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lib/FAST/Bio/DB/Taxonomy/entrez.pm  view on Meta::CPAN

 Args    : on set, new value (a scalar or undef, optional)

=cut

sub entrez_url{
    my $self = shift;

    return $self->{'_entrez_url'} = shift if @_;
    return $self->{'_entrez_url'};
}

=head2 entrez_params

 Title   : entrez_params
 Usage   : $obj->entrez_params($newval)
 Function: Get/set entrez params
 Returns : value of entrez_params (a hashref)
 Args    : on set, new value Hashref

=cut

sub entrez_params{
    my $self = shift;
    my $f;
    if( @_ ) {
	$f = $self->{'_entrez_params'} = shift;
    } else {
	$f = $self->{'_entrez_params'};
    }
    return %$f;
}

=head2 FAST::Bio::DB::WebBase methods

=cut

=head2 proxy_string

 Title   : proxy_string
 Usage   : my $proxy_string = $self->proxy_string($protocol)
 Function: Get the proxy string (plus user/pass )
 Returns : string
 Args    : protocol ('http' or 'ftp'), default 'http'

=head2 proxy

 Title   : proxy
 Usage   : $httpproxy = $db->proxy('http')  or
           $db->proxy(['http','ftp'], 'http://myproxy' )
 Function: Get/Set a proxy for use of proxy
 Returns : a string indicating the proxy
 Args    : $protocol : an array ref of the protocol(s) to set/get
           $proxyurl : url of the proxy to use for the specified protocol
           $username : username (if proxy requires authentication)
           $password : password (if proxy requires authentication)

=head2 authentication

 Title   : authentication
 Usage   : $db->authentication($user,$pass)
 Function: Get/Set authentication credentials
 Returns : Array of user/pass
 Args    : Array or user/pass

=cut

# make a Taxon object from data hash ref
sub _make_taxon {
    my ($self, $data) = @_;
    
    my $taxon = FAST::Bio::Taxon->new();
    
    my $taxid;
    while (my ($method, $value) = each %{$data}) {
        if ($method eq 'id') {
            $method = 'ncbi_taxid'; # since this is a real ncbi taxid, explicitly set it as one
            $taxid = $value;
        }
        $taxon->$method(ref($value) eq 'ARRAY' ? @{$value} : $value);
    }
    
    # we can't use -dbh or the db_handle() method ourselves or we'll go
    # infinite on the merge attempt
    $taxon->{'db_handle'} = $self;
    
    $self->_handle_internal_id($taxon);
    
    return $taxon;
}

1;