Raw content of Bio::EnsEMBL::ExternalData::Mole::DBSQL::LocationAdaptor
<![CDATA[package Bio::EnsEMBL::ExternalData::Mole::DBSQL::LocationAdaptor;
use strict;
use Bio::EnsEMBL::ExternalData::Mole::Location;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::ExternalData::Mole::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 (['location' , 'lcn']);
}
sub _columns {
my $self = shift;
return ( 'lcn.entry_id', 'lcn.flat_file',
'lcn.file_offset', 'lcn.blastdbtracking_id');
}
sub fetch_by_Entry {
my $self = shift;
my $entry = shift;
my $location_object = $self->fetch_by_entry_id($entry->dbID);
return $location_object;
}
sub fetch_by_entry_id {
my ($self, $entry_id) = @_;
my $constraint = "lcn.entry_id = '$entry_id'";
my ($location_obj) = @{ $self->generic_fetch($constraint) };
return $location_obj;
}
sub fetch_by_flat_file {
my ($self, $flat_file) = @_;
my $constraint = "lcn.flat_file = '$flat_file'";
my ($location_obj) = @{ $self->generic_fetch($constraint) };
return $location_obj;
}
sub fetch_by_blastdbtracking_id {
my ($self, $blastdbtracking_id) = @_;
my $constraint = "lcn.blastdbtracking_id = '$blastdbtracking_id'";
my ($location_obj) = @{ $self->generic_fetch($constraint) };
return $location_obj;
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my @out;
my ( $entry_id, $flat_file, $file_offset, $blastdbtracking_id );
$sth->bind_columns( \$entry_id, \$flat_file, \$file_offset, \$blastdbtracking_id );
while($sth->fetch()) {
push @out, Bio::EnsEMBL::ExternalData::Mole::Location->new(
-entry_id => $entry_id,
-adaptor => $self,
-flat_file => $flat_file,
-file_offset => $file_offset,
-blastdbtracking_id => $blastdbtracking_id,
);
}
return \@out;
}
1;
]]>