GitLab

added 2 new attributes in protein and dna alignFeatures to get the name of the external database and the displayable name

registry and not get_XXXAdaptor() explicitly.

In all the feature adaptors, use either _create_feature() or
_create_feature_fast() from BaseFeatureAdaptor in _objs_from_sth() to
create features.

added order as an optional argument to list_dbIDs, mosy useful for genes and transcripts so caching is maximised

modified execute calls to make compatible with other databases. Need to use bind_param first, with the type of the parameter, and execute later

bug fix in Bio::EnsEMBL::Feature
added import of warning method into DnaAlignFeatureAdaptor

fixes RepeatFeatureAdaptor::fetch_by_dbID

fixed some memory leak problems, store Analysis object will now happen on feature store. That could slow down the Pipeline

Updates so slices can handle negative strand, not finished yet, and not tested

-Sped up general feature retrieval a little bit

Fixed a bug in _objs_from_sth where the hit start coordinate was accidentally being used as the hit score.

-'Flatening' FeaturePair object so that it no longer contains 2 SeqFeatures; It is now isa SeqFeature with some additional Hit attributes (object still bhaves as if it contained two features
-Adding 'fast' constructors to DnaDnaAlignFeatures and PepDnaAlignFeatures
-Some other minor tweaks such as using bind columns instead of fetchrow_hashref

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

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

BaseFeatureAdaptor was returning list when it should have been returning scalar - fixed.  Added dbID to SimpleFeature, dbID of DnaDnaAlignFeatures and PepDnaAlignFeatures now set by their respective feature adaptors upon retrieval from the database

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!