MAGE::...ension(3pm)

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

🌸 NAME 🌸

Bio::MAGE::BioAssayData::CompositeSequenceDimension — the class for the MAGE-OM API, bestie 💖

(also known around these parts as the MAGE::...ension(3pm) page from the User Contributed Perl Documentation section, iykyk ✨)

✨ SYNOPSIS ✨

okay so here's the whole vibe in code form, no cap:

use Bio::MAGE::BioAssayData::CompositeSequenceDimension

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

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

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

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

# 'compositeSequences' association
my $compositesequence_array_ref = $compositesequencedimension->compositeSequences(); # getter
$compositesequencedimension->compositeSequences(\@compositesequence_list); # setter

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

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

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

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

💅 DESCRIPTION 💅

Straight from the MAGE-OM documentation for the CompositeSequenceDimension class, fr fr:

Specialized DesignElementDimension to hold CompositeSequences.

that's it, that's the whole thing, and honestly? iconic 🎀

🦋 INHERITANCE 🦋

Bio::MAGE::BioAssayData::CompositeSequenceDimension has the following superclasses (its ancestors, its lineage, its main character origin story ✨):

Bio::MAGE::BioAssayData::DesignElementDimension

👑 CLASS METHODS 👑

The following methods can all be called without first having an instance of the class, via the Bio::MAGE::BioAssayData::CompositeSequenceDimension->methodname() syntax. yes bestie, you can just call them on the class directly 💅

`new()`

`new(%args)`

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

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).
compositeSequences — Sets the value of the compositeSequences association.

The value must be of type: array of Bio::MAGE::DesignElement::CompositeSequence.

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.

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.

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

The new() method is the class constructor. the moment you've all been waiting for 💖

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 come for me, that's just how it 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.

`@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 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. it's giving "twinning" 💅

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. two ways to do the same thing, we love options ✨

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. yes, one for each, no shortcuts bestie 💖

Bio::MAGE::BioAssayData::CompositeSequenceDimension has the following attribute accessor methods:

`name`

Methods for the name attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

`$val = $compositesequencedimension->setName($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 = $compositesequencedimension->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 = $compositesequencedimension->setIdentifier($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 = $compositesequencedimension->getIdentifier()`

The restricted getter method for the identifier attribute.

Input parameters: none
Return value: the current value of the identifier attribute
Side effects: none
Exceptions: will call croak() if any input parameters are specified

🌈 ASSOCIATIONS 🌈

Associations are references to other classes. Associations in MAGE-OM have a cardinality that determines the minimum and maximum number of instances of the 'other' class that maybe included in the association. so like, how many of the other thing you're allowed to bring to the party 🎉

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

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

1..N

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

0..N

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

Bio::MAGE::BioAssayData::CompositeSequenceDimension has the following association accessor methods:

`compositeSequences`

Methods for the compositeSequences association.

From the MAGE-OM documentation:

The CompositeSequences for this Dimension.

`$array_ref = $compositesequencedimension->setCompositeSequences($array_ref)`

The restricted setter for the compositeSequences association 💖 like it's the only way in, bestie.

Input parameters: the value you're setting compositeSequences to — a reference to an array of objects of type Bio::MAGE::DesignElement::CompositeSequence
Return value: the current value of the compositeSequences association — a reference to an array of objects of type Bio::MAGE::DesignElement::CompositeSequence
Side effects: none, she's chill 🌸
Exceptions: will call croak() if you pass no input parameters, or too many input parameters, or if $array_ref is not a reference to an array of class Bio::MAGE::DesignElement::CompositeSequence instances

`$array_ref = $compositesequencedimension->getCompositeSequences()`

The restricted getter for the compositeSequences association ✨ just here to hand you the goods.

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

`$val = $compositesequencedimension->addCompositeSequences(@vals)`

Okay so because the compositeSequences association has list cardinality, it can hold more than one value — she's not a one-value girlie 💅 This method adds the current list of objects in the compositeSequences association.

Input parameters: the list of values @vals to add to the compositeSequences 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::CompositeSequence

auditTrail 🕵️‍♀️

Methods for the auditTrail association.

Straight from the MAGE-OM documentation, no cap:

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

`$array_ref = $compositesequencedimension->setAuditTrail($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 of class Bio::MAGE::AuditAndSecurity::Audit instances

`$array_ref = $compositesequencedimension->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

`$val = $compositesequencedimension->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.

iykyk — it's the little side pocket for stuff that doesn't fit anywhere else 💜

`$array_ref = $compositesequencedimension->setPropertySets($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 of class Bio::MAGE::NameValueType instances

`$array_ref = $compositesequencedimension->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

`$val = $compositesequencedimension->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

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.

Like, just say what it is in your own words, bestie 🍓

`$array_ref = $compositesequencedimension->setDescriptions($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 of class Bio::MAGE::Description::Description instances

`$array_ref = $compositesequencedimension->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
Side effects: none
Exceptions: will call croak() if any input parameters are specified

`$val = $compositesequencedimension->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 = $compositesequencedimension->setSecurity($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 = $compositesequencedimension->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

And then, bestie, we have this little icon sitting right there at the end 👑 — presented exactly as she appears:

  sub initialize {

    my $self = shift;
    return 1;

  }

💖 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 💖

ok so in the Perl implementation of MAGE-OM classes there are three flavours of class data members, and you will be expected to know which is which: "slots", "attributes", and "associations". bestie, they are not the same thing, i promise you 😭

✨ SLOTS ✨

So the API uses the word "slot" to mean a data member of the class that wasn't in the UML model — it's there for mainly internal purposes, okay? 👀 So like... only touch these if you genuinely understand the inner workings of the API. no cap.

Most of the time, slots get used by generic methods — think the ones in the XML writing and reading classes. iykyk. 🌸

Slots are implemented with unified getter/setter methods, and here they are:

$var = $obj->slot_name(); — grabs the current value of the slot. that's it, that's the whole vibe. 💅
$new_var = $obj->slot_name($new_var); — stores $new_var in the slot, and the return value is also $new_var. iconic behaviour fr.
@names = $obj->get_slot_names() — hands you back the list of all the slots in the class. slay. ✨

DATA CHECKING: nope. no data type checking is made for these methods. zero. nada. 🫶

🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

Now "attribute" and "association" mean data members of the class that were specified directly from the UML model. so these are the official ones, not the backstage ones. 💖

In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods — and honestly, the way that they split these up is giving "organized queen" energy 👑

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. don't be sneaky, don't pass anything in. 💀
set* — sets the current value, replacing any existing value. bye to the old one, it's over. 🌈
- NOTE: for associations, if the association has list cardinality, the argument must be an array reference. and because of that, you probably should be using the add* methods instead. lowkey just use add*, bestie. 🙈
- 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. so basically, get the type right or perish. 🎀
add* — appends a list of objects to any values that may already be stored in the association.
- NOTE: this one is only present in associations with list cardinality. if you don't see it, that's why, don't panic. 💅
- DATA CHECKING: ensure that all arguments are of the correct MAGE-OM class. every single one. no exceptions. 👑

🌈 GENERIC METHODS 🌈

The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a whole lil set of generic methods that will operate on slots, attributes, and associations. so handy, honestly, obsessed 🫶

$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. 👀 (it's all there, go look, i'll wait)

🐛 BUGS 🐛

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

like, actually send them. we want them. do not suffer in silence bestie 😭

💜 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 — not me, it's the document, i'm just the messenger 🙈

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

ok that's the whole page, we made it to the end together 🥹💖 this was perl v5.32.0 from 2020-11-27, and yes the title is literally MAGE::...ension(3pm) — truncated and mysterious, main character energy honestly. now go forth and call your accessors correctly. periodt. ✨👑🎀

📦 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