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lib/Bio/EnsEMBL/RNAProduct.pm  view on Meta::CPAN

=head2 start_Exon

  Arg [1]    : (optional) Bio::EnsEMBL::Exon || undef - start exon to assign
  Example    : $rnaproduct->start_Exon($exon1);
  Description: Getter/setter for the value of start_Exon, which denotes the
               exon at which RNAProduct starts.
  Returntype : Bio::EnsEMBL::Exon
  Exceptions : thrown on wrong argument type
  Caller     : general
  Status     : Stable

=cut

sub start_Exon {
  my ($self, $exon) = @_;

  if (defined($exon)) {

    # Normal setter
    assert_ref($exon, 'Bio::EnsEMBL::Exon');
    $self->{'start_exon'} = $exon;

  }
  elsif (@_ > 1) {
    # User has explicitly passed undef. Break connection to exon.
    delete( $self->{'start_exon'} );
  }

  return $self->{'start_exon'};
}


=head2 summary_as_hash

  Example       : $rnaproduct_summary = $rnaproduct->summary_as_hash();
  Description   : Retrieves a textual summary of this RNAProduct.
                  Not inherited from Feature.
  Returns       : hashref of arrays of descriptive strings
  Status        : Intended for internal use

=cut

sub summary_as_hash {
  my $self = shift;
  my %summary;
  my $id = $self->display_id;
  if ($self->version) {
    $id .= "." . $self->version;
  }
  $summary{'id'} = $id;
  $summary{'rnaproduct_id'} = $id;
  $summary{'genomic_start'} = $self->genomic_start;
  $summary{'genomic_end'} = $self->genomic_end;
  $summary{'length'} = $self->length;
  my $transcript = $self->transcript;
  $summary{'Parent'} = $transcript->display_id;
  return \%summary;
}


=head2 synchronise_attributes

  Example       : $rnaproduct->synchronise_attributes();
  Description   : Some RNAProduct attributes, e.g. stem-loop arm in case
                  of MicroRNA, use a local cache of their value for
                  convenience. Unless the corresponding setters update both
                  the cache value and the attribute (which would defeat
                  the convenience thing), we have to make sure the former
                  get propagated to the latter before storing the object
                  in the database:
                   - if no corresponding attribute exists, create one;
                   - if there is one, update its value.
                  Class-specific maps of attributes to synchronise are
                  provided by
                  RNAProductTypeMapper::class_attribute_cache_map() .
  Returntype    : none
  Exceptions    : throws if the object contains multiple attributes with the
                  given code and the choice which one to update is
                  ambiguous.
  Caller        : RNAProductAdaptor
  Status        : At Risk (In Development)

=cut

sub synchronise_attributes {
  my ($self) = @_;

  my $attribute_cache_map = Bio::EnsEMBL::Utils::RNAProductTypeMapper::mapper()
    ->class_attribute_cache_map(ref($self));

  while (my ($cache_key, $attr_code) = each %{$attribute_cache_map}) {
    my $existing_attributes = $self->get_all_Attributes($attr_code);
    my $n_existing_attrs = scalar @{$existing_attributes};
    if ($n_existing_attrs > 0) {
      # At the moment we do not support multiple occurrences of target
      # attributes at all
      if ($n_existing_attrs > 1) {
        throw("Object has multiple '$attr_code' attributes and we do not know"
              . " which one to update");
      }
      else {
        $existing_attributes->[0]->value($self->{$cache_key});
      }
    }
    else {
      # No corresponding attribute exists, most likely because we are
      # dealing with a newly created object which has never been pushed
      # to the database.
      $self->add_Attributes(Bio::EnsEMBL::Attribute->new(
        -CODE  => $attr_code,
        -VALUE => $self->{$cache_key},
      ));
    }
  }

  return;
}


=head2 transcript

  Arg [1]       : Transcript object (optional)
  Description   : Sets or retrieves the transcript object associated
                  with this RNAProduct object.
  Exceptions    : Throws if there is no adaptor or no dbID defined for
                  the RNAProduct object.
  Returntype    : Bio::EnsEMBL::Transcript

=cut

sub transcript {
  my ($self, $transcript) = @_;

  if (defined($transcript)) {

    # Normal setter
    assert_ref($transcript, 'Bio::EnsEMBL::Transcript');
    $self->{'transcript'} = $transcript;
    weaken($self->{'transcript'});    # Avoid circular references.

  } elsif (@_ > 1) {

    # User has explicitly passed undef. Break connection to transcript.
    delete( $self->{'transcript'} );