Raw content of Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::LocationAdaptor
<![CDATA[package Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::LocationAdaptor;
use strict;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::ExternalData::CDSTrack::Location;
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 (['Locations' , 'l']);
}
sub _columns {
my $self = shift;
return ( 'l.location_uid', 'l.chr_start', 'l.chr_stop');
}
sub fetch_by_dbID {
my $self = shift;
my $loc_id = shift;
throw("Require dbID for fetch_by_dbID")
unless ($loc_id);
my $constraint = "l.location_uid = '$loc_id'";
my ($loc_obj) = @{ $self->generic_fetch($constraint) };
return $loc_obj;
}
sub fetch_all_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 $chr = $gv->chromosome;
my $gv_id = $gv->dbID;
my (@loc_objs) = @{$self->fetch_all_by_group_version_id($gv_id, $chr)};
return \@loc_objs;
}
sub fetch_all_by_group_version_id {
my $self = shift;
my $gv_id = shift;
my $chr = shift;
my @loc_objs;
throw("Require group_version_id for fetch_by_group_version_id")
unless ($gv_id);
throw("Require chromosome for fetch_by_group_version_id")
unless ($chr);
my $sql = "SELECT lgv.location_uid ".
"FROM Locations_GroupVersions lgv ".
"WHERE lgv.group_version_uid = $gv_id ".
"AND lgv.chromosome = '$chr'";
my $sth = $self->prepare($sql);
$sth->execute();
while ( my $id = $sth->fetchrow()) {
push @loc_objs, $self->fetch_by_dbID($id);
}
return \@loc_objs;
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my @out;
my ($dbid, $exon_start, $exon_end);
$sth->bind_columns( \$dbid, \$exon_start, \$exon_end);
while($sth->fetch()) {
push @out, Bio::EnsEMBL::ExternalData::CDSTrack::Location->new(
-dbID => $dbid,
-exon_start => $exon_start + 1,
-exon_end => $exon_end + 1,
-adaptor => $self
);
}
return \@out;
}
1;
]]>