JAL-2629 fix file format issues preventing hmmsearch, jackhmmer running

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

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index 64802c7..b40b079 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -276,7 +276,13 @@ public class HMMSearch extends HmmerCommand
       AlignmentI al = af.getViewport().getAlignment();
       AlignmentI copy = new Alignment(al);
       deleteHmmSequences(copy);
-      exportStockholm(copy.getSequencesArray(), databaseFile, null);
+
+      SequenceI[] seqs = copy.getSequencesArray();
+
+      // hmmsearch fails if duplicate sequence names in file
+      renameDuplicates(seqs);
+
+      exportStockholm(copy.getSequencesArray(), databaseFile, null, true);
     }
 
     args.add(getFilePath(hmmFile, true));