Raw content of Bio::EnsEMBL::DBSQL::MetaContainer
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 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
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=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 $species = $meta_container->get_Species();
my @mapping_info =
@{ $meta_container->list_value_by_key('assembly.mapping') };
=head1 DESCRIPTION
An object that encapsulates specific access to core db meta data
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::MetaContainer;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::DBSQL::BaseMetaContainer;
use Bio::EnsEMBL::Utils::Exception;
use Bio::Species;
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseMetaContainer);
# add well known meta info get-functions below
=head2 get_Species
Arg [1] : none
Example : $species = $meta_container->get_Species();
Description: Obtains the species from this databases meta table
Returntype : Bio::Species
Exceptions : none
Caller : ?
Status : Stable
=cut
sub get_Species {
my $self = shift;
my $arrRef = $self->list_value_by_key( 'species.common_name' );
my $common_name;
if( @$arrRef ) {
$common_name = $arrRef->[0];
}
my $classification = $self->list_value_by_key( 'species.classification' );
if( ! @$classification ) {
return undef;
}
my $species = new Bio::Species;
$species->common_name( $common_name );
$species->classification( @$classification );
return $species;
}
=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 = shift;
my $arrRef = $self->list_value_by_key( 'species.taxonomy_id' );
if( @$arrRef ) {
return $arrRef->[0];
} else {
warning("Please insert meta_key 'species.taxonomy_id' " .
"in meta table at core db.\n");
}
}
=head2 get_default_assembly
Description: DEPRECATED. Use the version of the coordinate system you are
interested in instead.
Example: #use this instead
my ($highest_cs) = @{$db->get_CoordSystemAdaptor->fetch_all()};
my $assembly = $highest_cs->version();
=cut
sub get_default_assembly {
my $self = shift;
deprecate("Use version of coordinate system you are interested in instead.\n".
"Example:\n".
' ($cs) = @{$coord_system_adaptor->fetch_all()};'."\n" .
' $assembly = $cs->version();');
my ($cs) = @{$self->db->get_CoordSystemAdaptor->fetch_all()};
return $cs->version();
}
#
# TBD This method should be removed/deprecated
#
sub get_max_assembly_contig {
my $self = shift;
deprecate('This method should either be fixed or removed');
my $value_list = $self->list_value_by_key( "assembly.maxcontig" );
if( @$value_list ) {
return $value_list->[0];
} else {
return undef;
}
}
=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 = shift;
my $arrRef = $self->list_value_by_key( 'genebuild.start_date' );
if( @$arrRef ) {
return $arrRef->[0];
} else {
warning("Please insert meta_key 'genebuild.start_date' " .
"in meta table at core db.\n");
}
}
1;
]]>