Raw content of Bio::EnsEMBL::Compara::DBSQL::TaxonAdaptor
<![CDATA[#
# BioPerl module for Bio::EnsEMBL::Compara::DBSQL::TaxonAdaptor
#
# Cared by Abel Ureta-Vidal <abel@ebi.ac.uk>
#
# Copyright EnsEMBL
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
TaxonAdaptor - DESCRIPTION of Object
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 CONTACT
=head1 APPENDIX
=cut
package Bio::EnsEMBL::Compara::DBSQL::TaxonAdaptor;
use vars qw(@ISA);
use strict;
use Bio::EnsEMBL::Compara::Taxon;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception;
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_by_dbID [deprecated]
Title : fetch_by_dbID
Usage : $taxonadaptor->fetch_by_dbID($id);
Function: fetches a taxon given its internal database identifier (taxon_id)
Example : $taxonadaptor->fetch_by_dbID(1)
Returns : a Bio::EnsEMBL::Compara::Taxon object if found, undef otherwise
Args : an integer
=cut
sub fetch_by_dbID {
my ($self,$taxon_id) = @_;
deprecate("calling Bio::EnsEMBL::Compara::NCBITaxonAdaptor::fetch_node_by_taxon_id method instead.");
my $ncbi_ta = $self->db->get_NCBITaxonAdaptor;
return $ncbi_ta->fetch_node_by_taxon_id($taxon_id);
}
=head2 fetch_by_taxon_id [deprecated]
Title : fetch_by_taxon_id
Usage : $taxonadaptor->fetch_by_taxon_id($id);
Function: fetches a taxon given its internal database identifier (taxon_id)
Example : $taxonadaptor->fetch_by_taxon_id(1)
Returns : a Bio::EnsEMBL::Compara::Taxon object if found, undef otherwise
Args : an integer
=cut
sub fetch_by_taxon_id {
my ($self,$taxon_id) = @_;
deprecate("calling Bio::EnsEMBL::Compara::NCBITaxonAdaptor::fetch_node_by_taxon_id method instead.");
my $ncbi_ta = $self->db->get_NCBITaxonAdaptor;
return $ncbi_ta->fetch_node_by_taxon_id($taxon_id);
}
=head2 fetch_by_Family_Member_source [deprecated]
Title : fetch_by_Family_Member_source
Args[0] : Bio::EnsEMBL::Compara::Family object
Args[1] : string (member\'s source name)
Usage : @taxonArray = @$taxonAdaptor->fetch_by_Family_Member_source($family, 'ENSEMBLGENE');
Function: fetches all the taxon in a family of specified member source
Returns : reference to array of Bio::EnsEMBL::Compara::Taxon objects
=cut
sub fetch_by_Family_Member_source {
my ($self, $family, $source_name) = @_;
deprecate("calling Bio::EnsEMBL::Compara::Family::get_all_taxa_by_member_source_name method instead.");
return $family->get_all_taxa_by_member_source_name($source_name);
}
=head2 store [deprecated]
Title : store
Usage : $memberadaptor->store($member)
Function: Stores a taxon object only if it does not exists in the database
Example : $memberadaptor->store($member)
Returns : $member->dbID
Args : An Bio::EnsEMBL::Compara::Taxon object
=cut
sub store {
my ($self,$taxon) = @_;
deprecate("Bio::EnsEMBL::Compara::NCBITaxonAdaptor is now the new adaptor.
It does not have store method subroutine. The taxonomy data is imported from NCBI Taxonomy database.
Please read ensembl-compara/scripts/taxonomy/README-taxonomy for more information.");
return undef;
}
=head2 store_if_needed [deprecated]
Title : store_if_needed_if_needed
Usage : $memberadaptor->store($taxon)
Function: Stores a taxon object only if it does not exists in the database
Example : $memberadaptor->store($member)
Returns : $member->dbID
Args : An Bio::EnsEMBL::Compara::Taxon object
=cut
sub store_if_needed {
my ($self,$taxon) = @_;
deprecate("calling store method instead.");
return $self->store($taxon);
}
1;
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