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Bio-EUtilities-1.77
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/ Bio::Tools::EUtilities::Info::LinkInfo

NAME

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

VERSION

version 1.77

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 both einfo and elink, and centers on describing data that either describes how NCBI databases are linked together via link names, or how databases are linked to outside databases (LinkOut).

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

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     :
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

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 the Bioperl mailing list. Your participation is much appreciated.

bioperl-l@bioperl.org               - General discussion
https://bioperl.org/Support.html    - 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 of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bio-eutilities/issues

AUTHOR

Chris Fields <cjfields@bioperl.org>

COPYRIGHT

This software is copyright (c) 2006-2013 by Chris Fields.

This software is available under the same terms as the perl 5 programming language system itself.