=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2023] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut


=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
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;
