Bio::Tools::EUtilities::Info::LinkInfo.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::EUtilities::Info::LinkInfo - class for storing einfo link data

SYNOPSIS

     ## should not create instance directly; Bio::Tools::EUtilities does this ##
 
     # get a LinkInfo object using Bio:Tools::EUtilities    
     print "Link name: ",$link->get_link_name,"\n";
     print "Link name: ",$link->get_link_menu_name,"\n";
     print "Link desc: ",$link->get_link_description,"\n";
     print "DBFrom: ",$link->get_dbfrom,"\n"; # database linked from
     print "DBTo: ",$link->get_dbto,"\n"; # database linked to
 
 

DESCRIPTION

This class handles data output (XML) from einfo and elink.

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:

    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.
   http://bugzilla.open-bio.org/
 
 

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 _

new

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

get_database

  Title    : get_database
  Usage    : my $db = $info->get_database;
  Function : returns single database name (eutil-compatible).  This is the
             queried database. For elinks (which have 'db' and 'dbfrom')
             this is equivalent to db/dbto (use get_dbfrom() to for the latter)
  Returns  : string
  Args     : none
 
 

get_db (alias for get_database)

get_dbto (alias for get_database)

get_dbfrom

  Title    : get_dbfrom
  Usage    : my $origdb = $link->get_dbfrom;
  Function : returns referring database
  Returns  : string
  Args     : none
  Note     : alias for get_db()
 
 
  Title    : get_link_name
  Usage    : $ln = $link->get_link_name;
  Function : returns raw link name (eutil-compatible)
  Returns  : string
  Args     : none
 
 
  Title    : get_link_description
  Usage    : $desc = $link->get_link_description;
  Function : returns the (more detailed) link description
  Returns  : string
  Args     : none
 
 
  Title    : get_link_menu_name
  Usage    : my $mn = $link->get_link_menu_name;
  Function : returns formal menu name
  Returns  : string
  Args     : none
 
 

get_priority

  Title    : get_priority
  Usage    : my $mn = $link->get_priority;
  Function : returns priority ranking
  Returns  : integer
  Args     : none
  Note     : only set when using elink and cmd set to 'acheck'
 
 

get_html_tag

  Title    : get_html_tag
  Usage    : my $tag = $link->get_html_tag;
  Function : returns HTML tag
  Returns  : string
  Args     : none
  Note     : only set when using elink and cmd set to 'acheck'
 
 

get_url

  Title    : get_url
  Usage    : my $url = $link->get_url;
  Function : returns URL string; note that the string isn't usable directly but
             has the ID replaced with the tag <@UID@>
  Returns  : string
  Args     : none
  Note     : only set when using elink and cmd set to 'acheck'
 
 

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