Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


Bio::Tools::EUtilities::Info::FieldInfo - class for storing einfo field data


     #### 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->type;
     # 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 = $info->next_Link) {
         print "Link name: ",$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_Links; # 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: 1) a list of all available databases (when called w/o parameters) and 2) 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 (Field and Link) which can be iterated through or retrieved all at once, as demonstrated above. NOTE: Methods described for the Link and Field 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:


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.               - General discussion  - About the mailing lists


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

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.


Email cjfields at bioperl dot org


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


  Title    : new
  Note     : *** should not be called by end-users ***  
  Usage    : my $ct = Bio::Tools::EUtilities::Info::FieldInfo;
  Function : returns new FieldInfo instance
  Returns  : Bio::Tools::EUtilities::Info::FieldInfo instance
  Args     : none (all data added via _add_data, most methods are getters only)


  Title    : term_count
  Usage    : my $ct = $field->term_count;
  Function : returns number of terms for field 
  Returns  : integer
  Args     : none


  Title    : get_field_name
  Usage    : my $nm = $field->get_field_name;
  Function : returns the full name of the field
  Returns  : string
  Args     : none


  Title    : get_full_name
  Note     : alias of get_field_name()


  Title    : get_field_code
  Usage    : $field->get_field_code()
  Function : returns field code (abbreviation) used for queries
  Returns  : string
  Args     : none


  Title    : get_field_description
  Usage    : $field->get_field_description
  Function : returns field description
  Returns  : string
  Args     : none
  Note     : alias of get_description()


  Title    : is_date
  Usage    : if ($field->is_date) {...}
  Function : returns true if field contains date information
  Returns  : Boolean
  Args     : none


  Title    : is_singletoken
  Usage    : if ($field->is_singletoken) {...}
  Function : returns true if field has single value in docsums
  Returns  : Boolean
  Args     : none


  Title    : is_hierarchy
  Usage    : if ($field->is_hierarchy) {...}
  Function : returns true if field contains hierarchal values
  Returns  : Boolean
  Args     : none


  Title    : is_hidden
  Usage    : if ($field->is_hidden) {...}
  Function : returns true if field is hidden in docsums
  Returns  : Boolean
  Args     : none


  Title    : is_numerical
  Usage    : if ($field->is_numerical) {...}
  Function : returns true if field contains a numerical value
  Returns  : Boolean
  Args     : none


  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