temp push
[jalview.git] / src / jalview / jbgui / GDesktop.java
index 97ec9fe..9e15eea 100755 (executable)
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  */
 package jalview.jbgui;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Jalview;
+import jalview.io.FileFormatException;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.FlowLayout;
 import java.awt.Toolkit;
@@ -34,14 +38,15 @@ import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
 
 /**
- * DOCUMENT ME!
+ * abstract class super to jalview.gui.Desktop
  * 
- * @author $author$
- * @version $Revision$
  */
-public class GDesktop extends JFrame
+@SuppressWarnings("serial")
+// BH made abstract
+public abstract class GDesktop extends JFrame
 {
-  protected static JMenu windowMenu = new JMenu();
+
+  protected JMenu windowMenu = new JMenu(); // BH 2019.05.07 was static
 
   JMenuBar desktopMenubar = new JMenuBar();
 
@@ -73,20 +78,23 @@ public class GDesktop extends JFrame
 
   JMenuItem saveState = new JMenuItem();
 
+  JMenuItem saveAsState = new JMenuItem();
+
   JMenuItem loadState = new JMenuItem();
-  
+
   JMenu inputMenu = new JMenu();
 
+  // in JalviewJS
   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 inputSequence = new JMenuItem();
+
   JMenuItem closeAll = new JMenuItem();
 
   JMenuItem raiseRelated = new JMenuItem();
@@ -97,11 +105,17 @@ public class GDesktop extends JFrame
 
   JMenuItem garbageCollect = new JMenuItem();
 
+  protected JMenuItem groovyShell;
+
+  protected JCheckBoxMenuItem experimentalFeatures;
+
   protected JCheckBoxMenuItem showConsole = new JCheckBoxMenuItem();
 
-  protected JCheckBoxMenuItem showNews = new JCheckBoxMenuItem();
-  
+  // BH public for Runnable
+  public JCheckBoxMenuItem showNews = new JCheckBoxMenuItem();
+
   protected JMenuItem snapShotWindow = new JMenuItem();
+
   /**
    * Creates a new GDesktop object.
    */
@@ -116,11 +130,13 @@ public class GDesktop extends JFrame
       e.printStackTrace();
     }
 
-    if (!new jalview.util.Platform().isAMac())
+    if (Platform.allowMnemonics()) 
     {
+       //BH was !Platform.isAMacAndNotJS()) i.e. "JS or not Mac"
+       // but here we want just not a Mac, period, right?
       FileMenu.setMnemonic('F');
       inputLocalFileMenuItem.setMnemonic('L');
-      VamsasMenu.setMnemonic('V');
+      VamsasMenu.setMnemonic('V'); 
       inputURLMenuItem.setMnemonic('U');
       inputTextboxMenuItem.setMnemonic('C');
       quit.setMnemonic('Q');
@@ -138,23 +154,25 @@ public class GDesktop extends JFrame
    */
   private void jbInit() throws Exception
   {
-
+    setName(Jalview.getAppID("desktop"));
     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));
+    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);
@@ -163,16 +181,24 @@ public class GDesktop extends JFrame
     inputURLMenuItem.setText(MessageManager.getString("label.from_url"));
     inputURLMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        inputURLMenuItem_actionPerformed(null);
+        try
+        {
+          inputURLMenuItem_actionPerformed(null);
+        } catch (FileFormatException e1)
+        {
+          System.err.println("Error loading from URL: " + e1.getMessage());
+        }
       }
     });
-    inputTextboxMenuItem.setText(MessageManager
-            .getString("label.from_textbox"));
+    inputTextboxMenuItem
+            .setText(MessageManager.getString("label.from_textbox"));
     inputTextboxMenuItem
             .addActionListener(new java.awt.event.ActionListener()
             {
+              @Override
               public void actionPerformed(ActionEvent e)
               {
                 inputTextboxMenuItem_actionPerformed(null);
@@ -181,6 +207,7 @@ public class GDesktop extends JFrame
     quit.setText(MessageManager.getString("action.quit"));
     quit.addActionListener(new java.awt.event.ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         quit();
@@ -189,29 +216,31 @@ public class GDesktop extends JFrame
     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
+            .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);
+                documentationMenuItem_actionPerformed();
               }
             });
     this.getContentPane().setLayout(flowLayout1);
     windowMenu.setText(MessageManager.getString("label.window"));
-    preferences.setText(MessageManager.getString("label.preferences")
-            + "...");
+    preferences.setText(MessageManager.getString("label.preferences"));
     preferences.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         preferences_actionPerformed(e);
@@ -221,64 +250,80 @@ public class GDesktop extends JFrame
     saveState.setText(MessageManager.getString("action.save_project"));
     saveState.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        saveState_actionPerformed(e);
+        saveState_actionPerformed();
+      }
+    });
+    saveAsState.setText(MessageManager.getString("action.save_project_as"));
+    saveAsState.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        saveAsState_actionPerformed(e);
       }
     });
     loadState.setText(MessageManager.getString("action.load_project"));
     loadState.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        loadState_actionPerformed(e);
+        loadState_actionPerformed();
       }
     });
     inputMenu.setText(MessageManager.getString("label.input_alignment"));
-    vamsasStart.setText(MessageManager
-            .getString("label.new_vamsas_session") + "...");
+    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("label.load_vamsas_session") + "...");
+    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("label.save_vamsas_session") + "...");
+    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("label.fetch_sequences")
-            + "...");
+    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
+            .setText(MessageManager.getString("label.stop_vamsas_session"));
     vamsasStop.setVisible(false);
     vamsasStop.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         vamsasStop_actionPerformed(e);
@@ -287,42 +332,47 @@ public class GDesktop extends JFrame
     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.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.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
+            .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
+            .setText(MessageManager.getString("label.show_memory_usage"));
     showMemusage.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showMemusage_actionPerformed(e);
@@ -332,6 +382,7 @@ public class GDesktop extends JFrame
             .setText(MessageManager.getString("label.show_java_console"));
     showConsole.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         showConsole_actionPerformed(e);
@@ -340,20 +391,46 @@ public class GDesktop extends JFrame
     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);
@@ -364,6 +441,7 @@ public class GDesktop extends JFrame
     FileMenu.add(inputSequence);
     FileMenu.addSeparator();
     FileMenu.add(saveState);
+    FileMenu.add(saveAsState);
     FileMenu.add(loadState);
     FileMenu.addSeparator();
     FileMenu.add(quit);
@@ -376,10 +454,18 @@ public class GDesktop extends JFrame
     VamsasMenu.add(vamsasSave);
     VamsasMenu.add(vamsasStop);
     toolsMenu.add(preferences);
-    toolsMenu.add(showMemusage);
-    toolsMenu.add(showConsole);
-    toolsMenu.add(showNews);
-    toolsMenu.add(garbageCollect);
+    if (!Platform.isJS())
+    {
+      toolsMenu.add(showMemusage);
+      toolsMenu.add(showConsole);
+    }
+    if (!Platform.isJS())
+    {
+      toolsMenu.add(showNews);
+      toolsMenu.add(garbageCollect);
+      toolsMenu.add(groovyShell);
+    }
+    toolsMenu.add(experimentalFeatures);
     // toolsMenu.add(snapShotWindow);
     inputMenu.add(inputLocalFileMenuItem);
     inputMenu.add(inputURLMenuItem);
@@ -391,10 +477,18 @@ public class GDesktop extends JFrame
     // 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)
@@ -445,9 +539,10 @@ public class GDesktop extends JFrame
    * 
    * @param e
    *          DOCUMENT ME!
+   * @throws FileFormatException
    */
   protected void inputURLMenuItem_actionPerformed(
-          jalview.gui.AlignViewport av)
+          jalview.gui.AlignViewport av) throws FileFormatException
   {
   }
 
@@ -458,7 +553,7 @@ public class GDesktop extends JFrame
    *          DOCUMENT ME!
    */
   protected void inputTextboxMenuItem_actionPerformed(
-          jalview.gui.AlignViewport av)
+          AlignmentViewPanel avp)
   {
   }
 
@@ -479,13 +574,7 @@ public class GDesktop extends JFrame
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void documentationMenuItem_actionPerformed(ActionEvent e)
+  protected void documentationMenuItem_actionPerformed()
   {
   }
 
@@ -495,7 +584,7 @@ public class GDesktop extends JFrame
    * @param e
    *          DOCUMENT ME!
    */
-  public void SaveState_actionPerformed(ActionEvent e)
+  protected void preferences_actionPerformed(ActionEvent e)
   {
   }
 
@@ -505,17 +594,11 @@ public class GDesktop extends JFrame
    * @param e
    *          DOCUMENT ME!
    */
-  protected void preferences_actionPerformed(ActionEvent e)
+  public void saveState_actionPerformed()
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void saveState_actionPerformed(ActionEvent e)
+  public void saveAsState_actionPerformed(ActionEvent e)
   {
   }
 
@@ -525,7 +608,7 @@ public class GDesktop extends JFrame
    * @param e
    *          DOCUMENT ME!
    */
-  public void loadState_actionPerformed(ActionEvent e)
+  public void loadState_actionPerformed()
   {
   }