Raw content of Bio::EnsEMBL::ExternalData::Family::GenomeDB
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#
# Ensembl module for Bio::EnsEMBL::ExternalData::GenomeDB
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::ExternalData::Family::GenomeDB
=head1 SYNOPSIS
=head1 DESCRIPTION
=cut
package Bio::EnsEMBL::ExternalData::Family::GenomeDB;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Root;
@ISA = qw(Bio::EnsEMBL::Root);
sub new {
my($caller, $dba, $name, $assembly, $taxon_id, $dbID) = @_;
my $class = ref($caller) || $caller;
my $self = bless({}, $class);
$dba && $self->db_adaptor($dba);
$name && $self->name($name);
$assembly && $self->assembly($assembly);
$taxon_id && $self->taxon_id($taxon_id);
$dbID && $self->dbID($dbID);
return $self;
}
=head2 db_adaptor
Arg [1] : (optional) Bio::EnsEMBL::DBSQL::DBConnection $dba
The DBAdaptor containing sequence information for the genome
represented by this object.
Example : $gdb->db_adaptor($dba);
Description: Getter/Setter for the DBAdaptor containing sequence
information for the genome represented by this object.
Returntype : Bio::EnsEMBL::DBSQL::DBConnection
Exceptions : thrown if the argument is not a
Bio::EnsEMBL::DBSQL::DBConnection
Caller : general
=cut
sub db_adaptor{
my ( $self, $dba ) = @_;
if( $dba ) {
unless(ref $dba && $dba->isa('Bio::EnsEMBL::DBSQL::DBConnection')) {
$self->throw("dba arg must be a Bio::EnsEMBL::DBSQL::DBConnection" .
" not a [$dba]\n");
}
$self->{'_db_adaptor'} = $dba;
}
return $self->{'_db_adaptor'};
}
=head2 name
Arg [1] : (optional) string $value
Example : $gdb->name('Homo sapiens');
Description: Getter setter for the name of this genome database, usually
just the species name.
Returntype : string
Exceptions : none
Caller : general
=cut
sub name{
my ($self,$value) = @_;
if( defined $value) {
$self->{'name'} = $value;
}
return $self->{'name'};
}
=head2 dbID
Arg [1] : (optional) int $value the new value of this objects database
identifier
Example : $dbID = $genome_db->dbID;
Description: Getter/Setter for the internal identifier of this GenomeDB
Returntype : int
Exceptions : none
Caller : general
=cut
sub dbID{
my ($self,$value) = @_;
if( defined $value) {
$self->{'dbID'} = $value;
}
return $self->{'dbID'};
}
=head2 adaptor
Arg [1] : (optional) Bio::EnsEMBL::Compara::GenomeDBAdaptor $adaptor
Example : $adaptor = $GenomeDB->adaptor();
Description: Getter/Setter for the GenomeDB object adaptor used
by this GenomeDB for database interaction.
Returntype : Bio::EnsEMBL::Compara::GenomeDBAdaptor
Exceptions : none
Caller : general
=cut
sub adaptor{
my ($self,$value) = @_;
if( defined $value) {
$self->{'adaptor'} = $value;
}
return $self->{'adaptor'};
}
=head2 assembly
Arg [1] : (optional) string
Example : $gdb->assembly('NCBI_31');
Description: Getter/Setter for the assembly type of this genome db.
Returntype : string
Exceptions : none
Caller : general
=cut
sub assembly {
my $self = shift;
my $assembly = shift;
if($assembly) {
$self->{'assembly'} = $assembly;
}
return $self->{'assembly'};
}
=head2 taxon_id
Arg [1] : (optional) int
Example : $gdb->taxon_id('9606');
Description: Getter/Setter for the taxon id of the contained genome db
Returntype : int
Exceptions : none
Caller : general
=cut
sub taxon_id {
my $self = shift;
my $taxon_id = shift;
if($taxon_id) {
$self->{'taxon_id'} = $taxon_id;
}
return $self->{'taxon_id'};
}
=head2 has_consensus
Arg [1] : Bio::EnsEMBL::Compara::GenomeDB $genomedb
Example : none
Description: none
Returntype : int
Exceptions : none
Caller : general
=cut
sub has_consensus {
my ($self,$con_gdb) = @_;
# sanity check on the GenomeDB passed in
if( !defined $con_gdb || !$con_gdb->isa("Bio::EnsEMBL::Compara::GenomeDB")) {
$self->throw("No query genome specified or query is not a GenomeDB obj");
}
# and check that you are not trying to compare the same GenomeDB
if ( $con_gdb eq $self ) {
$self->throw("Trying to return consensus / " .
"query information from the same db");
}
my $consensus = $self->adaptor->check_for_consensus_db( $self, $con_gdb);
return $consensus;
}
=head2 has_query
Arg [1] : Bio::EnsEMBL::Compara::GenomeDB $genomedb
Example : none
Description: none
Returntype : int
Exceptions : none
Caller : general
=cut
sub has_query {
my ($self,$query_gdb) = @_;
# sanity check on the GenomeDB passed in
if( !defined $query_gdb ||
!$query_gdb->isa("Bio::EnsEMBL::Compara::GenomeDB")) {
$self->throw("No consensus genome specified or query is not a " .
"GenomeDB object");
}
# and check that you are not trying to compare the same GenomeDB
if ( $query_gdb eq $self ) {
$self->throw("Trying to return consensus / query information " .
"from the same db");
}
my $query = $self->adaptor->check_for_query_db( $self, $query_gdb );
return $query;
}
=head2 linked
Arg [1] : Bio::EnsEMBL::Compara::GenomeDB $genomedb
Example : none
Description: none
Returntype : int
Exceptions : none
Caller : general
=cut
sub linked_genomes {
my ( $self ) = @_;
my $links = $self->adaptor->get_all_db_links( $self );
return $links;
}
1;
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