X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=8c54b1e2f4e0bce042a4344496dc4bcb71d8512e;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=22202e55ffc68d1f454add4d5e2cd84847e0f382;hpb=a65993fd311b1a53617c5df3c84abfb78740a900;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 22202e5..8c54b1e 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.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.
  * 
@@ -31,6 +31,7 @@ import jalview.bin.Cache;
 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;
@@ -45,10 +46,10 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   private AppJmol appJmolWindow;
 
-  public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
+  public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
           SequenceI[][] sequenceIs, String[][] chains, String protocol)
   {
-    super(pdbentry, sequenceIs, chains, protocol);
+    super(sSm, pdbentry, sequenceIs, chains, protocol);
     appJmolWindow = appJmol;
   }
 
@@ -62,10 +63,10 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     {
       if (fr == null)
       {
-        fr = new FeatureRenderer((AlignmentPanel)alignment);
+        fr = new FeatureRenderer(ap);
       }
 
-      fr.transferSettings(((AlignmentPanel)alignment).
+      fr.transferSettings(ap.
               seqPanel.seqCanvas.getFeatureRenderer());
     }
 
@@ -126,8 +127,8 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source,topap;
-    // ignore events from unrelated or non-user interactive frames
-    if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || !appJmolWindow.isUsedforcolourby(ap))
+    // ignore events from panels not used to colour this view
+    if (!appJmolWindow.isUsedforcolourby(ap))
       return;
     if (!isLoadingFromArchive()) {
       colourBySequence(ap.av.getShowSequenceFeatures(), ap);