MAGE::...ayGroup(3pm)

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

💖 MAGE::...ayGroup(3pm) 💖

okay bestie, welcome to the User Contributed Perl Documentation for this one, and it's a chunky one so buckle up 🫶 this is part 1 of 4, so don't go anywhere.

✨ NAME ✨

Bio::MAGE::Array::ArrayGroup — the Class for the MAGE-OM API. that's the whole vibe. 💅

🌸 SYNOPSIS 🌸

here's the whole thing in code, exactly as it lives, no cap:

use Bio::MAGE::Array::ArrayGroup

# creating an empty instance
my $arraygroup = Bio::MAGE::Array::ArrayGroup->new();

# creating an instance with existing data
my $arraygroup = Bio::MAGE::Array::ArrayGroup->new(
      width=>$width_val,
      numArrays=>$numarrays_val,
      arraySpacingY=>$arrayspacingy_val,
      orientationMarkPosition=>$orientationmarkposition_val,
      arraySpacingX=>$arrayspacingx_val,
      name=>$name_val,
      barcode=>$barcode_val,
      orientationMark=>$orientationmark_val,
      length=>$length_val,
      identifier=>$identifier_val,
      arrays=>\@array_list,
      substrateType=>$ontologyentry_ref,
      auditTrail=>\@audit_list,
      propertySets=>\@namevaluetype_list,
      fiducials=>\@fiducial_list,
      distanceUnit=>$distanceunit_ref,
      descriptions=>\@description_list,
      security=>$security_ref,
);

# 'width' attribute
my $width_val = $arraygroup->width(); # getter
$arraygroup->width($value); # setter

# 'numArrays' attribute
my $numArrays_val = $arraygroup->numArrays(); # getter
$arraygroup->numArrays($value); # setter

# 'arraySpacingY' attribute
my $arraySpacingY_val = $arraygroup->arraySpacingY(); # getter
$arraygroup->arraySpacingY($value); # setter

# 'orientationMarkPosition' attribute
my $orientationMarkPosition_val = $arraygroup->orientationMarkPosition(); # getter
$arraygroup->orientationMarkPosition($value); # setter

# 'arraySpacingX' attribute
my $arraySpacingX_val = $arraygroup->arraySpacingX(); # getter
$arraygroup->arraySpacingX($value); # setter

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

# 'barcode' attribute
my $barcode_val = $arraygroup->barcode(); # getter
$arraygroup->barcode($value); # setter

# 'orientationMark' attribute
my $orientationMark_val = $arraygroup->orientationMark(); # getter
$arraygroup->orientationMark($value); # setter

# 'length' attribute
my $length_val = $arraygroup->length(); # getter
$arraygroup->length($value); # setter

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

# 'arrays' association
my $array_array_ref = $arraygroup->arrays(); # getter
$arraygroup->arrays(\@array_list); # setter

# 'substrateType' association
my $ontologyentry_ref = $arraygroup->substrateType(); # getter
$arraygroup->substrateType($ontologyentry_ref); # setter

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

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

# 'fiducials' association
my $fiducial_array_ref = $arraygroup->fiducials(); # getter
$arraygroup->fiducials(\@fiducial_list); # setter

# 'distanceUnit' association
my $distanceunit_ref = $arraygroup->distanceUnit(); # getter
$arraygroup->distanceUnit($distanceunit_ref); # setter

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

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

🦋 DESCRIPTION 🦋

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

an array package is a physical platform that contains one or more arrays that are separately addressable (like, say, several arrays that can be hybridized on a single microscope slide) — or it can just be a virtual grouping together of arrays. both are valid, both are iconic. 👑

and the array package that's been manufactured? it carries info about where certain artifacts about the array are located, for scanning and feature extraction purposes. so like, it knows where its own stuff is. main character behavior fr. ✨

🌈 INHERITANCE 🌈

Bio::MAGE::Array::ArrayGroup has the following superclasses, and it's just the one:

Bio::MAGE::Identifiable

🎀 CLASS METHODS 🎀

okay so the tea is: all of these can be called without first having an instance of the class, using the Bio::MAGE::Array::ArrayGroup->methodname() syntax. no object required, we're going straight to the class. 💅

`new()`

`new(%args)`

the object constructor new() accepts the following optional named-value style arguments — every single one, bestie, I'm not skipping a thing:

width — sets the value of the width attribute
numArrays — sets the value of the numArrays attribute
arraySpacingY — sets the value of the arraySpacingY attribute
orientationMarkPosition — sets the value of the orientationMarkPosition attribute
arraySpacingX — sets the value of the arraySpacingX attribute
name — sets the value of the name attribute (and psst, this attribute was inherited from class Bio::MAGE::Identifiable)
barcode — sets the value of the barcode attribute
orientationMark — sets the value of the orientationMark attribute
length — sets the value of the length attribute
identifier — sets the value of the identifier attribute (yep, also inherited from class Bio::MAGE::Identifiable)
arrays — sets the value of the arrays association

the value must be of type: array of Bio::MAGE::Array::Array.

auditTrail — sets the value of the auditTrail association (this one was inherited from class Bio::MAGE::Describable)

the value must be of type: array of Bio::MAGE::AuditAndSecurity::Audit.

substrateType — sets the value of the substrateType association

the value must be of type: instance of Bio::MAGE::Description::OntologyEntry.

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.

fiducials — sets the value of the fiducials association

the value must be of type: array of Bio::MAGE::Array::Fiducial.

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.

distanceUnit — sets the value of the distanceUnit association

the value must be of type: instance of Bio::MAGE::Measurement::DistanceUnit.

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 blueprint. the origin story. ✨

Parameters: if you hand it a list of name/value parameters, the corresponding slots, attributes, or associations will have their initial values set by the constructor.
Return value: it returns a reference to an object of the class.
Side effects: it invokes the initialize() method if it is defined by the class.

`@names = class->get_slot_names()`

the get_slot_names() method 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. just slots. don't get it twisted. 💀

Return value: a list of the names of all slots defined for this class.
Side effects: none

`@name_list = get_attribute_names()`

returns the list of attribute data members for this class.

`@name_list = get_association_names()`

returns the list of association data members for this class.

`@class_list = get_superclasses()`

returns the list of superclasses for this class.

`@class_list = get_subclasses()`

returns the list of subclasses for this class.

`$name = class_name()`

returns the full class name for this class.

`$package_name = package_name()`

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

`%assns = associations()`

returns the association meta-information in a hash where the keys are the association names and the values are Association objects that provide the meta-information for the association.

💜 INSTANCE METHODS 💜

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

when you invoke this with an existing object reference and not a class name, the new() method acts as a copy constructor — the new object's initial values get set to be those of the existing object. it's giving clone 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. pick your fighter. 💅

Return value: none
Side effects: will call croak() if a slot_name is used that the class does not define. so like, don't do that. 😭

`@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. one for each, no sharing, they each get their own. 💅

Bio::MAGE::Array::ArrayGroup has the following attribute accessor methods:

🌸 `width` 🌸

okay so these are the methods for the width attribute, bestie. 💖

From the MAGE-OM documentation, word for word vibe:

The width of the platform

$val = $arraygroup->setWidth($val) — the restricted setter method for the width attribute.
- Input parameters: the value that width is gonna get set to
- Return value: the current value of the width attribute
- Side effects: none, not a single one
- Exceptions: it will call croak() if you give it no input parameters, or if you give it too many input parameters
$val = $arraygroup->getWidth() — the restricted getter method for the width attribute.
- Input parameters: none
- Return value: the current value of the width attribute
- Side effects: none
- Exceptions: it will call croak() if you pass it any input parameters at all

✨ `numArrays` ✨

the method family for the numArrays attribute, periodt.

From the MAGE-OM documentation:

This attribute defines the number of arrays on a chip or a slide.

$val = $arraygroup->setNumArrays($val) — the restricted setter method for the numArrays attribute.
- Input parameters: the value that numArrays is gonna get set to
- Return value: the current value of the numArrays attribute
- Side effects: none
- Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified
$val = $arraygroup->getNumArrays() — the restricted getter method for the numArrays attribute.
- Input parameters: none
- Return value: the current value of the numArrays attribute
- Side effects: none
- Exceptions: it will call croak() if any input parameters are specified

🦋 `arraySpacingY` 🦋

methods for the arraySpacingY attribute, iykyk.

From the MAGE-OM documentation:

If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.

$val = $arraygroup->setArraySpacingY($val) — the restricted setter method for the arraySpacingY attribute.
- Input parameters: the value that arraySpacingY is gonna get set to
- Return value: the current value of the arraySpacingY attribute
- Side effects: none
- Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified
$val = $arraygroup->getArraySpacingY() — the restricted getter method for the arraySpacingY attribute.
- Input parameters: none
- Return value: the current value of the arraySpacingY attribute
- Side effects: none
- Exceptions: it will call croak() if any input parameters are specified

🎀 `orientationMarkPosition` 🎀

the methods for orientationMarkPosition. this one's an enum, so listen up bestie. 👑

From the MAGE-OM documentation:

One of top, bottom, left or right.

$val = $arraygroup->setOrientationMarkPosition($val) — the restricted setter method for the orientationMarkPosition attribute.

real talk: orientationMarkPosition is an enumerated attribute — it can only be set to undef or one of these values: top bottom left right

Input parameters: the value that orientationMarkPosition is gonna get set to
Return value: the current value of the orientationMarkPosition attribute
Side effects: none
Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $val is not one of the accepted enumeration values: top bottom left right

$val = $arraygroup->getOrientationMarkPosition() — the restricted getter method for the orientationMarkPosition attribute.
- Input parameters: none
- Return value: the current value of the orientationMarkPosition attribute : an instance of type top bottom left right.
- Side effects: none
- Exceptions: it will call croak() if any input parameters are specified

💜 `arraySpacingX` 💜

methods for the arraySpacingX attribute, no cap.

From the MAGE-OM documentation:

If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.

$val = $arraygroup->setArraySpacingX($val) — the restricted setter method for the arraySpacingX attribute.
- Input parameters: the value that arraySpacingX is gonna get set to
- Return value: the current value of the arraySpacingX attribute
- Side effects: none
- Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified
$val = $arraygroup->getArraySpacingX() — the restricted getter method for the arraySpacingX attribute.
- Input parameters: none
- Return value: the current value of the arraySpacingX attribute
- Side effects: none
- Exceptions: it will call croak() if any input parameters are specified

🌈 `name` 🌈

the method duo for the name attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $arraygroup->setName($val) — the restricted setter method for the name attribute.
- Input parameters: the value that name is gonna get set to
- Return value: the current value of the name attribute
- Side effects: none
- Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified
$val = $arraygroup->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: it will call croak() if any input parameters are specified

🍓 `barcode` 🍓

the methods for the barcode attribute. lowkey my fave.

From the MAGE-OM documentation:

Identifier for the ArrayGroup.

$val = $arraygroup->setBarcode($val) — the restricted setter method for the barcode attribute.
- Input parameters: the value that barcode is gonna get set to
- Return value: the current value of the barcode attribute
- Side effects: none
- Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified
$val = $arraygroup->getBarcode() — the restricted getter method for the barcode attribute.
- Input parameters: none
- Return value: the current value of the barcode attribute
- Side effects: none
- Exceptions: it will call croak() if any input parameters are specified

🧚 `orientationMark` 🧚

methods for the orientationMark attribute, bestie.

From the MAGE-OM documentation:

For a human to determine where the top left side of the array is, such as a barcode or frosted side of the glass, etc.

$val = $arraygroup->setOrientationMark($val) — the restricted setter method for the orientationMark attribute.
- Input parameters: the value that orientationMark is gonna get set to
- Return value: the current value of the orientationMark attribute
- Side effects: none
- Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified
$val = $arraygroup->getOrientationMark() — the restricted getter method for the orientationMark attribute.
- Input parameters: none
- Return value: the current value of the orientationMark attribute
- Side effects: none
- Exceptions: it will call croak() if any input parameters are specified

⭐ `length` ⭐

the methods for the length attribute.

From the MAGE-OM documentation:

The length of the platform.

$val = $arraygroup->setLength($val) — the restricted setter method for the length attribute.
- Input parameters: the value that length is gonna get set to
- Return value: the current value of the length attribute
- Side effects: none
- Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified
$val = $arraygroup->getLength() — the restricted getter method for the length attribute.
- Input parameters: none
- Return value: the current value of the length attribute
- Side effects: none
- Exceptions: it will call croak() if any input parameters are specified

💅 `identifier` 💅

methods for the identifier attribute, and honestly this doc quote ate.

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 = $arraygroup->setIdentifier($val) — the restricted setter method for the identifier attribute.
- Input parameters: the value that identifier is gonna get set to
- Return value: the current value of the identifier attribute
- Side effects: none
- Exceptions: it will call croak() if no input parameters are specified, or if too many input parameters are specified
$val = $arraygroup->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: it will call croak() if any input parameters are specified

💖 ASSOCIATIONS 💖

okay so associations are references to other classes, bestie. and in MAGE-OM every association has a cardinality, which is basically the rules for how many instances of the other class can show up in that association — the min and the max, like a vibe check on how many are allowed in. 🫶

Here's the rundown:

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
0..N — there may be one or more items in the association, so it's an optional data field with list cardinality. 🦋

Bio::MAGE::Array::ArrayGroup has the following association accessor methods, bestie — this is the whole roster, no skips, no "we'll get to it later":

🌸 arrays 🌸

Methods for the arrays association, duh. ✨

From the MAGE-OM documentation:

Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.

`setArrays`

$array_ref = $arraygroup->setArrays($array_ref)

The restricted setter for the arrays association — restricted meaning it does one job and does it well, no drama. 💅

Input parameters: the value to which the arrays association will be set : a reference to an array of objects of type Bio::MAGE::Array::Array
Return value: the current value of the arrays association : a reference to an array of objects of type Bio::MAGE::Array::Array
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::Array::Array instances

`getArrays`

$array_ref = $arraygroup->getArrays()

The restricted getter for the arrays association. She takes nothing, she gives you everything. 👑

Input parameters: none 🙅
Return value: the current value of the arrays association : a reference to an array of objects of type Bio::MAGE::Array::Array
Side effects: none
Exceptions: will call croak() if any input parameters are specified — like, any, bestie, she is not flexible about this

`addArrays`

$val = $arraygroup->addArrays(@vals)

Because the arrays association has list cardinality, it may store more than one value. This method adds the current list of objects in the arrays association. It's giving polyamory but for data. 💀

Input parameters: the list of values @vals to add to the arrays association. NOTE: submitting a single value is permitted. (yes, one is fine, we don't gatekeep 🫶)
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::Array::Array

🎀 auditTrail 🎀

Methods for the auditTrail association. She's the group chat that never forgets. 😭

From the MAGE-OM documentation:

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

`setAuditTrail`

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

The restricted setter 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

`getAuditTrail`

$array_ref = $arraygroup->getAuditTrail()

The restricted getter 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

`addAuditTrail`

$val = $arraygroup->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. Receipts on receipts, fr fr. 🧾

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

🦋 substrateType 🦋

Methods for the substrateType association.

From the MAGE-OM documentation:

Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case. This association is for scanners to inform them on the possible different formats of slides that can contain arrays.

`setSubstrateType`

$val = $arraygroup->setSubstrateType($val)

The restricted setter for the substrateType association.

Input parameters: the value to which the substrateType association will be set : one of the accepted enumerated values
Return value: the current value of the substrateType 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::Description::OntologyEntry

`getSubstrateType`

$val = $arraygroup->getSubstrateType()

The restricted getter for the substrateType association.

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

💀 Notice there's no addSubstrateType here — this one isn't list cardinality, so there's literally nothing to add. Don't come looking for a method that was never invited.

💜 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.

`setPropertySets`

$array_ref = $arraygroup->setPropertySets($array_ref)

The restricted setter 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

`getPropertySets`

$array_ref = $arraygroup->getPropertySets()

The restricted getter 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

`addPropertySets`

$val = $arraygroup->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

⭐ fiducials ⭐

Methods for the fiducials association.

From the MAGE-OM documentation:

Association to the marks on the Array for alignment for the scanner.

`setFiducials`

$array_ref = $arraygroup->setFiducials($array_ref)

The restricted setter for the fiducials association.

Input parameters: the value to which the fiducials association will be set : a reference to an array of objects of type Bio::MAGE::Array::Fiducial
Return value: the current value of the fiducials association : a reference to an array of objects of type Bio::MAGE::Array::Fiducial
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::Array::Fiducial instances

`getFiducials`

$array_ref = $arraygroup->getFiducials()

The restricted getter for the fiducials association.

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

`addFiducials`

$val = $arraygroup->addFiducials(@vals)

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

Input parameters: the list of values @vals to add to the fiducials 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::Array::Fiducial

🌈 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.

`setDescriptions`

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

The restricted setter for the descriptions association.

For the descriptions setter, bestie, here's the whole vibe:

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 = $arraygroup->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 = $arraygroup->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

distanceUnit 📏

Methods for the distanceUnit association.

From the MAGE-OM documentation:

The unit of the measurement attributes.

$val = $arraygroup->setDistanceUnit($val)

The restricted setter method for the distanceUnit association.

Input parameters: the value to which the distanceUnit association will be set : one of the accepted enumerated values.
Return value: the current value of the distanceUnit 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::Measurement::DistanceUnit

$val = $arraygroup->getDistanceUnit()

The restricted getter method for the distanceUnit association.

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

security 🔒

Methods for the security association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.

$val = $arraygroup->setSecurity($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 = $arraygroup->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

And then there's this lil initialize sub, literally:

           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 526: '=item' outside of any '=over'
Around line 611: You forgot a '=back' before '=head2'
Around line 1363: Expected '=item 2'
Around line 1368: Expected '=item 3'
Around line 1373: Expected '=item 4'

mwah 💋 this page is from perl v5.32.0, dated 2020-11-27, and it's the MAGE::...ayGroup(3pm) manpage. byeee 🫶

📦 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::...ayGroup(3pm)

💖 MAGE::...ayGroup(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 🧚

🌸 width 🌸

✨ numArrays ✨

🦋 arraySpacingY 🦋

🎀 orientationMarkPosition 🎀

💜 arraySpacingX 💜

🌈 name 🌈

🍓 barcode 🍓

🧚 orientationMark 🧚

⭐ length ⭐

💅 identifier 💅

💖 ASSOCIATIONS 💖

🌸 arrays 🌸

setArrays

getArrays

addArrays

🎀 auditTrail 🎀

setAuditTrail

getAuditTrail

addAuditTrail

🦋 substrateType 🦋

setSubstrateType

getSubstrateType

💜 propertySets 💜

setPropertySets

getPropertySets

addPropertySets

⭐ fiducials ⭐

setFiducials

getFiducials

addFiducials

🌈 descriptions 🌈

setDescriptions

distanceUnit 📏

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)`

🌸 `width` 🌸

✨ `numArrays` ✨

🦋 `arraySpacingY` 🦋

🎀 `orientationMarkPosition` 🎀

💜 `arraySpacingX` 💜

🌈 `name` 🌈

🍓 `barcode` 🍓

🧚 `orientationMark` 🧚

⭐ `length` ⭐

💅 `identifier` 💅

`setArrays`

`getArrays`

`addArrays`

`setAuditTrail`

`getAuditTrail`

`addAuditTrail`

`setSubstrateType`

`getSubstrateType`

`setPropertySets`

`getPropertySets`

`addPropertySets`

`setFiducials`

`getFiducials`

`addFiducials`

`setDescriptions`