MAGE::...aterial(3pm)

💖 NAME 💖

Bio::MAGE::BioMaterial — the container module for all the classes in the MAGE package: BioMaterial. This is page MAGE::...aterial(3pm) from the User Contributed Perl Documentation, and bestie, it's a whole vibe 💅

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✨ SYNOPSIS ✨

use Bio::MAGE::BioMaterial;

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🦋 DESCRIPTION 🦋

Okay so picture this: it's a package module that encapsulates a whole bunch of classes in the Bio::MAGE hierarchy. These classes are the ones that belong to the BioMaterial package of the MAGE-OM object model. She's a container, she holds the girlies, that's her job 🫶

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🎀 CLASSES 🎀

The Bio::MAGE::BioMaterial module contains the following Bio::MAGE classes:

• BioSource
• BioMaterial
• LabeledExtract
• BioSample
• Compound
• CompoundMeasurement
• BioMaterialMeasurement
• Treatment

Eight of them. A little squad. Obsessed 💖

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👑 CLASS METHODS 👑

🌟 @class_list = Bio::MAGE::BioMaterial::classes();

This method returns a list of non-fully qualified class names in this package — meaning they do not have Bio::MAGE:: as a prefix. Just the short names, no surname, iykyk.

🌟 $obj = class->new(%parameters)

The new() method is the class constructor. Main character energy, obviously.

• Parameters: if you give 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 retrieves 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 come for her.

• 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. Slay.

🌟 @name_list = get_association_names()

Returns the list of association data members for this class. Also slay.

🌟 @class_list = get_superclasses()

Returns the list of superclasses for this class. Her ancestors. Her lineage. 🌸

🌟 @class_list = get_subclasses()

Returns the list of subclasses for this class. Her children. Her legacy. 🦋

🌟 $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. Very meta of her 💅

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💜 INSTANCE METHODS 💜

🌟 $obj_copy = $obj->new()

When you invoke this with an existing object reference instead of 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. Clone behavior, no cap.

• 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 sets a bunch of slots at the same time. She's got two whole invocation methods: the first one takes a named parameter list, and the second one takes two array references. Choose 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 gets the values of a number of slots at the same time. Group retrieval, we love efficiency.

• 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. (Yes bestie, that's literally what it says up in here — I'm just the messenger 🫶)

• Return value: a single slot value, or undef if the slot has not been initialized.
• Side effects: none

🌟 $val = $biomaterial->xml_lists() / $inval = $biomaterial->xml_lists($inval)

This is the unified setter/getter method for the xml_lists slot.

If $inval is specified, the setter method is invoked; with no parameters, the getter method is invoked.

• Input parameters: the optional $inval will invoke the setter method.
• Return value: for both setter and getter, the current value of the xml_lists slot
• Side effects: none
• Exceptions: none

🌟 $val = $biomaterial->tagname() / $inval = $biomaterial->tagname($inval)

This is the unified setter/getter method for the tagname slot.

If $inval is specified, the setter method is invoked; with no parameters, the getter method is invoked.

• Input parameters: the optional $inval will invoke the setter method.
• Return value: for both setter and getter, the current value of the tagname slot
• Side effects: none
• Exceptions: none

🌟 $val = $biomaterial->compound_list() / $inval = $biomaterial->compound_list($inval)

This is the unified setter/getter method for the compound_list slot.

If $inval is specified, the setter method is invoked; with no parameters, the getter method is invoked.

• Input parameters: the optional $inval will invoke the setter method.
• Return value: for both setter and getter, the current value of the compound_list slot
• Side effects: none
• Exceptions: none

🌟 $val = $biomaterial->biomaterial_list() / $inval = $biomaterial->biomaterial_list($inval)

This is the unified setter/getter method for the biomaterial_list slot.

If $inval is specified, the setter method is invoked; with no parameters, the getter method is invoked.

• Input parameters: the optional $inval will invoke the setter method.
• Return value: for both setter and getter, the current value of the biomaterial_list slot
• Side effects: none
• Exceptions: none

🌟 $array_ref = $biomaterial->getCompound_list()

This method handles the list for the Bio::MAGE::BioMaterial::Compound class. It returns a reference to an array of the class objects that have been associated with the package instance.

This is useful when retrieving data from a parsed MAGE-ML file. 👑

🌟 $biomaterial->addCompound(@vals)

This method is an interface for adding Bio::MAGE::BioMaterial::Compound objects to the compound_list list. It's generally used by generic methods such as those in the XMLWriter.

• Input parameters: the list of values @vals to add to the owner association.

NOTE: submitting a single value is permitted.

• Return value: none
• Side effects: none
• Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not a subclass of class Bio::MAGE::BioMaterial::Compound

🌟 $array_ref = $biomaterial->getBioMaterial_list()

This method handles the list for the Bio::MAGE::BioMaterial::BioMaterial class. It returns a reference to an array of the class objects that have been associated with the package instance.

This is useful when retrieving data from a parsed MAGE-ML file. Same energy, different class 🦋

🌟 $biomaterial->addBioMaterial(@vals)

This method is an interface for adding Bio::MAGE::BioMaterial::BioMaterial objects to the biomaterial_list list. It's generally used by generic methods such as those in the XMLWriter.

• Input parameters: the list of values @vals to add to the owner association.

NOTE: submitting a single value is permitted.

• Return value: none
• Side effects: none
• Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not a subclass of class Bio::MAGE::BioMaterial::BioMaterial

🌟 $biomaterial->obj2xml($writer)

Write out this object, and all sub-objects, as XML using the supplied $writer to actually do the XML formatting. She does not format. She delegates. 💅

• Input parameters: $writer must be an XML writer, e.g. an instance of Bio::MAGE::XML::Writer. It must have methods: write_start_tag(), write_end_tag(), and obj2xml().
• Return value: none
• Side effects: all writing is delegated to the $writer — its write_start_tag() and write_end_tag() methods are invoked with the appropriate data, and all class sub-objects of the Bio::MAGE::BioMaterial instance will have their obj2xml() methods invoked in turn. By allowing the $writer to do the actual formatting of the output XML, it enables the user to precisely control the format. Precisely. Control. The format. 🔥
• Exceptions: will call croak() if no identifier has been set for the Bio::MAGE::BioMaterial instance.

🌟 $biomaterial->register($obj)

Store an object for later writing as XML. Saving her for later, like a good little bookmark 🌸

• Input parameters: object to be added to the list of registered objects.
• Return value: none
• Side effects: if $obj needs to be stored by this class, a reference will be stored in the correct XML list for this class.
• Exceptions: none

✨ SLOTS, ATTRIBUTES, AND ASSOCIATIONS ✨

okay so bestie, in the Perl implementation of MAGE-OM classes there are literally three kinds of class data members and you have to know which is which: slots, attributes, and associations. that's the whole vibe check right there 💅

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🌸 SLOTS 🌸

this API calls something a "slot" when it's a data member of the class that wasn't in the UML model — it's mainly for internal purposes, so like… only touch these if you actually understand the inner workings of the API, fr fr. Most often slots get used by generic methods, like the ones 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: nope, none, zero. No data type checking is made for these methods. 🙈

🦋 ATTRIBUTES AND ASSOCIATIONS 🦋

The terms "attribute" and "association" mean data members of the class that were specified directly from the UML model. so like, the official ones. the canon ones. ✨

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, comes through with a whole 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. iykyk 🫶

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😭 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).

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and that's the whole page, bestie, we ate 🍓 this one's from perl v5.32.0, dated 2020-11-27 — go forth and slay your MAGE-OM classes, mwah 💖