Christopher Fields > BioPerl-1.6.901 > Bio::Tools::EUtilities::Info

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Module Version: 1.006901   Source  

NAME ^

Bio::Tools::EUtilities::Info - interface class for storing einfo data

SYNOPSIS ^

  #### 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

DESCRIPTION ^

This class handles data output (XML) from einfo.

Einfo is capable of returning two types of information:

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

FEEDBACK ^

Mailing Lists

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

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web.

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR ^

Email cjfields at bioperl dot org

APPENDIX ^

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

rewind

 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

to_string

 Title    : to_string
 Usage    : $foo->to_string()
 Function : converts current object to string
 Returns  : none
 Args     : (optional) simple data for text formatting
 Note     : Used generally for debugging and for various print methods
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