X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=868f306b72843c90a0026e84502ffd9859de8079;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=0cc04f7dd029d31d668468c5bf648208b35e1975;hpb=6486a5333807ca300db4a28a6bf9899f5dddf5a6;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 0cc04f7..868f306 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -339,8 +339,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
       bl.setHgap(0);
       bl.setVgap(0);
       scriptWindow = new JPanel(bl);
+      scriptWindow.setVisible(false);
     };
-    
     jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null);
     jmb.newJmolPopup(true, "Jmol", true);
     jmb.evalStateCommand(command);
@@ -414,6 +414,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
   void closeViewer()
   {
     jmb.closeViewer();
+    
     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     jmb = null;
@@ -786,7 +787,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
     {
     }
   }
-  public void showConsole(boolean showConsole)
+public void showConsole(boolean showConsole)
   {
 
     if (showConsole)
@@ -818,7 +819,6 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
     validate();
   }
-
   class RenderPanel extends JPanel
   {
     final Dimension currentSize = new Dimension();