MAGE::...luster(3pm)

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

💖 NAME 💖

Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster — a whole class for the MAGE-OM API, bestie. 🦋

And yeah, the official page header says MAGE::...luster(3pm) under User Contributed Perl Documentation — that's this page, it's just abbreviated for the shelf. We're so back.

✨ SYNOPSIS ✨

Okay so here's the whole vibe of using this thing, literally every line:

  use Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster

  # creating an empty instance
  my $bioassaydatacluster = Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster->new();

  # creating an instance with existing data
  my $bioassaydatacluster = Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster->new(
        identifier=>$identifier_val,
        name=>$name_val,
        descriptions=>\@description_list,
        security=>$security_ref,
        auditTrail=>\@audit_list,
        nodes=>\@node_list,
        propertySets=>\@namevaluetype_list,
        clusterBioAssayData=>$bioassaydata_ref,
  );

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

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

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

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

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

  # 'nodes' association
  my $node_array_ref = $bioassaydatacluster->nodes(); # getter
  $bioassaydatacluster->nodes(\@node_list); # setter

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

  # 'clusterBioAssayData' association
  my $bioassaydata_ref = $bioassaydatacluster->clusterBioAssayData(); # getter
  $bioassaydatacluster->clusterBioAssayData($bioassaydata_ref); # setter

Getters AND setters for days. Setter gang where u at. 💅

🧚 DESCRIPTION 🧚

Straight from the MAGE-OM documentation for the "BioAssayDataCluster" class, no notes:

A mathematical method of higher level analysis whereby BioAssayData are grouped together into nodes.

Math girlies rise, that's the whole concept. 🍓

🌈 INHERITANCE 🌈

Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster has the following superclasses:

Bio::MAGE::Identifiable

So it inherited the family traits, iykyk. 👑

🌸 CLASS METHODS 🌸

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

Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster->methodname()

syntax. No object required, just raw class energy.

`new()`

`new(%args)`

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

identifier — Sets the value of the "identifier" attribute. Fun fact: this attribute was inherited from class Bio::MAGE::Identifiable.
name — Sets the value of the "name" attribute. Also inherited from class Bio::MAGE::Identifiable.
descriptions — Sets the value of the "descriptions" association. Inherited from class Bio::MAGE::Describable, bestie.

The value must be of type: array of Bio::MAGE::Description::Description.

auditTrail — Sets the value of the "auditTrail" association. Also inherited from class Bio::MAGE::Describable.

The value must be of type: array of Bio::MAGE::AuditAndSecurity::Audit.

security — Sets the value of the "security" association. Yep, inherited from class Bio::MAGE::Describable too.

The value must be of type: instance of Bio::MAGE::AuditAndSecurity::Security.

propertySets — Sets the value of the "propertySets" association. This one was inherited from class Bio::MAGE::Extendable.

The value must be of type: array of Bio::MAGE::NameValueType.

nodes — Sets the value of the "nodes" association. Homegrown, not inherited. ✨

The value must be of type: array of Bio::MAGE::HigherLevelAnalysis::Node.

clusterBioAssayData — Sets the value of the "clusterBioAssayData" association. Also its own thing.

The value must be of type: instance of Bio::MAGE::BioAssayData::BioAssayData.

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

The new() method is the class constructor, the blueprint, the main character.

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. Don't @ me, that's just how it is.

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

Side effects: none. Peaceful. 🕊️

`@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 era. 👯

Parameters: No input parameters are used in the copy constructor, the initial values are taken directly from the object to be copied.

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

Side effects: It invokes the initialize() method if it is defined by the class.

`$obj->set_slots(%parameters)`

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

The set_slots() method is used to set a number of slots at the same time. It has two different invocation methods. The first takes a named parameter list, and the second takes two array references. Pick your fighter. 🥊

Return value: none

Side effects: will call croak() if a slot_name is used that the class does not define. So like, don't make up slots, bestie. 😭

`@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, no sharing, very independent. ✨

Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster has the following attribute accessor methods:

`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 = $bioassaydatacluster->setIdentifier($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 = $bioassaydatacluster->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

`name`

Methods for the "name" attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $bioassaydatacluster->setName($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 = $bioassaydatacluster->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

🫶 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. Cardinality is basically the vibe check on how many friends this field is allowed to bring:

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

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

1..N

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

0..N

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

Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster has the following association accessor methods:

💬 descriptions

Methods for the descriptions association. Let's get into it 💖

From the MAGE-OM documentation:

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

$array_ref = $bioassaydatacluster->setDescriptions($array_ref) — the restricted setter method for the descriptions association.
- Input parameters: the value to which the descriptions association will be set : a reference to an array of objects of type Bio::MAGE::Description::Description
- Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description
- Side effects: none
- Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::Description::Description instances
$array_ref = $bioassaydatacluster->getDescriptions() — the restricted getter method for the descriptions association.
- Input parameters: none
- Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified
$val = $bioassaydatacluster->addDescriptions(@vals) — bestie, the descriptions association has list cardinality, so it can hold more than one value. This method adds the current list of objects sitting 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

📜 auditTrail

Methods for the auditTrail association. It's giving receipts ✨

From the MAGE-OM documentation:

A list of Audit instances that track changes to the instance of Describable.

$array_ref = $bioassaydatacluster->setAuditTrail($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 = $bioassaydatacluster->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 = $bioassaydatacluster->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

🔒 security

Methods for the security association. Protect the vibes 🫶

From the MAGE-OM documentation:

Information on the security for the instance of the class.

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

🏷️ 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 = $bioassaydatacluster->setPropertySets($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 = $bioassaydatacluster->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 = $bioassaydatacluster->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

🦋 nodes

Methods for the nodes association.

From the MAGE-OM documentation:

The nodes of the cluster.

$array_ref = $bioassaydatacluster->setNodes($array_ref) — the restricted setter method for the nodes association.
- Input parameters: the value to which the nodes association will be set : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::Node
- Return value: the current value of the nodes association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::Node
- 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::HigherLevelAnalysis::Node instances
$array_ref = $bioassaydatacluster->getNodes() — the restricted getter method for the nodes association.
- Input parameters: none
- Return value: the current value of the nodes association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::Node
- Side effects: none
- Exceptions: will call croak() if any input parameters are specified
$val = $bioassaydatacluster->addNodes(@vals) — because the nodes association has list cardinality, it may store more than one value. This method adds the current list of objects in the nodes association.
- Input parameters: the list of values @vals to add to the nodes 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::HigherLevelAnalysis::Node

🧬 clusterBioAssayData

Methods for the clusterBioAssayData association.

From the MAGE-OM documentation:

The BioAssayData whose values were used by the cluster algorithm.

$val = $bioassaydatacluster->setClusterBioAssayData($val) — the restricted setter method for the clusterBioAssayData association.
- Input parameters: the value to which the clusterBioAssayData association will be set : one of the accepted enumerated values.
- Return value: the current value of the clusterBioAssayData 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::BioAssayData::BioAssayData
$val = $bioassaydatacluster->getClusterBioAssayData() — the restricted getter for the clusterBioAssayData association. She's picky, bestie, she only wants the reading job 💅
- Input parameters: none — like, zero, nada, do not send anyone 🚫
- Return value: whatever clusterBioAssayData is holding rn — an instance of type Bio::MAGE::BioAssayData::BioAssayData ✨
- Side effects: none, she's a clean girl 🌸
- Exceptions: she will croak() at you if you dare pass any input parameters. Not a vibe. Do not test her. 💀

sub initialize {

  my $self = shift;
  return 1;

}

🌈 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 🌈

okay so in the Perl implementation of MAGE-OM classes there are three kinds of class data members, and you gotta know the difference: slots, attributes, and associations. Let's break it down 🫶

🎀 SLOTS 🎀

This API uses the term slot for a data member that wasn't in the UML model at all — it's mainly for internal stuff. So like, only touch it if you genuinely understand the inner workings of the API, no cap. Most of the time slots get used by generic methods like the ones in the XML writing and reading classes.

Slots are implemented with unified getter/setter methods:

$var = $obj->slot_name(); — grabs the current value of the slot 📥
$new_var = $obj->slot_name($new_var); — stores $new_var in the slot, and the return value is also $new_var (cute, she gives it right back) 🎁
@names = $obj->get_slot_names() — returns the list of all the slots in the class 📝

DATA CHECKING: No data type checking is made for these methods. She's trusting you fr fr. 🙈

💖 ATTRIBUTES AND ASSOCIATIONS 💖

The terms attribute and association mean data members of the class that were specified directly from the UML model. Iconic, model-accurate, we love to see it.

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. She asked for nothing and she means it 💅

set* — sets the current value, replacing any existing value. Out with the old ✨

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 instead. (Yeah bestie, add* is the move, listen to her 🫶)

DATA CHECKING: for attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure the argument is a reference to an array of instances of the correct MAGE-OM class; otherwise ensure there's a single argument of the correct MAGE-OM class. She checks, she cares, she's thorough 💖

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 her 😭

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, serves up a whole set of generic methods that 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 — the receipts are all there, go look 🔍

💀 BUGS 💀

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net). Do not suffer in silence bestie, tell the maintainers 🫶

👑 AUTHOR 👑

Jason E. Stewart (jasons 'at' cpan 'dot' org) — the main character who made all this happen ✨

🔥 SEE ALSO 🔥

perl(1).

🙈 POD ERRORS 🙈

Hey! The above document had some coding errors, which are explained below — not me, I'm just the messenger 💀

Around line 382:
- '=item' outside of any '=over'
Around line 467:
- You forgot a '=back' before '=head2'
Around line 639:
- Expected '=item 2'
Around line 644:
- Expected '=item 3'
Around line 649:
- Expected '=item 4'

and that's a wrap on this one, bestie 🎀 shoutout to perl v5.32.0, dated 2020-11-27, straight from the MAGE::...luster(3pm) era. go forth and cluster your bioassays 💅✨🦋

📦 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