X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=80fafe3697fefc143b7a608bf42338d31e56401b;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=edf2d45fd395b89ab8e25bcfaafcb57e36f8a897;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index edf2d45..80fafe3 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
@@ -50,7 +52,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
           AlignmentViewPanel alignment)
   {
     AlignmentPanel ap = (AlignmentPanel) alignment;
-    if (appletJmolBinding.ap.av.showSequenceFeatures)
+    if (appletJmolBinding.ap.av.isShowSequenceFeatures())
     {
       if (appletJmolBinding.fr == null)
       {
@@ -75,7 +77,9 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void sendConsoleEcho(String strEcho)
   {
     if (appletJmolBinding.scriptWindow == null)
+    {
       appletJmolBinding.showConsole(true);
+    }
 
     appletJmolBinding.history.append("\n" + strEcho);
   }
@@ -103,7 +107,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    colourBySequence(ap.av.isShowSequenceFeatures(), ap);
   }
 
   public void showUrl(String url)
@@ -136,10 +140,10 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
+  @Override
   public void refreshPdbEntries()
   {
-    // TODO Auto-generated method stub
-
+    // noop
   }
 
   @Override
@@ -162,20 +166,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   protected void releaseUIResources()
   {
     appletJmolBinding = null;
-    if (console != null)
-    {
-      try
-      {
-        console.setVisible(false);
-      } catch (Error e)
-      {
-      } catch (Exception x)
-      {
-      }
-      ;
-      console = null;
-    }
-
+    closeConsole();
   }
 
   @Override