conditional operator.

In fetch_all_by_Transcript():  Be absolutely sure not to add the
exon_transcript table twice.  Should solve a bug reported by Jan.

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.