GitLab

    fetch_by_contig_id(int) -> fetch_by_Contig(RawContig)
  store(int, list of Features) -> store(list of Features with attached contigs)

transcript IDs.

 home.....

consistency.  Other minor cosmetic changes of ordering of fields.

Added some more PODs, removed some methods from RawContigAdaptor, modified RawContig to work without removed methods

Added check to fetch_evidence_by_Exon to ensure exon has a dbID before trying to fetch the evidence

transform functionality in BaseAlignFeature should now work for slice -> raw contig other way still need implementing should also now split cigarlines nice where necessary

made sure end_phase was set explicitly when transforming sticky exons in Exon.pm

moved around some of the feature pair stuff again.  RepeatFeature now inherits from RepeatFeatureI, BaseFeature now inherits from RepeatFeature

un-deprecated GeneAdaptor->get_description which should not have been deprecated in first place (oops).
Added more PODs

Restructured ProxyAdaptors, now all inherit from ProxyAdaptor class.  Removed now unneeded interfaces (and threw out DBAdaptorI while at it).

and Updated DBConnection so that get_adaptor no longer checks the object type of adaptors