JAL-1177 propagate sequence associated annotation to dataset sequence

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 5fa37e3..cd817ab 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -997,6 +997,18 @@ public class Sequence implements SequenceI
       datasetSequence.setPDBId(getPDBId());
       setPDBId(null);
       datasetSequence.updatePDBIds();
+      if (annotation != null)
+      {
+        Vector<AlignmentAnnotation> _annot = annotation;
+        annotation = null;
+        for (AlignmentAnnotation aa : _annot)
+        {
+          aa.sequenceRef = datasetSequence;
+          aa.adjustForAlignment(); // uses annotation's own record of
+                                   // sequence-column mapping
+          datasetSequence.addAlignmentAnnotation(aa);
+        }
+      }
     }
     return datasetSequence;
   }