Raw content of Bio::EnsEMBL::Compara::Taxon
<![CDATA[# $Id: Taxon.pm,v 1.4 2005/12/13 16:47:20 jh7 Exp $
#
# Module to handle family members
#
# Cared for by Abel Ureta-Vidal <abel@ebi.ac.uk>
#
# Copyright Abel Ureta-Vidal
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Taxon - DESCRIPTION of Object
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 CONTACT
Abel Ureta-Vidal <abel@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::Taxon;
use strict;
use Bio::Species;
our @ISA = qw(Bio::Species);
# new() is inherited from Bio::Species
=head2 adaptor
Title : adaptor
Usage :
Function: give the adaptor if known
Example :
Returns :
Args :
=cut
sub adaptor {
my ($self, $value) = @_;
if (defined $value) {
$self->{'_adaptor'} = $value;
}
return $self->{'_adaptor'};
}
=head2 dbID
Title : dbID
Usage :
Function: get/set the dbID (taxon_id) of the taxon
Example :
Returns :
Args :
=cut
sub dbID {
my ($self,$value) = @_;
return $self->ncbi_taxid($value);
}
=head2 taxon_id
Title : taxon_id
Usage :
Function: get/set the taxon_id of the taxon
Example :
Returns : An integer
Args :
=cut
sub taxon_id {
my ($self,$value) = @_;
$self->warn("Taxon->taxon_id is a deprecated method!
Calling Taxon->ncbi_taxid instead!");
if (defined $value) {
return $self->ncbi_taxid($value);
}
return $self->ncbi_taxid;
}
=head2 ncbi_taxid
Title : ncbi_taxid
Usage :
Function: get/set the ncbi_taxid of the taxon
Example :
Returns : An integer
Args :
=cut
sub ncbi_taxid {
my ($self,$value) = @_;
# tricks for bioperl-07/bioperl-1-0-0 compliancy
bless $self, "Bio::Species";
if ($self->can("ncbi_taxid")) { # when using bioperl-1-0-0 and later
if (defined $value) {
$self->ncbi_taxid($value);
$self->{'_ncbi_taxid'} = $self->ncbi_taxid;
}
} else { # when using bioperl-07
if (defined $value) {
$self->{'_ncbi_taxid'} = $value;
}
}
bless $self, "Bio::EnsEMBL::Compara::Taxon";
return $self->{'_ncbi_taxid'};
}
=head2 validate_species_name
Title : validate_species_name
Usage :
Function: override the inherited method to disable all
species name checking since some swissprot species
are not valid by the Bioperl definition
e.g. SWISSPROT:APV1_DRONO has species novae-hollandiae
and the - causes this function to throw an exception
Example :
Returns : 1
Args :
=cut
sub validate_species_name{
my( $self, $string ) = @_;
return 1;
}
1;
]]>