=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.

=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>.


=head1 NAME

=head1 SYNOPSIS

=head1 DESCRIPTION

=cut

package Bio::EnsEMBL::Funcgen::DBSQL::PeakAdaptor;

use strict;
use base 'Bio::EnsEMBL::Funcgen::DBSQL::GenericFeatureAdaptor';
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );
use Bio::EnsEMBL::Utils::Exception qw( deprecate );

sub object_class {

    my $deprecation_message = 'Bio::EnsEMBL::Funcgen::DBSQL::'
      . 'PeakAdaptor::object_class has '
      . 'been deprecated along with the ' 
      . 'Bio::EnsEMBL::Funcgen::DBSQL::PeakAdaptor module. ' 
      . 'They will be removed in release 109.';
    deprecate($deprecation_message);

    return 'Bio::EnsEMBL::Funcgen::Peak';
}

sub _tables {

    my $deprecation_message = 'Bio::EnsEMBL::Funcgen::DBSQL::'
      . 'PeakAdaptor::_tables has '
      . 'been deprecated along with the ' 
      . 'Bio::EnsEMBL::Funcgen::DBSQL::PeakAdaptor module. ' 
      . 'They will be removed in release 109.';
    deprecate($deprecation_message);

  return ['peak', 'p']
}

sub insertion_method {

    my $deprecation_message = 'Bio::EnsEMBL::Funcgen::DBSQL::'
      . 'PeakAdaptor::insertion_method has '
      . 'been deprecated along with the ' 
      . 'Bio::EnsEMBL::Funcgen::DBSQL::PeakAdaptor module. ' 
      . 'They will be removed in release 109.';
    deprecate($deprecation_message);

    return 'insert ignore'
}

sub _columns {

    my $deprecation_message = 'Bio::EnsEMBL::Funcgen::DBSQL::'
      . 'PeakAdaptor::_columns has '
      . 'been deprecated along with the ' 
      . 'Bio::EnsEMBL::Funcgen::DBSQL::PeakAdaptor module. ' 
      . 'They will be removed in release 109.';
    deprecate($deprecation_message);

  return qw(
    p.peak_id               p.seq_region_id
    p.seq_region_start      p.seq_region_end
    p.seq_region_strand     p.peak_calling_id
    p.score                 p.summit
  );
}

=head2 fetch_all_by_PeakCalling

  Arg [1]    : Bio::EnsEMBL::Funcgen::PeakCalling
  Example    : None
  Description: Fetches a list of Peak objects by PeakCalling
  Returntype : Arrayref of Bio::EnsEMBL::Funcgen::Peak objects
  Exceptions : Throws if PeakCalling parameter is not specified
  Caller     : Internal
  Status     : At Risk

=cut

sub fetch_all_by_PeakCalling {

    my $deprecation_message = 'Bio::EnsEMBL::Funcgen::DBSQL::'
      . 'PeakAdaptor::fetch_all_by_PeakCalling has '
      . 'been deprecated along with the ' 
      . 'Bio::EnsEMBL::Funcgen::DBSQL::PeakAdaptor module. ' 
      . 'They will be removed in release 109.';
    deprecate($deprecation_message);

    my $self         = shift;
    my $peak_calling = shift;

    assert_ref($peak_calling, 'Bio::EnsEMBL::Funcgen::PeakCalling');

    my $constraint = 'peak_calling_id = ' . $peak_calling->dbID;

    return $self->fetch_all($constraint);
}

=head2 fetch_all_by_Slice_PeakCalling

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : Bio::EnsEMBL::Funcgen::PeakCalling
  Example    : None
  Description: Fetches a list of Peak objects by PeakCalling on a given Slice
  Returntype : Arrayref of Bio::EnsEMBL::Funcgen::Peak objects
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

=cut

sub fetch_all_by_Slice_PeakCalling {

  my $deprecation_message = 'Bio::EnsEMBL::Funcgen::DBSQL::'
    . 'PeakAdaptor::fetch_all_by_Slice_PeakCalling has '
    . 'been deprecated along with the ' 
    . 'Bio::EnsEMBL::Funcgen::DBSQL::PeakAdaptor module. ' 
    . 'They will be removed in release 109.';
  deprecate($deprecation_message);

  my $self         = shift;
  my $slice        = shift;
  my $peak_calling = shift;
  
  my $peak_calling_id = $peak_calling->dbID;
  my $features = $self->fetch_all_by_Slice_constraint(
    $slice, 
    "peak_calling_id = " . $peak_calling_id
  );
  return $features;
}

=head2 _fetch_overlapping_MotifFeatures

  Arg [1]    : Bio::EnsEMBL::Funcgen::Peak
  Example    : None
  Description: Fetches a list of MotifFeature objects that overlap
               with the Peak object
  Returntype : Arrayref of Bio::EnsEMBL::Funcgen::MotifFeature objects
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

=cut

sub _fetch_overlapping_MotifFeatures {
    my $deprecation_message = 'Bio::EnsEMBL::Funcgen::DBSQL::'
      . 'PeakAdaptor::_fetch_overlapping_MotifFeatures has '
      . 'been deprecated along with the ' 
      . 'Bio::EnsEMBL::Funcgen::DBSQL::PeakAdaptor module. ' 
      . 'They will be removed in release 109.';
    deprecate($deprecation_message);
    return;
}

sub _parse_bed_line {

  my $deprecation_message = 'Bio::EnsEMBL::Funcgen::DBSQL::'
    . 'PeakAdaptor::_parse_bed_line has '
    . 'been deprecated along with the ' 
    . 'Bio::EnsEMBL::Funcgen::DBSQL::PeakAdaptor module. ' 
    . 'They will be removed in release 109.';
  deprecate($deprecation_message);

  my $self     = shift;
  my $bed_line = shift;
  
  (
    my $seq_region_id,
    my $seq_region_start,
    my $seq_region_end,
    my $peak_id,
    my $score,
    my $strand,
  ) = split "\t", $bed_line;

  my $hash = {
    seq_region_name  => $seq_region_id,
    seq_region_start => $seq_region_start,
    seq_region_end   => $seq_region_end,
    peak_id          => $peak_id,
    score            => $score,
    strand           => $strand,
  };
  return $hash;
}

sub _bulk_export_to_bed_by_PeakCalling {

  my $deprecation_message = 'Bio::EnsEMBL::Funcgen::DBSQL::'
    . 'PeakAdaptor::_bulk_export_to_bed_by_PeakCalling has '
    . 'been deprecated along with the ' 
    . 'Bio::EnsEMBL::Funcgen::DBSQL::PeakAdaptor module. ' 
    . 'They will be removed in release 109.';
  deprecate($deprecation_message);

  my $self = shift;
  my $peak_calling = shift;
  #my $bed_fh       = shift;
  my @bed_fh       = @_;
  
  if (! defined $peak_calling) {
    throw("Peak calling parameter was undefined!");
  }
  
  my $species = $self->db->species;
  
  if ($species eq 'DEFAULT') {
    die;
  }
  
  my $slice_adaptor = Bio::EnsEMBL::Registry
    ->get_adaptor(
        $species, 
        'core', 
        'Slice'
    );

  my %seq_region_id_to_name_cache;

  $self->sql_helper->execute_no_return(
    -SQL          => 'select seq_region_id, seq_region_start, seq_region_end, peak_id, score, 0 from peak where peak_calling_id = ?',
    -PARAMS       => [ $peak_calling->dbID ],
    -USE_HASHREFS => 0,
    -CALLBACK     => sub {
        my $row = shift;
        
        my $seq_region_id = $row->[0];
        
        my $seq_region_name;
        if (exists $seq_region_id_to_name_cache{$seq_region_id}) {
          $seq_region_name = $seq_region_id_to_name_cache{$seq_region_id};
        } else {
          my $current_slice = $slice_adaptor->fetch_by_seq_region_id($seq_region_id);
          $seq_region_name = $current_slice->seq_region_name;
          $seq_region_id_to_name_cache{$seq_region_id} = $seq_region_name;
        }
        
        my $bed_line = join "\t", (
          $seq_region_name,
          $row->[1],
          $row->[2],
          $row->[3],
          $row->[4],
          $row->[5],
        );
        
        map { $_->print($bed_line . "\n"); } @bed_fh;
        return;
      },
  );
}

1;
