GitLab

the Ensembl Genomes project.

Formatting.

reset_DBADaptor also handles absent adaptor nicely, as well as an extra parameters hash for passing to the DBAdaptor constructor

modified method get_species_and_object_type to retrieve ExonAdaptor as well and changed implementation to make it easier to maintain

extra number (used by Ensembl Genomes) after the word "core", as in
"schizzosachromyces_pombe_core_0_51_1a".

Passes unit tests.

get_all_DBAdaptors_by_connection():

  Arg [1]    : string, name of database
  Returntype : reference to list of DBAdaptors
  Exceptions : none
  Example    : @dba = @{ Bio::EnsEMBL::Registry
                  ->get_all_DBAdaptors_by_dbname($dbname) };
  Status     : Stable


Some formatting.

expensive joins for single-species databases.

database names and making sure none of them are picked out when looking
for core (single species) databases.

Reformat of get_all_db_adaptors().

not just "%_core_51".

Using this code on databases not patched up to the v51 schema will fail.

A pre-merge tag was put in place just before this merge:

  pre-multispecies-merge (in ensembl/modules/Bio/EnsEMBL)