MAGE::...ssayMap(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::...ssayMap(3pm) page! It's User Contributed Perl Documentation, and it's all about Bio::MAGE::BioAssayData::BioAssayMap — Class for the MAGE-OM API. No cap, this is the whole vibe. 💅

🦋 SYNOPSIS 🦋

Here's the tea, fr fr — use it like this:

         use Bio::MAGE::BioAssayData::BioAssayMap

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

         # creating an instance with existing data
         my $bioassaymap = Bio::MAGE::BioAssayData::BioAssayMap->new(
               name=>$name_val,
               identifier=>$identifier_val,
               bioAssayMapTarget=>$derivedbioassay_ref,
               sourceBioAssays=>\@bioassay_list,
               auditTrail=>\@audit_list,
               propertySets=>\@namevaluetype_list,
               protocolApplications=>\@protocolapplication_list,
               descriptions=>\@description_list,
               security=>$security_ref,
         );

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

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

         # 'bioAssayMapTarget' association
         my $derivedbioassay_ref = $bioassaymap->bioAssayMapTarget(); # getter
         $bioassaymap->bioAssayMapTarget($derivedbioassay_ref); # setter

         # 'sourceBioAssays' association
         my $bioassay_array_ref = $bioassaymap->sourceBioAssays(); # getter
         $bioassaymap->sourceBioAssays(\@bioassay_list); # setter

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

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

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

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

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

That's the whole synopsis, periodt. 🎀

🌸 DESCRIPTION 🌸

From the MAGE-OM documentation for the BioAssayMap class:

The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays.

Like, that's literally the description, bestie. 🫶

👑 INHERITANCE 👑

Bio::MAGE::BioAssayData::BioAssayMap has the following superclasses:

Bio::MAGE::BioEvent::Map

So it's giving inherited energy. 💖

🌟 CLASS METHODS 🌟

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

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).
- 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.
- sourceBioAssays — Sets the value of the sourceBioAssays association The value must be of type: array of Bio::MAGE::BioAssay::BioAssay.
- bioAssayMapTarget — Sets the value of the bioAssayMapTarget association The value must be of type: instance of Bio::MAGE::BioAssay::DerivedBioAssay.
- 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.
- 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.
$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.

That's giving method moment. ✨

🦋 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::BioAssayData::BioAssayMap has the following attribute accessor methods:

name — Methods for the name attribute. From the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $bioassaymap->setName($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 = $bioassaymap->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 = $bioassaymap->setIdentifier($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 = $bioassaymap->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
0..N — there may be one or more items in the association, i.e. this is an optional data field, with list cardinality.

and that's the whole cardinality menu bestie — now let's get into the fun part where you actually grab the handles. 💅

Bio::MAGE::BioAssayData::BioAssayMap has the following association accessor methods: