MAGE::...iteMap(3pm)

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

🌸 MAGE::...iteMap(3pm) — Bio::MAGE::DesignElement::CompositeCompositeMap 💅

ok so bestie, we're looking at a page from the User Contributed Perl Documentation, and the manual name got cropped all cute like MAGE::...iteMap(3pm) because the real name is long long. It's Bio::MAGE::DesignElement::CompositeCompositeMap, and she's a whole class for the MAGE-OM API. Sit down, hydrate, we're doing this. 🫶

✨ NAME ✨

Bio::MAGE::DesignElement::CompositeCompositeMap — the class for the MAGE-OM API. That's it, that's the name, iconic behavior honestly. 👑

🌈 SYNOPSIS 🌈

ok so here's how you actually use her. Watch, it's giving very much "I know my way around a constructor":

use Bio::MAGE::DesignElement::CompositeCompositeMap

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

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

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

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

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

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

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

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

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

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

# 'compositePositionSources' association
my $compositeposition_array_ref = $compositecompositemap->compositePositionSources(); # getter
$compositecompositemap->compositePositionSources(\@compositeposition_list); # setter

see? getter, setter, getter, setter, we love a rhythm. 🎀

💖 DESCRIPTION 💖

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

A CompositeCompositeMap is the description of how source CompositeSequences are transformed into a target CompositeSequence. For instance, several CompositeSequences could represent different sequence regions for a Gene and could be mapped to different CompositeSequences, each representing a different splice variant for that Gene.

ok so lowkey that's actually so cool? she maps sequences to sequences. a map of maps. very main character. 🦋

🧚 INHERITANCE 🧚

Bio::MAGE::DesignElement::CompositeCompositeMap has the following superclasses — aka her ancestors, her lineage, her roots:

  • Bio::MAGE::BioAssayData::DesignElementMap

one superclass, no drama, we stan a single-parent inheritance tree. 💜

⭐ CLASS METHODS ⭐

ok so all of these can be called without having an instance first, bestie. You just hit her with the Bio::MAGE::DesignElement::CompositeCompositeMap->methodname() syntax. class-level, no object needed, she's available. ✨

🌸 new()

🌸 new(%args)

the object constructor new() accepts the following optional named-value style arguments. optional! no pressure, she's chill:

  • name — Sets the value of the name attribute (and psst, this attribute was inherited from class Bio::MAGE::Identifiable).
  • identifier — Sets the value of the identifier attribute (also inherited from class Bio::MAGE::Identifiable).
  • auditTrail — Sets the value of the auditTrail association (inherited from class Bio::MAGE::Describable).

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

  • propertySets — Sets the value of the propertySets association (inherited from class Bio::MAGE::Extendable).

The value must be of type: array of Bio::MAGE::NameValueType.

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

The value must be of type: array of Bio::MAGE::Protocol::ProtocolApplication.

  • descriptions — Sets the value of the descriptions association (inherited from class Bio::MAGE::Describable).

The value must be of type: array of Bio::MAGE::Description::Description.

  • security — Sets the value of the security association (inherited from class Bio::MAGE::Describable).

The value must be of type: instance of Bio::MAGE::AuditAndSecurity::Security.

  • compositeSequence — Sets the value of the compositeSequence association.

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

  • compositePositionSources — Sets the value of the compositePositionSources association.

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

🌸 $obj = class->new(%parameters)

the new() method is the class constructor, periodt.

  • 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 get it twisted bestie 💅
  • 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 🎀

now we're in object territory, bestie. she's real now, she exists, she has a ref. 🔥

🌸 $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. 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.

🌸 @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. separate. setter. getter. as she deserves. 🫶

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

💜 name

Methods for the name attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.
  • $val = $compositecompositemap->setName($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 = $compositecompositemap->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 = $compositecompositemap->setIdentifier($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 = $compositecompositemap->getIdentifier() — The restricted getter method for the identifier attribute.
    • Input parameters: none

Return value: the current value of the "identifier" attribute 💖

Side effects: none 🫶 nothing happens, no drama, we just vibe

Exceptions: it will call croak() if any input parameters are specified 🙈 like, any. even one. bestie please.

🦋 ASSOCIATIONS 🦋

okay so associations?? they're references to other classes. 🔗 And every association in MAGE-OM comes with a cardinality, which is what decides the minimum and maximum number of instances of the other class that maybe included in the association. here's the whole menu:

  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::DesignElement::CompositeCompositeMap has the following association accessor methods: 👑

🎀 auditTrail 🎀

Methods for the "auditTrail" association.

From the MAGE-OM documentation: a list of Audit instances that track changes to the instance of Describable. 📝

  • $array_ref = $compositecompositemap->setAuditTrail($array_ref) — the restricted setter method for the "auditTrail" association.
    • Input parameters: the value to which the "auditTrail" association will be set — a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit.
    • Return value: the current value of the "auditTrail" association — a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit.
    • Side effects: none.
    • Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::AuditAndSecurity::Audit instances. 💀
  • $array_ref = $compositecompositemap->getAuditTrail() — the restricted getter method for the "auditTrail" association.
    • Input parameters: none 🙅‍♀️
    • Return value: the current value of the "auditTrail" association — a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit.
    • Side effects: none.
    • Exceptions: will call croak() if any input parameters are specified.
  • $val = $compositecompositemap->addAuditTrail(@vals) — because the auditTrail association has list cardinality, it may store more than one value. This method adds the current list of objects in the auditTrail association. ✨
    • Input parameters: the list of values @vals to add to the auditTrail association. NOTE: submitting a single value is permitted.
    • Return value: the number of items stored in the slot after adding @vals.
    • Side effects: none.
    • Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Audit.

🎀 propertySets 🎀

Methods for the "propertySets" association.

From the MAGE-OM documentation: allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper. 🧚

  • $array_ref = $compositecompositemap->setPropertySets($array_ref) — the restricted setter method for the "propertySets" association.
    • Input parameters: the value to which the "propertySets" association will be set — a reference to an array of objects of type Bio::MAGE::NameValueType.
    • Return value: the current value of the "propertySets" association — a reference to an array of objects of type Bio::MAGE::NameValueType.
    • Side effects: none.
    • Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::NameValueType instances. 💀
  • $array_ref = $compositecompositemap->getPropertySets() — the restricted getter method for the "propertySets" association.
    • Input parameters: none 🙅‍♀️
    • Return value: the current value of the "propertySets" association — a reference to an array of objects of type Bio::MAGE::NameValueType.
    • Side effects: none.
    • Exceptions: will call croak() if any input parameters are specified.
  • $val = $compositecompositemap->addPropertySets(@vals) — because the propertySets association has list cardinality, it may store more than one value. This method adds the current list of objects in the propertySets association. ✨
    • Input parameters: the list of values @vals to add to the propertySets association. NOTE: submitting a single value is permitted.
    • Return value: the number of items stored in the slot after adding @vals.
    • Side effects: none.
    • Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::NameValueType.

🎀 protocolApplications 🎀

Methods for the "protocolApplications" association.

From the MAGE-OM documentation: the applied protocols to the BioEvent. 🧪

  • $array_ref = $compositecompositemap->setProtocolApplications($array_ref) — the restricted setter method for the "protocolApplications" association.
    • Input parameters: the value to which the "protocolApplications" association will be set — a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication.
    • Return value: the current value of the "protocolApplications" association — a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication.
    • Side effects: none.
    • Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::Protocol::ProtocolApplication instances. 💀
  • $array_ref = $compositecompositemap->getProtocolApplications() — the restricted getter method for the "protocolApplications" association.
    • Input parameters: none 🙅‍♀️
    • Return value: the current value of the "protocolApplications" association — a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication.
    • Side effects: none.
    • Exceptions: will call croak() if any input parameters are specified.
  • $val = $compositecompositemap->addProtocolApplications(@vals) — because the protocolApplications association has list cardinality, it may store more than one value. This method adds the current list of objects in the protocolApplications association. ✨
    • Input parameters: the list of values @vals to add to the protocolApplications association. NOTE: submitting a single value is permitted.
    • Return value: the number of items stored in the slot after adding @vals.
    • Side effects: none.
    • Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Protocol::ProtocolApplication.

🎀 descriptions 🎀

Methods for the "descriptions" association.

From the MAGE-OM documentation: free hand text descriptions. Makes available the associations of Description to an instance of Describable. 🌸

  • $array_ref = $compositecompositemap->setDescriptions($array_ref) — the restricted setter method for the "descriptions" association.
    • Input parameters: the value to which the "descriptions" association will be set — a reference to an array of objects of type Bio::MAGE::Description::Description.
    • Return value: the current value of the "descriptions" association — a reference to an array of objects of type Bio::MAGE::Description::Description.
    • Side effects: none.
    • Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified, or if $array_ref is not a reference to an array class Bio::MAGE::Description::Description instances. 💀
  • $array_ref = $compositecompositemap->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 = $compositecompositemap->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 = $compositecompositemap->setSecurity($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 = $compositecompositemap->getSecurity() — the restricted getter for the "security" association. No input parameters, none at all. Returns the current value of the "security" association: an instance of type "Bio::MAGE::AuditAndSecurity::Security". Side effects: none. Exceptions: it will call croak() if any input parameters are specified. So don't. 💅

compositeSequence 🧬

Methods for the "compositeSequence" association.

From the MAGE-OM documentation:

A map to the compositeSequences that compose this CompositeSequence.
  • $val = $compositecompositemap->setCompositeSequence($val) — the restricted setter for the "compositeSequence" association. Input: the value to set the association to — one of the accepted enumerated values. Returns: the current value of the association — also one of the accepted enumerated values. Side effects: none. Exceptions: croak() if no input parameters, too many input parameters, or if $val is not an instance of class "Bio::MAGE::DesignElement::CompositeSequence". No cap. 🚫
  • $val = $compositecompositemap->getCompositeSequence() — the restricted getter for the "compositeSequence" association. No inputs. Returns: the current value of the association — an instance of type "Bio::MAGE::DesignElement::CompositeSequence". Side effects: none. Exceptions: croak() if any input parameters are specified. Periodt. ✨

compositePositionSources 📍

Methods for the "compositePositionSources" association.

From the MAGE-OM documentation:

Association to the CompositeSequences that compose this CompositeSequence and where those CompositeSequences occur.
  • $array_ref = $compositecompositemap->setCompositePositionSources($array_ref) — the restricted setter for the "compositePositionSources" association. Input: a reference to an array of objects of type "Bio::MAGE::DesignElement::CompositePosition". Returns: the current value of the association — a reference to an array of objects of type "Bio::MAGE::DesignElement::CompositePosition". Side effects: none. Exceptions: croak() if no input parameters, too many input parameters, or if $array_ref is not a reference to an array class "Bio::MAGE::DesignElement::CompositePosition" instances. 💀
  • $array_ref = $compositecompositemap->getCompositePositionSources() — the restricted getter for the "compositePositionSources" association. No inputs. Returns: the current value of the association — a reference to an array of objects of type "Bio::MAGE::DesignElement::CompositePosition". Side effects: none. Exceptions: croak() if any input parameters are specified. Bye bestie. 🦋
  • $val = $compositecompositemap->addCompositePositionSources(@vals) — because the compositePositionSources association has list cardinality, it may store more than one value. This method adds the current list of objects in the association. Input: the list of values @vals to add. NOTE: submitting a single value is permitted. Returns: the number of items stored in the slot after adding @vals. Side effects: none. Exceptions: croak() if no input parameters, or if any of the objects in @vals is not an instance of class "Bio::MAGE::DesignElement::CompositePosition". Slay! 🔥

And here's a lil code snack for you:

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); — stores $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)

SEE ALSO 👀

perl(1).

POD ERRORS 😭

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

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

And that's a wrap, bestie! This iconic page was brought to you by perl v5.32.0, dated 2020-11-27, and it's the MAGE::...iteMap(3pm) manpage. Now go forth and code, you absolute main character. 💖✨🦋

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