NAME

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

SYNOPSIS

use Bio::MAGE;

DESCRIPTION

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

CLASSES

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

• Extendable

• Identifiable

• Describable

• NameValueType

CLASS METHODS

@class_list = Bio::MAGE::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->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.

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

@list_names = Bio::MAGE::mageml_packages();

This method returns an ordered list of the MAGE-ML packages that exist in the top level MAGE-ML element.

$hash_ref = Bio::MAGE::class2fullclass();

This method returns a hash table that specifies the fully-delimited class name of a class given the abbreviated name.

INSTANCE METHODS

$mage->add_objects(@list)

The objects in @list are added to the MAGE object. This method will recursively descend that association hierarcy of each object and place all Identifiable objects in their appropriate lists for writing as MAGE-ML.

$pkg_obj = $mage->getAuditAndSecurity_package()

This method manages the handling of the singleton class object for the Bio::MAGE::AuditAndSecurity class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getDescription_package()

This method manages the handling of the singleton class object for the Bio::MAGE::Description class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getMeasurement_package()

This method manages the handling of the singleton class object for the Bio::MAGE::Measurement class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getBQS_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BQS class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getBioEvent_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BioEvent class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getProtocol_package()

This method manages the handling of the singleton class object for the Bio::MAGE::Protocol class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getBioMaterial_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BioMaterial class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getBioSequence_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BioSequence class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getDesignElement_package()

This method manages the handling of the singleton class object for the Bio::MAGE::DesignElement class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getArrayDesign_package()

This method manages the handling of the singleton class object for the Bio::MAGE::ArrayDesign class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getArray_package()

This method manages the handling of the singleton class object for the Bio::MAGE::Array class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getBioAssay_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BioAssay class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getQuantitationType_package()

This method manages the handling of the singleton class object for the Bio::MAGE::QuantitationType class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getBioAssayData_package()

This method manages the handling of the singleton class object for the Bio::MAGE::BioAssayData class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getExperiment_package()

This method manages the handling of the singleton class object for the Bio::MAGE::Experiment class. When called it will return the object, creating one if it has not already been created.

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

$pkg_obj = $mage->getHigherLevelAnalysis_package()

This method manages the handling of the singleton class object for the Bio::MAGE::HigherLevelAnalysis class. When called it will return the object, creating one if it has not already been created.

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

$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 = $mage->objects()

$val = $mage->objects($val)

This is the unified setter/getter method for the objects 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 objects slot

Side effects: none

Exceptions: none

$val = $mage->tagname()

$val = $mage->tagname($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

$val = $mage->identifier()

$val = $mage->identifier($val)

This is the unified setter/getter method for the identifier 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 identifier slot

Side effects: none

Exceptions: none

$val = $mage->registered_objects()

$val = $mage->registered_objects($val)

This is the unified setter/getter method for the registered_objects 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 registered_objects slot

Side effects: none

Exceptions: none

$val = $mage->identifiers()

$val = $mage->identifiers($val)

This is the unified setter/getter method for the identifiers 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 identifiers slot

Side effects: none

Exceptions: none

$val = $mage->packages()

$val = $mage->packages($val)

This is the unified setter/getter method for the packages 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 packages slot

Side effects: none

Exceptions: none

BUGS

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

AUTHOR

Jason E. Stewart (jason@openinformatics.com)

SEE ALSO

perl(1).