From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 31 May 2018 16:34:56 +0000 (+0100)
Subject: JAL-2629 (probably not right issue) JAL-1950 - make a new alignment sequence version... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=dc768c72d1aeffd0184dc6da80bc00cddb921e70;p=jalview.git

JAL-2629 (probably not right issue) JAL-1950 - make a new alignment sequence version of HMM that was used to search the database before adding to results to avoid breaking jalview’s alignment data model!
---

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index a3ac034..409ef80 100644
--- 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);