merged

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index a83c688..3a6e603 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,6 +23,7 @@ package jalview.jbgui;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
 import jalview.io.FileFormats;
@@ -169,7 +170,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
 
-  protected JTabbedPane tabbedPane = jalview.jbgui.swing.JTabbedPane.createTabbedPane();
+  protected JTabbedPane tabbedPane = jalview.jbgui.GDesktop.createTabbedPane();
 
   protected JMenuItem reload = new JMenuItem();
 
@@ -1716,7 +1717,10 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(formatMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
-    alignFrameMenuBar.add(webService);
+    if (!Jalview.isJS())
+    {
+      alignFrameMenuBar.add(webService);
+    }
 
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
@@ -1734,10 +1738,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(exportAnnotations);
     fileMenu.add(loadTreeMenuItem);
     fileMenu.add(associatedData);
-    /*
-     * No VCF import in Jalview-JS
-     * @j2sNative
-     */
+    if (!Jalview.isJS())
     {
       fileMenu.add(loadVcf);
     }
@@ -1774,8 +1775,11 @@ public class GAlignFrame extends JInternalFrame
     hideMenu.add(hideAllSelection);
     hideMenu.add(hideAllButSelection);
     viewMenu.add(newView);
-    viewMenu.add(expandViews);
-    viewMenu.add(gatherViews);
+    if (!Jalview.isJS())
+    {
+      viewMenu.add(expandViews);
+      viewMenu.add(gatherViews);
+    }
     viewMenu.addSeparator();
     viewMenu.add(showMenu);
     viewMenu.add(hideMenu);
@@ -1835,17 +1839,26 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.addSeparator();
     calculateMenu.add(expandAlignment);
     calculateMenu.add(extractScores);
-    calculateMenu.addSeparator();
-    calculateMenu.add(runGroovy);
+    if (!Jalview.isJS())
+    {
+      calculateMenu.addSeparator();
+      calculateMenu.add(runGroovy);
+    }
 
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
-    exportImageMenu.add(htmlMenuItem);
+    if (!Jalview.isJS())
+    {
+      exportImageMenu.add(htmlMenuItem);
+    }
     exportImageMenu.add(epsFile);
     exportImageMenu.add(createPNG);
     exportImageMenu.add(createBioJS);
-    exportImageMenu.add(createSVG);
+    if (!Jalview.isJS())
+    {
+      exportImageMenu.add(createSVG);
+    }
     addSequenceMenu.add(addFromFile);
     addSequenceMenu.add(addFromText);
     addSequenceMenu.add(addFromURL);

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 11a558c..4b4d28d 100755 (executable)
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -21,6 +21,7 @@
 package jalview.jbgui;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.bin.Jalview;
 import jalview.io.FileFormatException;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -44,6 +45,23 @@ import javax.swing.JMenuItem;
  */
 public class GDesktop extends JFrame
 {
+
+  public static javax.swing.JTabbedPane createTabbedPane()
+  {
+    // now just always return JTabbedPane
+   return new javax.swing.JTabbedPane();
+//    // BH 2018 coercing jalview.jbgui.swing.JTabbedPane() for now
+//    if (/** @j2sNative false && */
+//    true)
+//    {
+//      // Java
+//      return new javax.swing.JTabbedPane();
+//    }
+//    // JavaScript
+//    return (javax.swing.JTabbedPane) (Object) new jalview.jbgui.swing.JTabbedPane();
+  }
+
+  
   protected static JMenu windowMenu = new JMenu();
 
   JMenuBar desktopMenubar = new JMenuBar();
@@ -225,7 +243,7 @@ public class GDesktop extends JFrame
               @Override
               public void actionPerformed(ActionEvent e)
               {
-                documentationMenuItem_actionPerformed(e);
+                documentationMenuItem_actionPerformed();
               }
             });
     this.getContentPane().setLayout(flowLayout1);
@@ -246,7 +264,7 @@ public class GDesktop extends JFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        saveState_actionPerformed(e);
+        saveState_actionPerformed();
       }
     });
     loadState.setText(MessageManager.getString("action.load_project"));
@@ -255,7 +273,7 @@ public class GDesktop extends JFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        loadState_actionPerformed(e);
+        loadState_actionPerformed();
       }
     });
     inputMenu.setText(MessageManager.getString("label.input_alignment"));
@@ -423,9 +441,12 @@ public class GDesktop extends JFrame
     desktopMenubar.add(windowMenu);
     FileMenu.add(inputMenu);
     FileMenu.add(inputSequence);
-    FileMenu.addSeparator();
-    FileMenu.add(saveState);
-    FileMenu.add(loadState);
+    if (!Jalview.isJS())
+    {
+      FileMenu.addSeparator();
+      FileMenu.add(saveState);
+      FileMenu.add(loadState);
+    }
     FileMenu.addSeparator();
     FileMenu.add(quit);
     HelpMenu.add(aboutMenuItem);
@@ -437,11 +458,17 @@ 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);
-    toolsMenu.add(groovyShell);
+    if (!Jalview.isJS())
+    {
+      toolsMenu.add(showMemusage);
+      toolsMenu.add(showConsole);
+    }
+    if (!Jalview.isJS())
+    {
+      toolsMenu.add(showNews);
+      toolsMenu.add(garbageCollect);
+      toolsMenu.add(groovyShell);
+    }
     toolsMenu.add(experimentalFeatures);
     // toolsMenu.add(snapShotWindow);
     inputMenu.add(inputLocalFileMenuItem);
@@ -551,13 +578,7 @@ public class GDesktop extends JFrame
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void documentationMenuItem_actionPerformed(ActionEvent e)
+  protected void documentationMenuItem_actionPerformed()
   {
   }
 
@@ -581,33 +602,11 @@ public class GDesktop extends JFrame
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void saveState_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void loadState_actionPerformed(ActionEvent e)
+  public void saveState_actionPerformed()
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void loadJalviewAlign_actionPerformed(ActionEvent e)
+  public void loadState_actionPerformed()
   {
   }