X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=3fccad754bd9d2ea3e9cc89e0a4759957c6cc016;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=009cefd90f6c8bd38ab42c2420724924ff2276ac;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 009cefd..3fccad7 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -20,8 +20,11 @@ package jalview.appletgui;
 import java.awt.Container;
 import java.util.BitSet;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
 
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolViewer;
@@ -36,15 +39,16 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   private AppletJmol appletJmolBinding;
 
-  public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry,
+  public AppletJmolBinding(AppletJmol appletJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
           SequenceI[][] seq, String[][] chains, String protocol)
   {
-    super(pdbentry, seq, chains, protocol);
+    super(sSm, pdbentry, seq, chains, protocol);
     appletJmolBinding = appletJmol;
   }
 
-  public jalview.api.FeatureRenderer getFeatureRenderer()
+  public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
+    AlignmentPanel ap = (AlignmentPanel)alignment;
     if (appletJmolBinding.ap.av.showSequenceFeatures)
     {
       if (appletJmolBinding.fr == null)
@@ -61,9 +65,9 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     return appletJmolBinding.fr;
   }
 
-  public jalview.api.SequenceRenderer getSequenceRenderer()
+  public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
-    return new SequenceRenderer(appletJmolBinding.ap.av);
+    return new SequenceRenderer(((AlignmentPanel)alignment).av);
   }
 
   public void sendConsoleEcho(String strEcho)
@@ -97,7 +101,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    colourBySequence(ap.av.getShowSequenceFeatures(), ap);
   }
 
   public void showUrl(String url)
@@ -169,4 +173,9 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
+  @Override
+  public void releaseReferences(Object svl)
+  {
+  }
+
 }