Info documentation.

  #### should not create instance directly; Bio::Tools::EUtilities does this ####

  my $info = Bio::Tools::EUtilities->new(-eutil => 'einfo',
                                         -file => 'einfo.xml');
  # can also use '-response' (for HTTP::Response objects) or '-fh' (for filehandles)

  # print available databases (if data is present)

  print join(', ',$info->get_available_databases),"\n";

  # get database info

  my $db = $info->get_database; # in case you forgot...
  my $desc = $info->get_description;
  my $nm = $info->get_menu_name;
  my $ct = $info->get_record_count;
  my $dt = $info->get_last_update;

  # EUtilDataI interface methods

  my $eutil = $info->eutil;
  my $type = $info->datatype;

  # iterate through Field and Link objects

  while (my $field = $info->next_Field) {
      print "Field code: ",$field->get_field_code,"\n";
      print "Field name: ",$field->get_field_name,"\n";
      print "Field desc: ",$field->get_field_description,"\n";
      print "DB  : ",$field->get_database,"\n";
      print "Term ct   : ",$field->get_term_count,"\n";
      for my $att (qw(is_date is_singletoken is_hierarchy is_hidden is_numerical)) {
          print "\tField $att\n" if $field->$att;
      }
  }

  my @fields = $info->get_Fields; # grab them all (useful for grep)

  while (my $link = $info->next_LinkInfo) {
      print "Link name: ",$link->get_link_name,"\n";
      print "Link desc: ",$link->get_link_description,"\n";
      print "DBFrom: ",$link->get_dbfrom,"\n"; # same as get_database()
      print "DBTo: ",$link->get_dbto,"\n"; # database linked to
  }

  my @links = $info->get_LinkInfo; # grab them all (useful for grep)

  $info->rewind(); # rewinds all iterators
  $info->rewind('links'); # rewinds Link iterator
  $info->rewind('fields'); # rewinds Field iterator

This class handles data output (XML) from einfo.
Einfo is capable of returning two types of information:

* A list of all available databases (when called w/o parameters)

* Information about a specific database.

The latter information includes the database description, record count, and
date/time stamp for the last update, among other things. It also includes a list
of fields (indices by which record data is stored which can be used in queries)
and links (crossrefs between related records in other databases at NCBI). Data
from the latter two are stored in two small subclasses (FieldInfo and LinkInfo)
which can be iterated through or retrieved all at once, as demonstrated above.
NOTE: Methods described for the LinkInfo and FieldInfo subclasses are unique to
those classes (as they retrieve data unique to those data types).
Further documentation for Link and Field subclass methods is included below.
For more information on einfo see:

   http://eutils.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html

sub _add_data {

    my ($self, $simple) = @_;
    if (exists $simple->{DbList} &&
        exists $simple->{DbList}->{DbName}) {
        $self->{'_available_databases'} = $simple->{DbList}->{DbName};
    }
    # start setting internal variables
    if (exists $simple->{DbInfo}) {
        for my $key (sort keys %{ $simple->{DbInfo} }) {
            my $data = 
            ($key eq 'FieldList') ? $simple->{DbInfo}->{$key}->{Field} :
            ($key eq 'LinkList' ) ? $simple->{DbInfo}->{$key}->{Link}  :
            $simple->{DbInfo}->{$key};
            if ($key eq 'FieldList' || $key eq 'LinkList') {
                for my $chunk (@{$data}) {
                    if (exists $simple->{DbInfo}->{DbName}) {
                        $chunk->{DbFrom} = $simple->{DbInfo}->{DbName};
                    }
                    my $type = ($key eq 'FieldList') ? 'FieldInfo' : 'LinkInfo';
                    my $obj = "Bio::Tools::EUtilities::Info::$type"->new(
                                           -eutil => 'einfo',
                                           -type => lc $type,
                                        -verbose => $self->verbose);
                    $obj->_add_data($chunk);
                    push @{ $self->{'_'.lc $type} }, $obj;
                }
            } else {
                $self->{'_'.lc $key} = $data;
            }
        }
    } else {
        map { $self->{'_'.lc $_} = $simple->{$_} unless ref $simple->{$_}} keys %$simple;
    }

}

sub to_string {

    my $self = shift;
    my $string = $self->SUPER::to_string;
    if (my @dbs = $self->get_databases) {
        $string .= sprintf("%-20s:%s\n\n", 'DB',
            $self->_text_wrap('', ' 'x20 .':', join(', ',@dbs)));
    }
    while (my $fi = $self->next_FieldInfo) {
        $string .= $fi->to_string."\n";
    }
    while (my $li = $self->next_LinkInfo) {
        $string .= $li->to_string."\n";
    }
    return $string;
}

1;

}

User feedback is an integral part of the evolution of this and other Bioperl
modules. Send your comments and suggestions preferably to one of the Bioperl
mailing lists. Your participation is much appreciated.

  bioperl-l@lists.open-bio.org               - General discussion
  http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists

 Title    : rewind
 Usage    : $info->rewind() # rewinds all (default)
            $info->rewind('links') # rewinds only links
 Function : 'rewinds' (resets) specified interators (all if no arg)
 Returns  : none
 Args     : [OPTIONAL] String: 
            'all'    - all iterators (default)
            'linkinfo'  - LinkInfo objects only
            'fieldinfo' - FieldInfo objects only

_add_data	No description	Code
to_string	Description	Code