external DB type strings contains '%' and use "LIKE" or "=" accordingly.
Document this behaviour in the POD of the method.  Also, safely quote
strings inserted into SQL.

In _type_by_external_db_id(): Fix documentation for method.

Both pointed out by Michael S.

  Fix misspelt "Exmaple".

  In AUTOLOAD(): warning() before throw(), otherwise not much joy.

Also get rid of inconsistency pointed out by Michael S.

  Fix documentation for register_assembled(), register_component(),
  _register_chained_special().

  Remove unused variable in _build_combined_mapper().

  Initialise $mid_cs_id in _register_chained_special() properly.

  Use splice() to remove a list element in register_all_chained() rather
  than setting the list length (say what?!).

#
# Title:
#   Rename 'go_xref' table to 'ontology_xref'.
#
# Description:
#   Rename the 'go_xref' table to make its use more generic.

transcripts:

1. protein_coding
2. nonsense_mediated_decay (if translatable)
3. non coding (may include NMD)

Ue non 'protein_coding' labelled transcript only if there are no
'protein_coding' labelled transcripts present.

Added OPTIONS section to DOC.

argument.

  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.

  Arg [1]       : Bio::EnsEMBL::Transcript transcript
  Example       : if ($transcriptA->equals($transcriptB)) { ... }
  Description   : Compares two transcripts 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 transcripts are *not* equal.
                  2. If the biotypes differ, then the transcripts are
                     *not* equal.
                  3. If both transcripts have stable IDs: if these are
                     the same, the transcripts are equal, otherwise not.
                  4. If both transcripts have the same number of exons
                     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-transcript is passed as the argument.

  Arg [1]       : Bio::EnsEMBL::Exon exon
  Example       : if ($exonA->equals($exonB)) { ... }
  Description   : Compares two exons 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 exons are *not* equal.
                  2. If both exons have stable IDs: if these are the
                     same, the exons are equal, otherwise not.
                  3. If the exons have the same start, end, strand, and
                     phase, then they are equal, otherwise not.

  Return type   : Boolean (0, 1)

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

Arg [1]       : Bio::EnsEMBL::Feature object
Example       : if ($featureA->equals($featureB)) { ... }
Description   : Compares two features using various criteria.  The
                test for eqality goes through the following list and
                terminates at the first true match:

               1. If the two features are the same object, they are
                  equal.

               2. If they are of different types (e.g., transcript and
                  gene), they are *not* equal.

               3. If they both have dbIDs: if these are equal, then they
                  are equal otherwise not.

               4. If they have slices and analysis objects: if analysis
                  dbIDs are the same and the seq_region_id are the same,
                  along with seq_region_start and seq_region_end, then
                  they are equal, otherwise not.

               If none of the above is able to determine equality,
               undef is returned.

Return type : tri-Boolean (0, 1, undef = "unknown")

Exceptions  : Thrown if a non-feature 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.

Thanks Bronwen for the heads up.

to zero and then update it when we know what the new internal ID of the
transcript is.

In load(): also load the canonical transcript.

("$f->slice(undef)").

warn user).

Also, comment out buggy EG code in project() (see "EG BUG: FIXME").

Also reformat is_toplevel() and is_reference().