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

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

okay so bestie, welcome to Bio::Tools::EUtilities::Link::LinkSet — Class for EUtils LinkSets. yes that's the whole name, it's giving long module name energy but we move 💅. This page comes to you from the User Contributed Perl Documentation, which is exactly what it sounds like — the people's docs, fr fr.

✨ VERSION ✨

version 1.77 — current, fresh, slaying 🌸

🎀 SYNOPSIS 🎀

# ...

look, the synopsis is literally just a comment. iconic behavior honestly. sometimes the vibe is mystery 💀

💖 DESCRIPTION 💖

# ...

also just a comment. no notes. the whole description is a mood. 🫶

what we do get is the full tour of every method this class has, so buckle up:

🌟 get_ids 🌟

  • Title: get_ids
  • Usage: my @ids = $linkset->get_ids
  • Function: hands you back the list of retrieved IDs
  • Returns: an array of IDs
  • Args: none
  • Notes: the Cmd / Description tea is as follows:
    • acheck — same as get_submitted_ids
    • lcheck — same as get_submitted_ids
    • ncheck — same as get_submitted_ids
    • prlinks — same as get_submitted_ids
    • llinks — same as get_submitted_ids
    • llinkslib — same as get_submitted_ids
    • neighbor — linked IDs for database in get_database
    • neighbor_history — linked IDs for database in get_database

💫 get_database 💫

  • Title: get_database
  • Usage: my $db = $info->get_database;
  • Function: returns a single database name (eutil-compatible). this is the queried database. for elinks (which have both 'db' and 'dbfrom') this is equivalent to db/dbto — use get_dbfrom() for the latter. heads up: this only ever returns the first db, and in some cases that's lowkey not what you want (say, when multiple dbs are queried)
  • Returns: string
  • Args: none
  • Notes: with all elink cmd arguments

💅 get_db (alias for get_database)

same thing, different name, no cap. call it whatever feels right bestie 🫶

💅 get_dbto (alias for get_database)

again — a whole other alias for get_database. the duality of (a) method 🎀

🌈 get_databases 🌈

  • Title: get_databases
  • Usage: my $string = $linkset->get_databases;
  • Function: retrieve databases referred to for this linkset — these may be present as a single database or embedded in
  • Returns: array of strings
  • Args: none
ngl the original Function line just kinda... ends there. mid-sentence. the sentence is giving cliffhanger 😭 but we are not about to invent the rest of it, so here it stands.

💅 get_dbs (alias for get_databases)

you guessed it — alias for get_databases. so many names for one vibe ✨

🦋 get_dbfrom 🦋

  • Title: get_dbfrom
  • Usage: my $string = $linkset->get_dbfrom;
  • Function: retrieve the originating database for this linkset
  • Returns: string
  • Args: none
  • Title: get_link_names
  • Usage: my $string = $linkset->get_link_names;
  • Function: retrieve eutil-compatible link names
  • Returns: array of strings
  • Args: none
  • Notes: each LinkSet can hold multiple LinkInfo objects (each one containing a link name). also, some LinkSets define a single link name. this returns an array with all unique linknames globbed from both sources, if they're present and defined 👑
  • Title: get_link_name
  • Usage: my $string = $linkset->get_link_name;
  • Function: retrieve an eutil-compatible link name
  • Returns: a single link name
  • Args: none

🌸 get_submitted_ids 🌸

  • Title: get_submitted_ids
  • Usage: my $string = $linkset->get_submitted_ids;
  • Function: retrieve the original ID list
  • Returns: string
  • Args: none

⭐ has_scores ⭐

  • Title: has_scores
  • Usage: if (my $linkset->has_scores) {...}
  • Function: returns TRUE if score data is present
  • Returns: Boolean
  • Args: none

🔥 get_scores 🔥

  • Title: get_scores
  • Usage: %scores = $linkset->get_scores;
  • Function: returns a flattened list or a hash ref containing ID => score pairs
  • Returns: hash or hash ref (depends on whether you're in list or scalar context, iykyk)
  • Args: none

👑 get_score_by_id 👑

  • Title: get_score_by_id
  • Usage: $score = $linkset->get_score_by_id($id);
  • Function: returns the score for one particular primary ID
  • Returns: integer
  • Args: [REQUIRED] Primary ID for the score lookup — do not skip this one bestie, it's required fr fr

💜 has_linkout 💜

  • Title: has_linkout
  • Usage: if ($linkset->has_linkout) {...}
  • Function: returns TRUE if the single ID present in this linkset has a linkout
  • Returns: boolean
  • Args: none
  • Notes: this checks cmd=lcheck (a boolean for a linkout) and also backchecks cmd=acheck for databases with the name 'LinkOut'

🎀 has_neighbor 🎀

  • Title: has_neighbor
  • Usage: if ($linkset->has_neighbor) {...}
  • Function: returns TRUE if the single ID present in this linkset has a neighbor in the same database
  • Returns: boolean
  • Args: none
  • Notes: this checks cmd=ncheck (boolean for a neighbor in the same database); no other checks are performed at this time
  • Title: next_UrlLink
  • Usage: while (my $url = $linkset->next_UrlLink) {...}
  • Function: iterate through UrlLink objects
  • Returns: Bio::Tools::EUtilities::Link::UrlLink
  • Args:
  • Title: get_UrlLinks
  • Usage: my @urls = $linkset->get_UrlLinks
  • Function: returns all UrlLink objects
  • Returns: list of Bio::Tools::EUtilities::Link::UrlLink
  • Args:

🦋 next_LinkInfo 🦋

  • Title: next_LinkInfo
  • Usage: while (my $info = $linkset->next_LinkInfo) {...}
  • Function: iterate through LinkInfo objects
  • Returns: Bio::Tools::EUtilities::Link::LinkInfo
  • Args:

🍓 get_LinkInfo 🍓

  • Title: get_LinkInfo
  • Usage: my @links = $linkset->get_LinkInfo
  • Function: returns all LinkInfo objects
  • Returns: list of Bio::Tools::EUtilities::Link::LinkInfo
  • Args:

🧚 rewind 🧚

  • Title: rewind
  • Usage:
$info->rewind() # rewinds all (default)
$info->rewind('links') # rewinds only links
  • Function: 'rewinds' (resets) the specified iterators — all of them if you pass no arg
  • Returns: none
  • Args: [OPTIONAL] String:
    • 'all' — all iterators (default)
    • 'linkinfo' or 'linkinfos' — LinkInfo objects only
    • 'urllinks' — UrlLink objects only

⭐ to_string ⭐

  • Title: to_string
  • Usage: $foo->to_string()
  • Function: converts the current object to a 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 literally an integral part of the evolution of this and other Bioperl modules — like, integral integral. send your comments and suggestions preferably to the Bioperl mailing list, and 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. there are lots of experienced, responsive experts who'll be able to look at the problem and quickly address it. and please include a thorough description of the problem, with code and data examples, if at all possible. the more detail the better, bestie 💅

🐛 Reporting bugs 🐛

report bugs to the Bioperl bug tracking system so we can 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>

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.

and that's the whole page, bestie — perl v5.40.0, dated 2025-01-27, User Contributed Perl Documentation 💅✨ go forth and link your sets 🦋

📦 where this page comes from