From 92fd3e4d77444c14bb899e9fcd07bd8d44fe7b1e Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 5 Aug 2016 11:22:14 +0100
Subject: [PATCH 1/1] JAL-2164 add transferred annotation to sequence

---
 src/MCview/PDBChain.java |    5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 885521b..cf794b6 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -29,8 +29,8 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureMapping;
 import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureMapping;
 
 import java.awt.Color;
 import java.util.List;
@@ -582,12 +582,13 @@ public class PDBChain
         {
           for (AlignmentAnnotation ana : sequence.getAnnotation())
           {
-            List<AlignmentAnnotation> transfer = sq
+            List<AlignmentAnnotation> transfer = dsq
                     .getAlignmentAnnotations(ana.getCalcId(), ana.label);
             if (transfer == null || transfer.size() == 0)
             {
               ana = new AlignmentAnnotation(ana);
               ana.liftOver(dsq, sqmpping);
+              dsq.addAlignmentAnnotation(ana);
               // mapping.transfer(ana);
             }
             else
-- 
1.7.10.2