Raw content of Bio::EnsEMBL::ExternalData::Mole::DBSQL::SequenceAdaptor
<![CDATA[package Bio::EnsEMBL::ExternalData::Mole::DBSQL::SequenceAdaptor;
use strict;
use Bio::EnsEMBL::ExternalData::Mole::Sequence;
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 (['sequence' , 'seq']);
}
sub _columns {
my $self = shift;
return ( 'seq.entry_id',
'seq.split_counter', 'seq.sequence');
}
sub fetch_by_Entry {
my $self = shift;
my $entry = shift;
my $sequence_object = $self->fetch_by_entry_id($entry->dbID);
return $sequence_object;
}
sub fetch_by_entry_id {
my ($self, $entry_id) = @_;
my $constraint = "seq.entry_id = '$entry_id'";
my ($sequence_obj) = @{ $self->generic_fetch($constraint) };
return $sequence_obj;
}
sub fetch_by_sequence {
my ($self, $seq) = @_;
my $constraint = "seq.sequence = '$seq'";
my ($sequence_obj) = @{ $self->generic_fetch($constraint) };
return $sequence_obj;
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my @out;
my ( $entry_id, $split_counter, $sequence );
$sth->bind_columns( \$entry_id, \$split_counter, \$sequence );
while($sth->fetch()) {
push @out, Bio::EnsEMBL::ExternalData::Mole::Sequence->new(
-entry_id => $entry_id,
-adaptor => $self,
-split_counter => $split_counter,
-sequence => $sequence,
);
}
return \@out;
}
1;
]]>