Bio::O...actory(3pm)

💖 Bio::O...actory — the Perl man page, but make it a group chat 💖

okay so bestie, welcome to Bio::Ontology::TermFactory, a page straight out of the User Contributed Perl Documentation collection. It's giving "small module, big feelings". Let's get into it 💅

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✨ NAME ✨

Bio::Ontology::TermFactory — the little factory that instantiates a brand new Bio::Ontology::TermI (or literally any class derived from it) for you. No cap. It just builds them. 🏭🦋

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🌸 SYNOPSIS 🌸

Here's the vibe in code form:

use Bio::Ontology::TermFactory;

# the default type is Bio::Ontology::Term
my $factory = Bio::Ontology::TermFactory->new(
                    -type => 'Bio::Ontology::GOterm');
my $term = $factory->create_object(-name => 'peroxisome',
                                   -ontology => 'Gene Ontology',
                                   -identifier => 'GO:0005777');

see how easy that was?? You spin up the factory, tell it what type you want, and it hands you a term. Main character energy fr fr ✨

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🎀 DESCRIPTION 🎀

So basically this object builds Bio::Ontology::TermI objects generically. That's the whole gig. It's a factory. It factories. Periodt. 🫶

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💌 FEEDBACK 💌

🧚 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Yes, integral. Your thoughts matter, babe. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated — like genuinely, they mean it. 💖

bioperl-l@bioperl.org                  - General discussion
http://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. Lowkey important: there are many experienced and reponsive experts who will be able look at the problem and quickly address it. So like, don't DM the maintainer, ask the group chat. 🙈

Please include a thorough description of the problem with code and data examples if at all possible. The more detail the better, bestie. Give them the whole story. 📝

🐛 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/bioperl-live/issues

Slay. Go forth and file that issue. 🐞🔥

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👑 AUTHOR - Hilmar Lapp 👑

Email hlapp at gmx.net

Shoutout to Hilmar. Iconic. 💜

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — iykyk, that underscore is the secret handshake. 🤫

🌈 new

• Title — new
• Usage — my $obj = Bio::Ontology::TermFactory->new();
• Function — Builds a new Bio::Ontology::TermFactory object ✨
• Returns — Bio::Ontology::TermFactory
• Args — -type => string, name of a Bio::Ontology::TermI derived class. The default is Bio::Ontology::Term.

See Bio::Ontology::TermI, Bio::Ontology::Term.

🦋 create_object

• Title — create_object
• Usage — my $term = $factory->create_object(<named parameters>);
• Function — Instantiates new Bio::Ontology::TermI (or one of its child classes)

This object allows us to genericize the instantiation of Term objects. genericize the instantiation... she's so versatile 💅

• Returns — Bio::Ontology::TermI compliant object. The return type is configurable using new(-type =>"...").
• Args — initialization parameters specific to the type of term object we want. Typically

-name        => $name
-identifier  => identifier for the term
-ontology    => ontology for the term

See Bio::Ontology::TermI.

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And that's the whole page, bestie. Go build some terms. You got this. 💜

This was perl v5.32.1, dated 2021-08-15, from the Bio::O...actory(3pm) corner of the world. Mwah. 🎀✨