GitLab

fix for ChainedAssemblyMapper to map using the destination slice if one is provided http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-108

<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.

Added sanity check to _objs_from_sth to allow fetching DnaAlignFeatures without a slice, so that we can retrieve userdata features for the entire genome

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