X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMBuild.java;fp=src%2Fjalview%2Fhmmer%2FHMMBuild.java;h=7c148582d136e19c4b528d2fdcea570f3985331d;hb=d71391d37943d1f6a5bf0af74996229f4d290cb0;hp=85abd502f01e8ffa21b4d87417a24acc0848d958;hpb=3e49da65865c812f4b2b81f40ef65c983f14aa83;p=jalview.git

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 85abd50..7c14858 100644
--- 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[] {}));