MAGE::...quence(3pm)

🧬 MAGE::...quence(3pm) β€” aka Bio::MAGE::DesignElement::CompositeSequence πŸ’–

User Contributed Perl Documentation Β· MAGE::...quence(3pm)

okay bestie, sit down, hydrate, because we're doing MAGE-OM today and honestly? it's giving structured biology data. this is the Perl module for the CompositeSequence class from the MAGE-OM API. no cap, it's a whole vibe.


✨ NAME ✨

Bio::MAGE::DesignElement::CompositeSequence β€” Class for the MAGE-OM API. that's it, that's the whole identity. πŸ’…


πŸ¦‹ SYNOPSIS πŸ¦‹

okay so here's how you actually use this thing. read it, love it, copy it:

use Bio::MAGE::DesignElement::CompositeSequence

# creating an empty instance
my $compositesequence = Bio::MAGE::DesignElement::CompositeSequence->new();

# creating an instance with existing data
my $compositesequence = Bio::MAGE::DesignElement::CompositeSequence->new(
      name=>$name_val,
      identifier=>$identifier_val,
      controlType=>$ontologyentry_ref,
      compositeCompositeMaps=>\@compositecompositemap_list,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      descriptions=>\@description_list,
      security=>$security_ref,
      biologicalCharacteristics=>\@biosequence_list,
      reporterCompositeMaps=>\@reportercompositemap_list,
);

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

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

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

# 'compositeCompositeMaps' association
my $compositecompositemap_array_ref = $compositesequence->compositeCompositeMaps(); # getter
$compositesequence->compositeCompositeMaps(\@compositecompositemap_list); # setter

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

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

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

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

# 'biologicalCharacteristics' association
my $biosequence_array_ref = $compositesequence->biologicalCharacteristics(); # getter
$compositesequence->biologicalCharacteristics(\@biosequence_list); # setter

# 'reporterCompositeMaps' association
my $reportercompositemap_array_ref = $compositesequence->reporterCompositeMaps(); # getter
$compositesequence->reporterCompositeMaps(\@reportercompositemap_list); # setter

every getter, every setter, every association, all up there. πŸ‘‘


🌸 DESCRIPTION 🌸

straight from the MAGE-OM documentation for the "CompositeSequence" class, and I'm quoting here because honestly the original ate:

A collection of Reporter or CompositeSequence Design Elements, annotated through the association to BioSequence.

so basically: a little squad of design elements, plus the biological sauce that explains them. iconic. 🧬✨


πŸ’œ INHERITANCE πŸ’œ

Bio::MAGE::DesignElement::CompositeSequence has the following superclasses, i.e. it got its whole lineage:

  • Bio::MAGE::DesignElement::DesignElement

yes bestie, it's a nepo baby and we love that for it. 🫢


πŸ‘‘ CLASS METHODS πŸ‘‘

the way that all of these can be called without having an instance first, using the

Bio::MAGE::DesignElement::CompositeSequence->methodname()

syntax. so you don't even need to commit to an object yet. lowkey freeing.

πŸŽ€ new()

πŸŽ€ new(%args)

the object constructor "new()" takes the following optional named-value style arguments. all optional, all named, all slay:

  • name β€” sets the value of the "name" attribute. (this attribute was inherited from class "Bio::MAGE::Identifiable".)
  • identifier β€” sets the value of the "identifier" attribute. (this attribute was inherited from class "Bio::MAGE::Identifiable".)
  • controlType β€” sets the value of the "controlType" association. (this association was inherited from class "Bio::MAGE::DesignElement::DesignElement".)
    • the value must be of type: instance of "Bio::MAGE::Description::OntologyEntry".
  • auditTrail β€” 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".
  • compositeCompositeMaps β€” sets the value of the "compositeCompositeMaps" association.
    • the value must be of type: array of "Bio::MAGE::DesignElement::CompositeCompositeMap".
  • propertySets β€” 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 β€” 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".
  • biologicalCharacteristics β€” sets the value of the "biologicalCharacteristics" association.
    • the value must be of type: array of "Bio::MAGE::BioSequence::BioSequence".
  • security β€” 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".
  • reporterCompositeMaps β€” sets the value of the "reporterCompositeMaps" association.
    • the value must be of type: array of "Bio::MAGE::DesignElement::ReporterCompositeMap".

πŸ’« $obj = class->new(%parameters)

the "new()" method is the class constructor. main character energy fr.

  • Parameters: if you give 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 is defined by the class.

πŸ’« @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. like, don't @ me, that's just how it is. πŸ™ˆ
  • Return value: a list of the names of all slots defined for this class.
  • Side effects: none.

πŸ’« @name_list = get_attribute_names()

returns the list of attribute data members for this class.

πŸ’« @name_list = get_association_names()

returns the list of association data members for this class.

πŸ’« @class_list = get_superclasses()

returns the list of superclasses for this class.

πŸ’« @class_list = get_subclasses()

returns the list of subclasses for this class.

πŸ’« $name = class_name()

returns the full class name for this class.

πŸ’« $package_name = package_name()

returns the base package name (i.e. no 'namespace::') of the package that contains this class.

πŸ’« %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 invoke it with an existing object reference instead of a class name, the "new()" method acts as a copy constructor β€” the new object's initial values get set to those of the existing object. it's giving clone era. πŸ‘―

  • 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 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 like, don't make stuff up. πŸ’€

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

the "get_slots()" method gets the values of a bunch 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, committed relationship. πŸ’ž

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

πŸ“ name

methods for the "name" attribute.

from the MAGE-OM documentation:

The potentially ambiguous common identifier.

🌸 $val = $compositesequence->setName($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. so like. exactly one. please. 😭

🌸 $val = $compositesequence->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. it takes nothing, bestie. zero. nada. ✨

πŸ“ 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.

so it's the "no duplicates allowed" string. very exclusive. very VIP. πŸ’…

🌸 $val = $compositesequence->setIdentifier($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.

The getter for the identifier attribute β€” you get to peek at it, that's it. That's the whole vibe. πŸ‘‘

  • Input parameters: none. Zero. Nada. Don't even try it.
  • Return value: whatever the identifier attribute is currently holding πŸ’–
  • Side effects: none, she's harmless
  • Exceptions: will call croak() if you pass any input parameters β€” like bestie, it's a getter, what are you even doing πŸ™ˆ

✨ ASSOCIATIONS ✨

Okay so associations are refs to other classes β€” like your class's little friendship circle πŸ’…. And every association in MAGE-OM comes with a cardinality, which is basically the "how many of these are we allowed to have" rule. It sets the minimum and maximum number of instances of the other class that can be in the association:

  1. There has to be exactly one item in the association, i.e. this is a mandatory data field. No item = no deal.
  2. 0..1 β€” there may be one item in the association, i.e. this is an optional data field. Maybe she's there, maybe she's not, we don't stress πŸ¦‹
  3. 1..N β€” there must be one or more items in the association, i.e. a mandatory data field, but with list cardinality. The whole squad is required, minimum one member 🫢
  4. 0..N β€” there may be one or more items in the association, i.e. an optional data field, with list cardinality. A whole crowd, or literally nobody. Whatever happens happens.

Bio::MAGE::DesignElement::CompositeSequence has the following association accessor methods:


controlType

Methods for the controlType association.

Straight from the MAGE-OM documentation:

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

$val = $compositesequence->setControlType($val)

The restricted setter method for the controlType association.

  • Input parameters: the value you want the controlType association set to β€” one of the accepted enumerated values.
  • Return value: the current value of the controlType association β€” 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::Description::OntologyEntry

$val = $compositesequence->getControlType()

The restricted getter method for the controlType association.

  • Input parameters: none
  • Return value: the current value of the controlType association β€” an instance of type Bio::MAGE::Description::OntologyEntry.
  • Side effects: none
  • Exceptions: will call croak() if any input parameters are specified

auditTrail

Methods for the auditTrail association.

Straight from the MAGE-OM documentation:

A list of Audit instances that track changes to the instance of Describable.

$array_ref = $compositesequence->setAuditTrail($array_ref)

The restricted setter method for the auditTrail association.

  • Input parameters: the value to which the auditTrail association will be set β€” a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
  • Return value: the current value of the auditTrail association β€” 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 = $compositesequence->getAuditTrail()

The restricted getter method for the auditTrail association.

  • Input parameters: none
  • Return value: the current value of the auditTrail association β€” 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 = $compositesequence->addAuditTrail(@vals)

Because the auditTrail association has list cardinality, it can hold more than one value. This method adds the current list of objects in the auditTrail association. It's giving "collect them all" energy ✨

  • 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

compositeCompositeMaps

Methods for the compositeCompositeMaps association.

Straight from the MAGE-OM documentation:

A map to the compositeSequences that compose this CompositeSequence.

$array_ref = $compositesequence->setCompositeCompositeMaps($array_ref)

The restricted setter method for the compositeCompositeMaps association.

  • Input parameters: the value to which the compositeCompositeMaps association will be set β€” a reference to an array of objects of type Bio::MAGE::DesignElement::CompositeCompositeMap
  • Return value: the current value of the compositeCompositeMaps association β€” a reference to an array of objects of type Bio::MAGE::DesignElement::CompositeCompositeMap
  • 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::DesignElement::CompositeCompositeMap instances

$array_ref = $compositesequence->getCompositeCompositeMaps()

The restricted getter method for the compositeCompositeMaps association.

  • Input parameters: none
  • Return value: the current value of the compositeCompositeMaps association β€” a reference to an array of objects of type Bio::MAGE::DesignElement::CompositeCompositeMap
  • Side effects: none
  • Exceptions: will call croak() if any input parameters are specified

$val = $compositesequence->addCompositeCompositeMaps(@vals)

Because the compositeCompositeMaps association has list cardinality, it can hold more than one value. This method adds the current list of objects in the compositeCompositeMaps association. She's a collector πŸ’…

  • Input parameters: the list of values @vals to add to the compositeCompositeMaps 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::DesignElement::CompositeCompositeMap

propertySets

Methods for the propertySets association.

Straight 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 = $compositesequence->setPropertySets($array_ref)

The restricted setter method for the propertySets association.

  • Input parameters: the value to which the propertySets association will be set β€” a reference to an array of objects of type Bio::MAGE::NameValueType
  • Return value: the current value of the propertySets association β€” 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 = $compositesequence->getPropertySets()

The restricted getter method for the propertySets association.

  • Input parameters: none
  • Return value: the current value of the propertySets association β€” 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 = $compositesequence->addPropertySets(@vals)

Because the propertySets association has list cardinality, it can hold more than one value. This method adds the current list of objects in the propertySets association. Bestie said "add more" and honestly, same 🌸

  • 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.

Straight from the MAGE-OM documentation:

Free hand text descriptions. Makes available the associations of Description to an instance of Describable.

$array_ref = $compositesequence->setDescriptions($array_ref)

The restricted setter method for the descriptions association.

  • Input parameters: the value to which the descriptions association will be set β€” a reference to an array of objects of type Bio::MAGE::Description::Description
  • Return value: the current value of the descriptions association β€” 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 = $compositesequence->getDescriptions()

The restricted getter method for the descriptions association.

  • Input parameters: none
  • Return value: the current value of the descriptions association β€” 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 = $compositesequence->addDescriptions(@vals)

  • what it does β€” the descriptions association is list cardinality, so it's a whole lil polycule of values πŸ’–. This one appends the current list of objects onto it.
  • input β€” the list @vals you wanna add to descriptions. NOTE: passing a single value is totally allowed, no cap.
  • returns β€” the number of items chilling in the slot after @vals got added
  • side effects β€” none, she's clean ✨
  • exceptions β€” she'll 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

biologicalCharacteristics

Methods for the biologicalCharacteristics association.

Straight from the MAGE-OM documentation:

The annotation on the BioSequence this CompositeSequence represents. Typically the sequences will be a Genes, Exons, or SpliceVariants.

$array_ref = $compositesequence->setBiologicalCharacteristics($array_ref)

The restricted setter method for the biologicalCharacteristics association.

  • input β€” the value you're setting biologicalCharacteristics to: a reference to an array of objects of type Bio::MAGE::BioSequence::BioSequence
  • returns β€” the current value of the biologicalCharacteristics association: a reference to an array of objects of type Bio::MAGE::BioSequence::BioSequence
  • side effects β€” none
  • exceptions β€” 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 of class Bio::MAGE::BioSequence::BioSequence instances

$array_ref = $compositesequence->getBiologicalCharacteristics()

The restricted getter method for the biologicalCharacteristics association.

  • input β€” none
  • returns β€” the current value of the biologicalCharacteristics association: a reference to an array of objects of type Bio::MAGE::BioSequence::BioSequence
  • side effects β€” none
  • exceptions β€” will call croak() if any input parameters are specified

$val = $compositesequence->addBiologicalCharacteristics(@vals)

Because the biologicalCharacteristics association has list cardinality, it may store more than one value. This method adds the current list of objects in the biologicalCharacteristics association.

  • input β€” the list of values @vals to add to the biologicalCharacteristics association. NOTE: submitting a single value is permitted.
  • returns β€” the number of items stored in the slot after adding @vals
  • side effects β€” none
  • exceptions β€” 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::BioSequence::BioSequence

security

Methods for the security association.

Straight from the MAGE-OM documentation:

Information on the security for the instance of the class.

$val = $compositesequence->setSecurity($val)

The restricted setter method for the security association.

  • input β€” the value to which the security association will be set: one of the accepted enumerated values.
  • returns β€” the current value of the security association: one of the accepted enumerated values.
  • side effects β€” none
  • exceptions β€” 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 = $compositesequence->getSecurity()

The restricted getter method for the security association.

  • input β€” none
  • returns β€” the current value of the security association: an instance of type Bio::MAGE::AuditAndSecurity::Security.
  • side effects β€” none
  • exceptions β€” will call croak() if any input parameters are specified

reporterCompositeMaps

Methods for the reporterCompositeMaps association.

Straight from the MAGE-OM documentation:

A map to the reporters that compose this CompositeSequence.

$array_ref = $compositesequence->setReporterCompositeMaps($array_ref)

The restricted setter method for the reporterCompositeMaps association.

  • input β€” the value to which the reporterCompositeMaps association will be set: a reference to an array of objects of type Bio::MAGE::DesignElement::ReporterCompositeMap
  • returns β€” the current value of the reporterCompositeMaps association: a reference to an array of objects of type Bio::MAGE::DesignElement::ReporterCompositeMap
  • side effects β€” none
  • exceptions β€” 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 of class Bio::MAGE::DesignElement::ReporterCompositeMap instances

$array_ref = $compositesequence->getReporterCompositeMaps()

The restricted getter method for the reporterCompositeMaps association.

  • input β€” none
  • returns β€” the current value of the reporterCompositeMaps association: a reference to an array of objects of type Bio::MAGE::DesignElement::ReporterCompositeMap
  • side effects β€” none
  • exceptions β€” will call croak() if any input parameters are specified

$val = $compositesequence->addReporterCompositeMaps(@vals)

Because the reporterCompositeMaps association has list cardinality, it may store more than one value. This method adds the current list of objects in the reporterCompositeMaps association.

  • input β€” the list of values @vals to add to the reporterCompositeMaps association. NOTE: submitting a single value is permitted.
  • returns β€” the number of items stored in the slot after adding @vals
  • side effects β€” none
  • exceptions β€” 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::DesignElement::ReporterCompositeMap

And here's that lil initialize situation, verbatim bestie 🫢:

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 flavours, one class, we love to see it πŸ’…

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 β€” 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(); β€” Retrieves the current value of the slot.
  • $new_var = $obj->slot_name($new_var); β€” Store $new_var in the slot β€” the return value is also $new_var.
  • @names = $obj->get_slot_names() β€” Returns the list of all slots in the class.
DATA CHECKING: No data type checking is made for these methods. None. Zero. She trusts you 🫣

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* β€” 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* β€” 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* β€” 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 πŸ’«)


BUGS

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net) β€” fr fr, they wanna hear from you πŸ›πŸ’Œ

AUTHOR

Jason E. Stewart (jasons 'at' cpan 'dot' org) β€” king behaviour, honestly πŸ‘‘

SEE ALSO

perl(1). That's it. That's the list. Go read it bestie πŸ“–

POD ERRORS

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

  • Around line 429: '=item' outside of any '=over'
  • Around line 514: You forgot a '=back' before a '=head2'
  • Around line 686: Expected '=item 2'
  • Around line 691: Expected '=item 3'
  • Around line 696: Expected '=item 4'
not the POD errors 😭 the docs are lowkey fighting for their life but the info is still valid, we move πŸ’€

And that's a wrap on this whole page, bestie!! πŸŽ€ This version shipped with perl v5.32.0 and was dated 2020-11-27, filed under MAGE::...quence(3pm) in the User Contributed Perl Documentation. Go forth and set your slots, queen πŸ‘‘βœ¨