Formatting
[jalview.git] / src / jalview / jbgui / GDesktop.java
index daea610..722a408 100755 (executable)
@@ -1,54 +1,53 @@
 /*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
 package jalview.jbgui;\r
 \r
 import java.awt.*;\r
 import java.awt.event.*;\r
-\r
 import javax.swing.*;\r
 \r
-\r
 /**\r
  * DOCUMENT ME!\r
  *\r
  * @author $author$\r
  * @version $Revision$\r
  */\r
-public class GDesktop extends JFrame\r
+public class GDesktop\r
+    extends JFrame\r
 {\r
-    protected static JMenu windowMenu = new JMenu();\r
-    JMenuBar desktopMenubar = new JMenuBar();\r
-    JMenu FileMenu = new JMenu();\r
-    JMenu HelpMenu = new JMenu();\r
-    protected JMenu VamsasMenu = new JMenu();\r
-    JMenuItem inputLocalFileMenuItem = new JMenuItem();\r
-    JMenuItem inputURLMenuItem = new JMenuItem();\r
-    JMenuItem inputTextboxMenuItem = new JMenuItem();\r
-    JMenuItem quit = new JMenuItem();\r
-    JMenuItem aboutMenuItem = new JMenuItem();\r
-    JMenuItem documentationMenuItem = new JMenuItem();\r
-    FlowLayout flowLayout1 = new FlowLayout();\r
-    JMenu toolsMenu = new JMenu();\r
-    JMenuItem preferences = new JMenuItem();\r
-    JMenuItem saveState = new JMenuItem();\r
-    JMenuItem loadState = new JMenuItem();\r
-    JMenu inputMenu = new JMenu();\r
+  protected static JMenu windowMenu = new JMenu();\r
+  JMenuBar desktopMenubar = new JMenuBar();\r
+  JMenu FileMenu = new JMenu();\r
+  JMenu HelpMenu = new JMenu();\r
+  protected JMenu VamsasMenu = new JMenu();\r
+  JMenuItem inputLocalFileMenuItem = new JMenuItem();\r
+  JMenuItem inputURLMenuItem = new JMenuItem();\r
+  JMenuItem inputTextboxMenuItem = new JMenuItem();\r
+  JMenuItem quit = new JMenuItem();\r
+  JMenuItem aboutMenuItem = new JMenuItem();\r
+  JMenuItem documentationMenuItem = new JMenuItem();\r
+  FlowLayout flowLayout1 = new FlowLayout();\r
+  JMenu toolsMenu = new JMenu();\r
+  JMenuItem preferences = new JMenuItem();\r
+  JMenuItem saveState = new JMenuItem();\r
+  JMenuItem loadState = new JMenuItem();\r
+  JMenu inputMenu = new JMenu();\r
   protected JMenuItem vamsasLoad = new JMenuItem();\r
   JMenuItem inputSequence = new JMenuItem();\r
   protected JMenuItem vamsasStop = new JMenuItem();\r
@@ -57,125 +56,127 @@ public class GDesktop extends JFrame
   JMenuItem minimizeAssociated = new JMenuItem();\r
 \r
   /**\r
-     * Creates a new GDesktop object.\r
-     */\r
-    public GDesktop()\r
+   * Creates a new GDesktop object.\r
+   */\r
+  public GDesktop()\r
+  {\r
+    try\r
     {\r
-        try\r
-        {\r
-            jbInit();\r
-            this.setJMenuBar(desktopMenubar);\r
-        }\r
-        catch (Exception e)\r
-        {\r
-            e.printStackTrace();\r
-        }\r
-\r
-        if (!System.getProperty("os.name").startsWith("Mac"))\r
-        {\r
-          FileMenu.setMnemonic('F');\r
-          inputLocalFileMenuItem.setMnemonic('L');\r
-          VamsasMenu.setMnemonic('V');\r
-          inputURLMenuItem.setMnemonic('U');\r
-          inputTextboxMenuItem.setMnemonic('C');\r
-          quit.setMnemonic('Q');\r
-          saveState.setMnemonic('S');\r
-          loadState.setMnemonic('L');\r
-          inputMenu.setMnemonic('I');\r
-        }\r
+      jbInit();\r
+      this.setJMenuBar(desktopMenubar);\r
+    }\r
+    catch (Exception e)\r
+    {\r
+      e.printStackTrace();\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @throws Exception DOCUMENT ME!\r
-     */\r
-    private void jbInit() throws Exception\r
+    if (!System.getProperty("os.name").startsWith("Mac"))\r
     {\r
-        FileMenu.setText("File");\r
-        HelpMenu.setText("Help");\r
-        VamsasMenu.setText("Vamsas");\r
-        VamsasMenu.setToolTipText("Share data with other vamsas applications.");\r
-        inputLocalFileMenuItem.setText("from File");\r
+      FileMenu.setMnemonic('F');\r
+      inputLocalFileMenuItem.setMnemonic('L');\r
+      VamsasMenu.setMnemonic('V');\r
+      inputURLMenuItem.setMnemonic('U');\r
+      inputTextboxMenuItem.setMnemonic('C');\r
+      quit.setMnemonic('Q');\r
+      saveState.setMnemonic('S');\r
+      loadState.setMnemonic('L');\r
+      inputMenu.setMnemonic('I');\r
+    }\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @throws Exception DOCUMENT ME!\r
+   */\r
+  private void jbInit()\r
+      throws Exception\r
+  {\r
+    FileMenu.setText("File");\r
+    HelpMenu.setText("Help");\r
+    VamsasMenu.setText("Vamsas");\r
+    VamsasMenu.setToolTipText("Share data with other vamsas applications.");\r
+    inputLocalFileMenuItem.setText("from File");\r
     inputLocalFileMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
-        java.awt.event.KeyEvent.VK_O, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+        java.awt.event.KeyEvent.VK_O,\r
+        Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
     inputLocalFileMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-            {\r
-                public void actionPerformed(ActionEvent e)\r
-                {\r
-                    inputLocalFileMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
-        inputURLMenuItem.setText("from URL");\r
-        inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-            {\r
-                public void actionPerformed(ActionEvent e)\r
-                {\r
-                    inputURLMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
-        inputTextboxMenuItem.setText("from Textbox");\r
-        inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-            {\r
-                public void actionPerformed(ActionEvent e)\r
-                {\r
-                    inputTextboxMenuItem_actionPerformed(null);\r
-                }\r
-            });\r
-        quit.setText("Quit");\r
-        quit.addActionListener(new java.awt.event.ActionListener()\r
-            {\r
-                public void actionPerformed(ActionEvent e)\r
-                {\r
-                    quit();\r
-                }\r
-            });\r
-        aboutMenuItem.setText("About");\r
-        aboutMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-            {\r
-                public void actionPerformed(ActionEvent e)\r
-                {\r
-                    aboutMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        documentationMenuItem.setText("Documentation");\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        inputLocalFileMenuItem_actionPerformed(null);\r
+      }\r
+    });\r
+    inputURLMenuItem.setText("from URL");\r
+    inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        inputURLMenuItem_actionPerformed(null);\r
+      }\r
+    });\r
+    inputTextboxMenuItem.setText("from Textbox");\r
+    inputTextboxMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        inputTextboxMenuItem_actionPerformed(null);\r
+      }\r
+    });\r
+    quit.setText("Quit");\r
+    quit.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        quit();\r
+      }\r
+    });\r
+    aboutMenuItem.setText("About");\r
+    aboutMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        aboutMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
+    documentationMenuItem.setText("Documentation");\r
     documentationMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
         java.awt.event.KeyEvent.VK_F1, 0, false));\r
     documentationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-            {\r
-                public void actionPerformed(ActionEvent e)\r
-                {\r
-                    documentationMenuItem_actionPerformed(e);\r
-                }\r
-            });\r
-        this.getContentPane().setLayout(flowLayout1);\r
-        windowMenu.setText("Window");\r
-        preferences.setText("Preferences...");\r
-        preferences.addActionListener(new ActionListener()\r
-            {\r
-                public void actionPerformed(ActionEvent e)\r
-                {\r
-                    preferences_actionPerformed(e);\r
-                }\r
-            });\r
-        toolsMenu.setText("Tools");\r
-        saveState.setText("Save Project");\r
-        saveState.addActionListener(new ActionListener()\r
-            {\r
-                public void actionPerformed(ActionEvent e)\r
-                {\r
-                    saveState_actionPerformed(e);\r
-                }\r
-            });\r
-        loadState.setText("Load Project");\r
-        loadState.addActionListener(new ActionListener()\r
-            {\r
-                public void actionPerformed(ActionEvent e)\r
-                {\r
-                    loadState_actionPerformed(e);\r
-                }\r
-            });\r
-        inputMenu.setText("Input Alignment");\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        documentationMenuItem_actionPerformed(e);\r
+      }\r
+    });\r
+    this.getContentPane().setLayout(flowLayout1);\r
+    windowMenu.setText("Window");\r
+    preferences.setText("Preferences...");\r
+    preferences.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        preferences_actionPerformed(e);\r
+      }\r
+    });\r
+    toolsMenu.setText("Tools");\r
+    saveState.setText("Save Project");\r
+    saveState.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        saveState_actionPerformed(e);\r
+      }\r
+    });\r
+    loadState.setText("Load Project");\r
+    loadState.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        loadState_actionPerformed(e);\r
+      }\r
+    });\r
+    inputMenu.setText("Input Alignment");\r
     vamsasLoad.setText("Start Vamsas Session...");\r
     vamsasLoad.setVisible(false);\r
     vamsasLoad.addActionListener(new ActionListener()\r
@@ -254,102 +255,104 @@ public class GDesktop extends JFrame
     //    inputMenu.add(vamsasLoad);\r
   }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  protected void inputLocalFileMenuItem_actionPerformed(jalview.gui.\r
+      AlignViewport av)\r
+  {\r
+  }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  protected void inputURLMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
+  {\r
+  }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport av)\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  protected void inputTextboxMenuItem_actionPerformed(jalview.gui.AlignViewport\r
+      av)\r
+  {\r
+  }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     */\r
-    protected void quit()\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   */\r
+  protected void quit()\r
+  {\r
+  }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    protected void aboutMenuItem_actionPerformed(ActionEvent e)\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  protected void aboutMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    protected void documentationMenuItem_actionPerformed(ActionEvent e)\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  protected void documentationMenuItem_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    public void SaveState_actionPerformed(ActionEvent e)\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  public void SaveState_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    protected void preferences_actionPerformed(ActionEvent e)\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  protected void preferences_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    public void saveState_actionPerformed(ActionEvent e)\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  public void saveState_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    public void loadState_actionPerformed(ActionEvent e)\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  public void loadState_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param e DOCUMENT ME!\r
-     */\r
-    public void loadJalviewAlign_actionPerformed(ActionEvent e)\r
-    {\r
-    }\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
+  public void loadJalviewAlign_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
 \r
   public void vamsasLoad_actionPerformed(ActionEvent e)\r
   {\r
@@ -360,6 +363,7 @@ public class GDesktop extends JFrame
   {\r
 \r
   }\r
+\r
   public void vamsasStop_actionPerformed(ActionEvent e)\r
   {\r
 \r