JAL-348 JAL-674 JAL-1564 TODO and implementation error message when liftOver is attem...

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 679681c..012ecb3 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -1134,6 +1134,11 @@ public class AlignmentAnnotation
    */
   public void liftOver(SequenceI sq, Mapping sp2sq)
   {
+    if (sp2sq.getMappedWidth() != sp2sq.getWidth())
+    {
+      // TODO: employ getWord/MappedWord to transfer annotation between cDNA and Protein reference frames
+      throw new Error("liftOver currently not implemented for transfer of annotation between different types of seqeunce");
+    }
     boolean mapIsTo = (sp2sq != null) ? (sp2sq.getTo() == sq || sp2sq
             .getTo() == sq.getDatasetSequence()) : false;