X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=d15b9eba7e3e4cc6c3c7bfbcd988e69db6aa8e05;hb=aaf78c2f304b237a9c800137126967ace9437c99;hp=c8d9ae32e7a3577bba8d983cf12533f1b7f9d57a;hpb=75dcf03278eac69e3dafbbf7c0d839e9087734f8;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index c8d9ae3..d15b9eb 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -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());
     }
 
@@ -127,7 +128,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   {
     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))
+    if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || !appJmolWindow.isUsedforcolourby(ap))
       return;
     if (!isLoadingFromArchive()) {
       colourBySequence(ap.av.getShowSequenceFeatures(), ap);