From: Jim Procter <j.procter@dundee.ac.uk>
Date: Wed, 15 Oct 2014 09:04:26 +0000 (+0100)
Subject: JAL-348 JAL-674 JAL-1564 TODO and implementation error message when liftOver is attem... 
X-Git-Tag: Jalview_2_9~169^2~27
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=61c11ca07415db042c5ddcbbc6255e1dce3e7b2f;p=jalview.git

JAL-348 JAL-674 JAL-1564 TODO and implementation error message when liftOver is attempted for a DNA/Protein mapping.
---

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 679681c..012ecb3 100755
--- 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;