From cb0b6d61c64714d571e89bc7f229a2c3626b4bdb Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 14 Aug 2006 09:51:25 +0000
Subject: [PATCH] end<start for empty sequences in Sequence[] from SeqCigar[]

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

diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index 08c66d2..3366dcd 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -417,7 +417,7 @@ public class SeqCigar
       SequenceI ref = alseqs[i].getRefSeq();
       seqs[i] = new Sequence(ref.getName(), g_seqs[i].toString(),
                              ref.getStart() + alseqs[i].start+bounds[0],
-                             ref.getStart() + alseqs[i].start+bounds[2]);
+                             ref.getStart() + alseqs[i].start+(bounds[2]==0 ? -1 : bounds[2]));
       seqs[i].setDatasetSequence(ref);
     }
     if (segments!=null) {
-- 
1.7.10.2