GitLab

  * Use fetch_all_by_Transcript() rather than translation() on the
    transcript to get the canonical translation (and any alternative
    translations).

  * ... then store the translation and any alternative translations.

Solves a problem stopping genebuilders from copying genes from one
database to another.

  * Correct documentation.
  * Use fetch_by_Transcript() to get canonical translation.
  * Modify SQL not to get canonical translation.

  * In the _list_dbIDs() method: Wrap the execute() in an eval() and
    throw() if it fails.

  * In the generic_fetch() method: For multi-species databases, make
    sure we're using the correct SQL table aliases for the seq_region
    and coord_system tables..

associated with the transcript.

get fetch all to ignore LRG_gene this makes it slower but if you are getting all the them then this will be insignificant time difference

Added sanity check to _objs_from_sth to allow fetching DnaAlignFeatures without a slice, so that we can retrieve userdata features for the entire genome

Always de-reference the value got from get_mapping_path().
Found by Magali.

translation ID, and ALWAYS update it to the correct translation ID
later, after storing the translation.

Avoids problems (the canonical_translation_id being duplicated) when
transferring transcripts with translations from another database.

Amonida found this.

  Fix store() so that the canonical_translation_id in the transcript
  table is updated if the translation gets a new dbID when it is stored.

The TranslationAdaptor now has a fetch_all_by_Transcript() method with
which it's possible to get all translations for a transcript.

The fetch_by_Transcript() method now uses the new
canonical_translation_id field in the transcript table to get the
canonical transcript.

For species without alternative initiation (all Core speaces today), the
semantics and the results are the same as before.

Using the API from now on, without patch_56_57_e.sql applied, will
result in SQL errors.

The TranscriptAdaptor now knows how to store the canonical translation ID.

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.