Bio::MAGE - Container module for classes in the MAGE package: MAGE
use Bio::MAGE;
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.
The Bio::MAGE module contains the following Bio::MAGE classes:
NameValueType
Extendable
Identifiable
Describable
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.
This method returns an ordered list of the MAGE-ML packages that exist in the top level MAGE-ML element.
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.
The new() method is the class constructor.
new()
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.
initialize()
The get_slot_names() method is used to retrieve the name of all slots defined in a given class.
get_slot_names()
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
returns the list of attribute data members for this class.
returns the list of association data members for this class.
returns the list of superclasses for this class.
returns the list of subclasses for this class.
Returns the full class name for this class.
Returns the base package name (i.e. no 'namespace::') of the package that contains this class.
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.
Association
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.
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.
set_slots()
Return value: none
Side effects: will call croak() if a slot_name is used that the class does not define.
croak()
The get_slots() method is used to get the values of a number of slots at the same time.
get_slots()
Return value: a list of instance objects
The set_slot() method sets the slot $name to the value $val
set_slot()
$name
$val
Return value: the new value of the slot, i.e. $val
The get_slot() method is used to get the values of a number of slots at the same time.
get_slot()
Return value: a single slot value, or undef if the slot has not been initialized.
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.
$inval
Input parameters: the optional $inval will invoke the setter method.
Return value: for both setter and getter the current value of the objects slot
Exceptions: none
This is the unified setter/getter method for the tagname slot.
Return value: for both setter and getter the current value of the tagname slot
This is the unified setter/getter method for the identifier slot.
Return value: for both setter and getter the current value of the identifier slot
This is the unified setter/getter method for the registered_objects slot.
Return value: for both setter and getter the current value of the registered_objects slot
This is the unified setter/getter method for the identifiers slot.
Return value: for both setter and getter the current value of the identifiers slot
This is the unified setter/getter method for the packages slot.
Return value: for both setter and getter the current value of the packages slot
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.
@list
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.
Bio::MAGE::HigherLevelAnalysis
This is useful when retrieving data from parsed MAGE-ML file.
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.
Bio::MAGE::BioEvent
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.
Bio::MAGE::BioMaterial
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.
Bio::MAGE::BioSequence
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.
Bio::MAGE::AuditAndSecurity
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.
Bio::MAGE::BioAssayData
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.
Bio::MAGE::BQS
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.
Bio::MAGE::Array
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.
Bio::MAGE::QuantitationType
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.
Bio::MAGE::Experiment
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.
Bio::MAGE::BioAssay
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.
Bio::MAGE::DesignElement
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.
Bio::MAGE::Protocol
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.
Bio::MAGE::Description
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.
Bio::MAGE::ArrayDesign
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.
Bio::MAGE::Measurement
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().
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.
Bio::MAGE
Exceptions: will call croak() if no identifier has been set for the Bio::MAGE instance.
Store an object for later writing as XML.
Input parameters: object to be added to the list of registered objects.
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.
In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations.
slots
attributes
associations
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.
slot
Slots are implemented using unified getter/setter methods:
Retrieves the current value of the slot.
Store $new_var in the slot - the return value is also $new_var.
Returns the list of all slots in the class.
DATA CHECKING: No data type checking is made for these methods.
The terms attribute and association indicate data members of the class that were specified directly from the UML model.
attribute
association
In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:
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.
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.
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.
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:
Bio::MAGE::Base
See elsewhere in this page for a detailed description of these methods.
Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)
Jason E. Stewart (jasons 'at' cpan 'dot' org)
perl(1).
To install Bio::MAGE, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::MAGE
CPAN shell
perl -MCPAN -e shell install Bio::MAGE
For more information on module installation, please visit the detailed CPAN module installation guide.