MAGE::...lement(3pm)

💖 Bio::MAGE::DesignElement::DesignElement — the manual page, but make it make sense 💖

okay bestie, sit down, hydrate, because we're reading the Bio::MAGE::DesignElement::DesignElement page from User Contributed Perl Documentation and honestly? it's giving ✨foundational✨. This is the MAGE-OM API in Perl form, and this class is the mom of a whole little family. Let's get into it. 🫶

---

✨ NAME ✨

Bio::MAGE::DesignElement::DesignElement — a whole class for the MAGE-OM API. No cap. 🎀

---

✨ SYNOPSIS ✨

Bestie, look at this. Just look at it. 🦋

use Bio::MAGE::DesignElement::DesignElement

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

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

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

# 'controlType' association
my $ontologyentry_ref = $designelement->controlType(); # getter
$designelement->controlType($ontologyentry_ref); # setter

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

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

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

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

⚠️ BIG ONE: Bio::MAGE::DesignElement::DesignElement is an abstract base class and should not be directly instantiated. The examples above are just showing you how subclass objects will behave. Do not try to new() this thing directly, I'm literally begging. 😭

---

✨ DESCRIPTION ✨

Straight from the MAGE-OM documentation for the "DesignElement" class, quoting it exactly:

An element of an array. This is generally of type feature but can be specified as reporters or compositeSequence for arrays that are abstracted from a physical array.

And here's the tea ☕: Bio::MAGE::DesignElement::DesignElement is an abstract base class and should not be directly instantiated. It's not here to be built — it's here to serve as an interface definition for its subclasses. It's the blueprint, not the house. 💅

---

✨ INHERITANCE ✨ (the family tree 🌳)

Bio::MAGE::DesignElement::DesignElement has the following superclasses:

• Bio::MAGE::Identifiable

And it has the following subclasses (its iconic children 👑):

• Bio::MAGE::DesignElement::Reporter
• Bio::MAGE::DesignElement::CompositeSequence
• Bio::MAGE::DesignElement::Feature

---

✨ CLASS METHODS ✨

These are the ones you can call without having an instance yet — using the Bio::MAGE::DesignElement::DesignElement->methodname() syntax. Class-method girlies, this is your moment. 🌸

new()

new(%args)

Bio::MAGE::DesignElement::DesignElement is an abstract base class and should not be directly instantiated using the "new()" constructor. It's only listed here so you can see what arguments its subclasses will accept. 🙈

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").
• controlType — Sets the value of the "controlType" 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".

$obj = class->new(%parameters)

The "new()" method is the class constructor. Periodt.

• Parameters: if you give it a list of name/value parameters, the corresponding slots, attributes, or associations will 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're not out here confused.

• 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 ✨

Now we're in object territory. Main character energy only. 👑

$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 are set to be those of the existing object. It's giving clone. 🪞

• 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 all at once. It has two different invocation methods — the first takes a named parameter list, and the second takes two array references. Choose 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 freestyle. 🐸

@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. Two methods, one attribute, iconic behavior. 💖

"Bio::MAGE::DesignElement::DesignElement" has the following attribute accessor methods:

name

Methods for the "name" attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $designelement->setName($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 = $designelement->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 = $designelement->setIdentifier($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 = $designelement->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 may be included in the association. Here's the vibe check on all four: 🌈

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::DesignElement::DesignElement has the following association accessor methods:

controlType

Methods for the "controlType" association.

From the MAGE-OM documentation:

If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.)

• $val = $designelement->setControlType($val) — the restricted setter for the controlType association.
  • Input parameters: the value you want controlType set to — and it's gotta be one of the accepted enumerated values.
  • Return value: the current value of the controlType association — one of the accepted enumerated values.
  • Side effects: none
  • Exceptions: it will call croak() 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 = $designelement->getControlType() — the restricted getter for the controlType association.
  • Input parameters: none
  • Return value: the current value of the controlType association — an instance of type Bio::MAGE::Description::OntologyEntry.
  • Side effects: none
  • Exceptions: it will call croak() if you pass any input parameters at all

---

🎧 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 = $designelement->setAuditTrail($array_ref) — the restricted setter for the auditTrail association.
  • Input parameters: the value you're setting auditTrail 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: it will call croak() if you pass no input parameters, or if you pass too many input parameters, or if $array_ref isn't a reference to an array of class Bio::MAGE::AuditAndSecurity::Audit instances
• $array_ref = $designelement->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: it will call croak() if you pass any input parameters at all
• $val = $designelement->addAuditTrail(@vals) — okay so auditTrail has list cardinality, which is the fancy way of saying it can hold 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: it will call croak() if you pass no input parameters, or if any of the objects in @vals isn't 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 = $designelement->setPropertySets($array_ref) — the restricted setter for the propertySets association.
  • Input parameters: the value you're setting propertySets 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: it will call croak() if you pass no input parameters, or if you pass too many input parameters, or if $array_ref isn't a reference to an array of class Bio::MAGE::NameValueType instances
• $array_ref = $designelement->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: it will call croak() if you pass any input parameters at all
• $val = $designelement->addPropertySets(@vals) — propertySets also has list cardinality, so it's not a one-value-only situation, bestie. 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: it will call croak() if you pass no input parameters, or if any of the objects in @vals isn't 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 = $designelement->setDescriptions($array_ref) — the restricted setter for the descriptions association.
  • Input parameters: the value you're setting descriptions 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: it will call croak() if you pass no input parameters, or if you pass too many input parameters, or if $array_ref isn't a reference to an array of class Bio::MAGE::Description::Description instances
• $array_ref = $designelement->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: it will call croak() if you pass any input parameters at all
• $val = $designelement->addDescriptions(@vals) — yep, descriptions has list cardinality too, so 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: it will call croak() if you pass no input parameters, or if any of the objects in @vals isn't 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 = $designelement->setSecurity($val) — the restricted setter for the security association.
  • Input parameters: the value you're setting security 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: it will call croak() 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::AuditAndSecurity::Security
• $val = $designelement->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: it will call croak() if you pass any input parameters at all

---

And then there's this lil thing hanging out at the bottom, no cap:

sub initialize {

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

}

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

okay bestie, in the Perl implementation of MAGE-OM classes there are literally three types of class data members: slots, attributes, and associations. periodt. 💅

🌸 SLOTS 🌸

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

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); — stores $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. no cap.

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 🙈

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

• Around line 366: '=item' outside of any '=over'
• Around line 451: You forgot a '=back' before '=head2'
• Around line 623: Expected '=item 2'
• Around line 628: Expected '=item 3'
• Around line 633: Expected '=item 4'

and that's the whole vibe check, bestie — this page's footer says perl v5.32.0, dated 2020-11-27, for MAGE::...lement(3pm). slay 💅✨