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).