X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;fp=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=703505880668d4b94761c344400318fddc12cd8b;hb=c5a7bc3f03aef928f1b06e5e9ab53d06970aeb12;hp=7844f57dddf4ecf6c5107ef8345f03ae2293719e;hpb=578c59366e6a562567a37ad03f66f3cd38272306;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 7844f57..7035058 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -34,7 +34,6 @@ import javajs.awt.Dimension;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.console.AppletConsole;
 import org.jmol.java.BS;
-import org.jmol.popup.JmolAwtPopup;
 
 class AppletJmolBinding extends JalviewJmolBinding
 {
@@ -117,7 +116,7 @@ class AppletJmolBinding extends JalviewJmolBinding
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+    colourBySequence(ap);
   }
 
   public void showUrl(String url)
@@ -134,9 +133,8 @@ class AppletJmolBinding extends JalviewJmolBinding
   public void newJmolPopup(boolean translateLocale, String menuName,
           boolean asPopup)
   {
-    jmolpopup = new JmolAwtPopup(); // is this used?
-    jmolpopup.jpiInitialize((viewer), menuName);
-
+    // jmolpopup = new JmolAwtPopup(); // is this used?
+    // jmolpopup.jpiInitialize((viewer), menuName);
   }
 
   @Override