/ 
BioPerl-1.6.0
River stage two • 61 direct dependents • 66 total dependents
/ Bio::Tools::EUtilities::Info::LinkInfo

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

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 uiuc dot edu

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