MAGE::...oAssay(3pm)

📦 version 20030502.3, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

✨ NAME ✨

okay bestie, welcome to the MAGE::...oAssay(3pm) page 💖 — it lives in the User Contributed Perl Documentation section, and today we're talking about one specific little icon:

Bio::MAGE::BioAssay::PhysicalBioAssay — Class for the MAGE-OM API 🧬

🦋 SYNOPSIS 🦋

no thoughts, just vibes, but the vibes are code. here's the whole thing, verbatim, no cap:

use Bio::MAGE::BioAssay::PhysicalBioAssay

# creating an empty instance
my $physicalbioassay = Bio::MAGE::BioAssay::PhysicalBioAssay->new();

# creating an instance with existing data
my $physicalbioassay = Bio::MAGE::BioAssay::PhysicalBioAssay->new(
      name=>$name_val,
      identifier=>$identifier_val,
      channels=>\@channel_list,
      bioAssayCreation=>$bioassaycreation_ref,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      physicalBioAssayData=>\@image_list,
      bioAssayFactorValues=>\@factorvalue_list,
      bioAssayTreatments=>\@bioassaytreatment_list,
      descriptions=>\@description_list,
      security=>$security_ref,
);

# 'name' attribute
my $name_val = $physicalbioassay->name(); # getter
$physicalbioassay->name($value); # setter

# 'identifier' attribute
my $identifier_val = $physicalbioassay->identifier(); # getter
$physicalbioassay->identifier($value); # setter

# 'channels' association
my $channel_array_ref = $physicalbioassay->channels(); # getter
$physicalbioassay->channels(\@channel_list); # setter

# 'bioAssayCreation' association
my $bioassaycreation_ref = $physicalbioassay->bioAssayCreation(); # getter
$physicalbioassay->bioAssayCreation($bioassaycreation_ref); # setter

# 'auditTrail' association
my $audit_array_ref = $physicalbioassay->auditTrail(); # getter
$physicalbioassay->auditTrail(\@audit_list); # setter

# 'propertySets' association
my $namevaluetype_array_ref = $physicalbioassay->propertySets(); # getter
$physicalbioassay->propertySets(\@namevaluetype_list); # setter

# 'physicalBioAssayData' association
my $image_array_ref = $physicalbioassay->physicalBioAssayData(); # getter
$physicalbioassay->physicalBioAssayData(\@image_list); # setter

# 'bioAssayFactorValues' association
my $factorvalue_array_ref = $physicalbioassay->bioAssayFactorValues(); # getter
$physicalbioassay->bioAssayFactorValues(\@factorvalue_list); # setter

# 'bioAssayTreatments' association
my $bioassaytreatment_array_ref = $physicalbioassay->bioAssayTreatments(); # getter
$physicalbioassay->bioAssayTreatments(\@bioassaytreatment_list); # setter

# 'descriptions' association
my $description_array_ref = $physicalbioassay->descriptions(); # getter
$physicalbioassay->descriptions(\@description_list); # setter

# 'security' association
my $security_ref = $physicalbioassay->security(); # getter
$physicalbioassay->security($security_ref); # setter

🌸 DESCRIPTION 🌸

so, straight from the MAGE-OM documentation for the "PhysicalBioAssay" class, and I'm quoting the vibe here:

A bioAssay created by the bioAssayCreation event (e.g. in gene expression analysis this event is represented by the hybridization event).

like… it's the assay that the creation event made. that's the whole personality 🫶

🎀 INHERITANCE 🎀

Bio::MAGE::BioAssay::PhysicalBioAssay has the following superclasses:

Bio::MAGE::BioAssay::BioAssay

so yes, it's giving nepo baby but make it OOP 💅 it inherits everything from BioAssay.

👑 CLASS METHODS 👑

the way that all of these can be called without having an instance first?? obsessed. you just go through the Bio::MAGE::BioAssay::PhysicalBioAssay->methodname() syntax and it works ✨

🌈 new()

🌈 new(%args)

the object constructor new() accepts the following optional named-value style arguments:

name — sets the value of the "name" attribute (this attribute was inherited from class Bio::MAGE::Identifiable).
identifier — sets the value of the "identifier" attribute (this attribute was inherited from class Bio::MAGE::Identifiable).
channels — sets the value of the "channels" association (this association was inherited from class Bio::MAGE::BioAssay::BioAssay).
- The value must be of type: array of Bio::MAGE::BioAssay::Channel.
auditTrail — sets the value of the "auditTrail" association (this association was inherited from class Bio::MAGE::Describable).
- The value must be of type: array of Bio::MAGE::AuditAndSecurity::Audit.
bioAssayCreation — sets the value of the "bioAssayCreation" association.
- The value must be of type: instance of Bio::MAGE::BioAssay::BioAssayCreation.
propertySets — sets the value of the "propertySets" association (this association was inherited from class Bio::MAGE::Extendable).
- The value must be of type: array of Bio::MAGE::NameValueType.
physicalBioAssayData — sets the value of the "physicalBioAssayData" association.
- The value must be of type: array of Bio::MAGE::BioAssay::Image.
bioAssayTreatments — sets the value of the "bioAssayTreatments" association.
- The value must be of type: array of Bio::MAGE::BioAssay::BioAssayTreatment.
bioAssayFactorValues — sets the value of the "bioAssayFactorValues" association (this association was inherited from class Bio::MAGE::BioAssay::BioAssay).
- The value must be of type: array of Bio::MAGE::Experiment::FactorValue.
descriptions — sets the value of the "descriptions" association (this association was inherited from class Bio::MAGE::Describable).
- The value must be of type: array of Bio::MAGE::Description::Description.
security — sets the value of the "security" association (this association was inherited from class Bio::MAGE::Describable).
- The value must be of type: instance of Bio::MAGE::AuditAndSecurity::Security.

🌈 $obj = class->new(%parameters)

the new() method is the class constructor, the main character fr fr 👑

Parameters: if you hand it a list of name/value parameters, the corresponding slots, attributes, or associations will have their initial values set by the constructor.
Return value: it returns a reference to an object of the class.
Side effects: it invokes the initialize() method if it is defined by the class.

🌈 @names = class->get_slot_names()

the get_slot_names() method is how you retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names. 💀 don't get got by this one.

Return value: a list of the names of all slots defined for this class.
Side effects: none

🌈 @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.

🌈 @class_list = get_subclasses()

returns the list of subclasses for this class.

🌈 $name = class_name()

returns the full class name for this class.

🌈 $package_name = package_name()

returns the base package name (i.e. no 'namespace::') of the package that contains this class.

🌈 %assns = associations()

returns the association meta-information in a hash where the keys are the association names and the values are Association objects that provide the meta-information for the association.

💅 INSTANCE METHODS 💅

💜 $obj_copy = $obj->new()

when it's invoked with an existing object reference and not a class name, the new() method acts as a copy constructor — and the new object's initial values get set to be those of the existing object. it's giving clone era 🪞

Parameters: no input parameters are used in the copy constructor, the initial values are taken directly from the object to be copied.
Return value: it returns a reference to an object of the class.
Side effects: it invokes the initialize() method if it is defined by the class.

💜 $obj->set_slots(%parameters)

💜 $obj->set_slots(@name_list, @value_list)

the set_slots() method is used to set a number of slots at the same time. it has two different invocation methods — the first takes a named parameter list, and the second takes two array references. versatile queen ✨

Return value: none
Side effects: will call croak() if a slot_name is used that the class does not define.

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

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

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.

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 has not been initialized.
Side effects: none

🧚 ATTRIBUTES 🧚

attributes are simple data types that belong to a single instance of a class. in the Perl implementation of the MAGE-OM classes, the interface to attributes is implemented using separate setter and getter methods for each attribute. slay, separation of concerns 🫶

Bio::MAGE::BioAssay::PhysicalBioAssay has the following attribute accessor methods:

🍓 name

methods for the "name" attribute.

from the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $physicalbioassay->setName($val)

the restricted setter method for the "name" attribute.

Input parameters: the value to which the "name" attribute will be set
Return value: the current value of the "name" attribute
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $physicalbioassay->getName()

the restricted getter method for the "name" attribute.

Input parameters: none
Return value: the current value of the "name" attribute
Side effects: none
Exceptions: will call croak() if any input parameters are specified

🍓 identifier

methods for the "identifier" attribute.

from the MAGE-OM documentation:

An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.

$val = $physicalbioassay->setIdentifier($val)

the restricted setter method for the "identifier" attribute.

Input parameters: the value to which the "identifier" attribute will be set
Return value: the current value of the identifier attribute
- Side effects: none, bestie. nothing. zero. nada. 💤
- Exceptions: it'll croak() if you pass no input parameters, or if you pass too many. pick a lane 💀
$val = $physicalbioassay->getIdentifier() — the restricted getter for the identifier attribute.
- Input parameters: none
- Return value: the current value of the identifier attribute
- Side effects: none
- Exceptions: croak() incoming if you specify any input parameters. it's a getter. it takes nothing. respect the boundary 🫶

💖 ASSOCIATIONS 💖

okay so associations are just references to other classes. and in MAGE-OM every association has a cardinality, which is basically the vibe check on how many of the 'other' class are allowed to show up:

There must be exactly one item in the association, i.e. this is a mandatory data field.
0..1

There may be one item in the association, i.e. this is an optional data field.

1..N

There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.

0..N

There may be one or more items in the association, i.e. this is an optional data field, with list cardinality.

Bio::MAGE::BioAssay::PhysicalBioAssay has the following association accessor methods, and yes we're doing all of them, no skips:

🌸 channels 🌸

Methods for the channels association.

From the MAGE-OM documentation: Channels can be non-null for all subclasses. For instance, collapsing across replicate features will create a DerivedBioAssay that will potentially reference channels.

$array_ref = $physicalbioassay->setChannels($array_ref) — the restricted setter for the channels association.
- Input parameters: the value to which the channels association will be set : a reference to an array of objects of type Bio::MAGE::BioAssay::Channel
- Return value: the current value of the channels association : a reference to an array of objects of type Bio::MAGE::BioAssay::Channel
- Side effects: none
- Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::BioAssay::Channel instances
$array_ref = $physicalbioassay->getChannels() — the restricted getter for the channels association.
- Input parameters: none
- Return value: the current value of the channels association : a reference to an array of objects of type Bio::MAGE::BioAssay::Channel
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified
$val = $physicalbioassay->addChannels(@vals) — because the channels association has list cardinality, it may store more than one value. this method adds the current list of objects in the channels association.
- Input parameters: the list of values @vals to add to the channels association. NOTE: submitting a single value is permitted.
- Return value: the number of items stored in the slot after adding @vals
- Side effects: none
- Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::BioAssay::Channel

🦋 auditTrail 🦋

Methods for the auditTrail association.

From the MAGE-OM documentation: A list of Audit instances that track changes to the instance of Describable.

$array_ref = $physicalbioassay->setAuditTrail($array_ref) — the restricted setter for the auditTrail association.
- Input parameters: the value to which the auditTrail association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
- Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
- Side effects: none
- Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::AuditAndSecurity::Audit instances
$array_ref = $physicalbioassay->getAuditTrail() — the restricted getter for the auditTrail association.
- Input parameters: none
- Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified
$val = $physicalbioassay->addAuditTrail(@vals) — because the auditTrail association has list cardinality, it may store more than one value. this method adds the current list of objects in the auditTrail association.
- Input parameters: the list of values @vals to add to the auditTrail association. NOTE: submitting a single value is permitted.
- Return value: the number of items stored in the slot after adding @vals
- Side effects: none
- Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Audit

🎀 bioAssayCreation 🎀

Methods for the bioAssayCreation association.

From the MAGE-OM documentation: The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event.

$val = $physicalbioassay->setBioAssayCreation($val) — the restricted setter for the bioAssayCreation association.
- Input parameters: the value to which the bioAssayCreation association will be set : one of the accepted enumerated values.
- Return value: the current value of the bioAssayCreation association : one of the accepted enumerated values.
- Side effects: none
- Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not an instance of class Bio::MAGE::BioAssay::BioAssayCreation
$val = $physicalbioassay->getBioAssayCreation() — the restricted getter for the bioAssayCreation association.
- Input parameters: none
- Return value: the current value of the bioAssayCreation association : an instance of type Bio::MAGE::BioAssay::BioAssayCreation.
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified

🍓 propertySets 🍓

Methods for the propertySets association.

From the MAGE-OM documentation: Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.

$array_ref = $physicalbioassay->setPropertySets($array_ref) — the restricted setter for the propertySets association.
- Input parameters: the value to which the propertySets association will be set : a reference to an array of objects of type Bio::MAGE::NameValueType
- Return value: the current value of the propertySets association : a reference to an array of objects of type Bio::MAGE::NameValueType
- Side effects: none
- Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::NameValueType instances
$array_ref = $physicalbioassay->getPropertySets() — the restricted getter for the propertySets association.
- Input parameters: none
- Return value: the current value of the propertySets association : a reference to an array of objects of type Bio::MAGE::NameValueType
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified
$val = $physicalbioassay->addPropertySets(@vals) — because the propertySets association has list cardinality, it may store more than one value. this method adds the current list of objects in the propertySets association.
- Input parameters: the list of values @vals to add to the propertySets association. NOTE: submitting a single value is permitted.
- Return value: the number of items stored in the slot after adding @vals
- Side effects: none
- Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::NameValueType

🧚 physicalBioAssayData 🧚

Methods for the physicalBioAssayData association.

From the MAGE-OM documentation: The Images associated with this PhysicalBioAssay by ImageAcquisition.

$array_ref = $physicalbioassay->setPhysicalBioAssayData($array_ref) — the restricted setter for the physicalBioAssayData association.
- Input parameters: the value to which the physicalBioAssayData association will be set : a reference to an array of objects of type Bio::MAGE::BioAssay::Image
- Return value: the current value of the physicalBioAssayData association : a reference to an array of objects of type Bio::MAGE::BioAssay::Image
- Side effects: none
- Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::BioAssay::Image instances
$array_ref = $physicalbioassay->getPhysicalBioAssayData() — the restricted getter for the physicalBioAssayData association.
- Input parameters: none
- Return value: the current value of the physicalBioAssayData association : a reference to an array of objects of type Bio::MAGE::BioAssay::Image
- Side effects: none

okay so finishing up that getter from the last bit — one last lil bullet and then we move on, promise 💖

Exceptions: will call croak() if any input parameters are specified — so bestie, pass it nothing. It's a getter, it wants zero things, it's low maintenance like that 💅

🧪 `bioAssayTreatments` 🧪

Methods for the bioAssayTreatments association.

From the MAGE-OM documentation:

The set of treatments undergone by this PhysicalBioAssay.

🌸 `$array_ref = $physicalbioassay->setBioAssayTreatments($array_ref)`

The restricted setter method for the bioAssayTreatments association.

Input parameters: the value to which the bioAssayTreatments association will be set : a reference to an array of objects of type Bio::MAGE::BioAssay::BioAssayTreatment
Return value: the current value of the bioAssayTreatments association : a reference to an array of objects of type Bio::MAGE::BioAssay::BioAssayTreatment
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::BioAssay::BioAssayTreatment instances 😭

🦋 `$array_ref = $physicalbioassay->getBioAssayTreatments()`

The restricted getter method for the bioAssayTreatments association.

Input parameters: none
Return value: the current value of the bioAssayTreatments association : a reference to an array of objects of type Bio::MAGE::BioAssay::BioAssayTreatment
Side effects: none ✨
Exceptions: will call croak() if any input parameters are specified 💀

🎀 `$val = $physicalbioassay->addBioAssayTreatments(@vals)`

Because the bioAssayTreatments association has list cardinality, it may store more than one value. This method adds the current list of objects in the bioAssayTreatments association.

Input parameters: the list of values @vals to add to the bioAssayTreatments association. NOTE: submitting a single value is permitted 👑
Return value: the number of items stored in the slot after adding @vals
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::BioAssay::BioAssayTreatment

💜 `bioAssayFactorValues` 💜

Methods for the bioAssayFactorValues association.

From the MAGE-OM documentation:

The values that this BioAssay is associated with for the experiment.

🌈 `$array_ref = $physicalbioassay->setBioAssayFactorValues($array_ref)`

The restricted setter method for the bioAssayFactorValues association.

Input parameters: the value to which the bioAssayFactorValues association will be set : a reference to an array of objects of type Bio::MAGE::Experiment::FactorValue
Return value: the current value of the bioAssayFactorValues association : a reference to an array of objects of type Bio::MAGE::Experiment::FactorValue
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::Experiment::FactorValue instances 😭

⭐ `$array_ref = $physicalbioassay->getBioAssayFactorValues()`

The restricted getter method for the bioAssayFactorValues association.

Input parameters: none
Return value: the current value of the bioAssayFactorValues association : a reference to an array of objects of type Bio::MAGE::Experiment::FactorValue
Side effects: none ✨
Exceptions: will call croak() if any input parameters are specified 💀

🧚 `$val = $physicalbioassay->addBioAssayFactorValues(@vals)`

Because the bioAssayFactorValues association has list cardinality, it may store more than one value. This method adds the current list of objects in the bioAssayFactorValues association.

Input parameters: the list of values @vals to add to the bioAssayFactorValues association. NOTE: submitting a single value is permitted 👑
Return value: the number of items stored in the slot after adding @vals
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Experiment::FactorValue

📝 `descriptions` 📝

Methods for the descriptions association.

From the MAGE-OM documentation:

Free hand text descriptions. Makes available the associations of Description to an instance of Describable.

🍓 `$array_ref = $physicalbioassay->setDescriptions($array_ref)`

The restricted setter method for the descriptions association.

Input parameters: the value to which the descriptions association will be set : a reference to an array of objects of type Bio::MAGE::Description::Description
Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::Description::Description instances 😭

🫶 `$array_ref = $physicalbioassay->getDescriptions()`

The restricted getter method for the descriptions association.

Input parameters: none
Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description
Side effects: none ✨
Exceptions: will call croak() if any input parameters are specified 💀

🌸 `$val = $physicalbioassay->addDescriptions(@vals)`

Because the descriptions association has list cardinality, it may store more than one value. This method adds the current list of objects in the descriptions association.

Input parameters: the list of values @vals to add to the descriptions association. NOTE: submitting a single value is permitted 👑
Return value: the number of items stored in the slot after adding @vals
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::Description

🔒 `security` 🔒

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.

💅 `$val = $physicalbioassay->setSecurity($val)`

The restricted setter method for the security association.

Input parameters: the value to which the security association will be set : one of the accepted enumerated values.
Return value: the current value of the security association : one of the accepted enumerated values.
Side effects: none ✨
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not an instance of class Bio::MAGE::AuditAndSecurity::Security

👑 `$val = $physicalbioassay->getSecurity()`

The restricted getter method for the security association.

Input parameters: none
Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.
Side effects: none ✨
Exceptions: will call croak() if any input parameters are specified 💀

and then — no transition, no warning, nothing — the page just drops this absolute curveball on us 🙈 like ma'am what is this doing here, anyway, here it is, verbatim, exactly as written:

sub initialize {

  my $self = shift;
  return 1;

}

💖 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 💖

okay bestie, listen up — in the Perl implementation of MAGE-OM classes, there are literally three kinds of class data members, and you gotta know which is which: slots, attributes, and associations. three flavors, one class, let's go 🍓

✨ SLOTS ✨

So this API uses the term "slot" to mean a data member of the class that was not present in the UML model, and it's used for mainly internal purposes — so use only if you understand the inner workings of the API. fr fr, don't go poking at the secret machinery 💅

Most often slots are used by generic methods, like the ones chilling in the XML writing and reading classes.

Slots are implemented using unified getter/setter methods — same method name, does both jobs depending on whether you hand it an argument:

$var = $obj->slot_name(); — retrieves 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 (it just hands it right back, so polite).
@names = $obj->get_slot_names() — returns the list of all slots in the class. the whole roster, iconic 👑

DATA CHECKING: No data type checking is made for these methods. like. none. zero. she will not catch your mistakes. 😭

🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

The terms "attribute" and "association" mean data members of the class that were specified directly from the UML model. so these are the official ones — the canon, not the internal secret ones.

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, an array reference is returned.
- DATA CHECKING: ensure that no argument is provided.
set* — sets the current value, replacing any existing value. out with the old, in with the new 💫
- NOTE: for associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.
- DATA CHECKING: for attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is 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. stacking, but make it legal 🧚
- NOTE: only present in associations with list cardinality.
- DATA CHECKING: ensure that all arguments are of the correct MAGE-OM class.

🌈 GENERIC METHODS 🌈

The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that will operate on slots, attributes, and associations. one base class, doing the absolute most for everybody 👑

$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. 👀

💀 BUGS 💀

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)

👑 AUTHOR 👑

Jason E. Stewart (jasons 'at' cpan 'dot' org)

🎀 SEE ALSO 🎀

perl(1).

🙈 POD ERRORS 🙈

Hey! The above document had some coding errors, which are explained below:

Around line 441: '=item' outside of any '=over'
Around line 526: You forgot a '=back' before '=head2'
Around line 698: Expected '=item 2'
Around line 703: Expected '=item 3'
Around line 708: Expected '=item 4'

and that's a wrap on this whole page, bestie 💖 it came to you from perl v5.32.0 and it's dated 2020-11-27 — now go forth, slay, and remember the holy trinity: no argument for get*, array ref for set*, and just use add* like the main character you are. periodt ✨

📦 where this page comes from

debian bookworm: libbio-mage-perl 20030502.3-6 · MIT
debian trixie: libbio-mage-perl 20030502.3-6 · MIT
ubuntu jammy: libbio-mage-perl 20030502.3-6 · MIT
ubuntu noble: libbio-mage-perl 20030502.3-6 · MIT
ubuntu resolute: libbio-mage-perl 20030502.3-6 · MIT
ubuntu stonking: libbio-mage-perl 20030502.3-6 · MIT
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-10-14: a language model's rewrite of the original, under its terms

MAGE::...oAssay(3pm)

✨ NAME ✨

🦋 SYNOPSIS 🦋

🌸 DESCRIPTION 🌸

🎀 INHERITANCE 🎀

👑 CLASS METHODS 👑

🌈 new()

🌈 new(%args)

🌈 $obj = class->new(%parameters)

🌈 @names = class->get_slot_names()

🌈 @name_list = get_attribute_names()

🌈 @name_list = get_association_names()

🌈 @class_list = get_superclasses()

🌈 @class_list = get_subclasses()

🌈 $name = class_name()

🌈 $package_name = package_name()

🌈 %assns = associations()

💅 INSTANCE METHODS 💅

💜 $obj_copy = $obj->new()

💜 $obj->set_slots(%parameters)

💜 $obj->set_slots(@name_list, @value_list)

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

💜 $val = $obj->set_slot($name,$val)

💜 $val = $obj->get_slot($name)

🧚 ATTRIBUTES 🧚

🍓 name

$val = $physicalbioassay->setName($val)

$val = $physicalbioassay->getName()

🍓 identifier

$val = $physicalbioassay->setIdentifier($val)

💖 ASSOCIATIONS 💖

🌸 channels 🌸

🦋 auditTrail 🦋

🎀 bioAssayCreation 🎀

🍓 propertySets 🍓

🧚 physicalBioAssayData 🧚

🧪 bioAssayTreatments 🧪

🌸 $array_ref = $physicalbioassay->setBioAssayTreatments($array_ref)

🦋 $array_ref = $physicalbioassay->getBioAssayTreatments()

🎀 $val = $physicalbioassay->addBioAssayTreatments(@vals)

💜 bioAssayFactorValues 💜

🌈 $array_ref = $physicalbioassay->setBioAssayFactorValues($array_ref)

⭐ $array_ref = $physicalbioassay->getBioAssayFactorValues()

🧚 $val = $physicalbioassay->addBioAssayFactorValues(@vals)

📝 descriptions 📝

🍓 $array_ref = $physicalbioassay->setDescriptions($array_ref)

🫶 $array_ref = $physicalbioassay->getDescriptions()

🌸 $val = $physicalbioassay->addDescriptions(@vals)

🔒 security 🔒

💅 $val = $physicalbioassay->setSecurity($val)

👑 $val = $physicalbioassay->getSecurity()

💖 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 💖

✨ SLOTS ✨

🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

🌈 GENERIC METHODS 🌈

💀 BUGS 💀

👑 AUTHOR 👑

🎀 SEE ALSO 🎀

🙈 POD ERRORS 🙈

🧪 `bioAssayTreatments` 🧪

🌸 `$array_ref = $physicalbioassay->setBioAssayTreatments($array_ref)`

🦋 `$array_ref = $physicalbioassay->getBioAssayTreatments()`

🎀 `$val = $physicalbioassay->addBioAssayTreatments(@vals)`

💜 `bioAssayFactorValues` 💜

🌈 `$array_ref = $physicalbioassay->setBioAssayFactorValues($array_ref)`

⭐ `$array_ref = $physicalbioassay->getBioAssayFactorValues()`

🧚 `$val = $physicalbioassay->addBioAssayFactorValues(@vals)`

📝 `descriptions` 📝

🍓 `$array_ref = $physicalbioassay->setDescriptions($array_ref)`

🫶 `$array_ref = $physicalbioassay->getDescriptions()`

🌸 `$val = $physicalbioassay->addDescriptions(@vals)`

🔒 `security` 🔒

💅 `$val = $physicalbioassay->setSecurity($val)`

👑 `$val = $physicalbioassay->getSecurity()`