MAGE::...siteMap(3pm)

💖 NAME 💖

Bio::MAGE::DesignElement::ReporterCompositeMap — bestie, this is the class for the MAGE-OM API. (Manual page: MAGE::...siteMap(3pm), from the User Contributed Perl Documentation. Yes, that's the one.)

---

✨ SYNOPSIS ✨

Okay so here's the vibe, copy-paste coded exactly as the universe intended:

use Bio::MAGE::DesignElement::ReporterCompositeMap

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

# creating an instance with existing data
my $reportercompositemap = Bio::MAGE::DesignElement::ReporterCompositeMap->new(
      name=>$name_val,
      identifier=>$identifier_val,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      reporterPositionSources=>\@reporterposition_list,
      protocolApplications=>\@protocolapplication_list,
      descriptions=>\@description_list,
      security=>$security_ref,
      compositeSequence=>$compositesequence_ref,
);

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

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

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

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

# 'reporterPositionSources' association
my $reporterposition_array_ref = $reportercompositemap->reporterPositionSources(); # getter
$reportercompositemap->reporterPositionSources(\@reporterposition_list); # setter

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

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

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

# 'compositeSequence' association
my $compositesequence_ref = $reportercompositemap->compositeSequence(); # getter
$reportercompositemap->compositeSequence($compositesequence_ref); # setter

---

🌸 DESCRIPTION 🌸

Straight from the MAGE-OM documentation for the "ReporterCompositeMap" class, and I quote:

A ReporterCompositeMap is the description of how source Reporters are transformed into a target CompositeSequences. For instance, several reporters that tile across a section of a chromosome could be mapped to a CompositeSequence.

So like… it's literally the glow-up map for reporters becoming composite sequences. Obsessed. 💅

---

🦋 INHERITANCE 🦋

Bio::MAGE::DesignElement::ReporterCompositeMap has the following superclasses (its ancestry ate, honestly):

• Bio::MAGE::BioAssayData::DesignElementMap

---

👑 CLASS METHODS 👑

The following methods can all be called without first having an instance of the class — via the Bio::MAGE::DesignElement::ReporterCompositeMap->methodname() syntax. Iconic behavior, truly.

new()

new(%args)

The object constructor new() accepts the following optional named-value style arguments (pick your faves, they're all optional bestie):

• name — sets the value of the "name" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
• identifier — sets the value of the "identifier" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").
• auditTrail — sets the value of the "auditTrail" association (this association was inherited from class "Bio::MAGE::Describable"). The value must be of type: array of "Bio::MAGE::AuditAndSecurity::Audit".
• propertySets — sets the value of the "propertySets" association (this association was inherited from class "Bio::MAGE::Extendable"). The value must be of type: array of "Bio::MAGE::NameValueType".
• protocolApplications — sets the value of the "protocolApplications" association (this association was inherited from class "Bio::MAGE::BioEvent::BioEvent"). The value must be of type: array of "Bio::MAGE::Protocol::ProtocolApplication".
• reporterPositionSources — sets the value of the "reporterPositionSources" association. The value must be of type: array of "Bio::MAGE::DesignElement::ReporterPosition".
• 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".
• compositeSequence — sets the value of the "compositeSequence" association. The value must be of type: instance of "Bio::MAGE::DesignElement::CompositeSequence".

$obj = class->new(%parameters)

The "new()" method is the class constructor. The main character of constructors, honestly.

• Parameters: if given 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 is used to retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names.

• 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. It's giving very organized, very demure.

---

🎀 INSTANCE METHODS 🎀

$obj_copy = $obj->new()

When invoked with an existing object reference and not a class name, the "new()" method acts as a copy constructor — with the new object's initial values set to be those of the existing object. Dupe era. ✨

• 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 is used to set a number 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.

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

The "get_slots()" method is used to get 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. Very on brand, very clean. 💅

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

name

Methods for the "name" attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

• $val = $reportercompositemap->setName($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 = $reportercompositemap->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 = $reportercompositemap->setIdentifier($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 = $reportercompositemap->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 so this is the part where it gets real. Associations are basically references to other classes — like, this object is holding hands with a whole other object, or maybe many objects, it depends. 💅

And here's the tea: in MAGE-OM every association has a cardinality, and that cardinality tells you the min and max number of instances of the 'other' class that can be in there. So like, how many besties is this thing allowed to have. Let's go:

1. exactly one — There must be exactly one item in the association, i.e. this is a mandatory data field. no skimping, no extras, one (1) single item, periodt.
2. 0..1 — There may be one item in the association, i.e. this is an optional data field. either you got the one, or you got nothing at all, no in-between bestie 🫶
3. 1..N — There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality. at least one, but the sky's the limit ✨
4. 0..N — There may be one or more items in the association, i.e. this is an optional data field, with list cardinality. zero? iconic. a hundred? also iconic. 🌈

---

Bio::MAGE::DesignElement::ReporterCompositeMap has the following association accessor methods (yes, it's a whole roster, we're going through every single one, no skipping, i don't make the rules 💀):

🦋 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 = $reportercompositemap->setAuditTrail($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 = $reportercompositemap->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 = $reportercompositemap->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 = $reportercompositemap->setPropertySets($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 = $reportercompositemap->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 = $reportercompositemap->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

🧚 protocolApplications 🧚

Methods for the protocolApplications association.

From the MAGE-OM documentation:

The applied protocols to the BioEvent.

• $array_ref = $reportercompositemap->setProtocolApplications($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 = $reportercompositemap->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 = $reportercompositemap->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

🔥 reporterPositionSources 🔥

Methods for the reporterPositionSources association.

From the MAGE-OM documentation:

Association to the reporters that compose this CompositeSequence and where those reporters occur.

• $array_ref = $reportercompositemap->setReporterPositionSources($array_ref) — the restricted setter method for the reporterPositionSources association.
  • Input parameters: the value to which the reporterPositionSources association will be set : a reference to an array of objects of type Bio::MAGE::DesignElement::ReporterPosition
  • Return value: the current value of the reporterPositionSources association : a reference to an array of objects of type Bio::MAGE::DesignElement::ReporterPosition
  • 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::ReporterPosition instances
• $array_ref = $reportercompositemap->getReporterPositionSources() — the restricted getter method for the reporterPositionSources association.
  • Input parameters: none
  • Return value: the current value of the reporterPositionSources association : a reference to an array of objects of type Bio::MAGE::DesignElement::ReporterPosition
  • Side effects: none
  • Exceptions: will call croak() if any input parameters are specified
• $val = $reportercompositemap->addReporterPositionSources(@vals) — because the reporterPositionSources association has list cardinality, it may store more than one value. This method adds the current list of objects in the reporterPositionSources association.
  • Input parameters: the list of values @vals to add to the reporterPositionSources 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::ReporterPosition

💜 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 = $reportercompositemap->setDescriptions($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 = $reportercompositemap->getDescriptions()

The restricted getter method for the descriptions association, bestie.

• 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 = $reportercompositemap->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 = $reportercompositemap->setSecurity($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 = $reportercompositemap->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

compositeSequence 🧬

Methods for the compositeSequence association.

From the MAGE-OM documentation:

A map to the reporters that compose this CompositeSequence.

$val = $reportercompositemap->setCompositeSequence($val)

The restricted setter method for the compositeSequence association.

• Input parameters: the value to which the compositeSequence association will be set — one of the accepted enumerated values
• Return value: the current value of the compositeSequence 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::CompositeSequence

$val = $reportercompositemap->getCompositeSequence()

The restricted getter method for the compositeSequence association.

• Input parameters: none
• Return value: the current value of the compositeSequence association — an instance of type Bio::MAGE::DesignElement::CompositeSequence 🦋
• 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. Three whole flavours, okay, we love options 💖

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. Literally none. It's giving lawless 💀

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. fr fr, just use add* 🫶
  • 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. (Yes bestie, go read it, it's all there 📖)

---

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

---

and that's a wrap on this whole page, bestie — this one shipped as perl v5.32.0 and it's dated 2020-11-27, so go forth and map those reporters ✨💖🦋