X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=cc6a785280449f17a83468c46d6d95551542ae38;hb=353cb52722490edcba2c13b18836b6d37c5455de;hp=e3c65da467fe22e84a4d8f6f11b60ed4234221e8;hpb=1f029391e9e263b132a62eaefcc2fe68badacfd6;p=jalview.git

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index e3c65da..cc6a785 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -38,7 +38,7 @@ import javax.swing.event.InternalFrameEvent;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
@@ -73,6 +73,10 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   private int myHeight = 150;
 
+  private JMenuItem writeFeatures = null;
+
+  private JMenu fetchAttributes = null;
+
   /**
    * Initialise menu options.
    */
@@ -84,10 +88,10 @@ 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"));
+    writeFeatures.setToolTipText(
+            MessageManager.getString("label.create_viewer_attributes_tip"));
     writeFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -98,10 +102,10 @@ public class ChimeraViewFrame extends StructureViewerBase
     });
     viewerActionMenu.add(writeFeatures);
 
-    final JMenu fetchAttributes = new JMenu(
-            MessageManager.getString("label.fetch_chimera_attributes"));
-    fetchAttributes.setToolTipText(
-            MessageManager.getString("label.fetch_chimera_attributes_tip"));
+    fetchAttributes = new JMenu(MessageManager.formatMessage(
+            "label.fetch_viewer_attributes", getViewerName()));
+    fetchAttributes.setToolTipText(MessageManager.formatMessage(
+            "label.fetch_viewer_attributes_tip", getViewerName()));
     fetchAttributes.addMouseListener(new MouseAdapter()
     {
 
@@ -114,6 +118,16 @@ 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
@@ -152,8 +166,8 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     // todo pull up?
     int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
-    statusBar.setText(
-            MessageManager.formatMessage("label.attributes_set", count));
+    statusBar.setText(MessageManager.formatMessage("label.attributes_set",
+            count, getViewerName()));
   }
 
   /**
@@ -280,8 +294,7 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @param ap
    */
   public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded,
-          SequenceI[][] seqs,
-          AlignmentPanel ap)
+          SequenceI[][] seqs, AlignmentPanel ap)
   {
     this();
     setAlignAddedStructures(alignAdded);
@@ -320,6 +333,7 @@ public class ChimeraViewFrame extends StructureViewerBase
                       getViewerName()),
               MessageManager.getString("label.error_loading_file"),
               JvOptionPane.ERROR_MESSAGE);
+      jmb.closeViewer(true);
       this.dispose();
       return;
     }
@@ -430,9 +444,15 @@ public class ChimeraViewFrame extends StructureViewerBase
           initChimera();
         } catch (Exception ex)
         {
-          Cache.log.error("Couldn't open Chimera viewer!", ex);
+          Console.error("Couldn't open Chimera viewer!", ex);
         }
       }
+      if (!jmb.isViewerRunning())
+      {
+        // nothing to do
+        // TODO: ensure we tidy up JAL-3619
+        return;
+      }
       int num = -1;
       for (PDBEntry pe : filePDB)
       {
@@ -475,12 +495,12 @@ public class ChimeraViewFrame extends StructureViewerBase
                     oomerror);
           } catch (Exception ex)
           {
-            Cache.log.error(
+            Console.error(
                     "Couldn't open " + pe.getFile() + " in Chimera viewer!",
                     ex);
           } finally
           {
-            Cache.log.debug("File locations are " + files);
+            Console.debug("File locations are " + files);
           }
         }
       }