MAGE::...ension(3pm)

💖 MAGE::Bio::MAGE::BioAssayData::DesignElementDimension(3pm) 💖

okay bestie, buckle up, this is a Perl module from the User Contributed Perl Documentation corner of the internet and it's giving very serious MAGE-OM energy. it's long, it's abstract, it's got inheritance drama. let's go 🫶

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✨ NAME ✨

Bio::MAGE::BioAssayData::DesignElementDimension — literally just a Class for the MAGE-OM API. that's it, that's the whole vibe.

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🌸 SYNOPSIS 🌸

use Bio::MAGE::BioAssayData::DesignElementDimension

# Bio::MAGE::BioAssayData::DesignElementDimension is an abstract base class and should not
# be directly instantiated. These examples indicate how subclass
# objects will behave

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

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

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

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

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

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

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💅 DESCRIPTION 💅

so, straight from the MAGE-OM documentation for the DesignElementDimension class, and I quote:

An ordered list of designElements. It will be realized as one of its three subclasses.

and then the important bit: Bio::MAGE::BioAssayData::DesignElementDimension is an abstract base class and should not be directly instantiated. nope. don't do it. instead it serves as an interface definition for its subclasses. it's the blueprint, not the house, iykyk 💀

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🦋 INHERITANCE 🦋

family tree time, and this one's kinda iconic ngl.

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

• Bio::MAGE::Identifiable

Bio::MAGE::BioAssayData::DesignElementDimension has the following subclasses:

• Bio::MAGE::BioAssayData::CompositeSequenceDimension
• Bio::MAGE::BioAssayData::ReporterDimension
• Bio::MAGE::BioAssayData::FeatureDimension

three kids, one parent, no cap. 👑

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🌟 CLASS METHODS 🌟

all of these can be called without having an instance of the class first, using the syntax:

Bio::MAGE::BioAssayData::DesignElementDimension->methodname()

🎀 new() 🎀

🎀 new(%args) 🎀

Bio::MAGE::BioAssayData::DesignElementDimension is an abstract base class, so pls do not directly instantiate it with the new() constructor. it's listed here purely to show you what arguments its subclasses will accept.

the object constructor new() accepts 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.
• 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. the main character fr.

• 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's defined by the class.

💜 @names = class->get_slot_names() 💜

the get_slot_names() method retrieves the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names. just so you know.

• 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.

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💖 INSTANCE METHODS 💖

🌈 $obj_copy = $obj->new() 🌈

when you invoke this with 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 those of the existing object. so cute, so useful.

• 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's 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. rude, but fair.

🌈 @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 gets 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

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🌸 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. very demure, very mindful.

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

🍓 name

methods for the name attribute.

from the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $designelementdimension->setName($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 = $designelementdimension->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 = $designelementdimension->setIdentifier($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 = $designelementdimension->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

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🔥 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. here's the breakdown bestie:

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.

3. 1..N

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

4. 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::BioAssayData::DesignElementDimension has the following association accessor methods:

🌈 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 = $designelementdimension->setAuditTrail($array_ref)

the restricted setter method for the auditTrail association.

So, setAuditTrail? Here's the tea, bestie: 💅

• What you pass in: the value you're setting the auditTrail association to — specifically, a reference to an array of Bio::MAGE::AuditAndSecurity::Audit objects.
• What you get back: the current value of the auditTrail association — again, a reference to an array of Bio::MAGE::AuditAndSecurity::Audit objects.
• Side effects: none, we love a clean queen. ✨
• Exceptions: it'll call croak() if you don't give it any input parameters, or if you give it too many, or if $array_ref isn't a reference to an array of Bio::MAGE::AuditAndSecurity::Audit instances. So don't play yourself. 😭

$array_ref = $designelementdimension->getAuditTrail() — the restricted getter for the auditTrail association.

• Input parameters: none. It's giving minimal.
• Return value: the current value of the auditTrail association — a reference to an array of Bio::MAGE::AuditAndSecurity::Audit objects.
• Side effects: none.
• Exceptions: will call croak() if any input parameters are specified. So keep your hands to yourself. 🙈

$val = $designelementdimension->addAuditTrail(@vals) — because auditTrail 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, so don't stress. 🫶
• 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 = $designelementdimension->setPropertySets($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 = $designelementdimension->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 = $designelementdimension->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 = $designelementdimension->setDescriptions($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 = $designelementdimension->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 = $designelementdimension->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 = $designelementdimension->setSecurity($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 = $designelementdimension->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.

And here's the initialize method, which is giving abstract base class energy — don't instantiate this, bestie:

           sub initialize {

             carp __PACKAGE__ . "::initialize: abstract base classes should not be instantiated";

           }

💖 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 💖

In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations. It's giving trio energy. 👑

🎀 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. So it's the wild west out here. 🤠

🌈 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. (iykyk) 💜

💀 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, plot twist 😭 — the doc above? It had some coding errors. And perl, being the messy little gossip that it is, is gonna tell us exactly where. No secrets here, everything's explained below 👇

• Around line 333 — '=item' outside of any '=over' — like, hello?? you can't just drop an =item with no =over to hold it. it's giving orphaned item energy 🫶
• Around line 418 — You forgot a '=back' before '=head2' — bestie you forgot the =back before the =head2 💅 close your list, it's rude to leave it hanging
• Around line 590 — Expected '=item 2' — it wanted the =item 2 and it did not get it, we've all been there 😭
• Around line 595 — Expected '=item 3' — same situation, now it wants =item 3 🎀
• Around line 600 — Expected '=item 4' — and yes, =item 4 was also expected. the list said "number me" and perl said "no" 😔

no cap, these are just warnings about the POD markup itself — the errors are in the doc's formatting, and perl is kindly snitching on every single one. nothing hidden, nothing skipped ✨

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and that's a wrap on this whole page, bestie 🎀 this lil masterpiece is from perl v5.32.0, dated 2020-11-27 — iconic, timeless, lowkey a legend. go forth and use it responsibly 💖✨🦋