In translation_id(): Update for this method.

All from Michael S.

throw() has the correct message (but leave it commented out since it
would stop circular genomes working).

In overlap_size(): Correct documentation.


All from Michael S.

Michael S.

Also, reformat method.

Michael S.

Michael S.

Also, reformat method.

message.  From Michael S.

Also, reformat method.

mentioning of return values as none are returned (and the rest of the
API is not expecting anything).  From Michael S.


Also, reformat method.

transcript's translation.

translation's transcript.

of the two slices into account.  From Michael S.

transcripts.

In get_all_DBEntries(): Document undocumented arguments.


From Michael S.

slice was given.  Noticed by Michael S.

From Michael S.

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.