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

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 8812dcc..49d7d4a 100755 (executable)
--- 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);
             }