GitLab

Formatting of SYNOPSIS code.

Passes unit tests.

get slice adaptor from the destination slice, rather then the current db - because userdata features are stored in a different db

changes introduced in release 52: new column description in external_db and new column in dna_align_feature

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