X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=380ec25c8adac307f62608bb84beae9d97ea66bd;hb=9745565701f82e6a975ac71254bcf07822d6d9dd;hp=89a912f9907f9575fbe0f09affe1c8dd9e44ad9a;hpb=2ab7b9b152018bb808693218ad88dc3778166492;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 89a912f..380ec25 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -20,25 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.bin.JalviewLite;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
-import jalview.io.StructureFile;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.CheckboxMenuItem;
 import java.awt.Color;
@@ -64,6 +45,25 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Vector;
 
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
 public class AppletJmol extends EmbmenuFrame implements
         // StructureListener,
         KeyListener, ActionListener, ItemListener
@@ -104,16 +104,16 @@ public class AppletJmol extends EmbmenuFrame implements
           MessageManager.getString("label.colourScheme_hydrophobic"));
 
   MenuItem helix = new MenuItem(
-          MessageManager.getString("label.colourScheme_helix_propensity"));
+          MessageManager.getString("label.colourScheme_helixpropensity"));
 
   MenuItem strand = new MenuItem(
-          MessageManager.getString("label.colourScheme_strand_propensity"));
+          MessageManager.getString("label.colourScheme_strandpropensity"));
 
   MenuItem turn = new MenuItem(
-          MessageManager.getString("label.colourScheme_turn_propensity"));
+          MessageManager.getString("label.colourScheme_turnpropensity"));
 
   MenuItem buried = new MenuItem(
-          MessageManager.getString("label.colourScheme_buried_index"));
+          MessageManager.getString("label.colourScheme_buriedindex"));
 
   MenuItem purinepyrimidine = new MenuItem(
           MessageManager.getString("label.colourScheme_purine/pyrimidine"));
@@ -335,7 +335,7 @@ public class AppletJmol extends EmbmenuFrame implements
             }
             FileParse fp = new FileParse(pdbentry.getFile(), protocol);
             fp.mark();
-            // reader = new MCview.PDBfile(fp);
+            // reader = new mc_view.PDBfile(fp);
             // could set ID, etc.
             // if (!reader.isValid())
             // {
@@ -411,7 +411,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
   void closeViewer()
   {
-    jmb.closeViewer();
+    jmb.closeViewer(true);
     jmb = null;
     this.setVisible(false);
   }