blosum62 must have its on consensus

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