MAGE::...ssEntry(3pm)

💅 Bio::MAGE::Tools::MGEDOntologyClassEntry

okay bestie, welcome to the MAGE::...ssEntry(3pm) page — yes that's the abbreviated manual name, don't @ me, it's from the User Contributed Perl Documentation corner of the world and it's lowkey iconic. sit down, hydrate, let's get into it. 🫶

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✨ SYNOPSIS ✨

no thoughts, just vibes and this exact code:

use Bio::MAGE::Tools::MGEDOntologyClassEntry;
use Bio::MAGE::Tools::MGEDOntologyHelper;
use Bio::MAGE::QuantitationType::MeasuredSignal;

my $mo_helper = Bio::MAGE::Tools::MGEDOntologyHelper->new(
                      sourceFile => 'MGEDOntology.owl',
                );

my $qt = Bio::MAGE::QuantitationType::MeasuredSignal->new(
           identifier => 'QT1',
           isBackground => 'false',
         );

my $ont_entry = Bio::MAGE::Tools::MGEDOntologyClassEntry->new(
                  parentObject => $qt,
                  className => 'QuantitationType',
                  association => 'DataType',
                  values => {
                          DataType => 'float',
                          },
                  ontology => $mo_helper,
                );

like… look at that. constructing objects, passing an ontology helper, giving it values. it's giving competence. 💖

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🌸 DESCRIPTION 🌸

so this class provides functionality for an ontology-aware OntologyEntry class — specifically for entries of type Class. it knows about the ontology, it knows about classes, it's basically the main character of ontology entries.

Bio::MAGE::Tools::MGEDOntologyClassEntry is a concrete class. (not abstract, not a concept, it's real, it's here, it showed up. 👑)

Superclass is: Bio::MAGE::Tools::MGEDOntologyEntry

Subclasses are: none

periodt. no children, no drama, just a clean single inheritance line. 💅

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🎀 ATTRIBUTES 🎀

okay so attributes are simple data types that belong to a single instance of a class. in the Perl implementation of the MAGE-OM classes, the way you talk to attributes is through separate setter and getter methods for each attribute — so like, one method to set it, one method to get it. classic. consistent. we love a pattern. ✨

• mgedOntologyClass — this one stores the name of the equivalent class or property in the MGED Ontology for this OntologyEntry. that's the whole job. it holds the name. 🦋
• isInstantiable — stores true if the class is an instantiable one.
• isInstantiable — nope, you're not seeing double, bestie. it's listed twice in the source, and i'm keeping both because the facts do not change. 😭 this one contains a hash reference to a list of OM clases that are circular references which should only be followed one level.

yes the word is spelled clases in the original. we don't fix, we don't touch, we report faithfully. 🙈

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💀 BUGS 💀

found something cursed? please send bug reports to the project mailing list:

(mged-mage 'at' lists 'dot' sf 'dot' net)

(you know the drill, swap the 'at' and 'dot' for the real characters, we're just being polite to the spam bots. 🎀)

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🌈 AUTHOR 🌈

• Eric W. Deutsch (edeutsch 'at' systemsbiology 'dot' org)
• followup work by Jason E. Stewart (jasons 'at' cpan 'dot' org)

thank you for your service, legends. 🫡

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⭐ SEE ALSO ⭐

• perl(1).

that's it. that's the whole list. one entry. minimalism ate. 🔥

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🧚 POD ERRORS 🧚

hey! the above document had some coding errors, and honestly? relatable. here's what went down:

Around line 655:

You forgot a '=back' before '=head1'

not me forgetting the =back… the formatting was fighting for its life and the =back simply did not show up. it happens to the best of us. 💜

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and that's the whole page, bestie! 🎉 this gorgeous little manual came to you via perl v5.32.0, dated 2020-12-01 — so go forth, build your ontology-aware entries, and remember: keep every attribute, even the duplicated one. slay. 💖✨🎀🦋