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Bio/DB/EntrezGene.pm  view on Meta::CPAN

# the new way to make modules a little more lightweight
sub new {
  my($class, @args) = @_;
  my $self = $class->SUPER::new(@args);
  # Seems that Bio::SeqIO::entrezgene requires this:
  $self->{_retrieval_type} = "tempfile"; 
  $self->request_format($self->default_format);
  return $self;
}

=head2 get_params

 Title   : get_params
 Usage   : my %params = $self->get_params($mode)
 Function: Returns key,value pairs to be passed to NCBI database
           for either 'batch' or 'single' sequence retrieval method
 Returns : A key,value pair hash
 Args    : 'single' or 'batch' mode for retrieval

=cut

sub get_params {
    my ($self, $mode) = @_;
    return defined $PARAMSTRING{$mode} ? %{$PARAMSTRING{$mode}} : 
		%{$PARAMSTRING{$DEFAULTMODE}};
}

=head2 default_format

 Title   : default_format
 Usage   : my $format = $self->default_format
 Function: Returns default sequence format for this module
 Returns : string
 Args    : none

=cut

sub default_format {
	return $DEFAULTFORMAT;
}

# from Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI

=head1 Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI

=head2 get_Seq_by_id

 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id(2)
 Function: Gets a Bio::Seq object by its name
 Returns : A Bio::Seq object
 Args    : Gene id
 Throws  : "id does not exist" exception

=head1 Routines implemented by Bio::DB::NCBIHelper

=head2 get_request

 Title   : get_request
 Usage   : my $url = $self->get_request
 Function: HTTP::Request
 Returns : 
 Args    : %qualifiers = a hash of qualifiers (ids, format, etc)

=head2 get_Stream_by_id

  Title   : get_Stream_by_id
  Usage   : $stream = $db->get_Stream_by_id( [$gid1, $gid2] );
  Function: Gets a series of Seq objects using Gene ids
  Returns : A Bio::SeqIO stream object
  Args    : A reference to an array of Gene ids

=head2 request_format

 Title   : request_format
 Usage   : my $format = $self->request_format;
           $self->request_format($format);
 Function: Get or set sequence format retrieval
 Returns : String representing format
 Args    : $format = sequence format

=cut

# override to force format
sub request_format {
    my ($self) = @_;
    return $self->SUPER::request_format($self->default_format());
}

1;

__END__