Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

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

diff --git a/src/jalview/gui/PymolViewer.java b/src/jalview/gui/PymolViewer.java
index c5a4c9a..d426051 100644 (file)
--- a/src/jalview/gui/PymolViewer.java
+++ b/src/jalview/gui/PymolViewer.java
@@ -14,7 +14,7 @@ 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;
@@ -210,7 +210,7 @@ public class PymolViewer extends StructureViewerBase
           initPymol();
         } catch (Exception ex)
         {
-          Cache.log.error("Couldn't open PyMOL viewer!", ex);
+          Console.error("Couldn't open PyMOL viewer!", ex);
         }
       }
       int num = -1;
@@ -249,12 +249,12 @@ public class PymolViewer extends StructureViewerBase
             binding.stashFoundChains(pdb, pe.getFile());
           } 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);
+            // Cache.debug("File locations are " + files);
           }
         }
       }
@@ -323,7 +323,7 @@ public class PymolViewer extends StructureViewerBase
       boolean opened = binding.openSession(pymolSessionFile);
       if (!opened)
       {
-        Cache.log.error(
+        Console.error(
                 "An error occurred opening PyMOL session file "
                 + pymolSessionFile);
       }
@@ -348,7 +348,7 @@ public class PymolViewer extends StructureViewerBase
   {
     return "PyMOL";
   }
-
+  JMenuItem writeFeatures = null;
   @Override
   protected void initMenus()
   {
@@ -357,7 +357,7 @@ public class PymolViewer 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"));
@@ -371,12 +371,19 @@ public class PymolViewer extends StructureViewerBase
     });
     viewerActionMenu.add(writeFeatures);
   }
+  
+  @Override
+  protected void buildActionMenu()
+  {
+    super.buildActionMenu();
+    viewerActionMenu.add(writeFeatures);
+  }
 
   protected void sendFeaturesToPymol()
   {
     int count = binding.sendFeaturesToViewer(getAlignmentPanel());
     statusBar.setText(
-            MessageManager.formatMessage("label.attributes_set", count));
+            MessageManager.formatMessage("label.attributes_set", count, getViewerName())); 
   }
 
 }