MAGE::...Design(3pm)

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

💖 NAME 💖

okay so bestie, welcome to the MAGE::...Design(3pm) page (user contributed Perl documentation, no cap) 💅. It's all about Bio::MAGE::ArrayDesign::ArrayDesign — Class for the MAGE-OM API. That's the whole vibe: one class, big main character energy, here to describe array designs. ✨

✨ SYNOPSIS ✨

Here's the code, exactly as it slays:

         use Bio::MAGE::ArrayDesign::ArrayDesign

         # creating an empty instance
         my $arraydesign = Bio::MAGE::ArrayDesign::ArrayDesign->new();

         # creating an instance with existing data
         my $arraydesign = Bio::MAGE::ArrayDesign::ArrayDesign->new(
               numberOfFeatures=>$numberoffeatures_val,
               version=>$version_val,
               name=>$name_val,
               identifier=>$identifier_val,
               auditTrail=>\@audit_list,
               propertySets=>\@namevaluetype_list,
               designProviders=>\@contact_list,
               protocolApplications=>\@protocolapplication_list,
               reporterGroups=>\@reportergroup_list,
               featureGroups=>\@featuregroup_list,
               descriptions=>\@description_list,
               security=>$security_ref,
               compositeGroups=>\@compositegroup_list,
         );

         # 'numberOfFeatures' attribute
         my $numberOfFeatures_val = $arraydesign->numberOfFeatures(); # getter
         $arraydesign->numberOfFeatures($value); # setter

         # 'version' attribute
         my $version_val = $arraydesign->version(); # getter
         $arraydesign->version($value); # setter

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

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

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

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

         # 'designProviders' association
         my $contact_array_ref = $arraydesign->designProviders(); # getter
         $arraydesign->designProviders(\@contact_list); # setter

         # 'protocolApplications' association
         my $protocolapplication_array_ref = $arraydesign->protocolApplications(); # getter
         $arraydesign->protocolApplications(\@protocolapplication_list); # setter

         # 'reporterGroups' association
         my $reportergroup_array_ref = $arraydesign->reporterGroups(); # getter
         $arraydesign->reporterGroups(\@reportergroup_list); # setter

         # 'featureGroups' association
         my $featuregroup_array_ref = $arraydesign->featureGroups(); # getter
         $arraydesign->featureGroups(\@featuregroup_list); # setter

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

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

         # 'compositeGroups' association
         my $compositegroup_array_ref = $arraydesign->compositeGroups(); # getter
         $arraydesign->compositeGroups(\@compositegroup_list); # setter

🌸 DESCRIPTION 🌸

From the MAGE-OM documentation for the ArrayDesign class:

Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features.

🦋 INHERITANCE 🦋

Bio::MAGE::ArrayDesign::ArrayDesign has the following superclasses:

Bio::MAGE::Identifiable

Bio::MAGE::ArrayDesign::ArrayDesign has the following subclasses:

Bio::MAGE::ArrayDesign::PhysicalArrayDesign

👑 CLASS METHODS 👑

The following methods can all be called without first having an instance of the class via the Bio::MAGE::ArrayDesign::ArrayDesign->methodname() syntax.

`new()`

`new(%args)`

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

numberOfFeatures — Sets the value of the numberOfFeatures attribute
version — Sets the value of the version attribute
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).
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.
designProviders — Sets the value of the designProviders association. The value must be of type: array of Bio::MAGE::AuditAndSecurity::Contact.
reporterGroups — Sets the value of the reporterGroups association. The value must be of type: array of Bio::MAGE::ArrayDesign::ReporterGroup.
protocolApplications — Sets the value of the protocolApplications association. The value must be of type: array of Bio::MAGE::Protocol::ProtocolApplication.
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.
featureGroups — Sets the value of the featureGroups association. The value must be of type: array of Bio::MAGE::ArrayDesign::FeatureGroup.
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.
compositeGroups — Sets the value of the compositeGroups association. The value must be of type: array of Bio::MAGE::ArrayDesign::CompositeGroup.

`$obj = class->new(%parameters)`

The new() method is the class constructor.

Parameters: if given 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 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.

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.

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.

`@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.

Bio::MAGE::ArrayDesign::ArrayDesign has the following attribute accessor methods:

`numberOfFeatures`

Methods for the numberOfFeatures attribute.

From the MAGE-OM documentation:

The number of features for this array

$val = $arraydesign->setNumberOfFeatures($val)

The restricted setter method for the numberOfFeatures attribute.

Input parameters: the value to which the numberOfFeatures attribute will be set

Return value: the current value of the numberOfFeatures attribute

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $arraydesign->getNumberOfFeatures()

The restricted getter method for the numberOfFeatures attribute.

Input parameters: none

Return value: the current value of the numberOfFeatures attribute

Side effects: none

Exceptions: will call croak() if any input parameters are specified

version 🌸

Okay bestie, this is the method bundle for the version attribute. Straight from the MAGE-OM docs, here's the whole vibe:

The version of this design.

$val = $arraydesign->setVersion($val)

The restricted setter method for the version attribute. It sets, it doesn't chat. Restricted means it only does the one job 💅

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

$val = $arraydesign->getVersion()

The restricted getter method for the version attribute. Give it nothing, it gives you the goods ✨

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

name 🎀

Methods for the name attribute. The MAGE-OM documentation says, and I quote:

The potentially ambiguous common identifier.

Yes bestie, potentially ambiguous — that's a real quote, that's the actual spec being honest with us 😭

$val = $arraydesign->setName($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 = $arraydesign->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. And here's the MAGE-OM lore, which honestly ate:

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.

See? name can be ambiguous, but identifier is the one with main character energy — it's unique within its scope, periodt. 💖

$val = $arraydesign->setIdentifier($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 = $arraydesign->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 🦋

Okay so this is the part where the classes start holding hands with other classes 🫶. Associations are references to other classes. And — important — 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:

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.

And Bio::MAGE::ArrayDesign::ArrayDesign has the following association accessor methods, bestie. Buckle in 💅

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 = $arraydesign->setAuditTrail($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 = $arraydesign->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 = $arraydesign->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. List cardinality means it's a hoarder and that's valid 🍓

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.

It's giving escape hatch for your pipeline's weird little extras, and honestly? Iconic. 🙈

$array_ref = $arraydesign->setPropertySets($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 = $arraydesign->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 = $arraydesign->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

designProviders 💖

Methods for the designProviders association.

From the MAGE-OM documentation:

The primary contact for information on the array design

That's the person you @ in the group chat when the array design is acting up, fr fr 🫶

$array_ref = $arraydesign->setDesignProviders($array_ref)

The restricted setter method for the designProviders association.

Input parameters: the value to which the designProviders association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
Return value: the current value of the designProviders association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
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::Contact instances

$array_ref = $arraydesign->getDesignProviders()

The restricted getter method for the designProviders association.

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

$val = $arraydesign->addDesignProviders(@vals)

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

Input parameters: the list of values @vals to add to the designProviders 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::Contact

reporterGroups 🌈

Methods for the reporterGroups association.

From the MAGE-OM documentation:

The grouping of like Reporter together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple ReporterGroups to segregate the technology types.

So yeah — mixing technologies on one array means you get multiple ReporterGroups to keep the technology types from getting all up in each other's business. Segregation, but make it data modelling 💀

$array_ref = $arraydesign->setReporterGroups($array_ref)

The restricted setter method for the reporterGroups association.

Input parameters: the value to which the reporterGroups association will be set — a reference to an array of objects of type Bio::MAGE::ArrayDesign::ReporterGroup 💫

Return value: the current value of the reporterGroups association — a reference to an array of objects of type Bio::MAGE::ArrayDesign::ReporterGroup

Side effects: none, she's chill 😌

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::ArrayDesign::ReporterGroup instances

`$array_ref = $arraydesign->getReporterGroups()`

The restricted getter for the reporterGroups association, bestie 🫶

Input parameters: none — she takes nothing, she just gives
Return value: the current value of the reporterGroups association — a reference to an array of objects of type Bio::MAGE::ArrayDesign::ReporterGroup
Side effects: none
Exceptions: will call croak() if any input parameters are specified

`$val = $arraydesign->addReporterGroups(@vals)`

Because the reporterGroups association has list cardinality, it may store more than one value. This method adds the current list of objects in the reporterGroups association. It's giving "the more the merrier" 💅

Input parameters: the list of values @vals to add to the reporterGroups 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::ArrayDesign::ReporterGroup

✨ protocolApplications ✨

Methods for the protocolApplications association.

From the MAGE-OM documentation:

Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array. 🧬

`$array_ref = $arraydesign->setProtocolApplications($array_ref)`

The restricted setter for the protocolApplications association.

Input parameters: the value to which the protocolApplications association will be set — a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication
Return value: the current value of the protocolApplications association — a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication
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::Protocol::ProtocolApplication instances

`$array_ref = $arraydesign->getProtocolApplications()`

The restricted getter for the protocolApplications association.

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

`$val = $arraydesign->addProtocolApplications(@vals)`

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

Input parameters: the list of values @vals to add to the protocolApplications 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::Protocol::ProtocolApplication

✨ 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 = $arraydesign->setDescriptions($array_ref)`

The restricted setter 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 = $arraydesign->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 = $arraydesign->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

✨ featureGroups ✨

Methods for the featureGroups association.

From the MAGE-OM documentation:

The grouping of like Features together. Typically for a physical array design, this will be a single grouping of features whose type might be PCR Product or Oligo. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple FeatureGroups to segregate the technology types. 🧪

`$array_ref = $arraydesign->setFeatureGroups($array_ref)`

The restricted setter for the featureGroups association.

Input parameters: the value to which the featureGroups association will be set — a reference to an array of objects of type Bio::MAGE::ArrayDesign::FeatureGroup
Return value: the current value of the featureGroups association — a reference to an array of objects of type Bio::MAGE::ArrayDesign::FeatureGroup
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::ArrayDesign::FeatureGroup instances

`$array_ref = $arraydesign->getFeatureGroups()`

The restricted getter for the featureGroups association.

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

`$val = $arraydesign->addFeatureGroups(@vals)`

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

Input parameters: the list of values @vals to add to the featureGroups 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::ArrayDesign::FeatureGroup

✨ security ✨

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class. 🔒

`$val = $arraydesign->setSecurity($val)`

The restricted setter 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 = $arraydesign->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

✨ compositeGroups ✨

Methods for the compositeGroups association.

From the MAGE-OM documentation:

The grouping of like CompositeSequence together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple CompositeGroups to segregate the technology types. 🧫

`$array_ref = $arraydesign->setCompositeGroups($array_ref)`

The restricted setter for the compositeGroups association.

Input parameters: the value to which the compositeGroups association will be set — a reference to an array of objects of type Bio::MAGE::ArrayDesign::CompositeGroup
Return value: the current value of the compositeGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::CompositeGroup
- 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::ArrayDesign::CompositeGroup instances
$array_ref = $arraydesign->getCompositeGroups() — the restricted getter method for the compositeGroups association. just reads it, doesn't touch it, we love a respectful king 💅
- Input parameters: none
- Return value: the current value of the compositeGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::CompositeGroup
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified
$val = $arraydesign->addCompositeGroups(@vals) — because the compositeGroups association has list cardinality, it may store more than one value. This method adds the current list of objects in the compositeGroups association. stack 'em up bestie, the more the merrier 🫶
- Input parameters: the list of values @vals to add to the compositeGroups 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::ArrayDesign::CompositeGroup

And then there's this little baby just vibing at the end of all that:

sub initialize {

  my $self = shift;
  return 1;

}

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

Okay so in the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations. three whole flavors, a whole trio, iconic behavior fr fr

🌸 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. ngl this is the backstage area, don't wander in unless you know the choreography 💀

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. none. zero. nada. it's giving "trust me bro" 😭

🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

The terms "attribute" and "association" indicate data members of the class that were specified directly from the UML model. the real ones, the canon 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.
- 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. bestie pls just use add*, the set* on a list is a trap okay
- 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. it's giving "go read the rest of the doc, i'm not your search engine" 💜

💀 BUGS 💀

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net) tell them everything bestie, they wanna know 🫶

🌈 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 510: '=item' outside of any '=over'
Around line 595: You forgot a '=back' before a '=head2'
Around line 911: Expected '=item 2'
Around line 916: Expected '=item 3'
Around line 921: Expected '=item 4'

and that's the whole page bestie, we ate and left no crumbs 💅✨ this one came from perl v5.32.0, dated 2020-11-27 — MAGE::...Design(3pm), no cap, iconic, 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