GitLab

updated ProteinAlignFeatureAdaptor DnaAlignFeatureAdaptor to extend new BaseAlignFeatureAdaptor thereby eliminating quite a few lines of duplicated code

ExonAdaptor this now expects to store new style supporting features is, storing alignfeatures then appropriate idss in supporting feature table which is now a linkage table

warning all other code for supporting features will be broken if you are using a new style supporting feature table or the store method will be broken if you are using an old style supporting feature table this will hopefully be fixed soon so update your supporting feature tables!

AssemblyMapper, altereed checking of seq->start to allow for negative numbers

AlignFeatures, added coordinate transforms, only slice->rawcontig implemented currently plus otehr methods to make new supportting feature storage work like dbID and contig

Exon, altered supporting feature storage

FeaturePair remove cigar accessor as it is just confusing!

Removed ChromosomeStats and ChromosomeStatsAdaptor.  They are no longer needed since their functionality is present in the Chromosome/ChromosomeAdaptor objects

Can now transform exon from coords in one slice to coords on another slice.  Removed register region call in slice constructor.  Regions are now registered in chunks on an as-needed basis so this wasn't needed anymore

fetch_by_contig_list now calls core_adaptor->fetch_by_contig_list instead of core_adaptor->fetch_by_stable_id

Sticky Exons were not working nicely. Attaching seq  currently not supported. Has probably to be fixed

-fixed and renamed fetch_by_clone_name in SliceAdaptor

-Deprecated SliceAdaptor related methods in StaticGoldenPathAdaptor
-Updated RepeatFeatureAdaptorI interface
-Updated ProxyRepeatFeatureAdaptor to implement interface changes
-Deprecated is_golden method of Clone

Repeats can now be created using Lite or Core database.  On the web they are created via faster lite database via ProxyRepeatFeature Adaptor.  Lazy loading of repeats should probably be introduced, since repeat features are not fully populated when created via Lite.

Added in_assembly method to AssemblyMapper, changed feature factory warning msg, deprecated get_Contig method in Clone