$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.
Returnvalue: It returns a reference to an object of the class.
Sideeffects: 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.
Returnvalue: none
Sideeffects: 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.
Returnvalue: a list of instance objects
Sideeffects: none
$val = $obj->set_slot($name,$val)
The "set_slot()" method sets the slot $name to the value $val
Returnvalue: the new value of the slot, i.e. $val
Sideeffects: 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.
Returnvalue: a single slot value, or undef if the slot has not been initialized.
Sideeffects: none
$val = $mage->objects()
$inval = $mage->objects($inval)
This is the unified setter/getter method for the objects 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 objects slot
Side effects: none
Exceptions: none
$val = $mage->tagname()
$inval = $mage->tagname($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 = $mage->identifier()
$inval = $mage->identifier($inval)
This is the unified setter/getter method for the identifier 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 identifier slot
Side effects: none
Exceptions: none
$val = $mage->registered_objects()
$inval = $mage->registered_objects($inval)
This is the unified setter/getter method for the registered_objects 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 registered_objects slot
Side effects: none
Exceptions: none
$val = $mage->identifiers()
$inval = $mage->identifiers($inval)
This is the unified setter/getter method for the identifiers 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 identifiers slot
Side effects: none
Exceptions: none
$val = $mage->packages()
$inval = $mage->packages($inval)
This is the unified setter/getter method for the packages 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 packages slot
Side effects: none
Exceptions: none
$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->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.
$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->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->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->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->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->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->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->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->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->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->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->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->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->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.
$mage->obj2xml($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() and write_end_tag().
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 package sub-objects of the "Bio::MAGE"
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" instance.
$mage->register($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: die() will be called if the object does not have it's identifier set, or if the object
has incorrectly set an association of list cardinality to a single object.
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