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Bio/Taxon.pm  view on Meta::CPAN

 Title   : genetic_code
 Usage   : $taxon->genetic_code($newval)
 Function: Get/set genetic code table
 Returns : value of genetic_code (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

=cut

sub genetic_code {
    my $self = shift;
    return $self->{'genetic_code'} = shift if @_;
    return $self->{'genetic_code'};
}


=head2 mitochondrial_genetic_code

 Title   : mitochondrial_genetic_code
 Usage   : $taxon->mitochondrial_genetic_code($newval)
 Function: Get/set mitochondrial genetic code table
 Returns : value of mitochondrial_genetic_code (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

=cut

sub mitochondrial_genetic_code {
    my $self = shift;
    return $self->{'mitochondrial_genetic_code'} = shift if @_;
    return $self->{'mitochondrial_genetic_code'};
}


=head2 create_date

 Title   : create_date
 Usage   : $taxon->create_date($newval)
 Function: Get/Set Date this node was created (in the database)
 Returns : value of create_date (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

=cut

sub create_date {
    my $self = shift;
    return $self->{'create_date'} = shift if @_;
    return $self->{'create_date'};
}


=head2 update_date

 Title   : update_date
 Usage   : $taxon->update_date($newval)
 Function: Get/Set Date this node was updated (in the database)
 Returns : value of update_date (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

=cut

sub update_date {
    my $self = shift;
    return $self->{'update_date'} = shift if @_;
    return $self->{'update_date'};
}


=head2 pub_date

 Title   : pub_date
 Usage   : $taxon->pub_date($newval)
 Function: Get/Set Date this node was published (in the database)
 Returns : value of pub_date (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

=cut

sub pub_date {
    my $self = shift;
    return $self->{'pub_date'} = shift if @_;
    return $self->{'pub_date'};
}


=head2 ancestor

 Title   : ancestor
 Usage   : my $ancestor_taxon = $taxon->ancestor()
 Function: Retrieve the ancestor taxon. Normally the database is asked what the
           ancestor is.

           If you manually set the ancestor (or you make a Bio::Tree::Tree with
           this object as an argument to new()), the database (if any) will not
           be used for the purposes of this method.

           To restore normal database behaviour, call ancestor(undef) (which
           would remove this object from the tree), or request this taxon again
           as a new Taxon object from the database.

 Returns : Bio::Taxon
 Args    : none

=cut

sub ancestor {
    my $self = shift;
    my $ancestor = $self->SUPER::ancestor(@_);
    if ($ancestor) {
        return $ancestor;
    }
    my $dbh = $self->db_handle;
    #*** could avoid the db lookup if we knew our current id was definitely
    #    information from the db...

    my $definitely_from_dbh = $self->_get_similar_taxon_from_db($self);
    return $dbh->ancestor($definitely_from_dbh);
}


=head2 get_Parent_Node