From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 30 Oct 2014 15:51:54 +0000 (+0000)
Subject: JAL-674 propagate annotation onto mapped sequence and its dataset sequence
X-Git-Tag: Jalview_2_9~155^2~15^2~14
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e7235e7d60595f9e3bec5fb65317681e594461c4;p=jalview.git

JAL-674 propagate annotation onto mapped sequence and its dataset sequence
---

diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 9236331..e4749c9 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -106,11 +106,27 @@ public class StructureMapping
    * 
    * @param ana
    * @return the copy that was remapped to the mapped sequence
+   * @note this method will create a copy and add it to the dataset sequence for
+   *       the mapped sequence as well as the mapped sequence (if it is not a
+   *       dataset sequence).
    */
   public AlignmentAnnotation transfer(AlignmentAnnotation ana)
   {
     AlignmentAnnotation ala_copy = new AlignmentAnnotation(ana);
-    ala_copy.remap(sequence, mapping, 0, -1, 1);
+    SequenceI ds = sequence;
+    while (ds.getDatasetSequence() != null)
+    {
+      ds = ds.getDatasetSequence();
+    }
+    ala_copy.remap(ds, mapping, 0, -1, 1);
+    ds.addAlignmentAnnotation(ala_copy);
+    if (ds != sequence)
+    {
+      // mapping wasn't to an original dataset sequence, so we make a copy on
+      // the mapped sequence too
+      ala_copy = new AlignmentAnnotation(ala_copy);
+      sequence.addAlignmentAnnotation(ala_copy);
+    }
     return ala_copy;
   }
 }