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#
# Title: Add canonical translations
#
# Description:
# Add a reference to the translation table in the transcript table to
# let the API to know which translation (out of possibly several) is the
# canonical one.
#
# This patch adds a 'canonical_translation_id' field (with an index)
# to the 'transcript' table and initiates it with the corresponding
# 'translation.transcript_id'.

#
# Title: Allow for NULLs in meta table.
#
# Description:
# Allow the meta_value field in the meta table to be NULL.

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