GitLab

Minor POD corrections

for the benefit of Region Report tool

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.

translation's transcript.

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

dbIDs are not available, use genomic start/end coordinates to figure out
whether "this" translation is the same as the canonical translation or
not.

them instead.  Bug fix for Amy.

-  @seqeds = sort { $b->start() <=> $a->start() } @seqeds;
+  # HACK:   The translation ENSP00000420939 somehow makes the next line
+  #         bomb out ($a or $b becomes undef) if the start() method
+  #         is used.  I haven't been able to find out why.  It has 10
+  #         Selenocysteine seqedits that looks correct.
+  #         /Andreas (release 59)
+  my @seqeds = sort { $b->{'start'} <=> $a->{'start'} } @seqeds;

transcript had to be fetched from the database.  If this happens, the
user is likely working in a translation-centric way, i.e. not going
through transcripts.  If the reference is weakened, the reference to
the transcript will be undef after the end of the code block, as the
transcript passes out of scope.

=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

Simplify cdna_start() and cdna_end() by use of transcript().

Scalar::Util::weaken() to avoid memory leak.

* Add a transcript() method to the Translation object to retrieve its
  Transcript.

* Modify seq() in Translation so that it temporarily swaps out the
  canonical translation of the transcript if needed.

Formatting of SYNOPSIS code.

Passes unit tests.

    my @edits = ('initial_met', '_selenocysteine', 'amino_acid_sub');
for Drosophila.  (Like Selenocysteine, but any amino acid including '*' can be substituted.)