GitLab

This means that CoordSystem, DensityType, Map::Marker, Map::Ditag, Map::Qtl,
MiscSet, OntologyTerm and SeqRegionSynonym have now a fast constructor available.

Accordingly, new_fast is removed from Analysis, Feature, DataFile, DBEntry, RepeatConsensus,
Translation and UnmappedObject together with the import of weaken and isweak from
Scalar::Util.

[ENSCORESW-262]. Customised the Exon summary as hash, gene and transcript summaries have been improved. Biotype mapper can ask objects for their SO term and knows Variation objects are already annotated with a code. BioType mapper caches SO retrieval so it is a massive speed increase for large result sets.

ENSCORESW-159. Fix for issue found with coding_region_start which was using the wrong method in the transcript object.

Replacing the 6 coordinate methods with versions which can operate on transcripts which have not been persisted to a database. The DBID is still used for caching purposes

for origin overlapping genes take into account exons with negative start and with start greater then end

exons of the genes overlapping chromosome origin are attached to the normal slice, but with negative coordinates

attached slice.

slice was given.  Noticed by Michael S.

  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.

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

_merge_ajoining_coords added to make sure that having more than one coord is wrong. Andy Yates wrote the code i just checked it and added it.

=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

Formatting of SYNOPSIS code.

Passes unit tests.

the coding region does not start/end in this exon, it also will not
end/start here.

    cdna_start()
    cdna_end()

    cdna_coding_start()
    cdna_coding_end()

    coding_region_start()
    coding_region_end()

Changed POD from saying "in genomic coordinates" to say "in
slice-relative coordinates":

    coding_region_start()
    coding_region_end()

No functional change.

Fixed comment.

    $exon->cdna_start($transcript);
        # Returns the start position of the exon in cDNA coordinates.

    $exon->cdna_end($transcript);
        # Returns the end position of the exon in cDNA coordinates.


    $exon->cdna_coding_start($transcript);
        # Returns the start position of the coding region of the exon
        # in cDNA coordinates.  Returns undef if the whole exon is
        # non-coding.

    $exon->cdna_coding_end($transcript);
        # Returns the end position of the coding region of the exon
        # in cDNA coordinates.  Returns undef if the whole exon is
        # non-coding.


    $exon->coding_region_start($transcript);
        # Returns the start position of the coding region of the exon in
        # genomic coordinates on the forward strand.  Returns undef if
        # the whole exon is non-coding.

    $exon->coding_region_end($transcript);
        # Returns the end position of the coding region of the exon in
        # genomic coordinates on the forward strand.  Returns undef if
        # the whole exon is non-coding.


Since an exon may be part of one or more transcripts, the relevant
transcript must be given as argument ot these methods.