From 284bf925b630de7591d7ecdece5d71f8dc330497 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 25 Nov 2005 17:57:57 +0000
Subject: [PATCH] Must follow alignmentPosition

---
 src/jalview/gui/SequenceRenderer.java |    2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index e95ca02..460c6d1 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -91,6 +91,8 @@ public class SequenceRenderer
 
       allGroups = av.alignment.findAllGroups(seq);
 
+      i = seq.findIndex(i);
+
       drawBoxes(seq, i,i, 0, 0, 1,1);
 
       return new Color(bi.getRGB(0, 0));
-- 
1.7.10.2