Raw content of Bio::EnsEMBL::Compara::DBSQL::TaxonAdaptor # # 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;