MAGE::BioAssay(3pm)

💖 NAME 💖

Bio::MAGE::BioAssay — okay so this is the container module for all the classes hanging out in the MAGE package: BioAssay. It's the group chat, and every class below is a member of it. 🫶

(Also, for the record, this page is MAGE::BioAssay(3pm) from the User Contributed Perl Documentation. Hi. Welcome. You're gonna do great.) 💅

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✨ SYNOPSIS ✨

use Bio::MAGE::BioAssay;

That's it. That's the whole vibe. One line and you're in. 🎀

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🦋 DESCRIPTION 🦋

So like, this is a package module, meaning it's not one class — it's a whole little friend group of classes that all live together in the Bio::MAGE hierarchy. They belong to the BioAssay package of the MAGE-OM object model. If you're building or parsing MAGE-OM stuff, this is your home base, bestie. 🏠✨

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👑 CLASSES 👑

The Bio::MAGE::BioAssay module contains the following Bio::MAGE classes, and no we're not skipping any of them, they all matter:

• PhysicalBioAssay
• DerivedBioAssay
• Image
• BioAssay
• Channel
• MeasuredBioAssay
• BioAssayCreation
• FeatureExtraction
• Hybridization
• ImageAcquisition
• BioAssayTreatment

Look at them. Eleven whole classes. Iconic behavior honestly. 🌈

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🌸 CLASS METHODS 🌸

These ones you call on the class itself, not on an object. Class-level energy. Main character, but for the whole package.

🌟 @class_list = Bio::MAGE::BioAssay::classes();

This hands you back a list of the non-fully qualified class names in this package — like, they do not have Bio::MAGE:: glued to the front. Short names only, cuties. ✂️

🌟 $obj = class->new(%parameters)

The new() method is the class constructor. The classic. The origin story. 🐣

• Parameters: if you hand it a list of name/value pairs, the matching slots, attributes, or associations get their initial values set right there by the constructor.
• Return value: a reference to an object of the class. Fresh out of the box. 🎁
• Side effects: it invokes the initialize() method if the class defines one.

🌟 @names = class->get_slot_names()

get_slot_names() is how you get the name of every slot defined in a given class.

NOTE: this list of names does not include attribute or association names. Slots only, bestie. Don't @ me.

• Return value: a list of the names of all slots defined for this class.
• Side effects: none. Chill as always. 😌

🌟 @name_list = get_attribute_names()

Returns the list of attribute data members for this class. 📋

🌟 @name_list = get_association_names()

Returns the list of association data members for this class. 🔗

🌟 @class_list = get_superclasses()

Returns the list of superclasses for this class. The ancestors. The ones who came before. 👑

🌟 @class_list = get_subclasses()

Returns the list of subclasses for this class. The babies. The heirs. 🐣

🌟 $name = class_name()

Returns the full class name for this class.

🌟 $package_name = package_name()

Returns the base package name — and that means no namespace:: prefix on it — of the package that contains this class. 📦

🌟 %assns = associations()

Returns the association meta-information as a hash. The keys are the association names, and the values are Association objects that carry the meta-information for that association. Meta. Very meta. 🔮

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💜 INSTANCE METHODS 💜

Now we're on the object level. You need an actual instance for these, okay?

💫 $obj_copy = $obj->new()

Plot twist: when you call new() on an existing object reference instead of a class name, it acts as a copy constructor — the brand new object's initial values get set to whatever the existing object's values are. Clone arc. 🧬

• Parameters: no input parameters are used in the copy constructor — the initial values are taken straight from the object being copied.
• Return value: a reference to an object of the class.
• Side effects: it invokes the initialize() method if the class defines one.

💫 $obj->set_slots(%parameters)

💫 $obj->set_slots(\@name_list, \@value_list)

set_slots() is the multitasker — it sets a whole bunch of slots at the same time. It has two different ways you can invoke it:

1. The first takes a named parameter list.
2. The second takes two array references.

• Return value: none.
• Side effects: it will call croak() if you use a slot_name that the class doesn't define. So like… don't make up slots. 🙈

💫 @obj_list = $obj->get_slots(@name_list)

get_slots() gets the values of a bunch of slots all at once. Bulk retrieve, we love efficiency. ⚡

• Return value: a list of instance objects.
• Side effects: none.

💫 $val = $obj->set_slot($name,$val)

The set_slot() method sets the slot $name to the value $val. One at a time, precise, intentional. 💅

• Return value: the new value of the slot, i.e. $val.
• Side effects: none.

💫 $val = $obj->get_slot($name)

The get_slot() method is used to get the values of a number of slots at the same time.

• Return value: a single slot value, or undef if the slot hasn't been initialized yet. Empty. Void. Nothing. 💀
• Side effects: none.

💫 $val = $bioassay->xml_lists()

💫 $inval = $bioassay->xml_lists($inval)

This is the unified setter/getter for the xml_lists slot. One method, two moods. ✨

If $inval is specified, the setter method gets invoked. With no parameters, the getter method gets invoked.

• Input parameters: the optional $inval will invoke the setter method.
• Return value: for both setter and getter, the current value of the xml_lists slot.
• Side effects: none.
• Exceptions: none.

💫 $val = $bioassay->tagname()

💫 $inval = $bioassay->tagname($inval)

This is the unified setter/getter for the tagname slot.

If $inval is specified, the setter method gets invoked. With no parameters, the getter method gets invoked.

• Input parameters: the optional $inval will invoke the setter method.
• Return value: for both setter and getter, the current value of the tagname slot.
• Side effects: none.
• Exceptions: none.

💫 $val = $bioassay->channel_list()

💫 $inval = $bioassay->channel_list($inval)

This is the unified setter/getter for the channel_list slot.

If $inval is specified, the setter method gets invoked. With no parameters, the getter method gets invoked.

• Input parameters: the optional $inval will invoke the setter method.
• Return value: for both setter and getter, the current value of the channel_list slot.
• Side effects: none.
• Exceptions: none.

💫 $val = $bioassay->bioassay_list()

💫 $inval = $bioassay->bioassay_list($inval)

This is the unified setter/getter for the bioassay_list slot.

If $inval is specified, the setter method gets invoked. With no parameters, the getter method gets invoked.

• Input parameters: the optional $inval will invoke the setter method.
• Return value: for both setter and getter, the current value of the bioassay_list slot.
• Side effects: none.
• Exceptions: none.

💫 $array_ref = $bioassay->getChannel_list()

This method handles the list for the Bio::MAGE::BioAssay::Channel class. It returns a reference to an array of the class objects that have been associated with the package instance. 🎀

This is genuinely useful when you're pulling data out of a parsed MAGE-ML file. Trust. 📂

💫 $bioassay->addChannel(@vals)

This one is the interface for adding Bio::MAGE::BioAssay::Channel objects to the channel_list list. It's generally used by generic methods, like the ones hanging out in the XMLWriter. 🛠️

• Input parameters: the list of values @vals to add to the owner association. NOTE: submitting a single value is permitted. One is fine. One is valid. 🫶
• Return value: none.
• Side effects: none.
• Exceptions: it will call croak() if no input parameters are specified, or if any of the objects in @vals is not a subclass of class Bio::MAGE::BioAssay::Channel. So like, check your types before you come in here, bestie. 😭

💫 $array_ref = $bioassay->getBioAssay_list()

This method handles the list for the Bio::MAGE::BioAssay::BioAssay class. It returns a reference to an array of the class objects that have been associated with the package instance. 🦋

This is useful when retrieving data from a parsed MAGE-ML file. (Yes, same energy as getChannel_list(). They're siblings.) 💕

💫 $bioassay->addBioAssay(@vals)

This is the interface for adding Bio::MAGE::BioAssay::BioAssay objects to the bioassay_list list. It's generally used by generic methods such as those in the XMLWriter. ✍️

• Input parameters: the list of values @vals to add to the owner association. NOTE: submitting a single value is permitted.
• Return value: none.
• Side effects: none.
• Exceptions: it will call croak() if no input parameters are specified, or if any of the objects in @vals is not a subclass of class Bio::MAGE::BioAssay::BioAssay. Again. Types. Check them. 🙈

💫 $bioassay->obj2xml($writer)

Write out this object, and all of its sub-objects, as XML — using the $writer you supply to actually do the XML formatting. 🪄

• Input parameters: $writer must be an XML writer, e.g. an instance of Bio::MAGE::XML::Writer. It must have these methods: write_start_tag(), write_end_tag(), and obj2xml().
• Return value: none.
• Side effects: literally all the writing gets delegated to the $writer. Its write_start_tag() and write_end_tag() methods get invoked with the appropriate data, and every class sub-object of the Bio::MAGE::BioAssay instance will have its own obj2xml() method invoked in turn. By letting the $writer do the actual formatting of the output XML, you get to precisely control the format. That's the whole point. That's the power move. 💅
• Exceptions: it will call croak() if no identifier has been set for the Bio::MAGE::BioAssay instance. So set your identifier, bestie. No identifier, no XML. Periodt. 🚫

💫 $bioassay->register($obj)

Stores an object so it can be written as XML later. Save it for the future. ⏳

• Input parameters: the object to be added to the list of registered objects.
• Return value: none.
• Side effects: if $obj needs to be stored by this class, a reference will get stored in the correct XML list for this class. Right place, right list. 🗂️
• Exceptions: none.

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okay that's the first half bestie, don't go anywhere, there's literally more 🫶✨

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

okay so bestie, in the Perl implementation of MAGE-OM classes there are three kinds of class data members, and you gotta know which is which: "slots", "attributes", and "associations". let's break them down one by one 🫶

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🎀 SLOTS 🎀

so "slot" is the API's word for a data member of the class that wasn't in the UML model at all — it exists for mainly internal purposes. it's giving backstage pass, not front-of-house. only touch these if you genuinely understand the inner workings of the API 💅 most of the time slots get used by generic methods, like the ones hanging out in the XML writing and reading classes.

slots are implemented using unified getter/setter methods:

• $var = $obj->slot_name(); — grabs the current value of the slot.
• $new_var = $obj->slot_name($new_var); — stores $new_var in the slot, and the return value is also $new_var. cute, right? it's giving echo.
• @names = $obj->get_slot_names() — hands you the list of every slot in the class.

🚨 DATA CHECKING: literally no data type checking is made for these methods. none. zero. you're on your own, bestie 😭

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🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

"attribute" and "association" are the terms for data members of the class that were specified directly from the UML model. these are the main-character data members, fr fr 👑

in the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:

• get* — retrieves the current value.
  • NOTE: for associations, if the association has list cardinality, you get back an array reference. keep that in mind or you'll be confused later, iykyk.
  • DATA CHECKING: ensures that no argument is provided. so don't be passing stuff in there 🙈
• set* — sets the current value, replacing whatever value was already there. it's a full glow-up, out with the old.
  • NOTE: for associations, if the association has list cardinality, the argument must be an array reference. and because of that whole situation, you probably should be using the add* methods instead. lowkey just use add*.
  • DATA CHECKING: for attributes, it ensures that a single value is provided as the argument. for associations, if the association has list cardinality, it ensures the argument is a reference to an array of instances of the correct MAGE-OM class; otherwise it ensures there's a single argument of the correct MAGE-OM class.
• add* — appends a list of objects to any values that may already be stored in the association. it's additive, it's generous, it's the friend who keeps bringing more people to the party ✨
  • NOTE: this one is only present in associations with list cardinality. if it's not there, that's why, don't come for me.
  • DATA CHECKING: ensures that all arguments are of the correct MAGE-OM class.

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💫 GENERIC METHODS 💫

the unified base class of all MAGE-OM classes, Bio::MAGE::Base, serves up a whole set of generic methods that operate on slots, attributes, and associations. one class to rule them all, periodt 👑

$val = $obj->get_slot($name)
\@list_ref = $obj->get_slots(@name_list);
$val = $obj->set_slot($name,$val)
$obj->set_slots(%parameters)
$obj->set_slots(\@name_list, \@value_list)

💡 see elsewhere in this page for a detailed description of these methods — they're already covered, bestie, go look 🌸

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💀 BUGS 💀

found a bug? not me manifesting that but okay. please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net) 🐛

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👑 AUTHOR 👑

Jason E. Stewart (jasons 'at' cpan 'dot' org) — the author, the icon, the legend 💜

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🌈 SEE ALSO 🌈

• perl(1) — go read it, bestie, it's foundational 🫶

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and that's the whole page, bestie!! this little masterpiece is perl v5.32.0 from 2020-11-27, filed under MAGE::BioAssay(3pm) — go forth and annotate your bioassays with main character energy 💖✨🎀🦋🌸