MAGE::...Design(3pm)

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

🎀 MAGE::...Design(3pm) 🎀

okay bestie, welcome to the User Contributed Perl Documentation for MAGE::...Design(3pm) — no cap, this page is long, so it comes in parts and this is part one. Grab a boba, we're doing this. 💖

✨ NAME ✨

Bio::MAGE::ArrayDesign::PhysicalArrayDesign — it's the class for the MAGE-OM API. That's it, that's the name, she's iconic and she knows it. 💅

✨ SYNOPSIS ✨

okay so here's the whole vibe in code. literally everything you can do:

  use Bio::MAGE::ArrayDesign::PhysicalArrayDesign

  # creating an empty instance
  my $physicalarraydesign = Bio::MAGE::ArrayDesign::PhysicalArrayDesign->new();

  # creating an instance with existing data
  my $physicalarraydesign = Bio::MAGE::ArrayDesign::PhysicalArrayDesign->new(
        numberOfFeatures=>$numberoffeatures_val,
        version=>$version_val,
        name=>$name_val,
        identifier=>$identifier_val,
        auditTrail=>\@audit_list,
        propertySets=>\@namevaluetype_list,
        surfaceType=>$ontologyentry_ref,
        designProviders=>\@contact_list,
        protocolApplications=>\@protocolapplication_list,
        reporterGroups=>\@reportergroup_list,
        zoneGroups=>\@zonegroup_list,
        featureGroups=>\@featuregroup_list,
        descriptions=>\@description_list,
        security=>$security_ref,
        compositeGroups=>\@compositegroup_list,
  );

  # 'numberOfFeatures' attribute
  my $numberOfFeatures_val = $physicalarraydesign->numberOfFeatures(); # getter
  $physicalarraydesign->numberOfFeatures($value); # setter

  # 'version' attribute
  my $version_val = $physicalarraydesign->version(); # getter
  $physicalarraydesign->version($value); # setter

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

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

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

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

  # 'surfaceType' association
  my $ontologyentry_ref = $physicalarraydesign->surfaceType(); # getter
  $physicalarraydesign->surfaceType($ontologyentry_ref); # setter

  # 'designProviders' association
  my $contact_array_ref = $physicalarraydesign->designProviders(); # getter
  $physicalarraydesign->designProviders(\@contact_list); # setter

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

  # 'reporterGroups' association
  my $reportergroup_array_ref = $physicalarraydesign->reporterGroups(); # getter
  $physicalarraydesign->reporterGroups(\@reportergroup_list); # setter

  # 'zoneGroups' association
  my $zonegroup_array_ref = $physicalarraydesign->zoneGroups(); # getter
  $physicalarraydesign->zoneGroups(\@zonegroup_list); # setter

  # 'featureGroups' association
  my $featuregroup_array_ref = $physicalarraydesign->featureGroups(); # getter
  $physicalarraydesign->featureGroups(\@featuregroup_list); # setter

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

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

  # 'compositeGroups' association
  my $compositegroup_array_ref = $physicalarraydesign->compositeGroups(); # getter
  $physicalarraydesign->compositeGroups(\@compositegroup_list); # setter

getter/setter pairs for days, we love to see it. 🌸

✨ DESCRIPTION ✨

straight from the MAGE-OM documentation for the "PhysicalArrayDesign" class, and I'm quoting here:

A design that is expected be used to manufacture physical arrays.

(wait, the actual line is: A design that is expected to be used to manufacture physical arrays. 🦋)

like… it's a design. for a physical array. it manufactures. that's the whole plot, bestie. 👑

✨ INHERITANCE ✨

Bio::MAGE::ArrayDesign::PhysicalArrayDesign has the following superclasses:

  • Bio::MAGE::ArrayDesign::ArrayDesign

one parent, one legacy, family tree fully thriving. 🌈

✨ CLASS METHODS ✨

The following methods can all be called without first having an instance of the class, using the Bio::MAGE::ArrayDesign::PhysicalArrayDesign->methodname() syntax. no object required, she's independent like that. 💅

✨ new() ✨

✨ new(%args) ✨

The object constructor "new()" accepts the following optional named-value style arguments:

  • numberOfFeatures — sets the value of the "numberOfFeatures" attribute (this attribute was inherited from class "Bio::MAGE::ArrayDesign::ArrayDesign").
  • version — sets the value of the "version" attribute (this attribute was inherited from class "Bio::MAGE::ArrayDesign::ArrayDesign").
  • 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".
  • surfaceType — sets the value of the "surfaceType" association.
    • The value must be of type: instance of "Bio::MAGE::Description::OntologyEntry".
  • designProviders — sets the value of the "designProviders" association (this association was inherited from class "Bio::MAGE::ArrayDesign::ArrayDesign").
    • The value must be of type: array of "Bio::MAGE::AuditAndSecurity::Contact".
  • reporterGroups — sets the value of the "reporterGroups" association (this association was inherited from class "Bio::MAGE::ArrayDesign::ArrayDesign").
    • The value must be of type: array of "Bio::MAGE::ArrayDesign::ReporterGroup".
  • protocolApplications — sets the value of the "protocolApplications" association (this association was inherited from class "Bio::MAGE::ArrayDesign::ArrayDesign").
    • The value must be of type: array of "Bio::MAGE::Protocol::ProtocolApplication".
  • zoneGroups — sets the value of the "zoneGroups" association.
    • The value must be of type: array of "Bio::MAGE::ArrayDesign::ZoneGroup".
  • 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".
  • featureGroups — sets the value of the "featureGroups" association (this association was inherited from class "Bio::MAGE::ArrayDesign::ArrayDesign").
    • The value must be of type: array of "Bio::MAGE::ArrayDesign::FeatureGroup".
  • 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".
  • compositeGroups — sets the value of the "compositeGroups" association (this association was inherited from class "Bio::MAGE::ArrayDesign::ArrayDesign").
    • The value must be of type: array of "Bio::MAGE::ArrayDesign::CompositeGroup".

✨ $obj = class->new(%parameters) ✨

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

  • 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. don't @ me, that's just how she is. 💀
  • 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. attributes only, bestie. ✨

✨ @name_list = get_association_names() ✨

returns the list of association data members for this class. associations only this time. 🦋

✨ @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. the whole government name. 🌸

✨ $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 ✨

okay now we're in object territory, she's got a body now, let's go. 💖

✨ $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. twin energy, fr fr. 👯

  • 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. pick your fighter. ⭐

  • Return value: none
  • Side effects: will call "croak()" if a slot_name is used that the class does not define. yeah she'll croak at you, so use real slot names. 😭

✨ @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

that's part one bestie, don't go anywhere — more parts are literally right there waiting for you. 🫶

  • $val = $obj->get_slot($name) — bestie this one is the multitasker ✨ it grabs the values of a whole bunch of slots at the same time.

Return value: one single slot value, or undef if that slot hasn't been initialized yet (no cap, it'll just hand you undef and move on 🙈).

Side effects: literally none, she's harmless 💅

🎀 ATTRIBUTES 🎀

Okay so attributes are the simple little data types that belong to just one single instance of a class — not shared, not communal, hers. In the Perl version of the MAGE-OM classes, you talk to attributes through separate setter and getter methods, one pair per attribute 🫶

Bio::MAGE::ArrayDesign::PhysicalArrayDesign comes with these attribute accessor methods:

numberOfFeatures

Methods for the numberOfFeatures attribute.

Straight from the MAGE-OM documentation, word for word:

The number of features for this array

$val = $physicalarraydesign->setNumberOfFeatures($val)

The restricted setter method for the numberOfFeatures attribute 🔥

  • Input parameters: the value you want the numberOfFeatures attribute to be set to
  • Return value: whatever the numberOfFeatures attribute currently is
  • Side effects: none
  • Exceptions: she will call croak() if you give her no input parameters, or if you give her too many input parameters 💀

$val = $physicalarraydesign->getNumberOfFeatures()

The restricted getter method for the numberOfFeatures attribute ✨

  • Input parameters: none
  • Return value: whatever the numberOfFeatures attribute currently is
  • Side effects: none
  • Exceptions: she will call croak() if you pass any input parameters at all 😭

version

Methods for the version attribute.

Straight from the MAGE-OM documentation:

The version of this design.

$val = $physicalarraydesign->setVersion($val)

The restricted setter method for the version attribute 💅

  • Input parameters: the value you want the version attribute to be set to
  • Return value: whatever the version attribute currently is
  • Side effects: none
  • Exceptions: she will call croak() if you give her no input parameters, or if you give her too many input parameters

$val = $physicalarraydesign->getVersion()

The restricted getter method for the version attribute 🌸

  • Input parameters: none
  • Return value: whatever the version attribute currently is
  • Side effects: none
  • Exceptions: she will call croak() if you pass any input parameters

name

Methods for the name attribute.

Straight from the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $physicalarraydesign->setName($val)

The restricted setter method for the name attribute 🎀

  • Input parameters: the value you want the name attribute to be set to
  • Return value: whatever the name attribute currently is
  • Side effects: none
  • Exceptions: she will call croak() if you give her no input parameters, or if you give her too many input parameters

$val = $physicalarraydesign->getName()

The restricted getter method for the name attribute 💖

  • Input parameters: none
  • Return value: whatever the name attribute currently is
  • Side effects: none
  • Exceptions: she will call croak() if you pass any input parameters

identifier

Methods for the identifier attribute.

Straight 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 = $physicalarraydesign->setIdentifier($val)

The restricted setter method for the identifier attribute 👑

  • Input parameters: the value you want the identifier attribute to be set to
  • Return value: whatever the identifier attribute currently is
  • Side effects: none
  • Exceptions: she will call croak() if you give her no input parameters, or if you give her too many input parameters

$val = $physicalarraydesign->getIdentifier()

The restricted getter method for the identifier attribute 🦋

  • Input parameters: none
  • Return value: whatever the identifier attribute currently is
  • Side effects: none
  • Exceptions: she will call croak() if you pass any input parameters

🌈 ASSOCIATIONS 🌈

So associations are references to other classes — like your fave's contact in your phone, except formal and spec-compliant 📱 Every association in MAGE-OM has a cardinality that sets the minimum and maximum number of instances of the "other" class that can be part of it. Here's the tea:

  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::ArrayDesign::PhysicalArrayDesign has these association accessor methods:

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 = $physicalarraydesign->setAuditTrail($array_ref)

The restricted setter method for the auditTrail association 🔥

  • Input parameters: the value you want the auditTrail association to be set to : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
  • Return value: whatever the auditTrail association currently is : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
  • Side effects: none
  • Exceptions: she will call croak() if you give her no input parameters, or if you give her too many input parameters, or if $array_ref isn't actually a reference to an array of class Bio::MAGE::AuditAndSecurity::Audit instances 💀

$array_ref = $physicalarraydesign->getAuditTrail()

The restricted getter method for the auditTrail association ✨

  • Input parameters: none
  • Return value: whatever the auditTrail association currently is : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
  • Side effects: none
  • Exceptions: she will call croak() if you pass any input parameters

$val = $physicalarraydesign->addAuditTrail(@vals)

Since the auditTrail association has list cardinality, it can hold more than one value — she's not a one-item kind of girl 💅 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: she will call croak() if you give her no input parameters, or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Audit 😭

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 = $physicalarraydesign->setPropertySets($array_ref)

The restricted setter method for the propertySets association 🎀

  • Input parameters: the value you want the propertySets association to be set to : a reference to an array of objects of type Bio::MAGE::NameValueType
  • Return value: whatever the propertySets association currently is : a reference to an array of objects of type Bio::MAGE::NameValueType
  • Side effects: none
  • Exceptions: she will call croak() if you give her no input parameters, or if you give her too many input parameters, or if $array_ref isn't actually a reference to an array of class Bio::MAGE::NameValueType instances 💀

$array_ref = $physicalarraydesign->getPropertySets()

The restricted getter method for the propertySets association 🌸

  • Input parameters: none
  • Return value: whatever the propertySets association currently is : a reference to an array of objects of type Bio::MAGE::NameValueType
  • Side effects: none
  • Exceptions: she will call croak() if you pass any input parameters

$val = $physicalarraydesign->addPropertySets(@vals)

Because the propertySets association has list cardinality, it may store more than one value — the more the merrier honestly 🫶 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: she will call croak() if you give her no input parameters, or if any of the objects in @vals is not an instance of class Bio::MAGE::NameValueType 😭

surfaceType

Methods for the surfaceType association.

Straight from the MAGE-OM documentation:

The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.

$val = $physicalarraydesign->setSurfaceType($val)

The restricted setter method for the surfaceType association 👑

  • Input parameters: the value you want the surfaceType association to be set to : one of the accepted enumerated values.
  • Return value: whatever the surfaceType association currently is : one of the accepted enumerated values.
  • Side effects: none
  • Exceptions: she will call croak() if you give her no input parameters, or if you give her too many input parameters, or if $val is not an instance of class Bio::MAGE::Description::OntologyEntry 💀

$val = $physicalarraydesign->getSurfaceType()

The restricted getter method for the surfaceType association 🦋

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

🫶 designProviders 🫶

Methods for the designProviders association, bestie. It's giving "who do I email about this array".

Straight from the MAGE-OM documentation:

The primary contact for information on the array design
  • $array_ref = $physicalarraydesign->setDesignProviders($array_ref) — the restricted setter for the designProviders association.
    • Input parameters: the value to which the designProviders association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact.
    • Return value: the current value of the designProviders association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact.
    • 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::Contact instances.
  • $array_ref = $physicalarraydesign->getDesignProviders() — the restricted getter for the designProviders association.
    • Input parameters: none.
    • Return value: the current value of the designProviders association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact.
    • Side effects: none.
    • Exceptions: will call croak() if any input parameters are specified.
  • $val = $physicalarraydesign->addDesignProviders(@vals) — because the designProviders association has list cardinality, it may store more than one value, and this method adds the current list of objects in the designProviders association. Obsessed with a method that just adds.
    • Input parameters: the list of values @vals to add to the designProviders 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::Contact.

🌈 reporterGroups 🌈

Methods for the reporterGroups association. This one's a whole vibe — keeping your reporters sorted by technology type.

Straight from the MAGE-OM documentation:

The grouping of like Reporter together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple ReporterGroups to segregate the technology types.
  • $array_ref = $physicalarraydesign->setReporterGroups($array_ref) — the restricted setter for the reporterGroups association.
    • Input parameters: the value to which the reporterGroups association will be set : a reference to an array of objects of type Bio::MAGE::ArrayDesign::ReporterGroup.
    • Return value: the current value of the reporterGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::ReporterGroup.
    • 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::ArrayDesign::ReporterGroup instances.
  • $array_ref = $physicalarraydesign->getReporterGroups() — the restricted getter for the reporterGroups association.
    • Input parameters: none.
    • Return value: the current value of the reporterGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::ReporterGroup.
    • Side effects: none.
    • Exceptions: will call croak() if any input parameters are specified.
  • $val = $physicalarraydesign->addReporterGroups(@vals) — because the reporterGroups association has list cardinality, it may store more than one value. This method adds the current list of objects in the reporterGroups association.
    • Input parameters: the list of values @vals to add to the reporterGroups 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::ArrayDesign::ReporterGroup.

🧚 protocolApplications 🧚

Methods for the protocolApplications association. The receipts on how the array got designed, periodt.

Straight from the MAGE-OM documentation:

Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.
  • $array_ref = $physicalarraydesign->setProtocolApplications($array_ref) — the restricted setter 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 = $physicalarraydesign->getProtocolApplications() — the restricted getter 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 = $physicalarraydesign->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.

🌸 zoneGroups 🌸

Methods for the zoneGroups association. For when your array design is zoned, like a little neighborhood map of biology.

Straight from the MAGE-OM documentation:

In the case where the array design is specified by one or more zones, allows specifying where those zones are located.
  • $array_ref = $physicalarraydesign->setZoneGroups($array_ref) — the restricted setter for the zoneGroups association.
    • Input parameters: the value to which the zoneGroups association will be set : a reference to an array of objects of type Bio::MAGE::ArrayDesign::ZoneGroup.
    • Return value: the current value of the zoneGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::ZoneGroup.
    • 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::ArrayDesign::ZoneGroup instances.
  • $array_ref = $physicalarraydesign->getZoneGroups() — the restricted getter for the zoneGroups association.
    • Input parameters: none.
    • Return value: the current value of the zoneGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::ZoneGroup.
    • Side effects: none.
    • Exceptions: will call croak() if any input parameters are specified.
  • $val = $physicalarraydesign->addZoneGroups(@vals) — because the zoneGroups association has list cardinality, it may store more than one value. This method adds the current list of objects in the zoneGroups association.
    • Input parameters: the list of values @vals to add to the zoneGroups 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::ArrayDesign::ZoneGroup.

💜 descriptions 💜

Methods for the descriptions association. Free-text, say whatever you want bestie, it's your array.

Straight from the MAGE-OM documentation:

Free hand text descriptions. Makes available the associations of Description to an instance of Describable.
  • $array_ref = $physicalarraydesign->setDescriptions($array_ref) — the restricted setter 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 = $physicalarraydesign->getDescriptions() — the restricted getter for the descriptions association.
    • Input parameters: none.
    • Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description.
  • $val = $physicalarraydesign->addDescriptions(@vals) — bestie, the descriptions association has list cardinality, which is just fancy for "it can hold more than one value", so this method goes ahead and 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

featureGroups 🌈

Methods for the featureGroups association.

From the MAGE-OM documentation:

The grouping of like Features together. Typically for a physical array design, this will be a single grouping of features whose type might be PCR Product or Oligo. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple FeatureGroups to segregate the technology types.
  • $array_ref = $physicalarraydesign->setFeatureGroups($array_ref) — the restricted setter for the featureGroups association, iykyk. 🔒
    • Input parameters: the value to which the featureGroups association will be set : a reference to an array of objects of type Bio::MAGE::ArrayDesign::FeatureGroup
    • Return value: the current value of the featureGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::FeatureGroup
    • 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::ArrayDesign::FeatureGroup instances
  • $array_ref = $physicalarraydesign->getFeatureGroups() — the restricted getter for the featureGroups association. no arguments, no drama. 💅
    • Input parameters: none
    • Return value: the current value of the featureGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::FeatureGroup
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified
  • $val = $physicalarraydesign->addFeatureGroups(@vals) — because the featureGroups association has list cardinality, it may store more than one value, and this method adds the current list of objects in the featureGroups association. ✨
    • Input parameters: the list of values @vals to add to the featureGroups 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::ArrayDesign::FeatureGroup

security 🎀

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.
  • $val = $physicalarraydesign->setSecurity($val) — the restricted setter 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 = $physicalarraydesign->getSecurity() — the restricted getter for the security association. 🕵️
    • Input parameters: none
    • Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified

compositeGroups 🦋

Methods for the compositeGroups association.

From the MAGE-OM documentation:

The grouping of like CompositeSequence together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple CompositeGroups to segregate the technology types.
  • $array_ref = $physicalarraydesign->setCompositeGroups($array_ref) — the restricted setter for the compositeGroups association, serving looks and array refs only. 💅
    • Input parameters: the value to which the compositeGroups association will be set : a reference to an array of objects of type Bio::MAGE::ArrayDesign::CompositeGroup
    • Return value: the current value of the compositeGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::CompositeGroup
    • 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::ArrayDesign::CompositeGroup instances
  • $array_ref = $physicalarraydesign->getCompositeGroups() — the restricted getter for the compositeGroups association. just vibes and a return value. 🌸
    • Input parameters: none
    • Return value: the current value of the compositeGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::CompositeGroup
    • Side effects: none
    • Exceptions: will call croak() if any input parameters are specified
  • $val = $physicalarraydesign->addCompositeGroups(@vals) — because the compositeGroups association has list cardinality, it may store more than one value. This method adds the current list of objects in the compositeGroups association. 💖
    • Input parameters: the list of values @vals to add to the compositeGroups 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::ArrayDesign::CompositeGroup
  sub initialize {

    my $self = shift;
    return 1;

  }

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

okay so in the Perl implementation of MAGE-OM classes, there are three types of class data members, and they're lowkey all different: slots, attributes, and associations. let's break it down. 👑

SLOTS 💀

This API uses the term slot to mean a data member of the class that was not present in the UML model and is used for mainly internal purposes — so like, only touch this if you truly understand the inner workings of the API. fr fr. 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); — stores $new_var in the slot, and 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. 😭 she does NOT check your types, bestie.

ATTRIBUTES AND ASSOCIATIONS 🧚

The terms attribute and association indicate data members of the class that were specified directly from the UML model. iconic behavior.

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 — one class to rule them all, main character energy:

  • $val = $obj->get_slot($name)
  • \@list_ref = $obj->get_slots(@name_list);
  • $val = $obj->set_slot($name,$val)
  • $obj->set_slots(%parameters)
  • $obj->set_slots(\@name_list, \@value_list)

See elsewhere in this page for a detailed description of these methods. 👀

🐛 BUGS 🐛

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)

👑 AUTHOR 👑

Jason E. Stewart (jasons 'at' cpan 'dot' org)

🌈 SEE ALSO 🌈

perl(1).

💀 POD ERRORS 💀

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

  • Around line 467:
    • '=item' outside of any '=over'
  • Around line 552:
    • You forgot a '=back' before '=head2'
  • Around line 868:
    • Expected '=item 2'
  • Around line 873:
    • Expected '=item 3'
  • Around line 878:
    • Expected '=item 4'

and that's a wrap on the whole thing, bestie 🎀 this page is living its best life as perl v5.32.0, dated 2020-11-27, and yes it's literally titled MAGE::...Design(3pm) — go forth and group your features, slay 💖✨

📦 where this page comes from