Raw content of Bio::EnsEMBL::ExternalData::Mole::DBSQL::AccessionAdaptor
<![CDATA[package Bio::EnsEMBL::ExternalData::Mole::DBSQL::AccessionAdaptor;
use strict;
use Bio::EnsEMBL::ExternalData::Mole::Accession;
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 (['accession' , 'a']);
}
sub _columns {
my $self = shift;
return ( 'a.accession_id', 'a.entry_id',
'a.accession', 'a.qualifier');
}
sub fetch_by_dbID {
my $self = shift;
my $id = shift;
my $constraint = "a.accession_id = '$id'";
my ($accession_obj) = @{ $self->generic_fetch($constraint) };
return $accession_obj;
}
sub fetch_by_Entry {
my $self = shift;
my $entry = shift;
my $sth = $self->prepare(
"SELECT a.accession_id ".
"FROM accession a ".
"WHERE a.entry_id = ?");
$sth->bind_param(1, $entry->dbID, SQL_INTEGER);
$sth->execute();
my $acc_id = $sth->fetchrow();
$sth->finish();
my $accession_object = $self->fetch_by_dbID($acc_id);
return $accession_object;
}
sub fetch_by_entry_id {
my ($self, $entry_id) = @_;
my $constraint = "a.entry_id = '$entry_id'";
my ($accession_obj) = @{ $self->generic_fetch($constraint) };
return $accession_obj;
}
sub fetch_by_accession {
my ($self, $acc) = @_;
my $constraint = "a.accession = '$acc'";
my ($accession_obj) = @{ $self->generic_fetch($constraint) };
return $accession_obj;
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my @out;
my ( $acc_id, $entry_id, $accession, $qualifier );
$sth->bind_columns( \$acc_id, \$entry_id, \$accession, \$qualifier );
while($sth->fetch()) {
push @out, Bio::EnsEMBL::ExternalData::Mole::Accession->new(
-dbID => $acc_id,
-entry_id => $entry_id,
-adaptor => $self,
-accession => $accession,
-qualifier => $qualifier,
);
}
return \@out;
}
1;
]]>