From 116786d279dcb83f05afd625ad6e39627a37e1e8 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 18 Apr 2005 16:03:51 +0000
Subject: [PATCH] blosum62 must have its on consensus

---
 src/jalview/gui/PopupMenu.java |    9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index b07dce8..398294b 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -408,6 +408,7 @@ public class PopupMenu extends JPopupMenu
 
       SliderPanel.showPIDSlider();
 
+
     }
     else // remove PIDColouring
     {
@@ -440,7 +441,13 @@ public class PopupMenu extends JPopupMenu
 
   protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
   {
-    getGroup().cs = new Blosum62ColourScheme();
+    SequenceGroup sg = getGroup();
+
+    sg.cs = new Blosum62ColourScheme();
+
+    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+                                               ap.av.alignment.getWidth()));
+
     refresh();
   }
 
-- 
1.7.10.2