JAL-2629 fix hmm on alignment being deleted upon running jackhmmer

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 3faa4f2..64802c7 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -275,11 +275,7 @@ public class HMMSearch extends HmmerCommand
       databaseFile = FileUtils.createTempFile("database", ".sto");
       AlignmentI al = af.getViewport().getAlignment();
       AlignmentI copy = new Alignment(al);
-      List<SequenceI> hmms = copy.getHmmSequences();
-      for (SequenceI hmmSeq : hmms)
-      {
-        copy.deleteSequence(hmmSeq);
-      }
+      deleteHmmSequences(copy);
       exportStockholm(copy.getSequencesArray(), databaseFile, null);
     }