MAGE::...TypeMap(3pm)

hey bestie 💖 so you pulled up a page from the User Contributed Perl Documentation and it's filed under MAGE::...TypeMap(3pm) — which is just the short label for the whole Bio::MAGE::BioAssayData::QuantitationTypeMap situation. this is part 1 of 3, so buckle up, there's more coming. 🎀

👑 NAME

Bio::MAGE::BioAssayData::QuantitationTypeMap — a class for the MAGE-OM API. short, sweet, self-explanatory, we love her. ✨

---

🌸 SYNOPSIS

okay so here's how you actually hang out with this class:

use Bio::MAGE::BioAssayData::QuantitationTypeMap

# creating an empty instance
my $quantitationtypemap = Bio::MAGE::BioAssayData::QuantitationTypeMap->new();

# creating an instance with existing data
my $quantitationtypemap = Bio::MAGE::BioAssayData::QuantitationTypeMap->new(
      name=>$name_val,
      identifier=>$identifier_val,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      protocolApplications=>\@protocolapplication_list,
      sourcesQuantitationType=>\@quantitationtype_list,
      descriptions=>\@description_list,
      security=>$security_ref,
      targetQuantitationType=>$quantitationtype_ref,
);

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

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

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

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

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

# 'sourcesQuantitationType' association
my $quantitationtype_array_ref = $quantitationtypemap->sourcesQuantitationType(); # getter
$quantitationtypemap->sourcesQuantitationType(\@quantitationtype_list); # setter

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

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

# 'targetQuantitationType' association
my $quantitationtype_ref = $quantitationtypemap->targetQuantitationType(); # getter
$quantitationtypemap->targetQuantitationType($quantitationtype_ref); # setter

---

💜 DESCRIPTION

straight from the MAGE-OM documentation for the QuantitationTypeMap class, and I am quoting:

A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType.

so bestie, she's literally the glow-up manual: she explains how source QuantitationTypes get math'd into a target QuantitationType. obsessed. ✨

---

🧬 INHERITANCE

Bio::MAGE::BioAssayData::QuantitationTypeMap comes from good stock. her superclasses are:

• Bio::MAGE::BioEvent::Map

that's the whole family tree she's claiming here. 💅

---

⭐ CLASS METHODS

every single one of these can be called without an instance first — you just hit the class name directly like Bio::MAGE::BioAssayData::QuantitationTypeMap->methodname(). no object needed, she picks up either way. 👑

🎀 new()

🎀 new(%args)

the object constructor new() takes these 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).
• 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.
• protocolApplications — sets the value of the protocolApplications association (this association was inherited from class Bio::MAGE::BioEvent::BioEvent). the value must be of type: array of Bio::MAGE::Protocol::ProtocolApplication.
• sourcesQuantitationType — sets the value of the sourcesQuantitationType association. the value must be of type: array of Bio::MAGE::QuantitationType::QuantitationType.
• 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.
• targetQuantitationType — sets the value of the targetQuantitationType association. the value must be of type: instance of Bio::MAGE::QuantitationType::QuantitationType.

🦋 $obj = class->new(%parameters)

the new() method is the class constructor, the one who makes objects happen.

• 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 how you 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 get it twisted. 🙈

• 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 you call it on an existing object reference instead of a class name, the new() method acts as a copy constructor — the new object's initial values get set to be those of the existing object. it's giving clone energy. 👯

• 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 sets a bunch 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. so like, don't invent slots, she will yell at you. 💀

🌈 @obj_list = $obj->get_slots(@name_list)

the get_slots() method gets 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. one for reading, one for writing, no crossover, we stay organized. 💅

Bio::MAGE::BioAssayData::QuantitationTypeMap has the following attribute accessor methods:

🌸 name

methods for the name attribute.

from the MAGE-OM documentation:

The potentially ambiguous common identifier.

• $val = $quantitationtypemap->setName($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 = $quantitationtypemap->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 = $quantitationtypemap->setIdentifier($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 = $quantitationtypemap->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 bestie, this is the part where it gets spicy. 🫶 Associations are literally just references to other classes, and in MAGE-OM every association has a cardinality — that's the thing that decides the min and max number of instances of the 'other' class that can be in the association. So like:

1. There must be exactly one item in the association, i.e. this is a mandatory data field. One. Just one. No notes. 💅
2. 0..1 — There may be one item in the association, i.e. this is an optional data field.
3. 1..N — There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality. Give me at least one, queen. 👑
4. 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::BioAssayData::QuantitationTypeMap has the following association accessor methods, no cap:

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 = $quantitationtypemap->setAuditTrail($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 = $quantitationtypemap->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 = $quantitationtypemap->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 = $quantitationtypemap->setPropertySets($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 = $quantitationtypemap->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 = $quantitationtypemap->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

protocolApplications

Methods for the protocolApplications association.

From the MAGE-OM documentation:

The applied protocols to the BioEvent.

• $array_ref = $quantitationtypemap->setProtocolApplications($array_ref) — The restricted setter method 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 = $quantitationtypemap->getProtocolApplications() — The restricted getter method 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 = $quantitationtypemap->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

sourcesQuantitationType

Methods for the sourcesQuantitationType association.

From the MAGE-OM documentation:

The QuantitationType sources for values for the transformation.

• $array_ref = $quantitationtypemap->setSourcesQuantitationType($array_ref) — The restricted setter method for the sourcesQuantitationType association.
  • Input parameters: the value to which the sourcesQuantitationType association will be set : a reference to an array of objects of type Bio::MAGE::QuantitationType::QuantitationType
  • Return value: the current value of the sourcesQuantitationType association : a reference to an array of objects of type Bio::MAGE::QuantitationType::QuantitationType
  • 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::QuantitationType::QuantitationType instances
• $array_ref = $quantitationtypemap->getSourcesQuantitationType() — The restricted getter method for the sourcesQuantitationType association.
  • Input parameters: none
  • Return value: the current value of the sourcesQuantitationType association : a reference to an array of objects of type Bio::MAGE::QuantitationType::QuantitationType
  • Side effects: none
  • Exceptions: will call croak() if any input parameters are specified
• $val = $quantitationtypemap->addSourcesQuantitationType(@vals) — Because the sourcesQuantitationType association has list cardinality, it may store more than one value. This method adds the current list of objects in the sourcesQuantitationType association.
  • Input parameters: the list of values @vals to add to the sourcesQuantitationType 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::QuantitationType::QuantitationType

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 = $quantitationtypemap->setDescriptions($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

So the exceptions for that setter? It 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 = $quantitationtypemap->getDescriptions() — The restricted getter method for the "descriptions" association. Like, it's the only way to peek, no cap.
  • Input parameters: none — don't even try it, bestie.
  • 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 = $quantitationtypemap->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. slay!
  • 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 = $quantitationtypemap->setSecurity($val) — The restricted setter method for the "security" association. You can set it, but only if you follow the rules, bestie.
  • Input parameters: the value to which the "security" association will be set : one of the accepted enumerated values.
  • Return value: the current value of the "security" association : one of the accepted enumerated values.
  • Side effects: none
  • Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not an instance of class Bio::MAGE::AuditAndSecurity::Security
• $val = $quantitationtypemap->getSecurity() — The restricted getter method for the "security" association. Look but don't touch, fr fr.
  • 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

targetQuantitationType 🎯

Methods for the "targetQuantitationType" association.

From the MAGE-OM documentation:

The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol.

• $val = $quantitationtypemap->setTargetQuantitationType($val) — The restricted setter method for the "targetQuantitationType" association. Set it, but only with the right vibe.
  • Input parameters: the value to which the "targetQuantitationType" association will be set : one of the accepted enumerated values.
  • Return value: the current value of the "targetQuantitationType" 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::QuantitationType::QuantitationType
• $val = $quantitationtypemap->getTargetQuantitationType() — The restricted getter method for the "targetQuantitationType" association. It's giving peek access only, bestie.
  • Input parameters: none
  • Return value: the current value of the "targetQuantitationType" association : an instance of type Bio::MAGE::QuantitationType::QuantitationType.
  • Side effects: none
  • Exceptions: will call croak() if any input parameters are specified

And here's that initialize sub, looking all cute:

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".

🌸 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) — like, don't be shy, they want to know.

👑 AUTHOR 👑

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

👀 SEE ALSO 👀

perl(1). — periodt.

💀 POD ERRORS 💀

Hey! The above document had some coding errors, which are explained below:

• Around line 395: '=item' outside of any '=over'
• Around line 480: You forgot a '=back' before '=head2'
• Around line 652: Expected '=item 2'
• Around line 657: Expected '=item 3'
• Around line 662: Expected '=item 4'

---

This manual page was brought to you by perl v5.32.0, dated 2020-11-27, from MAGE::...TypeMap(3pm). Stay iconic, bestie! 💖✨🦋