From 61c11ca07415db042c5ddcbbc6255e1dce3e7b2f Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 15 Oct 2014 10:04:26 +0100 Subject: [PATCH 1/1] JAL-348 JAL-674 JAL-1564 TODO and implementation error message when liftOver is attempted for a DNA/Protein mapping. --- src/jalview/datamodel/AlignmentAnnotation.java | 5 +++++ 1 file changed, 5 insertions(+) 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; -- 1.7.10.2