Bio-Biblio

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lib/Bio/DB/Biblio/eutils.pm  view on Meta::CPAN

    my $self = shift;

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


sub query_key {
    my $self = shift;

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

1;

__END__
=pod

=encoding utf-8

=head1 NAME

Bio::DB::Biblio::eutils - access to PubMed's bibliographic query service

=head1 VERSION

version 1.70

=head1 SYNOPSIS

Do not use this object directly, it is recommended to access it and use
it through the I<Bio::Biblio> module:

  use Bio::Biblio;
  use Bio::Biblio::IO;

  my $biblio = Bio::Biblio->new( -access => 'eutils' );
  $biblio->find("10336996");
  my $xml = $biblio->get_next;
  my $io = Bio::Biblio::IO->new( -data => $xml,
                                 -format => 'medlinexml' );
  my $article = $io->next_bibref();

The main documentation details are to be found in
L<Bio::DB::BiblioI>.

=head1 ATTRIBUTES

=head2 db

 Title   : db
 Usage   : $obj->db($newval)
 Function: specifies the database to search.  valid values are:

           pubmed, pmc, journals

           it is also possible to add the following, and i will do
           so on request:

           genome, nucleotide, protein, popset, snp, sequence, taxonomy

           pubmed is default.

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

=head2 has_next

  Title   : has_next
  Usage   : $has_next = $biblio->has_next();
  Function: check to see if there are more items to be retrieved
  Returns : 1 on true, undef on false
  Args    : none

=head1 METHODS

=head2 get_collection_id

  Title   : get_collection_id
  Usage   : $id = $biblio->get_collection_id();
  Function: returns WebEnv value from ESearch
  Returns : ESearch WebEnv value as a string
  Args    : none

=head2 reset_retrieval

  Title   : reset_retrieval
  Usage   : $biblio->reset_retrieval();
  Function: reset cursor in id list, see cursor()
  Returns : 1
  Args    : none

=head2 get_next

  Title   : get_next
  Usage   : $xml = $biblio->get_next();
  Function: return next record as xml
  Returns : an xml string
  Args    : none

=head2 get_more

  Title   : get_more
  Usage   : $xml = $biblio->get_more($more);
  Function: returns next $more records concatenated
  Returns : a string containing multiple xml documents
  Args    : an integer representing how many records to retrieve

=head2 find

  Title   : find
  Usage   : $biblio = $biblio->find($pubmed_query_phrase);
  Function: perform a PubMed query using Entrez ESearch
  Returns : a reference to the object on which the method was called
  Args    : a PubMed query phrase.  See
            http://eutils.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
            for help on how to construct a query.

=head2 get_all_ids



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