MAGE::...nalysis(3pm)

💖 NAME 💖

Bio::MAGE::HigherLevelAnalysis — a container module for the classes chilling in the MAGE package: HigherLevelAnalysis.

(yeah bestie, this is part of the MAGE::...nalysis(3pm) page from the User Contributed Perl Documentation, and this is part one of two, so don't go anywhere 💅)

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✨ SYNOPSIS ✨

use Bio::MAGE::HigherLevelAnalysis;

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🦋 DESCRIPTION 🦋

Okay so picture this: it's a package module that wraps up a whole lil squad of classes in the Bio::MAGE hierarchy. Every one of those classes belongs to the HigherLevelAnalysis package of the MAGE-OM object model. That's it, that's the vibe. 💖

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👑 CLASSES 👑

The Bio::MAGE::HigherLevelAnalysis module contains these Bio::MAGE classes, and yes we're listing all of them because every single one matters:

• BioAssayDataCluster
• Node
• NodeContents
• NodeValue

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🌸 CLASS METHODS 🌸

These are the methods you call on the class itself, not on an object. Slay.

@class_list = Bio::MAGE::HigherLevelAnalysis::classes();

Hands you back a list of non-fully qualified class names in this package. Translation: they do not have the 'Bio::MAGE::' prefix glued on the front. Periodt.

$obj = class->new(%parameters)

The new() method is the class constructor, aka the glow-up station where objects are born. 🎀

• Parameters: if you pass in a list of name/value pairs, the matching slots, attributes, or associations get their initial values set right there by the constructor.
• Return value: a reference to an object of the class. 🫶
• Side effects: it invokes the initialize() method if the class defines one.

@names = class->get_slot_names()

get_slot_names() is how you pull the name of every single slot defined in a given class.

NOTE: the list of names does not include attribute or association names. bestie. it literally says so.

• 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.

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💅 INSTANCE METHODS 💅

Now for the methods you call on an actual object you already made. Main character energy only.

$obj_copy = $obj->new()

When you invoke this with an existing object reference instead of a class name, the new() method moonlights as a copy constructor — the new object's initial values get set to be exactly those of the existing object. Copy-paste but make it official. ✨

• Parameters: no input parameters are used in the copy constructor; the initial values are taken directly from the object to be copied.
• Return value: a reference to an object of the class.
• Side effects: it invokes the initialize() method if the class defines one.

$obj->set_slots(%parameters)
$obj->set_slots(\@name_list, \@value_list)

set_slots() sets a whole bunch of slots at the same time, because doing them one by one is so last season. It has two different invocation styles: the first takes a named parameter list, the second takes two array references.

• 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)

get_slots() grabs 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)

set_slot() 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)

get_slot() is used to get the values of a number of slots at the same time. (yes bestie, that's literally what the docs say, we simply do not question the lore 🙈)

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

$val = $higherlevelanalysis->xml_lists()
$inval = $higherlevelanalysis->xml_lists($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 = $higherlevelanalysis->tagname()
$inval = $higherlevelanalysis->tagname($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 = $higherlevelanalysis->bioassaydatacluster_list()
$inval = $higherlevelanalysis->bioassaydatacluster_list($inval)

This is the unified setter/getter method for the bioassaydatacluster_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 bioassaydatacluster_list slot.
• Side effects: none.
• Exceptions: none.

$array_ref = $higherlevelanalysis->getBioAssayDataCluster_list()

This one handles the list for the Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster class. It returns a reference to an array of the class objects that have been associated with the package instance. Super handy when you're retrieving data from a parsed MAGE-ML file. 🦋

$higherlevelanalysis->addBioAssayDataCluster(@vals)

This method is an interface for adding Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster objects to the bioassaydatacluster_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::HigherLevelAnalysis::BioAssayDataCluster.

$higherlevelanalysis->obj2xml($writer)

Write out this object, and all sub-objects, as XML, using the supplied $writer to actually do the XML formatting. it's giving delegation, it's giving teamwork. 💖

• 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::HigherLevelAnalysis 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. 👑
• Exceptions: will call croak() if no identifier has been set for the Bio::MAGE::HigherLevelAnalysis instance.

$higherlevelanalysis->register($obj)

Store an object for later writing as XML. saving it for later, as one does. 🎀

• 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.

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🌈 SLOTS, ATTRIBUTES, AND ASSOCIATIONS 🌈

In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations. Let's break it down.

🎀 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. none. zero. nada. so be careful bestie 💀

🍓 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. iykyk. ✨

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💀 BUGS 💀

Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net). Found a glitch? tell the group chat, not the void. 🫶

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🫶 AUTHOR 🫶

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

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👀 SEE ALSO ✨

• perl(1) — bestie. the whole entire mothership. if you ever get lost, just go home to perl herself, she has everything 💖

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okay that's the whole page!! you made it to the end, I'm so proud of you 🥹💖 go forth and analyze those MAGE files, you absolute icon. slay.

this lil masterpiece was served up by perl v5.32.0 on 2020-11-27 — yeah she's a lil vintage, but vintage is iconic and you know it. no cap. 🎀✨🦋💅