From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Mon, 14 Aug 2017 14:51:48 +0000 (+0100)
Subject: JAL-2629 remove annotation when exporting for hmmbuild
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c9a198a4eb76592ff9091cdba7d0299a0345ba09;p=jalview.git

JAL-2629 remove annotation when exporting for hmmbuild
---

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();