MAGE::...rameter(3pm)

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

💖 MAGE::...rameter(3pm) 💖

okay so bestie, welcome to the User Contributed Perl Documentation page for MAGE::...rameter(3pm). We're decoding Bio::MAGE::Protocol::Parameter, and no cap, it's giving full MAGE-OM API main character energy. 💅✨

✨ NAME ✨

Bio::MAGE::Protocol::Parameter — Class for the MAGE-OM API. That's the whole name, periodt. 🫶

✨ SYNOPSIS ✨

Here's the code vibe, bestie. Copy it, run it, live your truth:

         use Bio::MAGE::Protocol::Parameter

         # creating an empty instance
         my $parameter = Bio::MAGE::Protocol::Parameter->new();

         # creating an instance with existing data
         my $parameter = Bio::MAGE::Protocol::Parameter->new(
               name=>$name_val,
               identifier=>$identifier_val,
               dataType=>$ontologyentry_ref,
               auditTrail=>\@audit_list,
               propertySets=>\@namevaluetype_list,
               descriptions=>\@description_list,
               security=>$security_ref,
               defaultValue=>$measurement_ref,
         );

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

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

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

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

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

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

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

         # 'defaultValue' association
         my $measurement_ref = $parameter->defaultValue(); # getter
         $parameter->defaultValue($measurement_ref); # setter

✨ DESCRIPTION ✨

From the MAGE-OM documentation for the "Parameter" class:

A Parameter is a replaceable value in a Parameterizable class. Examples of Parameters include: scanning wavelength, laser power, centrifuge speed, multiplicative errors, the number of input nodes to a SOM, and PCR temperatures.

✨ INHERITANCE ✨

Bio::MAGE::Protocol::Parameter has the following superclasses:

Bio::MAGE::Identifiable

✨ CLASS METHODS ✨

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

`new()`

`new(%args)`

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

name — Sets the value of the "name" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
identifier — Sets the value of the "identifier" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
dataType — Sets the value of the "dataType" association. 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".
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".
defaultValue — Sets the value of the "defaultValue" association. The value must be of type: instance of "Bio::MAGE::Measurement::Measurement".

`$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::Protocol::Parameter" has the following attribute accessor methods:

`name`

Methods for the "name" attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

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

The restricted getter method for the "name" attribute.

Input parameters: none

Return value: the current value of the "name" attribute

Side effects: none

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

`identifier`

Methods for the "identifier" attribute.

From the MAGE-OM documentation:

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

$val = $parameter->setIdentifier($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 = $parameter->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 ✨

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:

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::Protocol::Parameter has the following association accessor methods:

`dataType`

Methods for the "dataType" association.

From the MAGE-OM documentation:

The type of data generated by the parameter i.e. Boolean, float, etc...

$val = $parameter->setDataType($val) — the restricted setter for the dataType association 💅
- Input parameters: the value you're setting the dataType association to — one of the accepted enumerated values.
- Return value: the current value of the dataType association — one of the accepted enumerated values.
- Side effects: none, bestie, zero, nada ✨
- Exceptions: it will call croak() on you if you pass no input parameters, or if you pass too many input parameters, or if $val isn't an instance of class Bio::MAGE::Description::OntologyEntry 💀
$val = $parameter->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 you pass it any input parameters at all. it's a getter, it doesn't want your little gifts 😭

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 = $parameter->setAuditTrail($array_ref) — the restricted setter for the auditTrail association 💅
- Input parameters: the value you're setting the auditTrail association to — 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 = $parameter->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 = $parameter->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 = $parameter->setPropertySets($array_ref) — the restricted setter for the propertySets association 💅
- Input parameters: the value you're setting the propertySets association to — 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 = $parameter->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 = $parameter->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 💀

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 = $parameter->setDescriptions($array_ref) — the restricted setter for the descriptions association 💅
- Input parameters: the value you're setting the descriptions association to — 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 = $parameter->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 = $parameter->addDescriptions(@vals) — because the descriptions association has list cardinality, it may store more than one value. This method adds the current list of objects in the descriptions association 👑
- Input parameters: the list of values @vals to add to the descriptions association. NOTE: submitting a single value is permitted 🍓
- Return value: the number of items stored in the slot after adding @vals
- Side effects: none ⭐
- Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::Description 💀

security 🎀

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.

$val = $parameter->setSecurity($val) — the restricted setter for the security association 💅
- Input parameters: the value you're setting the security association to — 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 = $parameter->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 🙈

defaultValue 🎀

Methods for the defaultValue association.

From the MAGE-OM documentation:

Allows the optional specification of a default values and the unit for the Parameter

$val = $parameter->setDefaultValue($val) — the restricted setter for the defaultValue association 💅
- Input parameters: the value you're setting the defaultValue association to — one of the accepted enumerated values.
- Return value: the current value of the defaultValue 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::Measurement::Measurement 💀
$val = $parameter->getDefaultValue() — the restricted getter for the defaultValue association 🫶
- Input parameters: none
- Return value: the current value of the defaultValue association — an instance of type Bio::MAGE::Measurement::Measurement.
- Side effects: none 🌸
- Exceptions: will call croak() if any input parameters are specified 🙈

and then, right there in the middle of all that, there's this little guy:

sub initialize {

  my $self = shift;
  return 1;

}

iconic. no cap. 💖

💖 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 💖

okay so bestie, in the Perl implementation of MAGE-OM classes there are three kinds of class data members, and they are slots, attributes, and associations. that's the whole vibe of this section. let's get into it 💅

✨ SLOTS ✨

So this API calls a data member a "slot" when it wasn't even in the UML model and it's basically there for internal purposes. which means: only touch it if you genuinely understand the inner workings of the API, no cap 🙈. Most of the time slots are used by generic methods, like the ones hanging out in the XML writing and reading classes.

Slots get implemented with unified getter/setter methods, like so:

$var = $obj->slot_name(); — this one grabs the current value of the slot, that's it, that's the whole job ✨
$new_var = $obj->slot_name($new_var); — this one stores $new_var in the slot, and the return value is also $new_var (it literally hands it right back to you, generous queen 🫶)
@names = $obj->get_slot_names() — returns the list of all slots in the class 👑

DATA CHECKING: literally none. no data type checking is made for these methods. so like. be careful bestie 😭

🌸 ATTRIBUTES AND ASSOCIATIONS 🌸

okay so the words "attribute" and "association" mean data members of the class that came directly from the UML model. like, they're canon. they were always meant to be there 💜

And in the Perl implementation of MAGE-OM classes, the association and attribute accessors are built out of three separate methods:

get* — retrieves the current value.
- > NOTE: for associations, if the association has list cardinality, an array reference is returned. (iykyk)
- DATA CHECKING: ensures that no argument is provided.
set* — sets the current value, replacing whatever value was already there. out with the old, in with the new 💅
- > 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 fr fr, just use add*.
- DATA CHECKING: for attributes, it ensures a single value is provided as the argument. for associations, if the association has list cardinality, it ensures the argument is a reference to an array of instances of the correct MAGE-OM class — otherwise it ensures there's a single argument of the correct MAGE-OM class.
add* — appends a list of objects to any values that may already be stored in the association.
- > NOTE: this one is only present in associations with list cardinality. if it's not there, that's why bestie, don't panic 🫶
- DATA CHECKING: ensures that all arguments are of the correct MAGE-OM class.

🦋 GENERIC METHODS 🦋

The unified base class of all MAGE-OM classes, Bio::MAGE::Base, hooks you up with a whole set of generic methods that operate on slots, attributes, and associations. versatile icon behavior 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 — the tea is all there, I'm just not re-spilling it here 💖

🐛 BUGS 🐛

found a bug? send those bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net) — go off, tell them everything 📬

👑 AUTHOR 👑

Jason E. Stewart (jasons 'at' cpan 'dot' org) — the author, the moment, the legend 🫶

🌈 SEE ALSO 🌈

perl(1) — yeah that's it, that's the whole list. go read perl(1) bestie, it's giving foundation ✨

💀 POD ERRORS 💀

Hey! The above document had some coding errors, which are explained below — not me exposing the doc's messy era but okay, we're being transparent 🙈:

Around line 382:
- '=item' outside of any '=over'
Around line 467:
- You forgot a '=back' before a '=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 the whole page babes 🎀 this was perl v5.32.0, dated 2020-11-27 — vintage, iconic, and still slaying. stan 💜✨🦋

📦 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