=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>.

=cut

#
# Ensembl module for Bio::EnsEMBL::Variation::DBSQL::GenotypeCodeAdaptor
#
#

=head1 NAME

Bio::EnsEMBL::Variation::DBSQL::GenotypeCodeAdaptor

=head1 SYNOPSIS
  $reg = 'Bio::EnsEMBL::Registry';
  
  $reg->load_registry_from_db(-host => 'ensembldb.ensembl.org',-user => 'anonymous');
  
  $va = $reg->get_adaptor("human","variation","genotypecode");



=head1 DESCRIPTION

This adaptor provides database connectivity for GenotypeCode objects.
GenotypeCodes may be retrieved from the Ensembl variation database by
several means using this module.

GenotypeCode objects are internal objects utilised by the CompressedGenotype
adaptor - they are not intended for external use.

=head1 METHODS

=cut

use strict;
use warnings;

package Bio::EnsEMBL::Variation::DBSQL::GenotypeCodeAdaptor;

use Bio::EnsEMBL::Variation::DBSQL::BaseAdaptor;

use Bio::EnsEMBL::Variation::GenotypeCode;

use DBI qw(:sql_types);

our @ISA = ('Bio::EnsEMBL::Variation::DBSQL::BaseAdaptor');


sub fetch_all_by_dbID_list {
  my ($self, $id_list_ref) = @_;

  if(!defined($id_list_ref) || ref($id_list_ref) ne 'ARRAY') {
    throw("id_list list reference argument is required");
  }

  return [] if(!@$id_list_ref);

  my @out;
  
  # mysql is faster and we ensure that we do not exceed the max query size by
  # splitting large queries into smaller queries of 200 ids
  my $max_size = 200;
  my @id_list = @$id_list_ref;

  while(@id_list) {
    my @ids;
    if(@id_list > $max_size) {
      @ids = splice(@id_list, 0, $max_size);
    } else {
      @ids = splice(@id_list, 0);
    }

    my $id_str;
    if(@ids > 1)  {
      $id_str = " IN (" . join(',', @ids). ")";
    } else {
      $id_str = " = ?";
      $self->bind_param_generic_fetch($ids[0],SQL_INTEGER);
    }

    my $constraint = "gc.genotype_code_id $id_str";

    push @out, @{$self->generic_fetch($constraint)};
  }

  return \@out;
}

# 
sub fetch_all_single_bp {
	my $self = shift;
	
	my $constraint = "length(ac.allele) = 1";
	
	return $self->generic_fetch($constraint);
}

sub _objs_from_sth {
  my $self = shift;
  my $sth = shift;
	
	my $ploidy = $self->ploidy;
	
  my ($gt_code_id, $haplotype_id, $allele, $phased);
  my (@result, %gts);
  
  $sth->bind_columns(\$gt_code_id, \$haplotype_id, \$allele, \$phased);
  
	$gts{defined($phased) ? $phased : 'NULL'}{$gt_code_id}{$haplotype_id} = $allele while $sth->fetch;
	
  foreach $phased(keys %gts) {
    foreach $gt_code_id(keys %{$gts{$phased}}) {
      my @gt = map {$gts{$phased}{$gt_code_id}{$_}} sort {$a <=> $b} keys %{$gts{$phased}{$gt_code_id}};
      
      # splice it down to ploidy size
      @gt = splice @gt, 0, $ploidy;
      
      push @result, Bio::EnsEMBL::Variation::GenotypeCode->new_fast({
        dbID     => $gt_code_id,
        genotype => \@gt,
        phased   => $phased eq 'NULL' ? undef : $phased,
      });
    }
  }
  
  return \@result;
}

# method used by superclass to construct SQL
sub _tables { 
    return (['genotype_code','gc'],['allele_code','ac']);
}

sub _columns {
  return qw( gc.genotype_code_id gc.haplotype_id ac.allele gc.phased );
}

sub _default_where_clause {
	return 'gc.allele_code_id = ac.allele_code_id';
}

1;
