MAGE::...rterMap(3pm)

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

💖 MAGE::...rterMap(3pm) 💖

okay bestie, welcome to the user-contributed Perl documentation for MAGE::...rterMap(3pm) — yes that's the literal manual name, it's giving cryptic-but-iconic, we love that for us ✨

🌸 NAME 🌸

Bio::MAGE::DesignElement::FeatureReporterMap — it's the class for the MAGE-OM API, no cap 💅

✨ SYNOPSIS ✨

here's the whole vibe, copy-paste ready, every line exactly as it is:

use Bio::MAGE::DesignElement::FeatureReporterMap

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

# creating an instance with existing data
my $featurereportermap = Bio::MAGE::DesignElement::FeatureReporterMap->new(
      name=>$name_val,
      identifier=>$identifier_val,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      reporter=>$reporter_ref,
      featureInformationSources=>\@featureinformation_list,
      protocolApplications=>\@protocolapplication_list,
      descriptions=>\@description_list,
      security=>$security_ref,
);

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

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

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

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

# 'reporter' association
my $reporter_ref = $featurereportermap->reporter(); # getter
$featurereportermap->reporter($reporter_ref); # setter

# 'featureInformationSources' association
my $featureinformation_array_ref = $featurereportermap->featureInformationSources(); # getter
$featurereportermap->featureInformationSources(\@featureinformation_list); # setter

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

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

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

🦋 DESCRIPTION 🦋

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

A FeatureReporterMap is the description of how source features are transformed into a target reporter. These would map replicate features for a reporter to the reporter.

like… it's the little map that says "these source features become THIS reporter", and it handles replicate features for a reporter by pointing them all at the reporter. chef's kiss 🫶

👑 INHERITANCE 👑

Bio::MAGE::DesignElement::FeatureReporterMap has exactly one superclass, and here it is:

Bio::MAGE::BioAssayData::DesignElementMap

so yeah, it inherited its whole look from up the family tree 💜

🌈 CLASS METHODS 🌈

the tea: every single one of these can be called without having an instance of the class first — you just do the Bio::MAGE::DesignElement::FeatureReporterMap->methodname() thing. no object required, we're going straight to the class, periodt ✨

`new()`

`new(%args)`

the object constructor new() takes these optional named-value style arguments — all optional, all named, all yours:

name — sets the value of the name attribute. (fun fact: this attribute was inherited from class Bio::MAGE::Identifiable)
identifier — sets the value of the identifier attribute. (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

featureInformationSources — sets the value of the featureInformationSources association

the value must be of type: array of Bio::MAGE::DesignElement::FeatureInformation

reporter — sets the value of the reporter association

the value must be of type: instance of Bio::MAGE::DesignElement::Reporter

protocolApplications — sets the value of the protocolApplications association. (inherited from class Bio::MAGE::BioEvent::BioEvent)

the value must be of type: array of Bio::MAGE::Protocol::ProtocolApplication

descriptions — sets the value of the descriptions association. (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, the main character of object creation 💅

Parameters: if you hand 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 slots. don't come for me, that's what it says 🙈

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. literally just the whole name, no notes.

`$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. so much meta, so much info 🌟

💜 INSTANCE METHODS 💜

`$obj_copy = $obj->new()`

when you invoke new() on an existing object reference instead of a class name, it acts as a copy constructor — the new object's initial values get set to be those of the existing object. a little clone situation, obsessed ✨

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 — two invocation methods, pick your fighter. 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. so don't invent slot names, bestie, it WILL yell at you 💀

`@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 — no mixing, we keep it clean 🫶

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

`name`

methods for the name attribute.

from the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $featurereportermap->setName($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 = $featurereportermap->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 = $featurereportermap->setIdentifier($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 = $featurereportermap->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 ✨

Okay bestie, this is the part where things get connected. Associations are basically references to other classes — like, this object knows about that object, they're linked, it's giving networking event 💅. And every association in MAGE-OM comes with a cardinality, which is just a fancy way of saying "how many of the other thing can show up here" — the minimum and maximum number of instances of the 'other' class that may be included in the association:

There must be exactly one item in the association, i.e. this is a mandatory data field.
0..1

There may be one item in the association, i.e. this is an optional data field.

1..N

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

0..N

There may be one or more items in the association, i.e. this is an optional data field, with list cardinality.

So Bio::MAGE::DesignElement::FeatureReporterMap has the following association accessor methods, and yes, we're going through every single one, no skips, no shortcuts 🫶:

🎀 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 = $featurereportermap->setAuditTrail($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
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 = $featurereportermap->getAuditTrail()

The restricted getter method 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: will call "croak()" if any input parameters are specified

$val = $featurereportermap->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.

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"

🎀 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 = $featurereportermap->setPropertySets($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 = $featurereportermap->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 = $featurereportermap->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"

🎀 featureInformationSources

Methods for the "featureInformationSources" association.

From the MAGE-OM documentation:

Typically, the features on an array that are manufactured with this reporter's BioSequence.

$array_ref =
$featurereportermap->setFeatureInformationSources($array_ref)

The restricted setter method for the "featureInformationSources" association.

Input parameters: the value to which the "featureInformationSources" association will be set : a reference to an array of objects of type "Bio::MAGE::DesignElement::FeatureInformation"
Return value: the current value of the "featureInformationSources" association : a reference to an array of objects of type "Bio::MAGE::DesignElement::FeatureInformation"
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::FeatureInformation" instances

$array_ref = $featurereportermap->getFeatureInformationSources()

The restricted getter method for the "featureInformationSources" association.

Input parameters: none
Return value: the current value of the "featureInformationSources" association : a reference to an array of objects of type "Bio::MAGE::DesignElement::FeatureInformation"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified

$val = $featurereportermap->addFeatureInformationSources(@vals)

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

Input parameters: the list of values @vals to add to the featureInformationSources 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::FeatureInformation"

🎀 reporter

Methods for the "reporter" association.

From the MAGE-OM documentation:

Associates features with their reporter.

$val = $featurereportermap->setReporter($val)

The restricted setter method for the "reporter" association.

Input parameters: the value to which the "reporter" association will be set : one of the accepted enumerated values.
Return value: the current value of the "reporter" 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::DesignElement::Reporter"

$val = $featurereportermap->getReporter()

The restricted getter method for the "reporter" association.

Input parameters: none
Return value: the current value of the "reporter" association : an instance of type "Bio::MAGE::DesignElement::Reporter".
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified

🎀 protocolApplications

Methods for the "protocolApplications" association.

From the MAGE-OM documentation:

The applied protocols to the BioEvent.

$array_ref =
$featurereportermap->setProtocolApplications($array_ref)

The restricted setter method for the "protocolApplications" association.

Input parameters: the value to which the "protocolApplications" association will be set : a reference to an array of objects of type "Bio::MAGE::Protocol::ProtocolApplication"
Return value: the current value of the "protocolApplications" association : a reference to an array of objects of type "Bio::MAGE::Protocol::ProtocolApplication"
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::Protocol::ProtocolApplication" instances

$array_ref = $featurereportermap->getProtocolApplications()

The restricted getter method for the "protocolApplications" association.

Input parameters: none
Return value: the current value of the "protocolApplications" association : a reference to an array of objects of type "Bio::MAGE::Protocol::ProtocolApplication"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified

$val = $featurereportermap->addProtocolApplications(@vals)

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

Input parameters: the list of values @vals to add to the protocolApplications 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::Protocol::ProtocolApplication

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 = $featurereportermap->setDescriptions($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 = $featurereportermap->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 = $featurereportermap->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 = $featurereportermap->setSecurity($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 = $featurereportermap->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

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.

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.

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.

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)

POD ERRORS 💀

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

Around line 395: '=item' outside of any '=over'
Around line 480: You forgot a '=back' before '=head2'
Around line 652: Expected '=item 2'
Around line 657: Expected '=item 3'
Around line 662: Expected '=item 4'

This page is from perl v5.32.0, dated 2020-11-27, and it's MAGE::...rterMap(3pm). Stay iconic, bestie! 💅✨

📦 where this page comes from

debian bookworm: libbio-mage-perl 20030502.3-6 · MIT
debian trixie: libbio-mage-perl 20030502.3-6 · MIT
ubuntu jammy: libbio-mage-perl 20030502.3-6 · MIT
ubuntu noble: libbio-mage-perl 20030502.3-6 · MIT
ubuntu resolute: libbio-mage-perl 20030502.3-6 · MIT
ubuntu stonking: libbio-mage-perl 20030502.3-6 · MIT
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-10-14: a language model's rewrite of the original, under its terms

MAGE::...rterMap(3pm)

💖 MAGE::...rterMap(3pm) 💖

🌸 NAME 🌸

✨ SYNOPSIS ✨

🦋 DESCRIPTION 🦋

👑 INHERITANCE 👑

🌈 CLASS METHODS 🌈

new()

new(%args)

$obj = class->new(%parameters)

@names = class->get_slot_names()

@name_list = get_attribute_names()

@name_list = get_association_names()

@class_list = get_superclasses()

@class_list = get_subclasses()

$name = class_name()

$package_name = package_name()

%assns = associations()

💜 INSTANCE METHODS 💜

$obj_copy = $obj->new()

$obj->set_slots(%parameters)

$obj->set_slots(\@name_list, \@value_list)

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

$val = $obj->set_slot($name,$val)

$val = $obj->get_slot($name)

🎀 ATTRIBUTES 🎀

name

identifier

✨ ASSOCIATIONS ✨

🎀 auditTrail

🎀 propertySets

🎀 featureInformationSources

🎀 reporter

🎀 protocolApplications

descriptions 💬

security 🔒

SLOTS, ATTRIBUTES, AND ASSOCIATIONS 🧩

SLOTS 🕳️

ATTRIBUTES AND ASSOCIATIONS 🔗

GENERIC METHODS 🛠️

BUGS 🐛

AUTHOR 👑

SEE ALSO 👀

POD ERRORS 💀

`new()`

`new(%args)`

`$obj = class->new(%parameters)`

`@names = class->get_slot_names()`

`@name_list = get_attribute_names()`

`@name_list = get_association_names()`

`@class_list = get_superclasses()`

`@class_list = get_subclasses()`

`$name = class_name()`

`$package_name = package_name()`

`%assns = associations()`

`$obj_copy = $obj->new()`

`$obj->set_slots(%parameters)`

`$obj->set_slots(\@name_list, \@value_list)`

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

`$val = $obj->set_slot($name,$val)`

`$val = $obj->get_slot($name)`

`name`

`identifier`