JAL-2668 add tests for HMMER commands, annotation and io

[jalview.git] / src / jalview / hmmer / HMMERCommands.java

diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
index a5a4d7d..6a538fc 100644 (file)
--- a/src/jalview/hmmer/HMMERCommands.java
+++ b/src/jalview/hmmer/HMMERCommands.java
@@ -136,11 +136,6 @@ public class HMMERCommands
     if (seqs != null)
     {
       StockholmFile file = new StockholmFile(new Alignment(seqs));
-      boolean removeAnnots = false;
-      if (hmm == null)
-      {
-        removeAnnots = true;
-      }
       String output = file.print(seqs, false);
       PrintWriter writer = new PrintWriter(stoLocation);
       writer.println(output);
@@ -150,7 +145,9 @@ public class HMMERCommands
     if (hmm != null)
     {
       HMMFile file = new HMMFile(hmm);
-      file.exportFile(hmmLocation);
+      PrintWriter writer = new PrintWriter(hmmLocation);
+      writer.print(file.print());
+      writer.close();
     }
   }