From f879178793c14038180e56ddddbc1812fb9473ec Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 5 Sep 2017 14:04:17 +0100
Subject: [PATCH] JAL-2722 Reinstate allGroups value setting in
 getResidueColour

---
 src/jalview/gui/SequenceRenderer.java |    1 +
 1 file changed, 1 insertion(+)

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 5be7f55..0a1e8ef 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -95,6 +95,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public Color getResidueColour(final SequenceI seq, int position,
           FeatureColourFinder finder)
   {
+    allGroups = av.getAlignment().findAllGroups(seq);
     return resColourFinder.getResidueColour(av.getShowBoxes(),
             av.getResidueShading(),
             allGroups, seq, position,
-- 
1.7.10.2