From 5822ce76b5567bd164c7a0194eac22fa742295a8 Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Mon, 28 Aug 2017 11:27:30 +0100
Subject: [PATCH] JAL-2629 fix HMMER validation fail due to checking for HMM
 incorrectly

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index bb226a0..7c0ac95 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1316,7 +1316,7 @@ public class Preferences extends GPreferences
   {
     HMMBuildThread hmmbuild = new HMMBuildThread(alignment);
     hmmbuild.hmmbuildWaitTillComplete();
-    SequenceI hmmSeq = alignment.getSequenceAt(1);
+    SequenceI hmmSeq = alignment.getSequenceAt(0);
     HiddenMarkovModel hmm;
     if (hmmSeq.isHMMConsensusSequence() && hmmSeq.getHMM() != null)
     {
-- 
1.7.10.2