From: TZVanaalten <TZVanaalten@LS30916.ad.lifesci.dundee.ac.uk>
Date: Wed, 30 Aug 2017 16:42:13 +0000 (+0100)
Subject: JAL-2629 fix issue where HMM sequence would be longer than alignment
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6de4d198e26fea3248732d627a13799182f54574;p=jalview.git

JAL-2629 fix issue where HMM sequence would be longer than alignment
---

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index 2ff89c1..f940fbb 100644
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -372,7 +372,7 @@ public class HMMBuildThread implements Runnable
     {
       seq.insertCharAt(0, group.getStartRes(), '-');
       seq.insertCharAt(group.getEndRes() + 1,
-              alignment.getWidth() - group.getEndRes(), '-');
+              alignment.getWidth() - group.getEndRes() - 1, '-');
       seq.updateHMMMapping();
       SequenceI topSeq = group.getSequencesInOrder(alignment)[0];
       int topIndex = alignment.findIndex(topSeq);