Moved to RegulatoryFactorAdaptor.pm

modules/Bio/EnsEMBL/DBSQL/RegulatoryMotifAdaptor.pm

-#
-# EnsEMBL module for Bio::EnsEMBL::DBSQL::RegulatoryMotifAdaptor
-#
-# 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::RegulatoryMotifAdaptor
-
-=head1 
-
-$rma = $database_adaptor->get_RegulatoryMotifAdaptor();
-
-$regulatory_motif = $rma->fetch_by_dbID(132);
-$regulatory_motif = $rma->fetch_by_name('Motif1');
-@regulatory_motifs = $rma->fetch_all_by_type("promoter");
-
-$rma->store($rm1, $rm2, $rm3);
-
-=head1 DESCRIPTION
-
-This is an adaptor for the retrieval and storage of RegulatoryMotif objects.
-
-=head1 AUTHOR - Glenn Proctor
-
-Email glenn@ebi.ac.uk
-
-=head1 CONTACT
-
-Post questions to the EnsEMBL developer list ensembl-dev@ebi.ac.uk
-
-=head1 METHODS
-
-=cut
-
-package Bio::EnsEMBL::DBSQL::RegulatoryMotifAdaptor;
-
-use strict;
-use Bio::EnsEMBL::DBSQL::BaseAdaptor;
-use Bio::EnsEMBL::RegulatoryMotif;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
-
-use vars qw(@ISA);
-@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
-
-
-=head2 fetch_by_dbID
-
-  Arg [1]    : int $db_id
-               The database identifier for the RegulatoryMotif to obtain
-  Example    : $regulatory_motif = $rma->fetch_by_dbID(4);
-  Description: Obtains a RegulatoryMotif object from the database via its
-               primary key. 
-  Returntype : Bio::EnsEMBL::RegulatoryMotif
-  Exceptions : none
-  Caller     : general, Bio::EnsEMBL::RegulatoryMotifAdaptor
-
-=cut
-
-sub fetch_by_dbID {
-    my( $self, $db_id ) = @_;
-
-    my ($rc) = @{$self->_generic_fetch("regulatory_motif_id = $db_id")};
-
-    return $rc;
-}
-
-
-
-=head2 fetch_by_name
-
-  Arg [1]    : string $name
-               the name of the regulatory motif to obtain
-  Example    : $rc = $rma->fetch_by_name('Motif');
-  Description: Obtains a regulatory motif from the database via its name
-  Returntype : Bio::EnsEMBL::RegulatoryMotif
-  Exceptions : none
-  Caller     : general
-
-=cut
-
-sub fetch_by_name {
-    my( $self, $name ) = @_;
-
-    my ($rc) = @{$self->_generic_fetch("name = '$name'")};
-
-    return $rc;
-}
-
-
-=head2 fetch_all_by_type
-
-  Arg [1]    : string $type
-               the type of regulatory motif to obtain
-  Example    : $rm = $rma->fetch_all_by_type('promoter');
-  Description: Obtains all regulatory motifs of a particular type
-  Returntype : listREF of Bio::EnsEMBL::RegulatoryMotifs
-  Exceptions : none
-  Caller     : general
-
-=cut
-
-sub fetch_all_by_type {
-    my( $self, $type) = @_;
-
-    return $self->_generic_fetch("type = '$type'");
-}
-
-
-
-=head2 _generic_fetch
-
-  Arg [1]    : string $where_clause
-  Example    : none
-  Description: PRIVATE used to create RegulatoryMotif features from an
-               SQL constraint
-  Returntype : listref of Bio::EnsEMBL::RegulatoryMotif objects
-  Exceptions : none
-  Caller     : internal
-
-=cut
-
-sub _generic_fetch {
-
-    my ($self, $where_clause) = @_;
-
-    my ($regulatory_motif_id, $name, $type);
-
-    my $sth = $self->prepare(qq{
-        SELECT regulatory_motif_id, name, type
-        FROM regulatory_motif
-        WHERE }. $where_clause);
-
-    $sth->execute;
-    $sth->bind_columns(\$regulatory_motif_id, \$name, \$type);
-
-    my @motifs;
-    while ($sth->fetch) {
-        push @motifs, Bio::EnsEMBL::RegulatoryMotif->new(-DBID => $regulatory_motif_id,
-							 -NAME => $name,
-							 -TYPE => $type);
-      }
-    return \@motifs;
-}
-
-
-=head2 store
-
-  Arg [1]    : list of Bio::EnsEMBL::RegulatoryMotifs @motifs
-  Example    : $rma->store(@motifs);
-  Description: stores a list of RegulatoryMotif objects in the database
-  Returntype : none
-  Exceptions : none
-  Caller     : ?
-
-=cut
-
-sub store {
-  my( $self, @motifs ) = @_;
-
-  my $sth = $self->prepare("INSERT into regulatory_motif (name, type) VALUES (?,?)");
-
-  foreach my $rm (@motifs) {
-
-    my $name = $rm->name or throw("name not set");
-    my $type = $rm->type or throw("type not set");
-
-    $sth->execute($name, $type);
-
-    my $db_id = $sth->{'mysql_insertid'}
-    or throw("Didn't get an insertid from the INSERT statement");
-
-    $rm->dbID($db_id);
-    $rm->adaptor($self);
-  }
-}
-
-1;
-
-__END__
-