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Summary

TaxonAdaptor - DESCRIPTION of Object

Package variables

Included modules

Inherit

Bio::EnsEMBL::DBSQL::BaseAdaptor

Synopsis

Description

Methods

Methods description

 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

 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

 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

 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

Methods code

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;

}

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);

}

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;

}

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;

}

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