SeqRegionSynonymAdaptor.pm

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=head1 LICENSE
 
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=cut
 
 
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INTO 
=cut
 
package Bio::EnsEMBL::DBSQL::SeqRegionSynonymAdaptor;
use vars qw(@ISA);
use strict;
 
 
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw);
use Bio::EnsEMBL::SeqRegionSynonym;
 
@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
 
 
sub get_synonyms {
  my ($self, $seq_id) = @_;
  $self->bind_param_generic_fetch($seq_id, SQL_INTEGER);
  return $self->generic_fetch(qq{srs.seq_region_id = ?});
}
 
sub store {
  my $self = shift;
  my $syn = shift;
 
  return if($syn->is_stored($self->db));
 
  if(!defined($syn->seq_region_id)){
    throw("seq_region_id is needed to store a seq_region_synoym");
  }
 
  my $insert_ignore = $self->insert_ignore_clause();
  my $sth = $self->prepare("${insert_ignore} INTO seq_region_synonym (seq_region_id, synonym, external_db_id) VALUES (?, ?, ?)");
  $sth->bind_param(1, $syn->seq_region_id,  SQL_INTEGER);
  $sth->bind_param(2, $syn->name         ,  SQL_VARCHAR);
  $sth->bind_param(3, $syn->external_db_id, SQL_INTEGER);
  $sth->execute;
  $syn->{'dbID'} = $self->last_insert_id('seq_region_synonym_id', undef, 'seq_region_synonym');
  $sth->finish;
}
 
sub _tables {
  return (['seq_region_synonym', 'srs'], ['external_db','exdb']);
}
 
sub _columns {
  return qw(srs.seq_region_synonym_id srs.seq_region_id srs.synonym srs.external_db_id exdb.db_name exdb.db_display_name);
}
 
sub _left_join{
    return (['external_db',"exdb.external_db_id = srs.external_db_id"]);
}
 
sub _objs_from_sth {
  my ($self, $sth) = @_;
 
  my @results;
  my ($seq_id, $dbid, $alt_name, $ex_db, $dbname, $db_display_name);
  $sth->bind_columns(\$dbid, \$seq_id, \$alt_name, \$ex_db, \$dbname, \$db_display_name);
 
  push @results, Bio::EnsEMBL::SeqRegionSynonym->new(
    -adaptor         => $self,
    -synonym         => $alt_name,
    -dbID            => $dbid,
    -external_db_id  => $ex_db,
    -seq_region_id   => $seq_id,
    -dbname          => $dbname,
    -db_display_name => $db_display_name,
  ) while $sth->fetch();
 
  $sth->finish;
 
  return \@results;
}
 
sub _final_clause {
    return ' ORDER BY srs.seq_region_synonym_id'
}
 
1;