From bb2e1279398313648ae443a924cc9791bbbd17cd Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 6 Jul 2011 10:48:55 +0100
Subject: [PATCH] ensure selseq is trimmed to just sequences included in view
 (either all or just selectedRegionOnly) (JAL-724)

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

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index 2a93861..ebe8301 100644
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -107,7 +107,7 @@ public class AlignmentView
     {
       Vector sel = selection.getSequences(null);
       this.selected = new Vector();
-      selseqs = selection.getSequencesInOrder(alignment, false);
+      selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);
     }
     else
     {
-- 
1.7.10.2