JAL-3056 suppress menu options, and repoint Help, for JalviewJS

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index e890cb8..3e6e545 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -89,13 +89,21 @@ public class Jalview
 
   public static AlignFrame currentAlignFrame;
 
-  public static boolean isJS = /** @j2sNative true || */ // BH 2018
-          false;
+  /**
+   * Answers true if Jalview is running as Javascript, else false. The value is
+   * set at compile time.
+   * 
+   * @return
+   */
+  public static boolean isJS()
+  {
+    return /** @j2sNative true || */
+    false;
+  }
 
   static
   {
-
-    if (!isJS)
+    if (!isJS())
     { // BH 2018
     // grab all the rights we can the JVM
     Policy.setPolicy(new Policy()
@@ -199,7 +207,7 @@ public class Jalview
   void doMain(String[] args)
   {
 
-    if (!isJS)
+    if (!isJS())
     {
       System.setSecurityManager(null);
     }
@@ -530,7 +538,7 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!isJS && !file.startsWith("http://"))
+      if (!isJS() && !file.startsWith("http://"))
       {
         if (!(new File(file)).exists())
         {

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 81aacda..564f04a 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -41,6 +41,7 @@ import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
 import jalview.structure.StructureSelectionManager;
 import jalview.urls.IdOrgSettings;
+import jalview.util.BrowserLauncher;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -1377,19 +1378,24 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on requesting Help documentation
    */
   @Override
-  public void documentationMenuItem_actionPerformed(ActionEvent e)
+  public void documentationMenuItem_actionPerformed()
   {
     try
     {
-      Help.showHelpWindow();
+      if (Jalview.isJS())
+      {
+        BrowserLauncher.openURL("http://www.jalview.org/help.html");
+      }
+      else
+      {
+        Help.showHelpWindow();
+      }
     } catch (Exception ex)
     {
+      System.err.println("Error opening help: " + ex.getMessage());
     }
   }
 
@@ -1593,16 +1599,12 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Prompts the user to choose a file and then saves the Jalview state as a
+   * Jalview project file
    */
   @Override
-  public void saveState_actionPerformed(ActionEvent e)
+  public void saveState_actionPerformed()
   {
-    // TODO: JAL-3048 not needed for Jalview-JS
-
     JalviewFileChooser chooser = new JalviewFileChooser("jvp",
             "Jalview Project");
 
@@ -1668,16 +1670,11 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Prompts the user to choose a file and loads in as a Jalview project file
    */
   @Override
-  public void loadState_actionPerformed(ActionEvent e)
+  public void loadState_actionPerformed()
   {
-    // TODO: JAL-3048 not needed for Jalview-JS
-
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "jvp", "jar" },

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index b0fee88..95cbb61 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -444,7 +444,7 @@ public class AppletFormatAdapter
     {
       protocol = DataSourceType.URL;
     }
-    else if (jalview.bin.Jalview.isJS)
+    else if (jalview.bin.Jalview.isJS())
     {
       protocol = DataSourceType.RELATIVE_URL;
     }

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index a83c688..1910930 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;
@@ -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..9ffd701 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;
@@ -225,7 +226,7 @@ public class GDesktop extends JFrame
               @Override
               public void actionPerformed(ActionEvent e)
               {
-                documentationMenuItem_actionPerformed(e);
+                documentationMenuItem_actionPerformed();
               }
             });
     this.getContentPane().setLayout(flowLayout1);
@@ -246,7 +247,7 @@ 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 +256,7 @@ 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 +424,12 @@ 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 +441,17 @@ public class GDesktop extends JFrame
     VamsasMenu.add(vamsasSave);
     VamsasMenu.add(vamsasStop);
     toolsMenu.add(preferences);
-    toolsMenu.add(showMemusage);
-    toolsMenu.add(showConsole);
+    if (!Jalview.isJS())
+    {
+      toolsMenu.add(showMemusage);
+      toolsMenu.add(showConsole);
+    }
     toolsMenu.add(showNews);
-    toolsMenu.add(garbageCollect);
-    toolsMenu.add(groovyShell);
+    if (!Jalview.isJS())
+    {
+      toolsMenu.add(garbageCollect);
+      toolsMenu.add(groovyShell);
+    }
     toolsMenu.add(experimentalFeatures);
     // toolsMenu.add(snapShotWindow);
     inputMenu.add(inputLocalFileMenuItem);
@@ -551,13 +561,7 @@ public class GDesktop extends JFrame
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void documentationMenuItem_actionPerformed(ActionEvent e)
+  protected void documentationMenuItem_actionPerformed()
   {
   }
 
@@ -581,33 +585,11 @@ 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()
   {
   }
 

diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index 3d7d779..1b2b069 100755 (executable)
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -20,6 +20,7 @@
  */
 package jalview.jbgui;
 
+import jalview.bin.Jalview;
 import jalview.gui.JvSwingUtils;
 import jalview.util.MessageManager;
 
@@ -230,7 +231,10 @@ public class GUserDefinedColours extends JPanel
     okCancelPanel.add(applyButton);
     okCancelPanel.add(okButton);
     okCancelPanel.add(cancelButton);
-    lowerPanel.add(saveLoadPanel, java.awt.BorderLayout.NORTH);
+    if (!Jalview.isJS())
+    {
+      lowerPanel.add(saveLoadPanel, java.awt.BorderLayout.NORTH);
+    }
     lowerPanel.add(okCancelPanel, java.awt.BorderLayout.SOUTH);
 
     namePanel.add(schemeName, java.awt.BorderLayout.CENTER);