X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fhmmer%2FHMMBuild.java;h=85abd502f01e8ffa21b4d87417a24acc0848d958;hb=3e49da65865c812f4b2b81f40ef65c983f14aa83;hp=974d2b20f691d38113674a4b0686463e1b376e78;hpb=fbed76ebd126ac6152be48a717c4350e3229b5a5;p=jalview.git

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 974d2b2..85abd50 100644
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -202,7 +202,7 @@ public class HMMBuild extends HmmerCommand
       SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
       Hashtable sequencesHash = stashSequences(copyArray);
 
-      exportStockholm(copyArray, alignmentFile, ac);
+      exportStockholm(copyArray, alignmentFile, ac, false);
 
       recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));