From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 27 Nov 2014 14:32:52 +0000 (+0000)
Subject: JAL-674 patch to fix bug with showing reference annotation for legacy jalview example... 
X-Git-Tag: Jalview_2_9~138^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3ad07b11cf5c6c2a763fa9661252bb29ac4bc132;p=jalview.git

JAL-674 patch to fix bug with showing reference annotation for legacy jalview example file v2.7
---

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 8812dcc..49d7d4a 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -522,6 +522,7 @@ public class PDBChain
                   ana.getCalcId(), ana.label);
           if (transfer == null || transfer.size() == 0)
           {
+            ana = new AlignmentAnnotation(ana);
             ana.liftOver(sequence, shadowMap);
             ana.liftOver(dsq, sqmpping);
             dsq.addAlignmentAnnotation(ana);
@@ -542,6 +543,7 @@ public class PDBChain
                     .getAlignmentAnnotations(ana.getCalcId(), ana.label);
             if (transfer == null || transfer.size() == 0)
             {
+              ana = new AlignmentAnnotation(ana);
               ana.liftOver(dsq, sqmpping);
               // mapping.transfer(ana);
             }