<commit_before>package Bio::EnsEMBL::Compara::DBSQL::SequenceAdaptor;

use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);

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

sub fetch_by_dbID {
  my ($self, $sequence_id) = @_;

  my $sql = "SELECT sequence.sequence FROM sequence WHERE sequence_id = ?";
  my $sth = $self->prepare($sql);
  $sth->execute($sequence_id);

  my ($sequence) = $sth->fetchrow_array();
  $sth->finish();
  return $sequence;
}

sub fetch_other_sequence_by_member_id_type {
  my ($self, $member_id, $type) = @_;

  my $sql = "SELECT sequence FROM other_member_sequence WHERE member_id = ? AND seq_type = ?";
  my $sth = $self->prepare($sql);
  $sth->execute($member_id, $type);

  my ($seq) = $sth->fetchrow_array();
  $sth->finish();
  return $seq;
}


sub fetch_sequence_exon_bounded_by_member_id {
  my ($self, $member_id) = @_;
  deprecate('fetch_sequence_exon_bounded_by_member_id() is deprecated and will be removed in e72. Use fetch_other_sequence_by_member_id_type($member_id, "exon_bounded") instead.');
  return $self->fetch_other_sequence_by_member_id_type($member_id, 'exon_bounded');
}

sub fetch_sequence_cds_by_member_id {
  my ($self, $member_id) = @_;

  deprecate('fetch_sequence_cds_by_member_id() is deprecated and will be removed in e72. Use fetch_other_sequence_by_member_id_type($member_id, "cds") instead.');
  return $self->fetch_other_sequence_by_member_id_type($member_id, 'cds');
}


#
# STORE METHODS
#
################

sub store {<commit_msg>Removed deprecated methods from SequenceAdaptor<commit_after>package Bio::EnsEMBL::Compara::DBSQL::SequenceAdaptor;

use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);

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

sub fetch_by_dbID {
  my ($self, $sequence_id) = @_;

  my $sql = "SELECT sequence.sequence FROM sequence WHERE sequence_id = ?";
  my $sth = $self->prepare($sql);
  $sth->execute($sequence_id);

  my ($sequence) = $sth->fetchrow_array();
  $sth->finish();
  return $sequence;
}

sub fetch_other_sequence_by_member_id_type {
  my ($self, $member_id, $type) = @_;

  my $sql = "SELECT sequence FROM other_member_sequence WHERE member_id = ? AND seq_type = ?";
  my $sth = $self->prepare($sql);
  $sth->execute($member_id, $type);

  my ($seq) = $sth->fetchrow_array();
  $sth->finish();
  return $seq;
}


#
# STORE METHODS
#
################

sub store {
{'fraction_non_alphanumeric': 0.16422513492675406, 'fraction_numerical': 0.0015420200462606013, 'mean_word_length': 6.109589041095891, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 21, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '8349', 'n_tokens_mistral': 1003, 'n_tokens_neox': 960, 'n_words': 188}