From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 21 Jun 2016 09:18:54 +0000 (+0100)
Subject: JAL-1369 make sure the fake AlignmentI produced by getFullAlignment retains the curre... 
X-Git-Tag: Release_2_10_0~161^2~5^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d7a7562c9108c21a5dbc32ed4895cf788b748574;p=jalview.git

JAL-1369 make sure the fake AlignmentI produced by getFullAlignment retains the current reference sequence
---

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 0f57a02..db4c858 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -283,6 +283,7 @@ public class HiddenSequences
     fAlignmt.alignmentProperties = alignment.getProperties();
     fAlignmt.groups = alignment.getGroups();
     fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
+    fAlignmt.setSeqrep(alignment.getSeqrep());
 
     return fAlignmt;
   }