merged

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

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);