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 (file)
--- 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);