X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9b91255f50ba15bc43994c328c9457f6738509c0;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=b61d44b7a319ae3915b0a831a796965a9e354c0a;hpb=2026a420963f094072607c0495b6369ba96e60c0;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b61d44b..9b91255 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -662,11 +662,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     conservationMenuItem.setEnabled(!nucleotide);
     modifyConservation.setEnabled(!nucleotide);
     showGroupConservation.setEnabled(!nucleotide);
+    rnahelicesColour.setEnabled(nucleotide);
+    purinePyrimidineColour.setEnabled(nucleotide);
     // Remember AlignFrame always starts as protein
-    if (!nucleotide)
-    {
-      calculateMenu.remove(calculateMenu.getItemCount() - 2);
-    }
+    //if (!nucleotide)
+   // {
+   //   showTr
+   //   calculateMenu.remove(calculateMenu.getItemCount() - 2);
+   // }
   }
 
   /**
@@ -719,7 +722,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     autoCalculate.setSelected(av.autoCalculateConsensus);
     sortByTree.setSelected(av.sortByTree);
     listenToViewSelections.setSelected(av.followSelection);
-    
+    rnahelicesColour.setEnabled(av.alignment.hasRNAStructure());
+    rnahelicesColour.setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
     setShowProductsEnabled();
 
     updateEditMenuBar();