MAGE::...rement(3pm)

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

💖 MAGE::...rement(3pm) 💖

User Contributed Perl Documentation — MAGE::...rement(3pm)

okay bestie, sit down, grab a boba, because we're about to get into Bio::MAGE::BioMaterial::CompoundMeasurement and honestly? she's iconic. ✨

🌸 NAME 🌸

Bio::MAGE::BioMaterial::CompoundMeasurement — a whole class for the MAGE-OM API. no cap. 💅

✨ SYNOPSIS ✨

here's the vibe, in code, exactly as the universe intended:

use Bio::MAGE::BioMaterial::CompoundMeasurement

# creating an empty instance
my $compoundmeasurement = Bio::MAGE::BioMaterial::CompoundMeasurement->new();

# creating an instance with existing data
my $compoundmeasurement = Bio::MAGE::BioMaterial::CompoundMeasurement->new(
      measurement=>$measurement_ref,
      compound=>$compound_ref,
      propertySets=>\@namevaluetype_list,
);

# 'measurement' association
my $measurement_ref = $compoundmeasurement->measurement(); # getter
$compoundmeasurement->measurement($measurement_ref); # setter

# 'compound' association
my $compound_ref = $compoundmeasurement->compound(); # getter
$compoundmeasurement->compound($compound_ref); # setter

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

like, look at her go. getters AND setters. main character energy fr fr. 🫶

🦋 DESCRIPTION 🦋

straight from the MAGE-OM documentation for the "CompoundMeasurement" class, and I'm quoting here because we respect the source:

A CompoundMeasurement is a pairing of a source Compound and an amount (Measurement) of that Compound.

so basically it's a Compound + how much of that Compound = a CompoundMeasurement. it's giving "dynamic duo". 💜

🌈 INHERITANCE 🌈

Bio::MAGE::BioMaterial::CompoundMeasurement has the following superclasses, bestie:

  • Bio::MAGE::Extendable

she got it from her mama, iykyk. 👑

💅 CLASS METHODS 💅

the following methods can all be called without first having an instance of the class, via the Bio::MAGE::BioMaterial::CompoundMeasurement->methodname() syntax. class methods, not me. 💀

🎀 new() 🎀

🎀 new(%args) 🎀

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

  • measurement — sets the value of the "measurement" association. the value must be of type: instance of "Bio::MAGE::Measurement::Measurement".
  • 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".
  • compound — sets the value of the "compound" association. the value must be of type: instance of "Bio::MAGE::BioMaterial::Compound".

💖 $obj = class->new(%parameters) 💖

the "new()" method is the class constructor. the blueprint. the origin story. ✨

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. just so we're clear, 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. the government name, if you will. 👑

💖 $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. she's organized like that. 🎀

✨ INSTANCE METHODS ✨

💖 $obj_copy = $obj->new()

Okay so when you call this on an existing object reference instead of on a class name, new() lowkey becomes a copy constructor — the fresh object gets its starting values straight from the object you're copying. Iconic behaviour honestly.

  • Parameters: no input parameters are used in the copy constructor, because the initial values are taken directly from the object to be copied. She's self-sufficient. 💅
  • Return value: 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 your girl for setting a whole bunch of slots at the same time. She comes in two flavours of invocation: the first one takes a named parameter list, and the second one 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 don't get cute with made-up names, 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. So yes, one setter, one getter, per attribute. Very demure, very mindful.

Bio::MAGE::BioMaterial::CompoundMeasurement has the following attribute accessor methods:

🌈 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:

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

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

  1. 1..N

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

  1. 0..N

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

Bio::MAGE::BioMaterial::CompoundMeasurement has the following association accessor methods:

💅 measurement

Methods for the measurement association.

From the MAGE-OM documentation:

The amount of the Compound.

⭐ $val = $compoundmeasurement->setMeasurement($val)

The restricted setter method for the measurement association.

  • Input parameters: the value to which the measurement association will be set : one of the accepted enumerated values.
  • Return value: the current value of the measurement 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 = $compoundmeasurement->getMeasurement()

The restricted getter method for the measurement association.

  • Input parameters: none
  • Return value: the current value of the measurement association : an instance of type Bio::MAGE::Measurement::Measurement.
  • 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 = $compoundmeasurement->setPropertySets($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 = $compoundmeasurement->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 = $compoundmeasurement->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

🧚 compound

Methods for the compound association.

From the MAGE-OM documentation:

A Compound to be used to create another Compound.

🌸 $val = $compoundmeasurement->setCompound($val)

The restricted setter method for the compound association.

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

👑 $val = $compoundmeasurement->getCompound()

The restricted getter method for the compound association.

  • Input parameters: none
  • Return value: the current value of the compound association : an instance of type Bio::MAGE::BioMaterial::Compound.
  • Side effects: none
  • Exceptions: will call croak() if any input parameters are specified
sub initialize {

  my $self = shift;
  return 1;

}

🌈 SLOTS, ATTRIBUTES, AND ASSOCIATIONS

In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations. Three whole categories, bestie, keep up. 💅

💀 SLOTS

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

Slots are implemented using unified getter/setter methods:

  • $var = $obj->slot_name(); — Retrieves the current value of the slot.
  • $new_var = $obj->slot_name($new_var); — Store $new_var in the slot — the return value is also $new_var.
  • @names = $obj->get_slot_names() — Returns the list of all slots in the class.

DATA CHECKING: No data type checking is made for these methods.

🌟 ATTRIBUTES AND ASSOCIATIONS

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

In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:

  • get*

Retrieves the current value.

NOTE: For associations, if the association has list cardinality, an array reference is returned.

DATA CHECKING: Ensure that no argument is provided.

  • set*

Sets the current value, replacing any existing value.

NOTE: For associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.

DATA CHECKING: For attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is a single argument of the correct MAGE-OM class.

  • add*

NOTE: Only present in associations with list cardinality.

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

DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.

✨ GENERIC METHODS

The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that will operate on slots, attributes, and associations:

$val = $obj->get_slot($name)
\@list_ref = $obj->get_slots(@name_list);
$val = $obj->set_slot($name,$val)
$obj->set_slots(%parameters)
$obj->set_slots(\@name_list, \@value_list)

See elsewhere in this page for a detailed description of these methods. 👀

🐛 BUGS

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)

🫶 AUTHOR

Jason E. Stewart (jasons 'at' cpan 'dot' org)

👑 SEE ALSO

perl(1).

✨ POD ERRORS ✨

okay bestie so 💅 the doc above had a few little coding oopsies and we're gonna spill the tea about every single one. it's giving "the vibes were immaculate but the syntax was not" 😭 no cap.

  • Around line 323:
    • '=item' outside of any '=over'
  • Around line 408:
    • You forgot a '=back' before '=head2'
  • Around line 436:
    • Expected '=item 2'
  • Around line 441:
    • Expected '=item 3'
  • Around line 446:
    • Expected '=item 4'
bestie this is NOT a vibe check you wanna fail 💀 your =over and =back are out here living their main character lives with zero supervision. fix the pods, queen. periodt. 👑

and that's the whole page, fr fr 🫶 we went from NAME all the way to here and you ate every single section. iconic behavior honestly 🌟

this lil beauty came from perl v5.32.0, dated 2020-11-27, and it's serving MAGE::...rement(3pm) realness. go forth and perldoc responsibly, bestie 💖✨🦋

📦 where this page comes from