<commit_before>=head1 LICENSE

  Copyright (c) 1999-2013 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <<EMAIL>>.

  Questions may also be sent to the Ensembl help desk at
  <<EMAIL>>.

=cut

=head1 NAME

Bio::EnsEMBL::DBSQL::MetaContainer - Encapsulates all access to core
database meta information

=head1 SYNOPSIS

  my $meta_container =
    $registry->get_adaptor( 'Human', 'Core', 'MetaContainer' );

  my @mapping_info =
    @{ $meta_container->list_value_by_key('assembly.mapping') };
  
  my $scientific_name = $meta_container->get_scientific_name();

=head1 DESCRIPTION

  An object that encapsulates specific access to core db meta data

=head1 METHODS

=cut

package Bio::EnsEMBL::DBSQL::MetaContainer;

use strict;
use warnings;

use Bio::EnsEMBL::Utils::Exception qw/deprecate/;
use Bio::Species;


use base qw/Bio::EnsEMBL::DBSQL::BaseMetaContainer/;

# add well known meta info get-functions below

=head2 get_production_name

  Args          : none
  Example       : $species = $meta_container->get_production_name();
  Description   : Obtains the name of the species in a form usable as, for
                  example, a table name, file name etc.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

=cut

sub get_production_name {
  my ($self) = @_;
  return $self->single_value_by_key('species.production_name');
}

=head2 get_short_name

  Args          : none
  Example       : $species = $meta_container->get_short_name();
  Description   : Obtains the name of the species in a form usable as, for
                  example, a short label in a GUI.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

=cut

sub get_short_name {
  my ($self) = @_;
  return $self->single_value_by_key('species.short_name');
}

=head2 get_common_name

  Args          : none
  Example       : $species = $meta_container->get_common_name();
  Description   : Obtains the common name of the species.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

=cut

sub get_common_name {
  my ($self) = @_;
  return $self->single_value_by_key('species.common_name');
}

=head2 get_scientific_name

  Args          : none
  Example       : $species = $meta_container->get_scientific_name();
  Description   : Obtains the full scientific name of the species.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

=cut<commit_msg>get_short_name is now deprecated, that meta_key does not exist in ensembl databases any more we now have a display_name meta_key, added method get_display_name<commit_after>=head1 LICENSE

  Copyright (c) 1999-2013 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <<EMAIL>>.

  Questions may also be sent to the Ensembl help desk at
  <<EMAIL>>.

=cut

=head1 NAME

Bio::EnsEMBL::DBSQL::MetaContainer - Encapsulates all access to core
database meta information

=head1 SYNOPSIS

  my $meta_container =
    $registry->get_adaptor( 'Human', 'Core', 'MetaContainer' );

  my @mapping_info =
    @{ $meta_container->list_value_by_key('assembly.mapping') };
  
  my $scientific_name = $meta_container->get_scientific_name();

=head1 DESCRIPTION

  An object that encapsulates specific access to core db meta data

=head1 METHODS

=cut

package Bio::EnsEMBL::DBSQL::MetaContainer;

use strict;
use warnings;

use Bio::EnsEMBL::Utils::Exception qw/deprecate/;
use Bio::Species;


use base qw/Bio::EnsEMBL::DBSQL::BaseMetaContainer/;

# add well known meta info get-functions below

=head2 get_production_name

  Args          : none
  Example       : $species = $meta_container->get_production_name();
  Description   : Obtains the name of the species in a form usable as, for
                  example, a table name, file name etc.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

=cut

sub get_production_name {
  my ($self) = @_;
  return $self->single_value_by_key('species.production_name');
}

=head2 get_short_name

  Args          : none
  Example       : $species = $meta_container->get_short_name();
  Description   : Obtains the name of the species in a form usable as, for
                  example, a short label in a GUI.
  Returntype    : string
  Exceptions    : none
  Status        : Deprecated in release 74

=cut

sub get_short_name {
  my ($self) = @_;
  deprecate('Call is deprecated. short_name is not in use any more, use get_common_name instead');
  return $self->single_value_by_key('species.short_name');
}


=head2 get_display_name

  Args          : none
  Example       : $species = $meta_container->get_display_name();
  Description   : Obtains the name of the species in a form usable as, for
                  example, a short label in a GUI.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

=cut

sub get_display_name {
  my ($self) = @_;
  return $self->single_value_by_key('species.display_name');
}

=head2 get_common_name

  Args          : none
  Example       : $species = $meta_container->get_common_name();
  Description   : Obtains the common name of the species.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

=cut

sub get_common_name {
  my ($self) = @_;
  return $self->single_value_by_key('species.common_name');
}

=head2 get_scientific_name

  Args          : none
  Example       : $species = $meta_container->get_scientific_name();
  Description   : Obtains the full scientific name of the species.
  Returntype    : string
  Exceptions    : none
  Status        : Stable

=cut
{'fraction_non_alphanumeric': 0.0854378484749098, 'fraction_numerical': 0.006395539521154477, 'mean_word_length': 3.2769985974754556, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 33, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, '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': '4030889', 'n_tokens_mistral': 2002, 'n_tokens_neox': 1863, 'n_words': 581}