JAL-2447 EXPERIMENTAL preference (option in Tools menu)

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 915ef6f..354dc93 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1300,3 +1300,5 @@ warn.name_cannot_be_duplicate = User-defined URL names must be unique and cannot
 label.invalid_name = Invalid Name !
 label.output_seq_details = Output Sequence Details to list all database references
 label.urllinks = Links
+label.show_experimental = Enable experimental features
+label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details)
\ No newline at end of file

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index ec9feb7..ab6f6c8 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -100,35 +100,41 @@ public class ChimeraViewFrame extends StructureViewerBase
     savemenu.setVisible(false); // not yet implemented
     viewMenu.add(fitToWindow);
 
-    JMenuItem writeFeatures = new JMenuItem(
-            MessageManager.getString("label.create_chimera_attributes"));
-    writeFeatures.setToolTipText(MessageManager
-            .getString("label.create_chimera_attributes_tip"));
-    writeFeatures.addActionListener(new ActionListener()
+    /*
+     * exchange of Jalview features and Chimera attributes is for now
+     * an optionally enabled experimental feature
+     */
+    if (Desktop.instance.showExperimental())
     {
-      @Override
-      public void actionPerformed(ActionEvent e)
+      JMenuItem writeFeatures = new JMenuItem(
+              MessageManager.getString("label.create_chimera_attributes"));
+      writeFeatures.setToolTipText(MessageManager
+              .getString("label.create_chimera_attributes_tip"));
+      writeFeatures.addActionListener(new ActionListener()
       {
-        sendFeaturesToChimera();
-      }
-    });
-    viewerActionMenu.add(writeFeatures);
-
-    final JMenu fetchAttributes = new JMenu(
-            MessageManager.getString("label.fetch_chimera_attributes"));
-    fetchAttributes.setToolTipText(MessageManager
-            .getString("label.fetch_chimera_attributes_tip"));
-    fetchAttributes.addMouseListener(new MouseAdapter()
-    {
-
-      @Override
-      public void mouseEntered(MouseEvent e)
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          sendFeaturesToChimera();
+        }
+      });
+      viewerActionMenu.add(writeFeatures);
+
+      final JMenu fetchAttributes = new JMenu(
+              MessageManager.getString("label.fetch_chimera_attributes"));
+      fetchAttributes.setToolTipText(MessageManager
+              .getString("label.fetch_chimera_attributes_tip"));
+      fetchAttributes.addMouseListener(new MouseAdapter()
       {
-        buildAttributesMenu(fetchAttributes);
-      }
-    });
-    viewerActionMenu.add(fetchAttributes);
 
+        @Override
+        public void mouseEntered(MouseEvent e)
+        {
+          buildAttributesMenu(fetchAttributes);
+        }
+      });
+      viewerActionMenu.add(fetchAttributes);
+    }
   }
 
   /**

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 7d0eb7f..b8f8399 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -129,6 +129,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         DropTargetListener, ClipboardOwner, IProgressIndicator,
         jalview.api.StructureSelectionManagerProvider
 {
+  private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
 
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
@@ -327,19 +328,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     instance = this;
     doVamsasClientCheck();
 
-    groovyShell = new JMenuItem();
-    groovyShell.setText(MessageManager.getString("label.groovy_console"));
-    groovyShell.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        groovyShell_actionPerformed();
-      }
-    });
-    toolsMenu.add(groovyShell);
-    groovyShell.setVisible(true);
-
     doConfigureStructurePrefs();
     setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
@@ -394,6 +382,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     showConsole(showjconsole);
 
     showNews.setVisible(false);
+    
+    experimentalFeatures.setSelected(showExperimental());
 
     getIdentifiersOrgData();
 
@@ -490,6 +480,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             });
   }
 
+  /**
+   * Answers true if user preferences to enable experimental features is True
+   * (on), else false
+   * 
+   * @return
+   */
+  public boolean showExperimental()
+  {
+    String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
+            Boolean.FALSE.toString());
+    return Boolean.valueOf(experimental).booleanValue();
+  }
+
   public void doConfigureStructurePrefs()
   {
     // configure services
@@ -2492,8 +2495,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   }
 
-  protected JMenuItem groovyShell;
-
   /**
    * Accessor method to quickly get all the AlignmentFrames loaded.
    * 
@@ -2579,6 +2580,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /**
    * Add Groovy Support to Jalview
    */
+  @Override
   public void groovyShell_actionPerformed()
   {
     try
@@ -3393,4 +3395,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     }
   }
+
+  /**
+   * Sets the Preferences property for experimental features to True or False
+   * depending on the state of the controlling menu item
+   */
+  @Override
+  protected void showExperimental_actionPerformed(boolean selected)
+  {
+    Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
+  }
 }

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 63ecdaf..3e3691c 100755 (executable)
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -23,6 +23,7 @@ package jalview.jbgui;
 import jalview.api.AlignmentViewPanel;
 import jalview.io.FileFormatException;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.FlowLayout;
 import java.awt.Toolkit;
@@ -99,6 +100,10 @@ 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();
@@ -119,7 +124,7 @@ public class GDesktop extends JFrame
       e.printStackTrace();
     }
 
-    if (!new jalview.util.Platform().isAMac())
+    if (!Platform.isAMac())
     {
       FileMenu.setMnemonic('F');
       inputLocalFileMenuItem.setMnemonic('L');
@@ -374,6 +379,30 @@ public class GDesktop extends JFrame
         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()
     {
@@ -410,6 +439,8 @@ public class GDesktop extends JFrame
     toolsMenu.add(showConsole);
     toolsMenu.add(showNews);
     toolsMenu.add(garbageCollect);
+    toolsMenu.add(groovyShell);
+    toolsMenu.add(experimentalFeatures);
     // toolsMenu.add(snapShotWindow);
     inputMenu.add(inputLocalFileMenuItem);
     inputMenu.add(inputURLMenuItem);
@@ -421,6 +452,14 @@ 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