Bio::EnsEMBL::Compara::DBSQL TaxonAdaptor
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Summary
TaxonAdaptor - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::Compara::Taxon
Bio::EnsEMBL::DBSQL::BaseAdaptor
Bio::EnsEMBL::Utils::Exception
Inherit
Bio::EnsEMBL::DBSQL::BaseAdaptor
Synopsis
Description
Methods
fetch_by_Family_Member_sourceDescriptionCode
fetch_by_dbIDDescriptionCode
fetch_by_taxon_idDescriptionCode
storeDescriptionCode
store_if_neededDescriptionCode
Methods description
fetch_by_Family_Member_source [deprecated]code    nextTop
 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
fetch_by_dbID [deprecated]codeprevnextTop
 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
fetch_by_taxon_id [deprecated]codeprevnextTop
 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
store [deprecated]codeprevnextTop
 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
store_if_needed [deprecated]codeprevnextTop
 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 : $member->dbID
 Args    : An Bio::EnsEMBL::Compara::Taxon object
Methods code
fetch_by_Family_Member_sourcedescriptionprevnextTop
sub fetch_by_Family_Member_source {
  my ($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);
}
fetch_by_dbIDdescriptionprevnextTop
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);
}
fetch_by_taxon_iddescriptionprevnextTop
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);
}
storedescriptionprevnextTop
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;
}
store_if_neededdescriptionprevnextTop
sub store_if_needed {
  my ($self,$taxon) = @_;

  deprecate("calling store method instead.");
  return $self->store($taxon);
}

1;
}
General documentation
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