Raw content of Bio::EnsEMBL::ExternalData::Family::DBSQL::TaxonAdaptor
<![CDATA[# $Id: TaxonAdaptor.pm,v 1.7 2003/04/07 13:30:35 abel Exp $
#
# BioPerl module for Bio::EnsEMBL::ExternalData::Family::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::ExternalData::Family::DBSQL::TaxonAdaptor;
use vars qw(@ISA);
use strict;
#use Bio::Species;
use Bio::EnsEMBL::ExternalData::Family::Taxon;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_by_dbID
Title : fetch_by_dbID
Usage : $taxonadaptor->fetch_by_dbID($id);
Function: fetches a taxon given its internal database identifier (taxon_id)
Example : $taxonadaptor->fetch_by_dbID(1)
Returns : a Bio::EnsEMBL::ExternalData::Family::Taxon object if found, undef otherwise
Args : an integer
=cut
sub fetch_by_dbID {
my ($self,$taxon_id) = @_;
$self->throw("Should give a defined taxon_id as argument\n") unless (defined $taxon_id);
my $q = "SELECT taxon_id,genus,species,sub_species,common_name,classification
FROM taxon
WHERE taxon_id= ?";
$q = $self->prepare($q);
$q->execute($taxon_id);
if (defined (my $rowhash = $q->fetchrow_hashref)) {
my $taxon = new Bio::EnsEMBL::ExternalData::Family::Taxon;
$taxon->ncbi_taxid($taxon_id); #for bioperl-1-0-0 on
$taxon->sub_species($rowhash->{sub_species});
my @classification = split /\s+/,$rowhash->{classification};
$taxon->classification(@classification);
$taxon->common_name($rowhash->{common_name});
return $taxon;
}
return undef;
}
=head2 fetch_by_taxon_id
Title : fetch_by_taxon_id
Usage : $taxonadaptor->fetch_by_taxon_id($id);
Function: fetches a taxon given its internal database identifier (taxon_id)
Example : $taxonadaptor->fetch_by_taxon_id(1)
Returns : a Bio::EnsEMBL::ExternalData::Family::Taxon object if found, undef otherwise
Args : an integer
=cut
sub fetch_by_taxon_id {
my ($self,$taxon_id) = @_;
$self->throw("Should give a defined taxon_id as argument\n") unless (defined $taxon_id);
return $self->fetch_by_dbID($taxon_id);
}
=head2 store
Title : store
Usage : $memberadaptor->store($member)
Function: Stores a taxon object into the database
Example : $memberadaptor->store($member)
Returns : $member->dbID
Args : An Bio::EnsEMBL::ExternalData::Taxon object
=cut
sub store {
my ($self,$taxon) = @_;
$taxon->isa('Bio::EnsEMBL::ExternalData::Family::Taxon') ||
$self->throw("You have to store a Bio::EnsEMBL::ExternalData::Family::Taxon object, not a $taxon");
my $q = "INSERT INTO taxon (taxon_id,genus,species,sub_species,common_name,classification)
VALUES (?,?,?,?,?,?)";
my $sth = $self->prepare($q);
$sth->execute($taxon->ncbi_taxid,$taxon->genus,$taxon->species,$taxon->sub_species,$taxon->common_name,join " ",$taxon->classification);
$taxon->adaptor($self);
return $taxon->dbID;
}
=head2 store_if_needed
Title : store_if_needed_if_needed
Usage : $memberadaptor->store($taxon)
Function: Stores a taxon object only if it doesn't exists in the database
Example : $memberadaptor->store($member)
Returns : $member->dbID
Args : An Bio::EnsEMBL::ExternalData::Taxon object
=cut
sub store_if_needed {
my ($self,$taxon) = @_;
my $q = "select taxon_id from taxon where taxon_id=?";
$q = $self->prepare($q);
$q->execute($taxon->ncbi_taxid);
my $rowhash = $q->fetchrow_hashref;
if ($rowhash->{taxon_id}) {
return $rowhash->{external_db_id};
} else {
return $self->store($taxon);
}
}
1;
]]>