MetaContainer.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
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
 
=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::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_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
sub get_scientific_name {
  my ($self) = @_;
  return $self->single_value_by_key('species.scientific_name');
}
 
=head2 get_division
 
  Args          : none
  Example       : $div = $meta_container->get_division();
  Description   : Obtains the Ensembl Genomes division to which the species belongs.
  Returntype    : string
  Exceptions    : none
  Status        : Stable
 
=cut
sub get_division {
  my ($self) = @_;
  return $self->single_value_by_key('species.division');
}
 
=head2 get_taxonomy_id
 
  Arg [1]    : none
  Example    : $tax_id = $meta_container->get_taxonomy_id();
  Description: Retrieves the taxonomy id from the database meta table
  Returntype : string
  Exceptions : none
  Caller     : ?
  Status     : Stable
 
=cut
 
sub get_taxonomy_id {
  my ($self) = @_;
  return $self->single_value_by_key('species.taxonomy_id', 1);
}
 
=head2 get_genebuild
 
  Arg [1]    : none
  Example    : $tax_id = $meta_container->get_genebuild();
  Description: Retrieves the genebuild from the database meta table
  Returntype : string
  Exceptions : none
  Caller     : ?
  Status     : Stable
 
=cut
 
sub get_genebuild {
  my ($self) = @_;
  return $self->single_value_by_key('genebuild.start_date', 1);
}
 
=head2 get_genebuild
 
  Example    : $classification = $meta_container->get_classification();
  Description: Retrieves the classification held in the backing database minus
               any species specific levels. This means that the first element
               in the array will be subfamily/family level ascending to
               superkingdom
  Returntype : ArrayRef[String]
  Exceptions : none
  Caller     : ?
  Status     : Stable
 
=cut
 
sub get_classification {
  my ($self) = @_;
  my $classification = $self->list_value_by_key('species.classification');
  my $copy = [@{$classification}];
  splice(@{$copy}, 0, 1); # remove the Homo sapiens
  return $copy;
}
 
 
1;