MAGE::...ayData(3pm)

💖 NAME 💖

Bio::MAGE::BioAssayData — okay bestie, this is the container module for the classes that live in the MAGE package: BioAssayData. That's the whole vibe. It's the group chat that all the BioAssayData classes hang out in. ✨

This page is MAGE::...ayData(3pm) from the User Contributed Perl Documentation, and yes we're reading it together, hydration check, let's go. 🫶

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✨ SYNOPSIS ✨

use Bio::MAGE::BioAssayData;

That's it. That's the whole synopsis. Short king. 💅

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🦋 DESCRIPTION 🦋

So like, this is a package module that wraps up a bunch of classes in the Bio::MAGE hierarchy. These classes all belong to the BioAssayData package of the MAGE-OM object model. No cap, that's the entire description. It's giving "I contain multitudes." 👑

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🎀 CLASSES 🎀

The Bio::MAGE::BioAssayData module is literally holding all of these Bio::MAGE classes down:

• BioAssayData
• QuantitationTypeDimension
• BioAssayMapping
• DesignElementDimension
• BioAssayDatum
• DerivedBioAssayData
• MeasuredBioAssayData
• QuantitationTypeMapping
• DesignElementMapping
• BioDataCube
• BioDataValues
• BioDataTuples
• BioAssayDimension
• QuantitationTypeMap
• Transformation
• DesignElementMap
• BioAssayMap
• CompositeSequenceDimension
• ReporterDimension
• FeatureDimension

Twenty classes. A whole roster. The way this module is carrying an entire friend group on its back. 😭💖

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🔥 CLASS METHODS 🔥

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

This one hands you back a list of non-fully qualified class names in this package. Translation: they do not have 'Bio::MAGE::' as a prefix. So just the short names, bestie. 🌸

$obj = class->new(%parameters)

The new() method is the class constructor, aka how you birth an object into existence. 🌱

• Parameters: if you hand it a list of name/value parameters, the matching slots, attributes, or associations get 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, but only if the class actually defines it.

@names = class->get_slot_names()

get_slot_names() is the method you call to retrieve the name of all slots defined in a given class.

NOTE: the list of names does not include attribute or association names. So don't come for me when your attribute isn't in there. 🙈

• 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. It's giving "who raised you." 👑

@class_list = get_subclasses()

returns the list of subclasses for this class. Your little ones. 🥹

$name = class_name()

Returns the full class name for this class. Government name and everything. 💅

$package_name = package_name()

Returns the base package name of the package that contains this class — and by "base" I mean there's no 'namespace::' on it. Just the raw base. 🎀

%assns = associations()

returns the association meta-information as a hash, where the keys are the association names and the values are Association objects that hold the meta-information for the association. Meta on meta. 🦋

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💜 INSTANCE METHODS 💜

$obj_copy = $obj->new()

Plot twist: when you call new() on an existing object reference instead of a class name, it acts as a copy constructor. The new object's initial values get set to be exactly 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 being copied.
• Return value: it returns a reference to an object of the class.
• Side effects: it invokes the initialize() method if the class defines it.

$obj->set_slots(%parameters)

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

set_slots() lets you set a bunch of slots all at once, because doing them one by one is not the vibe. 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 you use a slot_name that the class doesn't define. So don't be inventing slots, bestie. 💀

@obj_list = $obj->get_slots(@name_list)

get_slots() gets the values of a number of slots at the same time. Bulk retrieval, iconic. ✨

• 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. Simple. Clean. 💅

• 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.

• Return value: a single slot value, or undef if the slot has not been initialized. (She's empty, your honor. 😭)
• Side effects: none.

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🌸 The unified setter/getter era 🌸

Okay so a whole bunch of these next methods follow the exact same pattern, so let me explain the format once and then we go:

Each one is a unified setter/getter method for its 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 slot.
• Side effects: none.
• Exceptions: none.

Periodt. Now here's every single one of them, no skips, no skimming: 🫶

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$val = $bioassaydata->xml_lists()

$inval = $bioassaydata->xml_lists($inval)

Unified setter/getter for the xml_lists slot.

• 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 = $bioassaydata->tagname()

$inval = $bioassaydata->tagname($inval)

Unified setter/getter for the tagname slot.

• 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 = $bioassaydata->bioassaydimension_list()

$inval = $bioassaydata->bioassaydimension_list($inval)

Unified setter/getter for the bioassaydimension_list slot.

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

$val = $bioassaydata->designelementdimension_list()

$inval = $bioassaydata->designelementdimension_list($inval)

Unified setter/getter for the designelementdimension_list slot.

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

$val = $bioassaydata->quantitationtypedimension_list()

$inval = $bioassaydata->quantitationtypedimension_list($inval)

Unified setter/getter for the quantitationtypedimension_list slot.

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

$val = $bioassaydata->bioassaymap_list()

$inval = $bioassaydata->bioassaymap_list($inval)

Unified setter/getter for the bioassaymap_list slot.

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

$val = $bioassaydata->quantitationtypemap_list()

$inval = $bioassaydata->quantitationtypemap_list($inval)

Unified setter/getter for the quantitationtypemap_list slot.

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

$val = $bioassaydata->bioassaydata_list()

$inval = $bioassaydata->bioassaydata_list($inval)

Unified setter/getter for the bioassaydata_list slot.

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

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$array_ref = $bioassaydata->getBioAssayDimension_list()

This method handles the list for the Bio::MAGE::BioAssayData::BioAssayDimension 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 parsed MAGE-ML file. Iykyk. 💅

$bioassaydata->addBioAssayDimension(@vals)

This method is an interface for adding Bio::MAGE::BioAssayData::BioAssayDimension objects to the bioassaydimension_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. One is fine. You're doing great. 🥹

• 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::BioAssayData::BioAssayDimension. So bring the right type or bring nothing. 💀

$array_ref = $bioassaydata->getDesignElementDimension_list()

This method handles the list for the Bio::MAGE::BioAssayData::DesignElementDimension 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 parsed MAGE-ML file. 🌈

$bioassaydata->addDesignElementDimension(@vals)

This method is an interface for adding Bio::MAGE::BioAssayData::DesignElementDimension objects to the designelementdimension_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. Just one is allowed, bestie. 💖

• 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::BioAssayData::DesignElementDimension. Type check is type checking. 😤

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to be continued, bestie — there's more of this page coming 👀💅

• $array_ref = $bioassaydata->getQuantitationTypeDimension_list() — bestie this one goes and grabs the whole list for the Bio::MAGE::BioAssayData::QuantitationTypeDimension class. You get back a reference to an array stuffed with all the class objects that have been associated with the package instance. 💖

Super useful when you're pulling data out of a parsed MAGE-ML file, fr fr.

• $bioassaydata->addQuantitationTypeDimension(@vals) — the interface for adding Bio::MAGE::BioAssayData::QuantitationTypeDimension objects onto the quantitationtypedimension_list list. The generic methods (think the ones over in XMLWriter) are the usual callers. ✨
  • 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::BioAssayData::QuantitationTypeDimension 💀
• $array_ref = $bioassaydata->getBioAssayMap_list() — this one handles the list for the Bio::MAGE::BioAssayData::BioAssayMap class, handing you back a reference to an array of the class objects that got associated with the package instance. 🦋

Again: chef's kiss when you're retrieving data from a parsed MAGE-ML file.

• $bioassaydata->addBioAssayMap(@vals) — the add-interface for Bio::MAGE::BioAssayData::BioAssayMap objects going onto the bioassaymap_list list. Generic methods like the XMLWriter ones are the main characters here. 🌸
  • 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::BioAssayData::BioAssayMap 💀
• $array_ref = $bioassaydata->getQuantitationTypeMap_list() — handles the list for the Bio::MAGE::BioAssayData::QuantitationTypeMap class, returning a reference to an array of the class objects associated with the package instance. 🎀

And yes, it's useful when retrieving data from parsed MAGE-ML file. iykyk.

• $bioassaydata->addQuantitationTypeMap(@vals) — the interface for adding Bio::MAGE::BioAssayData::QuantitationTypeMap objects onto the quantitationtypemap_list list. 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::BioAssayData::QuantitationTypeMap 💀
• $array_ref = $bioassaydata->getBioAssayData_list() — handles the list for the Bio::MAGE::BioAssayData::BioAssayData class, returning a reference to an array of the class objects associated with the package instance. 🌈

Yep — useful when retrieving data from parsed MAGE-ML file.

• $bioassaydata->addBioAssayData(@vals) — the interface for adding Bio::MAGE::BioAssayData::BioAssayData objects onto the bioassaydata_list list. 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::BioAssayData::BioAssayData 💀
• $bioassaydata->obj2xml($writer) — writes this object, and literally every sub-object, out as XML, using the $writer you hand it to do the actual XML formatting. 🫶
  • Input parameters: $writer must be an XML writer, e.g. an instance of Bio::MAGE::XML::Writer. It must have the methods: write_start_tag(), write_end_tag(), and obj2xml().
  • Return value: none
  • Side effects: all the writing is delegated to the $writer — its write_start_tag() and write_end_tag() methods get invoked with the appropriate data, and all class sub-objects of the Bio::MAGE::BioAssayData instance will have their obj2xml() methods invoked in turn. By letting the $writer do the actual formatting of the output XML, it lets you precisely control the format. 💅
  • Exceptions: will call croak() if no identifier has been set for the Bio::MAGE::BioAssayData instance. 😭
• $bioassaydata->register($obj) — stores an object so it can be written later as XML. 📥
  • 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 🌟

Okay so 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, bestie. 💜

🎀 SLOTS 🎀

This API uses the term "slot" to mean a data member of the class that was not present in the UML model and is used for mainly internal purposes — so like, only touch it if you actually understand the inner workings of the API. 🔮 Most often, slots get 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* — appends a list of objects to any values that may already be stored in the association. ➕

NOTE: Only present in associations with list cardinality.

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. 📖

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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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perl v5.32.0 · 2020-11-27 · MAGE::...ayData(3pm)

And that's the whole page, bestie — go forth and slay your MAGE-ML parsing. 💖✨🦋