X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=6ee68e878992459ac9ae36a366adbcd95785abe9;hb=69dd054a99ba910b138e84c8db62a11ee7c3ef37;hp=808e30b46ca29c7a04a211e7bf4a149c7abdbb20;hpb=966863a176d02eb6182ff5df1e755ec8757b9899;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 808e30b..6ee68e8 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * 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.
- * 
+ *  
  * 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 
@@ -37,16 +37,18 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   private AppletJmol appletJmolBinding;
 
-  public AppletJmolBinding(AppletJmol appletJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
+  public AppletJmolBinding(AppletJmol appletJmol,
+          StructureSelectionManager sSm, PDBEntry[] pdbentry,
           SequenceI[][] seq, String[][] chains, String protocol)
   {
     super(sSm, pdbentry, seq, chains, protocol);
     appletJmolBinding = appletJmol;
   }
 
-  public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+  public jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (AlignmentPanel)alignment;
+    AlignmentPanel ap = (AlignmentPanel) alignment;
     if (appletJmolBinding.ap.av.showSequenceFeatures)
     {
       if (appletJmolBinding.fr == null)
@@ -63,9 +65,10 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     return appletJmolBinding.fr;
   }
 
-  public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+  public jalview.api.SequenceRenderer getSequenceRenderer(
+          AlignmentViewPanel alignment)
   {
-    return new SequenceRenderer(((AlignmentPanel)alignment).av);
+    return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
 
   public void sendConsoleEcho(String strEcho)
@@ -118,8 +121,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   {
 
     jmolpopup = new JmolPopup();
-    jmolpopup.initialize(viewer, translateLocale, menuName,
-            asPopup);
+    jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -149,8 +151,9 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
           Container consolePanel, String buttonsToShow)
   {
-    //return new org.jmol.console.AppletConsole(viewer2, consolePanel);
-    JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole().getAppConsole(viewer2);
+    // return new org.jmol.console.AppletConsole(viewer2, consolePanel);
+    JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole()
+            .getAppConsole(viewer2);
     return appc;
   }
 
@@ -178,10 +181,11 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void releaseReferences(Object svl)
   {
   }
+
   @Override
   public void resizeInnerPanel(String data)
   {
     // TODO Auto-generated method stub
-    
+
   }
 }