MAGE::...dicator(3pm)

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

💖 MAGE::...dicator(3pm) 💖

okay bestie, gather round, because we're about to read a whole Perl manpage together and honestly? it's giving iconic. this is the User Contributed Perl Documentation for MAGE::...dicator(3pm), and yes we're doing all of it. no skimming. no skipping. we eat the whole plate. 🍓

✨ NAME ✨

Bio::MAGE::QuantitationType::ConfidenceIndicator — it's the class for the MAGE-OM API. that's the whole name, that's the whole job, periodt. 💅

🌈 SYNOPSIS 🌈

okay so first things first, you use it:

use Bio::MAGE::QuantitationType::ConfidenceIndicator

# Bio::MAGE::QuantitationType::ConfidenceIndicator is an abstract base class and should not
# be directly instantiated. These examples indicate how subclass
# objects will behave

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

# 'isBackground' attribute
my $isBackground_val = $confidenceindicator->isBackground(); # getter
$confidenceindicator->isBackground($value); # setter

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

# 'dataType' association
my $ontologyentry_ref = $confidenceindicator->dataType(); # getter
$confidenceindicator->dataType($ontologyentry_ref); # setter

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

# 'channel' association
my $channel_ref = $confidenceindicator->channel(); # getter
$confidenceindicator->channel($channel_ref); # setter

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

# 'confidenceIndicators' association
my $confidenceindicator_array_ref = $confidenceindicator->confidenceIndicators(); # getter
$confidenceindicator->confidenceIndicators(\@confidenceindicator_list); # setter

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

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

# 'scale' association
my $ontologyentry_ref = $confidenceindicator->scale(); # getter
$confidenceindicator->scale($ontologyentry_ref); # setter

# 'targetQuantitationType' association
my $quantitationtype_ref = $confidenceindicator->targetQuantitationType(); # getter
$confidenceindicator->targetQuantitationType($quantitationtype_ref); # setter

# 'quantitationTypeMaps' association
my $quantitationtypemap_array_ref = $confidenceindicator->quantitationTypeMaps(); # getter
$confidenceindicator->quantitationTypeMaps(\@quantitationtypemap_list); # setter
🫶 heads up bestie: every single one of those examples is showing you how a subclass object behaves. you do not instantiate this class directly. she's abstract. she's a concept. she's the blueprint, not the house. 💀

🦋 DESCRIPTION 🦋

so. from the MAGE-OM documentation for the "ConfidenceIndicator" class, word for word:

"Indication of some measure of confidence for a standard quantitation type."

that's it, that's the vibe. a little whisper of "how sure are we about this number" attached to a standard quantitation type. 🎀

now the important part, and I need you to lock in:

Bio::MAGE::QuantitationType::ConfidenceIndicator is an abstract base class and should not be directly instantiated. no cap. instead, she serves as an interface definition for her subclasses. she's the friend who sets the group's aesthetic and then lets everyone else show up in it. main character energy, zero solo appearances. ✨

👑 INHERITANCE 👑

Bio::MAGE::QuantitationType::ConfidenceIndicator has the following superclasses:

  • Bio::MAGE::QuantitationType::StandardQuantitationType

and she has the following subclasses:

  • Bio::MAGE::QuantitationType::Error
  • Bio::MAGE::QuantitationType::PValue
  • Bio::MAGE::QuantitationType::ExpectedValue

so she's got one parent and three gorgeous children. a whole family tree, thriving. 🌸

💅 CLASS METHODS 💅

the following methods can all be called without first having an instance of the class, using the

Bio::MAGE::QuantitationType::ConfidenceIndicator->methodname()

syntax. yes, you can just yell at the class directly. she answers. 💖

🌟 new()

🌟 new(%args)

okay so Bio::MAGE::QuantitationType::ConfidenceIndicator is an abstract base class and should not be directly instantiated using the "new()" constructor. it's listed here purely to show you what arguments will be accepted for its subclasses. it's like reading the menu for a restaurant that's only open to family. 😭

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").
  • isBackground — sets the value of the "isBackground" attribute (this attribute was inherited from class "Bio::MAGE::QuantitationType::QuantitationType").
  • identifier — sets the value of the "identifier" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
  • dataType — sets the value of the "dataType" association (this association was inherited from class "Bio::MAGE::QuantitationType::QuantitationType").

the value must be of type: instance of "Bio::MAGE::Description::OntologyEntry".

  • 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".

  • 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".

  • channel — sets the value of the "channel" association (this association was inherited from class "Bio::MAGE::QuantitationType::QuantitationType").

the value must be of type: instance of "Bio::MAGE::BioAssay::Channel".

  • confidenceIndicators — sets the value of the "confidenceIndicators" association (this association was inherited from class "Bio::MAGE::QuantitationType::QuantitationType").

the value must be of type: array of "Bio::MAGE::QuantitationType::ConfidenceIndicator".

  • 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".

  • scale — sets the value of the "scale" association (this association was inherited from class "Bio::MAGE::QuantitationType::QuantitationType").

the value must be of type: instance of "Bio::MAGE::Description::OntologyEntry".

  • 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".

  • targetQuantitationType — sets the value of the "targetQuantitationType" association.

the value must be of type: instance of "Bio::MAGE::QuantitationType::QuantitationType".

  • quantitationTypeMaps — sets the value of the "quantitationTypeMaps" association (this association was inherited from class "Bio::MAGE::QuantitationType::QuantitationType").

the value must be of type: array of "Bio::MAGE::BioAssayData::QuantitationTypeMap".

💜 $obj = class->new(%parameters)

the "new()" method is the class constructor. the moment. the birth. 🦋

Parameters: if you hand her a list of name/value parameters, the corresponding slots, attributes, or associations will get their initial values set by the constructor.

Return value: she returns a reference to an object of the class.

Side effects: she invokes the "initialize()" method if it's defined by the class. sneaky little extra step, but she's thorough. 💅

💜 @names = class->get_slot_names()

the "get_slot_names()" method grabs the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names. so don't come for her about what's missing. 🙈

Return value: a list of the names of all slots defined for this class.

Side effects: none. she's lowkey chill.

💜 @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. so like, just the last name. no middle names. 🎀

💜 %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. it's giving receipts, honestly. 🧾

🌸 INSTANCE METHODS 🌸

🌈 $obj_copy = $obj->new()

when you invoke this with an existing object reference and not a class name, the "new()" method acts as a copy constructor — with the new object's initial values set to be those of the existing object. clone her. duplicate her. she doesn't mind. 💖

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's defined by the class.

🌈 $obj->set_slots(%parameters)

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

the "set_slots()" method sets a number of slots at the same time. two different invocation methods, because why have one way when you can have two:

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

Return value: none

Side effects: will call "croak()" if a slot_name is used that the class does not define. so bestie, if you make up a slot name, she will croak at you. loud. 🐸

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

the "get_slots()" method grabs 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. (uninitialized slots are just ✨mysterious✨.)

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. one to give, one to receive. a whole relationship. 🫶

"Bio::MAGE::QuantitationType::ConfidenceIndicator" has the following attribute accessor methods:

🌟 name

methods for the "name" attribute.

from the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $confidenceindicator->setName($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 = $confidenceindicator->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

🦋 isBackground 🦋

Methods for the isBackground attribute.

From the MAGE-OM documentation:

Indicates whether the quantitation has been measured from the background or from the feature itself.

$val = $confidenceindicator->setIsBackground($val)

The restricted setter method for the isBackground attribute.

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

$val = $confidenceindicator->getIsBackground()

The restricted getter method for the isBackground attribute.

  • Input parameters: none
  • Return value: the current value of the isBackground 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 = $confidenceindicator->setIdentifier($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
  • Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $confidenceindicator->getIdentifier()

The restricted getter method for the identifier attribute.

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

💜 ASSOCIATIONS 💜

ok bestie, deep breath, this is the part where classes start holding hands with other classes. Associations are references to other classes. And in MAGE-OM, an association has a cardinality that decides the minimum and maximum number of instances of the other class that maybe included in the association:

  1. There must be exactly one item in the association, i.e. this is a mandatory data field.
  2. 0..1

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

  1. 1..N

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

  1. 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::QuantitationType::ConfidenceIndicator has the following association accessor methods:

✨ dataType ✨

Methods for the dataType association.

From the MAGE-OM documentation:

The specific type for the quantitations. From a controlled vocabulary of {float, int, boolean, etc.}

$val = $confidenceindicator->setDataType($val)

The restricted setter method for the dataType association.

  • Input parameters: the value to which the dataType association will be set : one of the accepted enumerated values.
  • Return value: the current value of the dataType 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::Description::OntologyEntry

$val = $confidenceindicator->getDataType()

The restricted getter method for the dataType association.

  • Input parameters: none
  • Return value: the current value of the dataType association : an instance of type Bio::MAGE::Description::OntologyEntry.
  • Side effects: none
  • Exceptions: will call croak() if any input parameters are specified

🎀 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 = $confidenceindicator->setAuditTrail($array_ref)

The restricted setter method 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 = $confidenceindicator->getAuditTrail()

The restricted getter method 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 = $confidenceindicator->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

🌟 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 = $confidenceindicator->setPropertySets($array_ref)

The restricted setter method 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 = $confidenceindicator->getPropertySets()

The restricted getter method 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 = $confidenceindicator->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

🌈 channel 🌈

Methods for the channel association.

From the MAGE-OM documentation:

The optional channel associated with the QuantitationType.

$val = $confidenceindicator->setChannel($val)

The restricted setter method for the channel association.

  • Input parameters: the value to which the channel association will be set : one of the accepted enumerated values.
  • Return value: the current value of the channel 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::Channel

$val = $confidenceindicator->getChannel()

The restricted getter method for the channel association.

  • Input parameters: none
  • Return value: the current value of the channel association : an instance of type Bio::MAGE::BioAssay::Channel.
  • Side effects: none
  • Exceptions: will call croak() if any input parameters are specified

🫶 confidenceIndicators 🫶

Methods for the confidenceIndicators association.

From the MAGE-OM documentation:

The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.
  • $array_ref = $confidenceindicator->setConfidenceIndicators($array_ref) — the restricted setter for the confidenceIndicators association</p> 💖
    • Input parameters: the value you're handing to confidenceIndicators — a reference to an array of Bio::MAGE::QuantitationType::ConfidenceIndicator objects
    • Return value: the current value of confidenceIndicators — a reference to an array of Bio::MAGE::QuantitationType::ConfidenceIndicator objects
    • Side effects: none, she's squeaky clean ✨
    • 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::QuantitationType::ConfidenceIndicator instances 😤
  • $array_ref = $confidenceindicator->getConfidenceIndicators() — the restricted getter for the confidenceIndicators association</p> 🫶
    • Input parameters: none, babes, hands off 👋
    • Return value: the current value of confidenceIndicators — a reference to an array of Bio::MAGE::QuantitationType::ConfidenceIndicator objects
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified 💀
  • $val = $confidenceindicator->addConfidenceIndicators(@vals) — because confidenceIndicators has list cardinality, it can hold more than one value, and this is the girl that adds to the current list of objects in the association 🎀
    • Input parameters: the list of values @vals to add to confidenceIndicators. NOTE: submitting a single value is permitted — one is a list too, she doesn't judge 💅
    • 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::QuantitationType::ConfidenceIndicator

🌸 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 = $confidenceindicator->setDescriptions($array_ref) — the restricted setter for the descriptions association</p>
    • Input parameters: the value you're setting descriptions to — a reference to an array of Bio::MAGE::Description::Description objects
    • Return value: the current value of descriptions — a reference to an array of Bio::MAGE::Description::Description objects
    • 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 = $confidenceindicator->getDescriptions() — the restricted getter for the descriptions association</p> ✨
    • Input parameters: none
    • Return value: the current value of descriptions — a reference to an array of Bio::MAGE::Description::Description objects
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified
  • $val = $confidenceindicator->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

🔥 scale 🔥

Methods for the scale association.

From the MAGE-OM documentation:

Indication of how to interpret the value. From a suggested vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER}
  • $val = $confidenceindicator->setScale($val) — the restricted setter for the scale association</p>
    • Input parameters: the value you're setting scale to — one of the accepted enumerated values
    • Return value: the current value of scale — 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::Description::OntologyEntry 💀
  • $val = $confidenceindicator->getScale() — the restricted getter for the scale association</p> 👑
    • Input parameters: none
    • Return value: the current value of scale — an instance of type Bio::MAGE::Description::OntologyEntry
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified

🔒 security 🔒

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.
  • $val = $confidenceindicator->setSecurity($val) — the restricted setter for the security association</p> 🫶
    • Input parameters: the value you're setting security to — one of the accepted enumerated values
    • Return value: the current value of security — 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 = $confidenceindicator->getSecurity() — the restricted getter for the security association</p> ✨
    • Input parameters: none
    • Return value: the current value of security — an instance of type Bio::MAGE::AuditAndSecurity::Security
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified

🎯 targetQuantitationType 🎯

Methods for the targetQuantitationType association.

From the MAGE-OM documentation:

The association between a ConfidenceIndicator and the QuantitationType its is an indicator for.
  • $val = $confidenceindicator->setTargetQuantitationType($val) — the restricted setter for the targetQuantitationType association</p>
    • Input parameters: the value you're setting targetQuantitationType to — one of the accepted enumerated values
    • Return value: the current value of targetQuantitationType — 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::QuantitationType::QuantitationType 😤
  • $val = $confidenceindicator->getTargetQuantitationType() — the restricted getter for the targetQuantitationType association</p> 🌈
    • Input parameters: none
    • Return value: the current value of targetQuantitationType — an instance of type Bio::MAGE::QuantitationType::QuantitationType
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified

🧚 quantitationTypeMaps 🧚

Methods for the quantitationTypeMaps association.

From the MAGE-OM documentation:

The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.
  • $array_ref = $confidenceindicator->setQuantitationTypeMaps($array_ref) — the restricted setter for the quantitationTypeMaps association</p> 💖
    • Input parameters: the value you're setting quantitationTypeMaps to — a reference to an array of Bio::MAGE::BioAssayData::QuantitationTypeMap objects
    • Return value: the current value of quantitationTypeMaps — a reference to an array of Bio::MAGE::BioAssayData::QuantitationTypeMap objects
    • 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::BioAssayData::QuantitationTypeMap instances
  • $array_ref = $confidenceindicator->getQuantitationTypeMaps() — the restricted getter for the quantitationTypeMaps association</p> 💅
    • Input parameters: none
    • Return value: the current value of quantitationTypeMaps — a reference to an array of Bio::MAGE::BioAssayData::QuantitationTypeMap objects
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified
  • $val = $confidenceindicator->addQuantitationTypeMaps(@vals) — because the quantitationTypeMaps association has list cardinality, it may store more than one value. This method adds the current list of objects in the quantitationTypeMaps association 🍓
    • Input parameters: the list of values @vals to add to the quantitationTypeMaps 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::BioAssayData::QuantitationTypeMap

and then the page literally just starts showing you the source, like, mid-breath:

sub initialize {

(yes bestie we're going there — the code continues in the next part, hold on 🫶)

             carp __PACKAGE__ . "::initialize: abstract base classes should not be instantiated";

           }

🌸 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 🌸

okay so bestie, in the Perl implementation of MAGE-OM classes there are literally three types of class data members: slots, attributes, and associations. periodt.

✨ SLOTS ✨

This API uses the term slot to indicate a data member of the class that was not present in the UML model and is used for mainly internal purposes - use only if you understand the inner workings of the API. Most often slots are used by generic methods such as those in the XML writing and reading classes.

Slots are implemented using unified getter/setter methods:

  • $var = $obj->slot_name(); — Retrieves the current value of the slot.
  • $new_var = $obj->slot_name($new_var); — Store $new_var in the slot - the return value is also $new_var.
  • @names = $obj->get_slot_names() — Returns the list of all slots in the class.
DATA CHECKING: No data type checking is made for these methods.

💖 ATTRIBUTES AND ASSOCIATIONS 💖

The terms attribute and association indicate data members of the class that were specified directly from the UML model.

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.
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* — NOTE: Only present in associations with list cardinality.

Appends a list of objects to any values that may already be stored in the association.

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:

$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 435: '=item' outside of any '=over'
  • Around line 520: You forgot a '=back' before '=head2'
  • Around line 764: Expected '=item 2'
  • Around line 769: Expected '=item 3'
  • Around line 774: Expected '=item 4'

This page came from perl v5.32.0, dated 2020-11-27, and it's the MAGE::...dicator(3pm) manual page. slay. 💅✨

📦 where this page comes from