JAL-1015 refactor tooltip html generation code to jalview.io.SequenceAnnotationReport

[jalview.git] / src / jalview / gui / AppJmolBinding.java

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 3b915ae..df62eab 100644 (file)
--- 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.
  * 
@@ -61,13 +61,12 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
     if (ap.av.showSequenceFeatures)
     {
-      if (fr == null)
+      if (fr==null)
       {
-        fr = new FeatureRenderer(ap);
+        fr=ap.cloneFeatureRenderer();
+      } else {
+        ap.updateFeatureRenderer(fr);
       }
-
-      fr.transferSettings(ap.
-              seqPanel.seqCanvas.getFeatureRenderer());
     }
 
     return fr;
@@ -152,7 +151,8 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
           boolean asPopup)
   {
 
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
+    jmolpopup = new JmolPopup();
+    jmolpopup.initialize(viewer, translateLocale, menuName,
             asPopup);
   }