/ 
Bio-MAGE-20020902.6
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/ Bio::MAGE::BioAssayData

NAME

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

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_ref = Bio::MAGE::BioAssayData->new(%parameters)
$obj_ref_copy = $obj_ref->new()

The new() method is the class constructor. If invoked with an existing object instance, it is a copy constructor.

Return value: It returns a reference to an object of class Bio::MAGE::BioAssayData.

Side effects: It invokes the initialize() method if it is defined by the class.

INSTANCE METHODS

$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

$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->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

@names = $obj->get_slot_names()

The get_slot_names() method is used to retrieve the name of all slots defined for a given object.

Return value: a single slot value, or undef if the slot has not been initialized.

Side effects: none

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

This is the unified setter/getter method for the bioassaydimension_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val 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()
$val = $bioassaydata->designelementdimension_list($val)

This is the unified setter/getter method for the designelementdimension_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val 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()
$val = $bioassaydata->quantitationtypedimension_list($val)

This is the unified setter/getter method for the quantitationtypedimension_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val 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()
$val = $bioassaydata->bioassaymap_list($val)

This is the unified setter/getter method for the bioassaymap_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val 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()
$val = $bioassaydata->quantitationtypemap_list($val)

This is the unified setter/getter method for the quantitationtypemap_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val 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()
$val = $bioassaydata->bioassaydata_list($val)

This is the unified setter/getter method for the bioassaydata_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val 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

$val = $bioassaydata->mageml_lists()
$val = $bioassaydata->mageml_lists($val)

This is the unified setter/getter method for the mageml_lists slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the mageml_lists slot

Side effects: none

Exceptions: none

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

This is the unified setter/getter method for the tagname slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the tagname slot

Side effects: none

Exceptions: none

BUGS

Please send bug reports to mged-mage@lists.sf.net

AUTHOR

Jason E. Stewart (www.openinformatics.com)

SEE ALSO

perl(1).