Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL InterpretationAdaptor
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Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::DBSQL::BaseAdaptor
Bio::EnsEMBL::ExternalData::CDSTrack::DBSQL::DBAdaptor
Bio::EnsEMBL::ExternalData::CDSTrack::Interpretation
Bio::EnsEMBL::Storable
Bio::EnsEMBL::Utils::Argument qw ( rearrange )
Bio::EnsEMBL::Utils::Exception qw ( deprecate throw warning stack_trace_dump )
Inherit
Bio::EnsEMBL::DBSQL::BaseAdaptor
Synopsis
No synopsis!
Description
No description!
Methods
_columns
No description
Code
_left_join
No description
Code
_objs_from_sth
No description
Code
_tables
No description
Code
fetch_by_dbID
No description
Code
Methods description
None available.
Methods code
_columnsdescriptionprevnextTop
sub _columns {
  my $self = shift;
  return ( 'i.interpretation_uid', 'i.ccds_uid', 'i.group_uid', 'i.group_version_uid', 'i.accession_uid', 
  'i.parent_interpretation_uid', 'i.date_time', 'i.comment', 'i.val_description', 'i.char_val', 'i.integer_val', 
  'i.float_val', 'i.interpretation_type_uid', 'i.interpretation_subtype_uid', 'i.acc_rejection_uid', 'i.interpreter_uid', 
  'i.program_uid', 'i.reftrack_uid',  'isub.interpretation_subtype');
}
_left_joindescriptionprevnextTop
sub _left_join {
  return ( [ 'InterpretationSubtypes', "i.interpretation_subtype_uid = isub.interpretation_subtype_uid" ]);
}
_objs_from_sthdescriptionprevnextTop
sub _objs_from_sth {
  my ($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;
}
_tablesdescriptionprevnextTop
sub _tables {
  my $self = shift;
  return (['Interpretations' , 'i'],['InterpretationSubtypes', 'isub']);
}
fetch_by_dbIDdescriptionprevnextTop
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;
}
General documentation
No general documentation available.