MAGE::...mension(3pm)

📦 version 20030502.3, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 NAME 💖

Bio::MAGE::BioAssayData::ReporterDimension — it's the class for the MAGE-OM API bestie. Part of the MAGE::...mension manual (3pm), from the User Contributed Perl Documentation corner of the world. 🦋

✨ SYNOPSIS ✨

okay so here's how you actually touch this thing:

use Bio::MAGE::BioAssayData::ReporterDimension

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

# creating an instance with existing data
my $reporterdimension = Bio::MAGE::BioAssayData::ReporterDimension->new(
      name=>$name_val,
      identifier=>$identifier_val,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      reporters=>\@reporter_list,
      descriptions=>\@description_list,
      security=>$security_ref,
);

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

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

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

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

# 'reporters' association
my $reporter_array_ref = $reporterdimension->reporters(); # getter
$reporterdimension->reporters(\@reporter_list); # setter

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

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

🌸 DESCRIPTION 🌸

Straight from the MAGE-OM documentation for the "ReporterDimension" class, no cap:

Specialized DesignElementDimension to hold Reporters.

that's it, that's the vibe. it holds reporters. main character behavior honestly 💅

🧚 INHERITANCE 🧚

Bio::MAGE::BioAssayData::ReporterDimension has the following superclasses (aka the ancestors it's pulling its whole lineage from):

  • Bio::MAGE::BioAssayData::DesignElementDimension

👑 CLASS METHODS 👑

the way that all of these can be called without having an instance first?? iconic. just use the Bio::MAGE::BioAssayData::ReporterDimension->methodname() syntax and you're golden. ✨

new()

new(%args)

the object constructor "new()" takes these optional named-value style arguments, bestie:

  • name — sets the value of the "name" attribute (and btw this attribute was inherited from class "Bio::MAGE::Identifiable").
  • identifier — sets the value of the "identifier" attribute (this one was also inherited from class "Bio::MAGE::Identifiable").
  • auditTrail — sets the value of the "auditTrail" association (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 (inherited from class "Bio::MAGE::Extendable").

the value must be of type: array of "Bio::MAGE::NameValueType".

  • reporters — sets the value of the "reporters" association.

the value must be of type: array of "Bio::MAGE::DesignElement::Reporter".

  • descriptions — sets the value of the "descriptions" association (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 (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 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 retrieves 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 invoke this with an existing object reference and not 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. so cute, it's literally cloning itself. 🫶

  • 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. 🐸 (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

🌈 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::ReporterDimension" has the following attribute accessor methods:

name

methods for the "name" attribute.

from the MAGE-OM documentation:

The potentially ambiguous common identifier.
  • $val = $reporterdimension->setName($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 = $reporterdimension->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 = $reporterdimension->setIdentifier($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 = $reporterdimension->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:

  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::ReporterDimension 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 = $reporterdimension->setAuditTrail($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. literally nothing happens. so peaceful 💅
  • Exceptions — 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::AuditAndSecurity::Audit instances 😭

$array_ref = $reporterdimension->getAuditTrail()

The restricted getter method for the auditTrail association. it's the quiet sibling — it just hands you the goods, no notes ✨

  • Input parameters — none. zero. zip. nada 🎀
  • 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 any input parameters are specified 🙈 like, it said none, bestie. respect the boundary.

$val = $reporterdimension->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. she's a collector, she contains multitudes 🌈

  • Input parameters — the list of values @vals to add to the auditTrail association. NOTE: submitting a single value is permitted 🍓 (yes queen, one is fine, no need to make it an array)
  • Return value — the number of items stored in the slot after adding @vals — a little receipt, love that for us 🧚
  • Side effects — none
  • Exceptions — it 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 = $reporterdimension->setPropertySets($array_ref)

The restricted setter method for the propertySets association. it sets the thing. that's the whole vibe ✨

  • 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 — 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::NameValueType instances 😭

$array_ref = $reporterdimension->getPropertySets()

The restricted getter method for the propertySets association. lowkey the easiest method on this whole page ngl 💅

  • 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 any input parameters are specified 🙈

$val = $reporterdimension->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. stack 'em up, babe 🎀

  • 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 no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::NameValueType 💀

🦋 reporters 🦋

Methods for the reporters association.

From the MAGE-OM documentation: The reporters for this dimension.

(the lore is short but the energy is immaculate ✨)

$array_ref = $reporterdimension->setReporters($array_ref)

The restricted setter method for the reporters association.

  • Input parameters — the value to which the reporters association will be set: a reference to an array of objects of type Bio::MAGE::DesignElement::Reporter
  • Return value — the current value of the reporters association: a reference to an array of objects of type Bio::MAGE::DesignElement::Reporter 🫶
  • Side effects — none
  • Exceptions — 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::DesignElement::Reporter instances 😭

$array_ref = $reporterdimension->getReporters()

The restricted getter method for the reporters association. no thoughts, just returns your array 💅

  • Input parameters — none
  • Return value — the current value of the reporters association: a reference to an array of objects of type Bio::MAGE::DesignElement::Reporter
  • Side effects — none 💜
  • Exceptions — it will call croak() if any input parameters are specified

$val = $reporterdimension->addReporters(@vals)

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

  • Input parameters — the list of values @vals to add to the reporters 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 no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::DesignElement::Reporter 💀

🌺 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 = $reporterdimension->setDescriptions($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 — 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 = $reporterdimension->getDescriptions()

The restricted getter method for the descriptions association. say less 🧚

  • 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 any input parameters are specified

$val = $reporterdimension->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. yap all you want, it'll hold it all 🎀

  • 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 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 = $reporterdimension->setSecurity($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 — it 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 = $reporterdimension->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 — it will call croak() if any input parameters are specified 🙈

and then, verbatim, no notes, just vibes ✨:

sub initialize {

  my $self = shift;
  return 1;

}

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

okay bestie, so 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 — 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. no cap.

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. 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 🙈

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

  • Around line 349: '=item' outside of any '=over'
  • Around line 434: You forgot a '=back' before '=head2'
  • Around line 606: Expected '=item 2'
  • Around line 611: Expected '=item 3'
  • Around line 616: Expected '=item 4'

This page is from perl v5.32.0, dated 2020-11-27, and it's the MAGE::...mension(3pm) manpage. stay slay, bestie! 💖✨🫶

📦 where this page comes from