GitLab

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

deprecated Chromosome::get_landmark_MarkerFeatures - Slice::get_landmark_MarkerFeatures should be used instead

more POD writing for ChromosomeAdaptor and BaseFeatureAdaptor\ deprecated landmark_MarkerFeature methods in ChromosomeAdaptor, Slice should be used instead

-Removed cruft file Range.pm
-Renamed Chromosome chromosome_id() method to dbID()

Added some sanity checks to ChromosomeAdaptor, Fixed some more bugs in SliceAdaptor in which chromosome id was being used as chromosome name

Fixed bug in Gene and Transcript in which start, end, and strand was sometimes not recalculated after a transform.

Fixed bug in SliceAdaptor::fetch_by_gene_stable_id method in which slice chromosome was sometimes incorrectly set