MAGE::...tAbsent(3pm)

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

👑 MAGE::...tAbsent(3pm) 👑

User Contributed Perl Documentation — yeah bestie, this is that page. Sit down, get a snack, we're doing MAGE-OM Perl modules today and honestly? it's giving very structured. 🍓

✨ NAME ✨

Bio::MAGE::QuantitationType::PresentAbsent — the class for the MAGE-OM API 💅

🌸 SYNOPSIS 🌸

Okay so here's the whole vibe in code. Every line, exactly as it lives:

  use Bio::MAGE::QuantitationType::PresentAbsent

  # creating an empty instance
  my $presentabsent = Bio::MAGE::QuantitationType::PresentAbsent->new();

  # creating an instance with existing data
  my $presentabsent = Bio::MAGE::QuantitationType::PresentAbsent->new(
        name=>$name_val,
        isBackground=>$isbackground_val,
        identifier=>$identifier_val,
        dataType=>$ontologyentry_ref,
        auditTrail=>\@audit_list,
        channel=>$channel_ref,
        propertySets=>\@namevaluetype_list,
        confidenceIndicators=>\@confidenceindicator_list,
        descriptions=>\@description_list,
        scale=>$ontologyentry_ref,
        security=>$security_ref,
        quantitationTypeMaps=>\@quantitationtypemap_list,
  );

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

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

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

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

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

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

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

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

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

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

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

  # 'quantitationTypeMaps' association
  my $quantitationtypemap_array_ref = $presentabsent->quantitationTypeMaps(); # getter
  $presentabsent->quantitationTypeMaps(\@quantitationtypemap_list); # setter

🦋 DESCRIPTION 🦋

Straight from the MAGE-OM documentation for the "PresentAbsent" class, and I quote:

Indicates relative presence or absence. From the enumeration AbsoluteCallTypeEnum {Present | Absent | Marginal | No call} or ComparisonCallTypeEnum {Increase I Marginal Increase | Decrease | Marginal Decrease | No change | No Call | Unknown }, as specified by the dataType.

Periodt. That's the whole point of this class — it's the "was it there or not, and how sure are we" energy. 🫶

🌈 INHERITANCE 🌈

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

  • Bio::MAGE::QuantitationType::StandardQuantitationType

So it's lowkey built on top of that one. Family tree moment. 👑

💜 CLASS METHODS 💜

All of these can be called without having an instance first — you just go straight through the class like this:

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

new()

new(%args)

The object constructor "new()" accepts the following optional named-value style arguments — yes, all eleven of them, no skipping:

  • 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".

  • 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".

  • 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".

  • 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. It's the main character of this whole page honestly. 🌟

Parameters: if you hand it a list of name/value parameters, the corresponding slots, attributes, or associations get 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 used to retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names. Just so you're not out here confused, bestie. 🙈

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 invoked 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 slay. ✨

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.

Return value: none

Side effects: will call "croak()" if a slot_name is used that the class does not define. Yes, it will yell at you. Don't test it for fun. 💀

@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. Two methods per attribute, always, no exceptions. 💅

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

name

Methods for the "name" attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $presentabsent->setName($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 = $presentabsent->getName()

The restricted getter for the "name" attribute. Yeah, "restricted" — meaning it wants nothing from you, bestie. It's a getter, it just hands over the goods ✨

  • 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 = $presentabsent->setIsBackground($val)

The restricted setter for the "isBackground" attribute. Give it a value, it sets the value, we move on 💅

  • 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 = $presentabsent->getIsBackground()

The restricted getter 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 = $presentabsent->setIdentifier($val)

The restricted setter for the "identifier" attribute. Unambiguous, unique, iconic. periodt.

  • 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 = $presentabsent->getIdentifier()

The restricted getter 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 🌈

Associations are references to other classes. Associations in MAGE-OM have a cardinality that determines the minimum and maximum number of instances of the 'other' class that maybe included in the association. (Yes, "maybe" — that's the original wording, don't come for me 🙈)

  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.
  3. 1..N — There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
  4. 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::PresentAbsent 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 = $presentabsent->setDataType($val)

The restricted setter 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 = $presentabsent->getDataType()

The restricted getter 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 = $presentabsent->setAuditTrail($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 = $presentabsent->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 = $presentabsent->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. It's giving "yes, and" energy 🫶

  • 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 = $presentabsent->setPropertySets($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 = $presentabsent->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 = $presentabsent->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 = $presentabsent->setChannel($val)

The restricted setter 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 = $presentabsent->getChannel()

The restricted getter 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 = $presentabsent->setConfidenceIndicators($array_ref)

The restricted setter for the "confidenceIndicators" association.

  • Input parameters: the value to which the "confidenceIndicators" association will be set : a reference to an array of objects of type Bio::MAGE::QuantitationType::ConfidenceIndicator
  • Return value: the current value of the "confidenceIndicators" association : a reference to an array of objects of type Bio::MAGE::QuantitationType::ConfidenceIndicator
  • Side effects: none, bestie. Literally nothing happens. 🫶
  • Exceptions: it WILL call croak() on you if you pass no input parameters, if you pass too many input parameters, or if $array_ref isn't a reference to an array of class Bio::MAGE::QuantitationType::ConfidenceIndicator instances 😭 no cap
  • $array_ref = $presentabsent->getConfidenceIndicators() — the restricted getter for the confidenceIndicators association. Just vibing, just reading, not touching 💅
    • Input parameters: none 🚫
    • Return value: the current value of the confidenceIndicators association — a reference to an array of objects of type Bio::MAGE::QuantitationType::ConfidenceIndicator ✨
    • Side effects: none
    • Exceptions: it'll call croak() if you specify any input parameters at all
  • $val = $presentabsent->addConfidenceIndicators(@vals) — because the confidenceIndicators association has list cardinality, it can hold more than one value, so this one adds the current list of objects into it. The way that this just keeps stacking them 👑
    • Input parameters: the list of values @vals to add to the confidenceIndicators association. NOTE: submitting a single value is permitted — a party of one is still a party 🎀
    • 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 = $presentabsent->setDescriptions($array_ref) — the restricted setter for the descriptions association. You're setting the whole array, no half measures 🔒
    • 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 = $presentabsent->getDescriptions() — the restricted getter 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 = $presentabsent->addDescriptions(@vals) — since 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. Collect them all, fr fr 🦋
    • 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 = $presentabsent->setSecurity($val) — the restricted setter for the security association. Lock it down, bestie 🗝️
    • 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 = $presentabsent->getSecurity() — the restricted getter 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

📏 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 = $presentabsent->setScale($val) — the restricted setter for the scale association.
    • Input parameters: the value to which the scale association will be set — one of the accepted enumerated values.
    • Return value: the current value of the scale 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 = $presentabsent->getScale() — the restricted getter for the scale association.
    • Input parameters: none
    • Return value: the current value of the scale association — an instance of type Bio::MAGE::Description::OntologyEntry. ⭐
    • 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 = $presentabsent->setQuantitationTypeMaps($array_ref) — the restricted setter for the quantitationTypeMaps association. Drop the whole array in, main character energy 🔥
    • Input parameters: the value to which the quantitationTypeMaps association will be set — a reference to an array of objects of type Bio::MAGE::BioAssayData::QuantitationTypeMap
    • Return value: the current value of the quantitationTypeMaps association — a reference to an array of objects of type Bio::MAGE::BioAssayData::QuantitationTypeMap
    • 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 = $presentabsent->getQuantitationTypeMaps() — the restricted getter for the quantitationTypeMaps association.
    • Input parameters: none
    • Return value: the current value of the quantitationTypeMaps association — a reference to an array of objects of type Bio::MAGE::BioAssayData::QuantitationTypeMap 🌈
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified
  • $val = $presentabsent->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. More is more, periodt 💅
    • 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 there's this little guy just sitting there at the bottom of the file, doing absolutely the most by doing the least 😌

sub initialize {

  my $self = shift;
  return 1;

}

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

ok so in the Perl implementation of MAGE-OM classes there are literally three types of class data members, and bestie you need to know all three: "slots", "attributes", and "associations". let's go 🫶

🌸 SLOTS 🌸

so this API uses the word "slot" to mean a data member of the class that was not in the UML model — it's there for mainly internal purposes. translation: only touch this if you actually 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. iykyk 💅

slots are implemented with unified getter/setter methods, and the way that they're unified is honestly iconic:

  • $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? you get your thing back.
  • @names = $obj->get_slot_names() — returns the list of every slot in the class. all of them. the whole squad.
DATA CHECKING: no data type checking is made for these methods. none. zero. it's giving free-for-all 🙈

🦋 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 real, official ones, 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. literally do not pass anything. hands off 🙅‍♀️
  • set* — sets the current value, replacing any existing value. the old value? gone. periodt.
NOTE: for associations, if the association has list cardinality, the argument must be an array reference. and because of that, you probably should be using the add* methods instead. like, just use add*, bestie, it's the vibe 💅
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. so, yeah, the type check goes hard here.
  • add* — appends a list of objects to any values that may already be stored in the association.
NOTE: only present in associations with list cardinality. if it's not there, that's why. don't come for me 🌸
DATA CHECKING: ensure that all arguments are of the correct MAGE-OM class. all of them. every single one 🎀

🎀 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. it's the main character of the inheritance tree, honestly:

$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. (yes, go look, it's all there 🫶)

💀 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. not me reading the error log like it's a group chat 💀

Around line 390:

  • '=item' outside of any '=over'

Around line 475:

  • you forgot a '=back' before a '=head2'

Around line 719:

  • expected '=item 2'

Around line 724:

  • expected '=item 3'

Around line 729:

  • expected '=item 4'

and that's a wrap on this whole page, bestie!! 🫶✨ this was perl v5.32.0, dated 2020-11-27, and it's the MAGE::...tAbsent(3pm) manpage — slay, go forth and query your slots responsibly 💖

📦 where this page comes from