Raw content of Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::InterpretationAdaptor 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;