From d9a5e7ac4957e98089c082e629d6e79dd5d30199 Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Mon, 14 Aug 2017 15:13:06 +0100
Subject: [PATCH] JAL-2629 fix expected length error for hmmbuild by
 uniquifying sequences

---
 src/jalview/hmmer/HMMBuildThread.java |   12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index d1039f9..48796e4 100644
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -73,14 +73,13 @@ public class HMMBuildThread implements Runnable
     {
     try
     {
+        SequenceI[] array;
         List<SequenceI> seqs = alignment
                 .getHMMConsensusSequences(true);
         cmds.setHmmSeqs(seqs);
         if (group != null)
         {
-          SequenceI[] array = group.getSelectionAsNewSequences(alignment);
-
-          cmds.exportData(array, stoTemp, null, null);
+          array = group.getSelectionAsNewSequences(alignment);
         }
         else
         {
@@ -88,9 +87,12 @@ public class HMMBuildThread implements Runnable
           {
             alignment.padGaps();
           }
-          cmds.exportData(alignment.getSequencesArray(), stoTemp, null,
-                  null);
+          array = alignment.getSequencesArray();
         }
+        cmds.uniquifySequences(array);
+        cmds.exportData(array, stoTemp, null, null);
+        jalview.analysis.SeqsetUtils.deuniquify(cmds.hash, array);
+
     } catch (FileNotFoundException e)
     {
       // TODO Auto-generated catch block
-- 
1.7.10.2