RegulatoryFeatureAdaptor.pm

#
# EnsEMBL module for Bio::EnsEMBL::DBSQL::RegulatoryFeatureAdaptor
#
# Copyright EMBL/EBI
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::EnsEMBL::DBSQL::RegulatoryFeatureAdaptor

=head1 SYNOPSIS

$rfa = $database_adaptor->get_RegulatoryFeatureAdaptor();

my $regulatory_feature = $rfa->fetch_by_dbID(1234);

=head1 DESCRIPTION

This is an adaptor for the retrieval and storage of RegulatoryFeature objects
from the database.  Most of the implementation is in the superclass BaseFeatureAdaptor.

=head1 AUTHOR - Glenn Proctor

=head1 CONTACT

Post questions to the EnsEMBL developer list: ensembl-dev@ebi.ac.uk

=head1 METHODS

=cut

package Bio::EnsEMBL::DBSQL::RegulatoryFeatureAdaptor;

use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::RegulatoryFeature;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);

use vars qw(@ISA);

@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);




=head2 fetch_all_by_Slice

  Arg [1]    : Bio::EnsEMBL::Slice $slice
  Arg [2]    : (optional) string $logic_name
               Limits RepeatFeatures obtained to those having an Analysis with
               of the specified logic_name.  If no logic name is specified
               Repeats of all analysis types are retrieved.
  Example    : @rfeats = @{$rfa->fetch_all_by_Slice($slice, 'miRanda')};
  Description: Retrieves regulatory features overlapping the area designated by
               the provided slice argument.  Returned features will be in
               in the same coordinate system as the provided slice and will
               have coordinates relative to the slice start.
  Returntype : reference to a list of Bio::EnsEMBL::RegulatoryFeatures.
  Exceptions : throw on bad argument
  Caller     : Slice::get_all_RegulatoryFeatures

=cut

sub fetch_all_by_Slice {
  my $self = shift;
  my $slice = shift;
  my $logic_name = shift;