Raw content of Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::CcdsAdaptor
<![CDATA[package Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::CcdsAdaptor;
use strict;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::ExternalData::CDSTrack::Ccds;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning stack_trace_dump );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use vars '@ISA';
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
sub _tables {
my $self = shift;
return (['CcdsUids' , 'cu']);
}
sub _columns {
my $self = shift;
return ( 'cu.ccds_uid', 'cu.group_uid', 'cu.latest_version' );
}
sub fetch_by_dbID {
my $self = shift;
my $ccds_id = shift;
throw("Require dbID for fetch_by_dbID")
unless ($ccds_id);
my $constraint = "cu.ccds_uid = '$ccds_id'";
my ($ccds_obj) = @{ $self->generic_fetch($constraint) };
return $ccds_obj;
}
sub fetch_by_GroupVersion {
my $self = shift;
my $gv = shift;
if (!ref $gv || !$gv->isa('Bio::EnsEMBL::ExternalData::CDSTrack::GroupVersion') ) {
throw("Must provide a Bio::EnsEMBL::ExternalData::CDSTrack::GroupVersion object");
}
my $gv_id = $gv->dbID;
my ($ccds_obj) = $self->fetch_by_group_version_id($gv_id);
return $ccds_obj;
}
sub fetch_by_group_version_id {
my $self = shift;
my $gv_id = shift;
throw("Require group_version_id for fetch_by_group_version_id")
unless ($gv_id);
my $sql = "SELECT cu.ccds_uid ".
"FROM CcdsUids cu, GroupVersions gv ".
"WHERE cu.group_uid = gv.group_uid ".
"AND gv.group_version_uid = '$gv_id'";
my $sth = $self->prepare($sql);
$sth->execute();
my ($id) = $sth->fetchrow();
my $ccds_obj;
if (defined $id){
$ccds_obj = $self->fetch_by_dbID($id);
}
return $ccds_obj;
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my @out;
my ($ccds_id, $group_id, $latest_version);
$sth->bind_columns( \$ccds_id, \$group_id, \$latest_version);
while($sth->fetch()) {
push @out, Bio::EnsEMBL::ExternalData::CDSTrack::Ccds->new(
-dbID => $ccds_id,
-group_id => $group_id,
-latest_version => $latest_version,
-adaptor => $self
);
}
return \@out;
}
1;
]]>