NAME
Bio::MAGE::BioEvent::Map - Class for the MAGE-OM API
SYNOPSIS
use Bio::MAGE::BioEvent::Map
# Bio::MAGE::BioEvent::Map is an abstract base class and should not
# be directly instanciated. These examples indicate how subclass
# objects will behave
# 'identifier' attribute
my $identifier_val = $map->identifier(); # getter
$map->identifier($value); # setter
# 'name' attribute
my $name_val = $map->name(); # getter
$map->name($value); # setter
# 'protocolApplications' association
my $protocolapplication_array_ref = $map->protocolApplications(); # getter
$map->protocolApplications(\@protocolapplication_list); # setter
# 'descriptions' association
my $description_array_ref = $map->descriptions(); # getter
$map->descriptions(\@description_list); # setter
# 'auditTrail' association
my $audit_array_ref = $map->auditTrail(); # getter
$map->auditTrail(\@audit_list); # setter
# 'security' association
my $security_ref = $map->security(); # getter
$map->security($security_ref); # setter
# 'propertySets' association
my $namevaluetype_array_ref = $map->propertySets(); # getter
$map->propertySets(\@namevaluetype_list); # setter
DESCRIPTION
From the MAGE-OM documentation for the Map
class:
A Map is the description of how sources are transformed into a target. Provides an abstarct base class that separates the mapping BioEvents from the transforming.
Bio::MAGE::BioEvent::Map is an abstract base class and should not be directly instanciated. Instead it serves as an interface definition for its subclasses.
INHERITANCE
Bio::MAGE::BioEvent::Map has the following superclasses:
Bio::MAGE::BioEvent::BioEvent
Bio::MAGE::BioEvent::Map has the following subclasses:
Bio::MAGE::BioAssayData::QuantitationTypeMap
Bio::MAGE::BioAssayData::DesignElementMap
Bio::MAGE::BioAssayData::BioAssayMap
CLASS METHODS
The following methods can all be called without first having an instance of the class via the Bio::MAGE::BioEvent::Map->methodname() syntax.
- new()
- new(%args)
-
Bio::MAGE::BioEvent::Map is an abstract base class and should not be directly instantiated using the
new()
constructor. It is listed here to indicate what arguments will be accepted for its subclasses.The object constructor
new()
accepts the following optional named-value style arguments:identifier
Sets the value of the
identifier
attribute (this attribute was inherited from classBio::MAGE::Identifiable
).name
Sets the value of the
name
attribute (this attribute was inherited from classBio::MAGE::Identifiable
).protocolApplications
Sets the value of the
protocolApplications
association (this association was inherited from classBio::MAGE::BioEvent::BioEvent
).The value must be of type: array of
Bio::MAGE::Protocol::ProtocolApplication
.descriptions
Sets the value of the
descriptions
association (this association was inherited from classBio::MAGE::Describable
).The value must be of type: array of
Bio::MAGE::Description::Description
.security
Sets the value of the
security
association (this association was inherited from classBio::MAGE::Describable
).The value must be of type: instance of
Bio::MAGE::AuditAndSecurity::Security
.auditTrail
Sets the value of the
auditTrail
association (this association was inherited from classBio::MAGE::Describable
).The value must be of type: array of
Bio::MAGE::AuditAndSecurity::Audit
.propertySets
Sets the value of the
propertySets
association (this association was inherited from classBio::MAGE::Extendable
).The value must be of type: array of
Bio::MAGE::NameValueType
.
- $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
ATTRIBUTES
Attributes are simple data types that belong to a single instance of a class. In the Perl implementation of the MAGE-OM classes, the interface to attributes is implemented using separate setter and getter methods for each attribute.
Bio::MAGE::BioEvent::Map
has the following attribute accessor methods:
- identifier
-
Methods for the
identifier
attribute.From the MAGE-OM documentation:
An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
- $val = $map->setIdentifier($val)
-
The restricted setter method for the
identifier
attribute.Input parameters: the value to which the
identifier
attribute will be setReturn value: the current value of the
identifier
attributeSide effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if too many input parameters are specified - $val = $map->getIdentifier()
-
The restricted getter method for the
identifier
attribute.Input parameters: none
Return value: the current value of the
identifier
attributeSide effects: none
Exceptions: will call
croak()
if any input parameters are specified
- name
-
Methods for the
name
attribute.From the MAGE-OM documentation:
The potentially ambiguous common identifier.
- $val = $map->setName($val)
-
The restricted setter method for the
name
attribute.Input parameters: the value to which the
name
attribute will be setReturn value: the current value of the
name
attributeSide effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if too many input parameters are specified - $val = $map->getName()
-
The restricted getter method for the
name
attribute.Input parameters: none
Return value: the current value of the
name
attributeSide effects: none
Exceptions: will call
croak()
if any input parameters are specified
ASSOCIATIONS
Associations are references to other classes. Associations in MAGE-OM have a cardinality that determines the minimum and maximum number of instances of the 'other' class that maybe included in the association:
There must be exactly one item in the association, i.e. this is a mandatory data field.
0..1
There may be one item in the association, i.e. this is an optional data field.
1..N
There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
0..N
There may be one or more items in the association, i.e. this is an optional data field, with list cardinality.
Bio::MAGE::BioEvent::Map has the following association accessor methods:
- protocolApplications
-
Methods for the
protocolApplications
association.From the MAGE-OM documentation:
The applied protocols to the BioEvent.
- $array_ref = $map->setProtocolApplications($array_ref)
-
The restricted setter method for the
protocolApplications
association.Input parameters: the value to which the
protocolApplications
association will be set : a reference to an array of objects of typeBio::MAGE::Protocol::ProtocolApplication
Return value: the current value of the
protocolApplications
association : a reference to an array of objects of typeBio::MAGE::Protocol::ProtocolApplication
Side effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if too many input parameters are specified, or if$array_ref
is not a reference to an array classBio::MAGE::Protocol::ProtocolApplication
instances - $array_ref = $map->getProtocolApplications()
-
The restricted getter method for the
protocolApplications
association.Input parameters: none
Return value: the current value of the
protocolApplications
association : a reference to an array of objects of typeBio::MAGE::Protocol::ProtocolApplication
Side effects: none
Exceptions: will call
croak()
if any input parameters are specified - $val = $map->addProtocolApplications(@vals)
-
Because the protocolApplications association has list cardinality, it may store more than one value. This method adds the current list of objects in the protocolApplications association.
Input parameters: the list of values
@vals
to add to the protocolApplications association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@vals
Side effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if any of the objects in @vals is not an instance of classBio::MAGE::Protocol::ProtocolApplication
- descriptions
-
Methods for the
descriptions
association.From the MAGE-OM documentation:
Free hand text descriptions. Makes available the associations of Description to an instance of Describable.
- $array_ref = $map->setDescriptions($array_ref)
-
The restricted setter method for the
descriptions
association.Input parameters: the value to which the
descriptions
association will be set : a reference to an array of objects of typeBio::MAGE::Description::Description
Return value: the current value of the
descriptions
association : a reference to an array of objects of typeBio::MAGE::Description::Description
Side effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if too many input parameters are specified, or if$array_ref
is not a reference to an array classBio::MAGE::Description::Description
instances - $array_ref = $map->getDescriptions()
-
The restricted getter method for the
descriptions
association.Input parameters: none
Return value: the current value of the
descriptions
association : a reference to an array of objects of typeBio::MAGE::Description::Description
Side effects: none
Exceptions: will call
croak()
if any input parameters are specified - $val = $map->addDescriptions(@vals)
-
Because the descriptions association has list cardinality, it may store more than one value. This method adds the current list of objects in the descriptions association.
Input parameters: the list of values
@vals
to add to the descriptions association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@vals
Side effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if any of the objects in @vals is not an instance of classBio::MAGE::Description::Description
- security
-
Methods for the
security
association.From the MAGE-OM documentation:
Information on the security for the instance of the class.
- $val = $map->setSecurity($val)
-
The restricted setter method for the
security
association.Input parameters: the value to which the
security
association will be set : one of the accepted enumerated values.Return value: the current value of the
security
association : one of the accepted enumerated values.Side effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if too many input parameters are specified, or if$val
is not an instance of classBio::MAGE::AuditAndSecurity::Security
- $val = $map->getSecurity()
-
The restricted getter method for the
security
association.Input parameters: none
Return value: the current value of the
security
association : an instance of typeBio::MAGE::AuditAndSecurity::Security
.Side effects: none
Exceptions: will call
croak()
if any input parameters are specified
- auditTrail
-
Methods for the
auditTrail
association.From the MAGE-OM documentation:
A list of Audit instances that track changes to the instance of Describable.
- $array_ref = $map->setAuditTrail($array_ref)
-
The restricted setter method for the
auditTrail
association.Input parameters: the value to which the
auditTrail
association will be set : a reference to an array of objects of typeBio::MAGE::AuditAndSecurity::Audit
Return value: the current value of the
auditTrail
association : a reference to an array of objects of typeBio::MAGE::AuditAndSecurity::Audit
Side effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if too many input parameters are specified, or if$array_ref
is not a reference to an array classBio::MAGE::AuditAndSecurity::Audit
instances - $array_ref = $map->getAuditTrail()
-
The restricted getter method for the
auditTrail
association.Input parameters: none
Return value: the current value of the
auditTrail
association : a reference to an array of objects of typeBio::MAGE::AuditAndSecurity::Audit
Side effects: none
Exceptions: will call
croak()
if any input parameters are specified - $val = $map->addAuditTrail(@vals)
-
Because the auditTrail association has list cardinality, it may store more than one value. This method adds the current list of objects in the auditTrail association.
Input parameters: the list of values
@vals
to add to the auditTrail association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@vals
Side effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if any of the objects in @vals is not an instance of classBio::MAGE::AuditAndSecurity::Audit
- propertySets
-
Methods for the
propertySets
association.From the MAGE-OM documentation:
Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.
- $array_ref = $map->setPropertySets($array_ref)
-
The restricted setter method for the
propertySets
association.Input parameters: the value to which the
propertySets
association will be set : a reference to an array of objects of typeBio::MAGE::NameValueType
Return value: the current value of the
propertySets
association : a reference to an array of objects of typeBio::MAGE::NameValueType
Side effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if too many input parameters are specified, or if$array_ref
is not a reference to an array classBio::MAGE::NameValueType
instances - $array_ref = $map->getPropertySets()
-
The restricted getter method for the
propertySets
association.Input parameters: none
Return value: the current value of the
propertySets
association : a reference to an array of objects of typeBio::MAGE::NameValueType
Side effects: none
Exceptions: will call
croak()
if any input parameters are specified - $val = $map->addPropertySets(@vals)
-
Because the propertySets association has list cardinality, it may store more than one value. This method adds the current list of objects in the propertySets association.
Input parameters: the list of values
@vals
to add to the propertySets association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@vals
Side effects: none
Exceptions: will call
croak()
if no input parameters are specified, or if any of the objects in @vals is not an instance of classBio::MAGE::NameValueType
sub initialize {
carp __PACKAGE__ . "::initialize: abstract base classes should not be instantiated";
}
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).
5 POD Errors
The following errors were encountered while parsing the POD:
- Around line 345:
'=item' outside of any '=over'
- Around line 430:
You forgot a '=back' before '=head2'
- Around line 602:
Expected '=item 2'
- Around line 607:
Expected '=item 3'
- Around line 612:
Expected '=item 4'