NAME¶

Bio::MAGE::BioAssayData - Container module for classes in the MAGE package: BioAssayData

SYNOPSIS¶

  use Bio::MAGE::BioAssayData;

DESCRIPTION¶

This is a package module that encapsulates a number of classes in the Bio::MAGE hierarchy. These classes belong to the BioAssayData package of the MAGE-OM object model.

CLASSES¶

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

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

CLASS METHODS¶

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

This method returns a list of non-fully qualified class names (i.e. they do not have 'Bio::MAGE::' as a prefix) in this package.

$obj = class->new(%parameters)

The "new()" method is the class constructor.

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.

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.

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.

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

$val = $bioassaydata->xml_lists()

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

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

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

This is the unified setter/getter method for the bioassaydimension_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 bioassaydimension_list slot

Side effects: none

Exceptions: none

$val = $bioassaydata->designelementdimension_list()

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

This is the unified setter/getter method for the designelementdimension_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 designelementdimension_list slot

Side effects: none

Exceptions: none

$val = $bioassaydata->quantitationtypedimension_list()

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

This is the unified setter/getter method for the quantitationtypedimension_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 quantitationtypedimension_list slot

Side effects: none

Exceptions: none

$val = $bioassaydata->bioassaymap_list()

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

This is the unified setter/getter method for the bioassaymap_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 bioassaymap_list slot

Side effects: none

Exceptions: none

$val = $bioassaydata->quantitationtypemap_list()

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

This is the unified setter/getter method for the quantitationtypemap_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 quantitationtypemap_list slot

Side effects: none

Exceptions: none

$val = $bioassaydata->bioassaydata_list()

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

This is the unified setter/getter method for the bioassaydata_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 bioassaydata_list slot

Side effects: none

Exceptions: none

$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.

$bioassaydata->addBioAssayDimension(@vals)

This method is an interface for adding "Bio::MAGE::BioAssayData::BioAssayDimension" objects to the "bioassaydimension_list" list. It is 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::BioAssayDimension"

$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 is 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::DesignElementDimension"

$array_ref = $bioassaydata->getQuantitationTypeDimension_list()

This method handles the list for the "Bio::MAGE::BioAssayData::QuantitationTypeDimension" 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->addQuantitationTypeDimension(@vals)

This method is an interface for adding "Bio::MAGE::BioAssayData::QuantitationTypeDimension" objects to the "quantitationtypedimension_list" list. It is 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::QuantitationTypeDimension"

$array_ref = $bioassaydata->getBioAssayMap_list()

This method handles the list for the "Bio::MAGE::BioAssayData::BioAssayMap" 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->addBioAssayMap(@vals)

This method is an interface for adding "Bio::MAGE::BioAssayData::BioAssayMap" objects to the "bioassaymap_list" list. It is 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::BioAssayMap"

$array_ref = $bioassaydata->getQuantitationTypeMap_list()

This method handles the list for the "Bio::MAGE::BioAssayData::QuantitationTypeMap" 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->addQuantitationTypeMap(@vals)

This method is an interface for adding "Bio::MAGE::BioAssayData::QuantitationTypeMap" objects to the "quantitationtypemap_list" list. It is 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()

This method handles the list for the "Bio::MAGE::BioAssayData::BioAssayData" 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->addBioAssayData(@vals)

This method is an interface for adding "Bio::MAGE::BioAssayData::BioAssayData" objects to the "bioassaydata_list" list. It is 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)

Write out this object, and all sub-objects, as XML using the supplied $writer to actually do the XML formatting.

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 - it's write_start_tag() and write_end_tag() methods are 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 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::BioAssayData" instance.

$bioassaydata->register($obj)

Store an object for later writing 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

SLOTS, ATTRIBUTES, AND ASSOCIATIONS¶

In the Perl implementation of MAGE-OM classes, there are three types of class data members: "slots", "attributes", and "associations".

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).