From cc04412e8052d7c2546e8e7ffdcdcf8dc579f10a Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Mon, 28 Aug 2017 11:26:23 +0100
Subject: [PATCH] JAL-2629 fix issue where HMM would not be added to alignment

---
 src/jalview/io/FileLoader.java |    1 +
 1 file changed, 1 insertion(+)

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index fd8429b..73fbc88 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -427,6 +427,7 @@ public class FileLoader implements Runnable
                       .getSequenceAt(alignment.getAbsoluteHeight() - 1);
               seq.setIsHMMConsensusSequence(true);
               alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+              alignment.insertSequenceAt(0, seq);
               viewport.getAlignPanel().adjustAnnotationHeight();
               viewport.updateSequenceIdColours();
 
-- 
1.7.10.2