JAL-2629 uniquify all hmmer command sequence outputs

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

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 85abd50..7c14858 100644 (file)
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -199,10 +199,11 @@ public class HMMBuild extends HmmerCommand
       // TODO rather than copy alignment data we should anonymize in situ -
       // export/File import could use anonymization hash to reinstate references
       // at import level ?
+
       SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
       Hashtable sequencesHash = stashSequences(copyArray);
 
-      exportStockholm(copyArray, alignmentFile, ac, false);
+      exportStockholm(copyArray, alignmentFile, ac);
 
       recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));