WormBase/website — pull request #3083 by sibyl229 (2014-08-27 20:24:25+00:00)
Title: Sequence refactor

Done
- remove duplicate subroutines in Cds.pm - those weren't actually called
- extract subroutines from print_sequence in Role::Sequence
- attempt to simplify control flow in print_sequence
- Missing markup for CDS in /species/c_elegans/transcript/ZK131.5#05--10

TODO
- add more test case, as I learn the expected outcome for different classes
- Question: The Predicted Exons in the table below Not correspond to the CDS highlighting in the sequence? The exons boundaries listed here is based on data in Ace. Not the GFF. Also these are exons, not cds. Is this okay?
- Question: Do we expect any highlighting for coding pseudogene?
- Question: what kind of sequence object has ``$self->object->Properties eq 'cDNA'``?

Hi @tharris, could you please take do a quick review at the modified print_sequence function? Thanks a lot! https://github.com/WormBase/website/blob/sequence-refactor/lib/WormBase/API/Role/Sequence.pm#L938