Bio-DB-Das-Chado

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lib/Bio/DB/Das/Chado.pm  view on Meta::CPAN

feature appears in the database.

NOTE: This currently raises a "not-implemented" exception, as the
BioSQL API does not appear to provide this functionality.

=cut

sub types {
  my $self = shift;
  my ($enumerate) =  $self->_rearrange([qw(ENUMERATE)],@_);
  $self->throw_not_implemented;
  #if lincoln didn't need to implement it, neither do I!
}

=head2 get_feature_by_alias, get_features_by_alias 

 Title   : get_features_by_alias
 Usage   : $db->get_feature_by_alias(@args)
 Function: return list of feature whose name or synonyms match
 Returns : a list of Bio::Das::Chado::Segment::Feature objects
 Args    : See below

lib/Bio/DB/Das/Chado/Segment/Feature.pm  view on Meta::CPAN

           from 1 to 10000
 Example :
 Returns : TRUE on success
 Args    : a Bio::PrimarySeqI compliant object

=cut

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

  $self->throw_not_implemented();
}

=head2 display_name()

  Title   : display_name
  Function: aliased to uniquename() for Bio::SeqFeatureI compatibility

=cut

*display_name = \&group;

lib/Bio/DB/Das/Chado/Segment/Feature.pm  view on Meta::CPAN

  Function: ???
  Returns :
  Args    :


=cut

sub get_tagset_values {
  my ($self,%arg) = @_;

  $self->throw_not_implemented();
}

=head2 gff_string()

  Title   : gff_string
  Usage   :
  Function: ???
  Returns :
  Args    :

lib/Bio/DB/Das/Chado/Segment/Feature.pm  view on Meta::CPAN

  Usage   :
  Function: ???
  Returns :
  Args    :

=cut

#sub seq {
#  my ($self,%arg) = @_;
#
#  $self->throw_not_implemented();
#}

=head2 seq_id()

  Title   : seq_id
  Usage   : $obj->seq_id($newval)
  Function: Set or get the name of the reference sequence that the feature 
            resides on.
  Returns : value of seq_id (a scalar)
  Args    : on set, new value (a scalar or undef, optional)