From c9a198a4eb76592ff9091cdba7d0299a0345ba09 Mon Sep 17 00:00:00 2001
From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Mon, 14 Aug 2017 15:51:48 +0100
Subject: [PATCH] JAL-2629 remove annotation when exporting for hmmbuild

---
 src/jalview/hmmer/HMMERCommands.java |    8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
index 136ad5c..4f1dbc6 100644
--- a/src/jalview/hmmer/HMMERCommands.java
+++ b/src/jalview/hmmer/HMMERCommands.java
@@ -124,8 +124,12 @@ public class HMMERCommands
     if (seqs != null)
     {
       StockholmFile file = new StockholmFile(new Alignment(seqs));
-      file.setSeqs(seqs);
-      String output = file.print();
+      boolean removeAnnots = false;
+      if (hmm == null)
+      {
+        removeAnnots = true;
+      }
+      String output = file.print(seqs, false, removeAnnots);
       PrintWriter writer = new PrintWriter(stoLocation);
       writer.println(output);
       writer.close();
-- 
1.7.10.2