Bio::Tools::EUtilities::Info::LinkInfo(3)

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()

  get_link_name
 Title    : get_link_name
 Usage    : $ln = $link->get_link_name;
 Function : returns raw link name (eutil-compatible)
 Returns  : string
 Args     : none

  get_link_description
 Title    : get_link_description
 Usage    : $desc = $link->get_link_description;
 Function : returns the (more detailed) link description
 Returns  : string
 Args     : none

  get_link_menu_name
 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