X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=e78938a9277883ca8c3df8ca800012cfd56e257a;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=9d98585289c510d3a7b0c9fae11cd62a431e2c55;hpb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;p=jalview.git

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 9d98585..e78938a 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -73,10 +73,11 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   private int myHeight = 150;
 
-  private JMenuItem writeFeatures=null;
+  private JMenuItem writeFeatures = null;
 
-  private JMenu fetchAttributes=null;
-/**
+  private JMenu fetchAttributes = null;
+
+  /**
    * Initialise menu options.
    */
   @Override
@@ -89,8 +90,8 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     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
@@ -101,10 +102,10 @@ public class ChimeraViewFrame extends StructureViewerBase
     });
     viewerActionMenu.add(writeFeatures);
 
-    fetchAttributes = new JMenu(
-            MessageManager.formatMessage("label.fetch_viewer_attributes",getViewerName()));
-    fetchAttributes.setToolTipText(
-            MessageManager.formatMessage("label.fetch_viewer_attributes_tip",getViewerName()));
+    fetchAttributes = new JMenu(MessageManager.formatMessage(
+            "label.fetch_viewer_attributes", getViewerName()));
+    fetchAttributes.setToolTipText(MessageManager.formatMessage(
+            "label.fetch_viewer_attributes_tip", getViewerName()));
     fetchAttributes.addMouseListener(new MouseAdapter()
     {
 
@@ -116,6 +117,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     });
     viewerActionMenu.add(fetchAttributes);
   }
+
   @Override
   protected void buildActionMenu()
   {
@@ -123,8 +125,9 @@ public class ChimeraViewFrame extends StructureViewerBase
     // 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
@@ -163,8 +166,8 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     // todo pull up?
     int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
-    statusBar.setText(
-            MessageManager.formatMessage("label.attributes_set", count, getViewerName()));
+    statusBar.setText(MessageManager.formatMessage("label.attributes_set",
+            count, getViewerName()));
   }
 
   /**
@@ -213,7 +216,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     initMenus();
 
     addingStructures = false;
-    worker = new Thread(this);
+    worker = new Thread(this, "OpenChimera");
     worker.start();
 
     this.addInternalFrameListener(new InternalFrameAdapter()
@@ -291,8 +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);
@@ -331,6 +333,7 @@ public class ChimeraViewFrame extends StructureViewerBase
                       getViewerName()),
               MessageManager.getString("label.error_loading_file"),
               JvOptionPane.ERROR_MESSAGE);
+      jmb.closeViewer(true);
       this.dispose();
       return;
     }
@@ -444,6 +447,12 @@ public class ChimeraViewFrame extends StructureViewerBase
           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)
       {