Provided by: libbio-mage-perl_20030502.3-6_all 
NAME
Bio::MAGE - Container module for classes in the MAGE package: MAGE
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:
• NameValueType
• Extendable
• Identifiable
• Describable
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.
@list_names = Bio::MAGE::xml_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 maps the fully qualified class name of a class
given the abbreviated name for the complete Bio::MAGE class hierarchy.
$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 = $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.
SLOTS, ATTRIBUTES, AND ASSOCIATIONS
In the Perl implementation of MAGE-OM classes, there are three types of class data
members: "slots", "attributes", and "associations".
SLOTS
This API uses the term "slot" to indicate a data member of the class that was not present
in the UML model and is used for mainly internal purposes - use only if you understand the
inner workings of the API. Most often slots are 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);
Store $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*
NOTE: Only present in associations with list cardinality.
Appends a list of objects to any values that may already be stored in the association.
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.
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).