From b55d5f8c5ce50ee068c8345c1bdb3dbc711a74df Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 21 Apr 2014 16:02:03 +0100
Subject: [PATCH] JAL-1466 don't include empty columns if no upstream sequence
 data available for aligned subsequences

---
 src/jalview/analysis/AlignmentUtils.java |    2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 5bbdc4a..85699a4 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -28,7 +28,7 @@ public class AlignmentUtils
     for (SequenceI s:core.getSequences())
     {
       SequenceI newSeq = s.deriveSequence();
-      if (newSeq.getStart()>maxoffset)
+      if (newSeq.getStart()>maxoffset && newSeq.getDatasetSequence().getStart()<s.getStart())
       {
         maxoffset = newSeq.getStart();
       }
-- 
1.7.10.2