Bio::T...nkInfo(3pm)

📦
version 1.77 · 4 versions
, in debian trixie, ubuntu resolute, ubuntu stonking

💖 Bio::Tools::EUtilities::Info::LinkInfo 💖

okay so bestie, welcome to the User Contributed Perl Documentation for this one. The page is officially called Bio::T...nkInfo(3pm) because manpages love to truncate things dramatically, but the actual module is Bio::Tools::EUtilities::Info::LinkInfo and it is exactly what it sounds like: a little class that holds onto einfo link data. No cap. ✨

🌸 NAME 🌸

Bio::Tools::EUtilities::Info::LinkInfo — a class for storing einfo link data. that's it, that's the job, and she does it beautifully 🎀

🦋 VERSION 🦋

version 1.77 — iconic, timeless, no notes 💅

✨ 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
important bestie!! don't you dare call new yourself. Bio::Tools::EUtilities handles that for you. you just vibe with the object it hands you 🫶

👑 DESCRIPTION 👑

So this class handles data output (XML) from both einfo and elink, and its whole main character energy is describing data that either explains how NCBI databases get linked together via link names, or how databases get linked out to outside databases (LinkOut). it's giving matchmaker but for databases. 💖

Further documentation for Link and Field subclass methods is included below, so keep scrolling, we're not done.

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)

okay so lowkey: do not call this. The Note literally has triple asterisks around "should not be called by end-users" which is manpage for "bestie I am begging you." It returns a new LinkInfo instance, it takes no args, all the data gets added via _add_data, and most of the methods are getters only. Let the parent class do it. periodt. 🙈

🍓 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

returns a single database name that's eutil-compatible. This is the queried database. And heads up for elinks (which have 'db' and 'dbfrom'): this is equivalent to db/dbto, so if you actually wanted the latter, use get_dbfrom(). Returns a string, takes no args. 🧚

💜 get_db (alias for get_database)

💜 get_dbto (alias for get_database)

yep, both of these are literally just aliases for get_database. same girl, different nickname. use whichever one vibes with your code. ✨

🌸 get_dbfrom 🌸

Title    : get_dbfrom
Usage    : my $origdb = $link->get_dbfrom;
Function : returns referring database
Returns  : string
Args     : none
Note     :

returns the referring database. Returns a string, takes no args, and the Note is genuinely empty so there's nothing extra to spill. 🎀

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

returns the raw link name, eutil-compatible and unbothered. Returns a string, takes no args. 💅

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

returns the link description, and yes it's the more detailed one — the deluxe edition. Returns a string, takes no args. ⭐

Title    : get_link_menu_name
Usage    : my $mn = $link->get_link_menu_name;
Function : returns formal menu name
Returns  : string
Args     : none

returns the formal menu name, because apparently this link has a whole government name. Returns a string, takes no args. 👑

🔥 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'

returns the priority ranking as an integer, no args. But listen: the Note says it's only set when using elink and cmd set to 'acheck'. so if it's empty, that's not a bug, that's just the vibe check not being run. 💀

💜 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'

returns the HTML tag. Returns a string, takes no args. Same deal as above — only set when using elink and cmd set to 'acheck'. don't come for her if it's undefined. 🫶

💖 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'

returns a URL string — but bestie, read this part carefully: the string isn't usable directly, because the ID has been replaced with the tag <@UID@>. so you gotta swap that back in yourself. Returns a string, takes no args. And yep, 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

converts the current object to a string. Returns none, and takes an optional arg of simple data for text formatting. Mostly this is for debugging and for all the various print methods. it's giving "just here to help you peek under the hood." 🔥

💌 FEEDBACK 💌

💜 Mailing lists 💜

User feedback is an integral part of the evolution of this and other Bioperl modules. So send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated, fr fr. 🫶

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. (yes, "reponsive" — we're quoting the manpage's own typo, she's doing her best 💅)

🎀 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> — legend behaviour. 💖

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. slay, share-alike, etc. ✨

and that's the whole page bestie!! 🎉 this was rendered with perl v5.40.0 on 2025-01-27, so go forth and link those databases, you absolute icon 💅🦋💖

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