JAL-1620 version bump and release notes

[jalview.git] / src / MCview / PDBChain.java

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 408108b..9cf7097 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -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);
@@ -534,24 +535,25 @@ public class PDBChain
       }
       else
       {
-      if (sequence != null && sequence.getAnnotation() != null)
-      {
-        for (AlignmentAnnotation ana : sequence.getAnnotation())
+        if (sequence != null && sequence.getAnnotation() != null)
         {
-          List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
-                  ana.getCalcId(), ana.label);
-          if (transfer == null || transfer.size() == 0)
-          {
-            ana.liftOver(dsq, sqmpping);
-            // mapping.transfer(ana);
-          }
-          else
+          for (AlignmentAnnotation ana : sequence.getAnnotation())
           {
-            continue;
+            List<AlignmentAnnotation> transfer = sq
+                    .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+            if (transfer == null || transfer.size() == 0)
+            {
+              ana = new AlignmentAnnotation(ana);
+              ana.liftOver(dsq, sqmpping);
+              // mapping.transfer(ana);
+            }
+            else
+            {
+              continue;
+            }
           }
         }
       }
-      }
       if (false)
       {
         // Useful for debugging mappings - adds annotation for mapped position