Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / src / jalview / gui / ChimeraViewFrame.java

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 810f40d..34410f1 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
@@ -51,7 +52,6 @@ import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-
 /**
  * GUI elements for handling an external chimera display
  * 
@@ -62,6 +62,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 {
   private JalviewChimeraBinding jmb;
 
+
   /*
    * Path to Chimera session file. This is set when an open Jalview/Chimera
    * session is saved, or on restore from a Jalview project (if it holds the
@@ -69,11 +70,15 @@ public class ChimeraViewFrame extends StructureViewerBase
    */
   private String chimeraSessionFile = null;
 
+
   private int myWidth = 500;
 
   private int myHeight = 150;
 
-  /**
+  private JMenuItem writeFeatures=null;
+
+  private JMenu fetchAttributes=null;
+/**
    * Initialise menu options.
    */
   @Override
@@ -84,7 +89,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     savemenu.setVisible(false); // not yet implemented
     viewMenu.add(fitToWindow);
 
-    JMenuItem writeFeatures = new JMenuItem(
+    writeFeatures = new JMenuItem(
             MessageManager.getString("label.create_viewer_attributes"));
     writeFeatures.setToolTipText(MessageManager
             .getString("label.create_viewer_attributes_tip"));
@@ -98,7 +103,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     });
     viewerActionMenu.add(writeFeatures);
 
-    final JMenu fetchAttributes = new JMenu(
+    fetchAttributes = new JMenu(
             MessageManager.getString("label.fetch_chimera_attributes"));
     fetchAttributes.setToolTipText(
             MessageManager.getString("label.fetch_chimera_attributes_tip"));
@@ -114,6 +119,15 @@ public class ChimeraViewFrame extends StructureViewerBase
     viewerActionMenu.add(fetchAttributes);
   }
 
+  @Override
+  protected void buildActionMenu()
+  {
+    super.buildActionMenu();
+    // add these back in after menu is refreshed
+    viewerActionMenu.add(writeFeatures);
+    viewerActionMenu.add(fetchAttributes);
+    
+  };
   /**
    * Query the structure viewer for its residue attribute names and add them as
    * items off the attributes menu
@@ -223,7 +237,6 @@ public class ChimeraViewFrame extends StructureViewerBase
     return new JalviewChimeraBindingModel(this,
             ap.getStructureSelectionManager(), pdbentrys, seqs, null);
   }
-
   /**
    * Create a new viewer from saved session state data including Chimera session
    * file
@@ -315,7 +328,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     if (!jmb.launchChimera())
     {
-      JvOptionPane.showMessageDialog(Desktop.desktop,
+      JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
               MessageManager.formatMessage("label.open_viewer_failed",
                       getViewerName()),
               MessageManager.getString("label.error_loading_file"),
@@ -412,7 +425,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     if (errormsgs.length() > 0)
     {
 
-      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
               MessageManager.formatMessage(
                       "label.pdb_entries_couldnt_be_retrieved", new Object[]
                       { errormsgs.toString() }),
@@ -491,7 +504,8 @@ public class ChimeraViewFrame extends StructureViewerBase
 
       /*
        * ensure that any newly discovered features (e.g. RESNUM)
-       * are added to any open feature settings dialog
+       * are notified to the FeatureRenderer (and added to any 
+       * open feature settings dialog)
        */
       FeatureRenderer fr = getBinding().getFeatureRenderer(null);
       if (fr != null)
@@ -522,6 +536,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     worker = null;
   }
 
+
   @Override
   public void makePDBImage(TYPE imageType)
   {
@@ -535,6 +550,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     return jmb;
   }
 
+
   @Override
   public ViewerType getViewerType()
   {