()
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void aboutMenuItem_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void documentationMenuItem_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void SaveState_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void preferences_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void saveState_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void loadState_actionPerformed(ActionEvent e)
-    {
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void loadJalviewAlign_actionPerformed(ActionEvent e)
-    {
-    }
-
-  public void vamsasLoad_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  public void inputSequence_actionPerformed(ActionEvent e)
-  {
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.jbgui;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.io.FileFormatException;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+import java.awt.FlowLayout;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class GDesktop extends JFrame
+{
+  protected static JMenu windowMenu = new JMenu();
+
+  JMenuBar desktopMenubar = new JMenuBar();
+
+  JMenu FileMenu = new JMenu();
+
+  JMenu HelpMenu = new JMenu();
+
+  protected JMenu VamsasMenu = new JMenu();
+
+  protected JMenu VamsasStMenu = new JMenu();
+
+  JMenuItem inputLocalFileMenuItem = new JMenuItem();
+
+  JMenuItem inputURLMenuItem = new JMenuItem();
+
+  JMenuItem inputTextboxMenuItem = new JMenuItem();
+
+  JMenuItem quit = new JMenuItem();
+
+  JMenuItem aboutMenuItem = new JMenuItem();
+
+  JMenuItem documentationMenuItem = new JMenuItem();
+
+  FlowLayout flowLayout1 = new FlowLayout();
+
+  protected JMenu toolsMenu = new JMenu();
+
+  JMenuItem preferences = new JMenuItem();
+
+  JMenuItem saveState = new JMenuItem();
+
+  JMenuItem loadState = new JMenuItem();
+
+  JMenu inputMenu = new JMenu();
+
+  protected JMenuItem vamsasStart = new JMenuItem();
+
+  protected JMenuItem vamsasImport = new JMenuItem();
+
+  protected JMenuItem vamsasSave = new JMenuItem();
+
+  JMenuItem inputSequence = new JMenuItem();
+
+  protected JMenuItem vamsasStop = new JMenuItem();
+
+  JMenuItem closeAll = new JMenuItem();
+
+  JMenuItem raiseRelated = new JMenuItem();
+
+  JMenuItem minimizeAssociated = new JMenuItem();
+
+  protected JCheckBoxMenuItem showMemusage = new JCheckBoxMenuItem();
+
+  JMenuItem garbageCollect = new JMenuItem();
+
+  protected JMenuItem groovyShell;
+
+  protected JCheckBoxMenuItem experimentalFeatures;
+
+  protected JCheckBoxMenuItem showConsole = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem showNews = new JCheckBoxMenuItem();
+
+  protected JMenuItem snapShotWindow = new JMenuItem();
+
+  /**
+   * Creates a new GDesktop object.
+   */
+  public GDesktop()
+  {
+    try
+    {
+      jbInit();
+      this.setJMenuBar(desktopMenubar);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+
+    if (!Platform.isAMac())
+    {
+      FileMenu.setMnemonic('F');
+      inputLocalFileMenuItem.setMnemonic('L');
+      VamsasMenu.setMnemonic('V');
+      inputURLMenuItem.setMnemonic('U');
+      inputTextboxMenuItem.setMnemonic('C');
+      quit.setMnemonic('Q');
+      saveState.setMnemonic('S');
+      loadState.setMnemonic('L');
+      inputMenu.setMnemonic('I');
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @throws Exception
+   *           DOCUMENT ME!
+   */
+  private void jbInit() throws Exception
+  {
+
+    FileMenu.setText(MessageManager.getString("action.file"));
+    HelpMenu.setText(MessageManager.getString("action.help"));
+    VamsasMenu.setText("Vamsas");
+    VamsasMenu.setToolTipText(MessageManager
+            .getString("label.share_data_vamsas_applications"));
+    VamsasStMenu.setText(MessageManager.getString("label.connect_to"));
+    VamsasStMenu.setToolTipText(
+            MessageManager.getString("label.join_existing_vamsas_session"));
+    inputLocalFileMenuItem
+            .setText(MessageManager.getString("label.load_tree_from_file"));
+    inputLocalFileMenuItem.setAccelerator(
+            javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O,
+                    Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(),
+                    false));
+    inputLocalFileMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                inputLocalFileMenuItem_actionPerformed(null);
+              }
+            });
+    inputURLMenuItem.setText(MessageManager.getString("label.from_url"));
+    inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          inputURLMenuItem_actionPerformed(null);
+        } catch (FileFormatException e1)
+        {
+          System.err.println("Error loading from URL: " + e1.getMessage());
+        }
+      }
+    });
+    inputTextboxMenuItem
+            .setText(MessageManager.getString("label.from_textbox"));
+    inputTextboxMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                inputTextboxMenuItem_actionPerformed(null);
+              }
+            });
+    quit.setText(MessageManager.getString("action.quit"));
+    quit.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        quit();
+      }
+    });
+    aboutMenuItem.setText(MessageManager.getString("label.about"));
+    aboutMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        aboutMenuItem_actionPerformed(e);
+      }
+    });
+    documentationMenuItem
+            .setText(MessageManager.getString("label.documentation"));
+    documentationMenuItem.setAccelerator(javax.swing.KeyStroke
+            .getKeyStroke(java.awt.event.KeyEvent.VK_F1, 0, false));
+    documentationMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              @Override
+              public void actionPerformed(ActionEvent e)
+              {
+                documentationMenuItem_actionPerformed(e);
+              }
+            });
+    this.getContentPane().setLayout(flowLayout1);
+    windowMenu.setText(MessageManager.getString("label.window"));
+    preferences.setText(MessageManager.getString("label.preferences"));
+    preferences.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        preferences_actionPerformed(e);
+      }
+    });
+    toolsMenu.setText(MessageManager.getString("label.tools"));
+    saveState.setText(MessageManager.getString("action.save_project"));
+    saveState.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        saveState_actionPerformed(true);
+      }
+    });
+    JMenuItem saveAsJaxb = new JMenuItem("Save Project as JAXB");
+    saveAsJaxb.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        saveState_actionPerformed(false);
+      }
+    });
+    loadState.setText(MessageManager.getString("action.load_project"));
+    loadState.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadState_actionPerformed(true);
+      }
+    });
+    JMenuItem loadAsJaxb = new JMenuItem("Load Project as JAXB");
+    loadAsJaxb.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadState_actionPerformed(false);
+      }
+    });
+    inputMenu.setText(MessageManager.getString("label.input_alignment"));
+    vamsasStart
+            .setText(MessageManager.getString("label.new_vamsas_session"));
+    vamsasStart.setVisible(false);
+    vamsasStart.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        vamsasStart_actionPerformed(e);
+      }
+    });
+    vamsasImport.setText(
+            MessageManager.getString("action.load_vamsas_session"));
+    vamsasImport.setVisible(false);
+    vamsasImport.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        vamsasImport_actionPerformed(e);
+      }
+    });
+    vamsasSave.setText(
+            MessageManager.getString("action.save_vamsas_session"));
+    vamsasSave.setVisible(false);
+    vamsasSave.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        vamsasSave_actionPerformed(e);
+      }
+    });
+    inputSequence
+            .setText(MessageManager.getString("action.fetch_sequences"));
+    inputSequence.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        inputSequence_actionPerformed(e);
+      }
+    });
+    vamsasStop
+            .setText(MessageManager.getString("label.stop_vamsas_session"));
+    vamsasStop.setVisible(false);
+    vamsasStop.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        vamsasStop_actionPerformed(e);
+      }
+    });
+    closeAll.setText(MessageManager.getString("action.close_all"));
+    closeAll.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        closeAll_actionPerformed(e);
+      }
+    });
+    raiseRelated.setText(
+            MessageManager.getString("action.raise_associated_windows"));
+    raiseRelated.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        raiseRelated_actionPerformed(e);
+      }
+    });
+    minimizeAssociated.setText(
+            MessageManager.getString("action.minimize_associated_windows"));
+    minimizeAssociated.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        minimizeAssociated_actionPerformed(e);
+      }
+    });
+    garbageCollect
+            .setText(MessageManager.getString("label.collect_garbage"));
+    garbageCollect.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        garbageCollect_actionPerformed(e);
+      }
+    });
+    showMemusage
+            .setText(MessageManager.getString("label.show_memory_usage"));
+    showMemusage.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showMemusage_actionPerformed(e);
+      }
+    });
+    showConsole
+            .setText(MessageManager.getString("label.show_java_console"));
+    showConsole.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showConsole_actionPerformed(e);
+      }
+    });
+    showNews.setText(MessageManager.getString("label.show_jalview_news"));
+    showNews.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showNews_actionPerformed(e);
+      }
+    });
+    groovyShell = new JMenuItem();
+    groovyShell.setText(MessageManager.getString("label.groovy_console"));
+    groovyShell.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        groovyShell_actionPerformed();
+      }
+    });
+    experimentalFeatures = new JCheckBoxMenuItem();
+    experimentalFeatures
+            .setText(MessageManager.getString("label.show_experimental"));
+    experimentalFeatures.setToolTipText(
+            MessageManager.getString("label.show_experimental_tip"));
+    experimentalFeatures.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showExperimental_actionPerformed(experimentalFeatures.isSelected());
+      }
+    });
+
+    snapShotWindow.setText(MessageManager.getString("label.take_snapshot"));
+    snapShotWindow.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        snapShotWindow_actionPerformed(e);
+      }
+    });
+
+    desktopMenubar.add(FileMenu);
+    desktopMenubar.add(toolsMenu);
+    VamsasMenu.setVisible(false);
+    desktopMenubar.add(VamsasMenu);
+    desktopMenubar.add(HelpMenu);
+    desktopMenubar.add(windowMenu);
+    FileMenu.add(inputMenu);
+    FileMenu.add(inputSequence);
+    FileMenu.addSeparator();
+    FileMenu.add(saveState);
+    FileMenu.add(saveAsJaxb);
+    FileMenu.add(loadState);
+    FileMenu.add(loadAsJaxb);
+    FileMenu.addSeparator();
+    FileMenu.add(quit);
+    HelpMenu.add(aboutMenuItem);
+    HelpMenu.add(documentationMenuItem);
+    VamsasMenu.add(VamsasStMenu);
+    VamsasStMenu.setVisible(false);
+    VamsasMenu.add(vamsasStart);
+    VamsasMenu.add(vamsasImport);
+    VamsasMenu.add(vamsasSave);
+    VamsasMenu.add(vamsasStop);
+    toolsMenu.add(preferences);
+    toolsMenu.add(showMemusage);
+    toolsMenu.add(showConsole);
+    toolsMenu.add(showNews);
+    toolsMenu.add(garbageCollect);
+    toolsMenu.add(groovyShell);
+    toolsMenu.add(experimentalFeatures);
+    // toolsMenu.add(snapShotWindow);
+    inputMenu.add(inputLocalFileMenuItem);
+    inputMenu.add(inputURLMenuItem);
+    inputMenu.add(inputTextboxMenuItem);
+    windowMenu.add(closeAll);
+    windowMenu.add(raiseRelated);
+    windowMenu.add(minimizeAssociated);
+    windowMenu.addSeparator();
+    // inputMenu.add(vamsasLoad);
+  }
+
+  protected void showExperimental_actionPerformed(boolean selected)
+  {
+  }
+
+  protected void groovyShell_actionPerformed()
+  {
+  }
+
+  protected void snapShotWindow_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showConsole_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showNews_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void showMemusage_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void garbageCollect_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  protected void vamsasStMenu_actionPerformed()
+  {
+  }
+
+  public void vamsasSave_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  protected void inputLocalFileMenuItem_actionPerformed(
+          jalview.gui.AlignViewport av)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   * @throws FileFormatException
+   */
+  protected void inputURLMenuItem_actionPerformed(
+          jalview.gui.AlignViewport av) throws FileFormatException
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  protected void inputTextboxMenuItem_actionPerformed(
+          AlignmentViewPanel avp)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  protected void quit()
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  protected void aboutMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  protected void documentationMenuItem_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void SaveState_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  protected void preferences_actionPerformed(ActionEvent e)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void saveState_actionPerformed(boolean asCastor)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void loadState_actionPerformed(boolean asCastor)
+  {
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void loadJalviewAlign_actionPerformed(ActionEvent e)
+  {
+  }
+
+  public void vamsasStart_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void inputSequence_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void vamsasStop_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void closeAll_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void raiseRelated_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void minimizeAssociated_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void vamsasImport_actionPerformed(ActionEvent e)
+  {
+  }
+}