skip it.

have a corresponding 'species.stable_id_prefix' meta key it should not
be skipped completely.  Solves a problem with Eugene's yeast database.

* Correction to a previous commit regarding a multi-species regular
  expression.

* Add registration of multi-species user upload databases.

* Add registration of multi-species functional genomics databases.

Yates).

Reformat.

Genomes might have more than one species per single stable ID prefix.
The patch takes care of that possibility.

databases (again, patch from Andy).

  Arg [1]    : Species name to retrieve aliases for
               (may be an alias as well).
  Example    : Bio::EnsEMBL::Registry->get_all_aliases('Homo sapiens');
  Description: Returns all known aliases for a given species (but not the
               species name/alias that was given).
  Returntype : ArrayRef of all known aliases
  Exceptions : none
  Status     : Development

a throw() on failure.

argument in the corresponding method in TranscriptAdaptor to insert a
constraint (limiting to a set of transcript IDs).

The new code did not take into account HAP/PAR regions.

a new fourth argument which is a constraint.

Although the new code was efficient, it did not take HAP/PAR regions
into consideration.

corrspond to actual object types that one may use to get an adaptor.

Currently, the stable IDs for the following types of objects are
detected:

  Gene
  Transcript
  Translation
  Exon
  ProteinTree
  Family
  NCTree
  SNP
  RegulatoryFeature

for which there is no species.stable_id_prefix meta entry onto
the the list of databases to query as fallback.  This solves
Eugene's problem with S.cerevisiae.

transcripts by dbID list.  Duplicate code from TranscriptAdaptor to load
exons for these transcripts as well, in a similar manner.

This solves Bronwen's and Steve's problem of running out of memory when
fetching a small subset of genes from a large slice with millions of
transcripts.

GeneAdaptor for efficiency.

into $ex_id, not the other way around :-/

documentation.

similar cleanup in GeneAdaptor.

fetch_all_by_Slice().

'merged_IG_gene' and 'havana_IG_gene' respectively.

direct_xref replace with seperate table for gene, transcript and translation so sql needed to be changed