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result in infinite recursion.

for the benefit of Region Report tool

Also minor POD corrections.

Add the following proxy methods:

* get_all_object_xrefs()    alias for get_all_DBEntries()
* get_all_xrefs()           alias for get_all_DBLinks()

These have no documentation as of yet.

canonical transcript.

transcripts.

In get_all_DBEntries(): Document undocumented arguments.


From Michael S.

  Arg [1]       : Bio::EnsEMBL::Gene gene
  Example       : if ($geneA->equals($geneB)) { ... }
  Description   : Compares two genes for equality.
                  The test for eqality goes through the following list
                  and terminates at the first true match:

                  1. If Bio::EnsEMBL::Feature::equals() returns false,
                     then the genes are *not* equal.
                  2. If the biotypes differ, then the genes are *not*
                     equal.
                  3. If both genes have stable IDs: if these are the
                     same, the genes are equal, otherwise not.
                  4. If both genes have the same number of transcripts
                     and if these are (when compared pair-wise sorted by
                     start-position and length) the same, then they are
                     equal, otherwise not.

  Return type   : Boolean (0, 1)

  Exceptions    : Thrown if a non-gene is passed as the argument.

for the canonical transcript in the canonical_transcript() method of the
Gene object, and also use it in the store() method in GeneAdaptor to
properly set the canonical transcript of genes.

In load(): also load the canonical transcript.

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

=head2 load

  Arg [1]       : Boolean $load_xrefs
                  Load (or don't load) xrefs.  Default is to load xrefs.
  Example       : $translation->load();
  Description   : The Ensembl API makes extensive use of
                  lazy-loading.  Under some circumstances (e.g.,
                  when copying genes between databases), all data of
                  an object needs to be fully loaded.  This method
                  loads the parts of the object that are usually
                  lazy-loaded.
  Returns       : Nothing.

=cut

canonical_transcript() method warn about not being able to fetch the
canonical transcript when there's no adptor attached to the gene.

internal ID of the transcript instead of the transcript itself.  The
canonical_transcript() method will then lazy load the transcript.

This speeds up the gene adaptor code.

The old semantics is maintained.

Formatting of SYNOPSIS code.

Passes unit tests.

added 2 new columns in the table: canonical_transcript_id and canonical_annotation and the respective methods in the API to get/set this new information

Change POSIX import to prevent it importing unused functions (e.g. remove which conflicts with the remove method defined in Gene).