JAL-2629 (probably not right issue) JAL-1950 - make a new alignment sequence version...

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index a3ac034..409ef80 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -362,6 +362,7 @@ public class HMMSearch extends HmmerCommand
 
       int seqCount = Math.min(seqs.length, seqsToReturn);
       SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
+      hmmSeq = hmmSeq.deriveSequence(); // otherwise all bad things happen
       hmmAndSeqs[0] = hmmSeq;
       System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);