Raw content of Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::InterpretationAdaptor
<![CDATA[package Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::InterpretationAdaptor;
use strict;
use Bio::EnsEMBL::Storable;
use Bio::EnsEMBL::ExternalData::CDSTrack::Interpretation;
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 (['Interpretations' , 'i'],['InterpretationSubtypes', 'isub']);
}
sub _columns {
my $self = shift;
return ( 'i.interpretation_uid', 'i.ccds_uid', 'i.group_uid', 'i.group_version_uid', 'i.accession_uid',
'i.parent_interpretation_uid', 'i.date_time', 'i.comment', 'i.val_description', 'i.char_val', 'i.integer_val',
'i.float_val', 'i.interpretation_type_uid', 'i.interpretation_subtype_uid', 'i.acc_rejection_uid', 'i.interpreter_uid',
'i.program_uid', 'i.reftrack_uid', 'isub.interpretation_subtype');
}
sub _left_join {
return ( [ 'InterpretationSubtypes', "i.interpretation_subtype_uid = isub.interpretation_subtype_uid" ]);
}
sub fetch_by_dbID {
my $self = shift;
my $int_id = shift;
throw("Require dbID for fetch_by_dbID")
unless ($int_id);
my $constraint = "i.interpretation_uid = '$int_id'";
my ($int_obj) = @{ $self->generic_fetch($constraint) };
return $int_obj;
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my @out;
my ($dbid, $ccds_id, $group_id, $group_version_id, $accession_id);
my ($parent_interpretation_id, $date_time, $comment, $val_description, $char_val, $integer_val);
my ($float_val, $interpretation_type_id, $interpretation_subtype_id, $acc_rejection_id, $interpreter_id);
my ($program_id, $reftrack_id, $interpretation_subtype);
$sth->bind_columns( \$dbid, \$ccds_id, \$group_id, \$group_version_id, \$accession_id,
\$parent_interpretation_id, \$date_time, \$comment, \$val_description, \$char_val, \$integer_val,
\$float_val, \$interpretation_type_id, \$interpretation_subtype_id, \$acc_rejection_id, \$interpreter_id,
\$program_id, \$reftrack_id, \$interpretation_subtype);
while($sth->fetch()) {
push @out, Bio::EnsEMBL::ExternalData::CDSTrack::Interpretation->new(
-dbID => $dbid,
-ccds_id => $ccds_id,
-group_id => $group_id,
-group_version_id => $group_version_id,
-accession_id => $accession_id,
-parent_interpretation_id => $parent_interpretation_id,
-date_time => $date_time,
-comment => $comment,
-val_description => $val_description,
-char_val => $char_val,
-integer_val => $integer_val,
-float_val => $float_val,
-interpretation_type_id => $interpretation_type_id,
-interpretation_subtype_id => $interpretation_subtype_id,
-acc_rejection_id => $acc_rejection_id,
-interpreter_id => $interpreter_id,
-program_id => $program_id,
-reftrack_id => $reftrack_id,
-interpretation_subtype => $interpretation_subtype,
-adaptor => $self
);
}
return \@out;
}
1;
]]>