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 (file)
--- 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();