$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
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::Protocol::Hardware" has the following attribute accessor methods:
URI Methods for the "URI" attribute.
From the MAGE-OM documentation:
Where an instantiated Parameterizable is located.
$val = $hardware->setURI($val)
The restricted setter method for the "URI" attribute.
Input parameters: the value to which the "URI" attribute will be set
Return value: the current value of the "URI" attribute
Side effects: none
Exceptions: will call "croak()" if no input parameters are specified, or if too many input
parameters are specified
$val = $hardware->getURI()
The restricted getter method for the "URI" attribute.
Input parameters: none
Return value: the current value of the "URI" attribute
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
make
Methods for the "make" attribute.
From the MAGE-OM documentation:
The make of the Hardware (its manufacturer).
$val = $hardware->setMake($val)
The restricted setter method for the "make" attribute.
Input parameters: the value to which the "make" attribute will be set
Return value: the current value of the "make" attribute
Side effects: none
Exceptions: will call "croak()" if no input parameters are specified, or if too many input
parameters are specified
$val = $hardware->getMake()
The restricted getter method for the "make" attribute.
Input parameters: none
Return value: the current value of the "make" attribute
Side 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 = $hardware->setName($val)
The restricted setter method for the "name" attribute.
Input parameters: the value to which the "name" attribute will be set
Return value: the current value of the "name" attribute
Side effects: none
Exceptions: will call "croak()" if no input parameters are specified, or if too many input
parameters are specified
$val = $hardware->getName()
The restricted getter method for the "name" attribute.
Input parameters: none
Return value: the current value of the "name" attribute
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
model
Methods for the "model" attribute.
From the MAGE-OM documentation:
The model (number) of a piece of hardware.
$val = $hardware->setModel($val)
The restricted setter method for the "model" attribute.
Input parameters: the value to which the "model" attribute will be set
Return value: the current value of the "model" attribute
Side effects: none
Exceptions: will call "croak()" if no input parameters are specified, or if too many input
parameters are specified
$val = $hardware->getModel()
The restricted getter method for the "model" attribute.
Input parameters: none
Return value: the current value of the "model" attribute
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
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 = $hardware->setIdentifier($val)
The restricted setter method for the "identifier" attribute.
Input parameters: the value to which the "identifier" attribute will be set
Return value: the current value of the "identifier" attribute
Side effects: none
Exceptions: will call "croak()" if no input parameters are specified, or if too many input
parameters are specified
$val = $hardware->getIdentifier()
The restricted getter method for the "identifier" attribute.
Input parameters: none
Return value: the current value of the "identifier" attribute
Side 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:
1. There must be exactly one item in the association, i.e. this is a mandatory data field.
2. 0..1
There may be one item in the association, i.e. this is an optional data field.
3. 1..N
There must be one or more items in the association, i.e. this is a mandatory data field, with list
cardinality.
4. 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::Protocol::Hardware has the following association accessor methods:
parameterTypes
Methods for the "parameterTypes" association.
From the MAGE-OM documentation:
The description of the parameters for the Parameterizable class instance.
$array_ref = $hardware->setParameterTypes($array_ref)
The restricted setter method for the "parameterTypes" association.
Input parameters: the value to which the "parameterTypes" association will be set : a reference
to an array of objects of type "Bio::MAGE::Protocol::Parameter"
Return value: the current value of the "parameterTypes" association : a reference to an array of
objects of type "Bio::MAGE::Protocol::Parameter"
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 class
"Bio::MAGE::Protocol::Parameter" instances
$array_ref = $hardware->getParameterTypes()
The restricted getter method for the "parameterTypes" association.
Input parameters: none
Return value: the current value of the "parameterTypes" association : a reference to an array of
objects of type "Bio::MAGE::Protocol::Parameter"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $hardware->addParameterTypes(@vals)
Because the parameterTypes association has list cardinality, it may store more than one value.
This method adds the current list of objects in the parameterTypes association.
Input parameters: the list of values @vals to add to the parameterTypes 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 class "Bio::MAGE::Protocol::Parameter"
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 = $hardware->setAuditTrail($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 type "Bio::MAGE::AuditAndSecurity::Audit"
Return value: the current value of the "auditTrail" association : a reference to an array of
objects of type "Bio::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 class
"Bio::MAGE::AuditAndSecurity::Audit" instances
$array_ref = $hardware->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 type "Bio::MAGE::AuditAndSecurity::Audit"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $hardware->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 class "Bio::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 = $hardware->setPropertySets($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 type "Bio::MAGE::NameValueType"
Return value: the current value of the "propertySets" association : a reference to an array of
objects of type "Bio::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 class
"Bio::MAGE::NameValueType" instances
$array_ref = $hardware->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 type "Bio::MAGE::NameValueType"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $hardware->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 class "Bio::MAGE::NameValueType"
hardwareManufacturers
Methods for the "hardwareManufacturers" association.
From the MAGE-OM documentation:
Contact for information on the Hardware.
$array_ref = $hardware->setHardwareManufacturers($array_ref)
The restricted setter method for the "hardwareManufacturers" association.
Input parameters: the value to which the "hardwareManufacturers" association will be set : a
reference to an array of objects of type "Bio::MAGE::AuditAndSecurity::Contact"
Return value: the current value of the "hardwareManufacturers" association : a reference to an
array of objects of type "Bio::MAGE::AuditAndSecurity::Contact"
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 class
"Bio::MAGE::AuditAndSecurity::Contact" instances
$array_ref = $hardware->getHardwareManufacturers()
The restricted getter method for the "hardwareManufacturers" association.
Input parameters: none
Return value: the current value of the "hardwareManufacturers" association : a reference to an
array of objects of type "Bio::MAGE::AuditAndSecurity::Contact"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $hardware->addHardwareManufacturers(@vals)
Because the hardwareManufacturers association has list cardinality, it may store more than one
value. This method adds the current list of objects in the hardwareManufacturers association.
Input parameters: the list of values @vals to add to the hardwareManufacturers 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 class "Bio::MAGE::AuditAndSecurity::Contact"
softwares
Methods for the "softwares" association.
From the MAGE-OM documentation:
Associates Hardware and Software together.
$array_ref = $hardware->setSoftwares($array_ref)
The restricted setter method for the "softwares" association.
Input parameters: the value to which the "softwares" association will be set : a reference to an
array of objects of type "Bio::MAGE::Protocol::Software"
Return value: the current value of the "softwares" association : a reference to an array of
objects of type "Bio::MAGE::Protocol::Software"
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 class
"Bio::MAGE::Protocol::Software" instances
$array_ref = $hardware->getSoftwares()
The restricted getter method for the "softwares" association.
Input parameters: none
Return value: the current value of the "softwares" association : a reference to an array of
objects of type "Bio::MAGE::Protocol::Software"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $hardware->addSoftwares(@vals)
Because the softwares association has list cardinality, it may store more than one value. This
method adds the current list of objects in the softwares association.
Input parameters: the list of values @vals to add to the softwares 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 class "Bio::MAGE::Protocol::Software"
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 = $hardware->setDescriptions($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 type "Bio::MAGE::Description::Description"
Return value: the current value of the "descriptions" association : a reference to an array of
objects of type "Bio::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 class
"Bio::MAGE::Description::Description" instances
$array_ref = $hardware->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 type "Bio::MAGE::Description::Description"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $hardware->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 class "Bio::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 = $hardware->setSecurity($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 class
"Bio::MAGE::AuditAndSecurity::Security"
$val = $hardware->getSecurity()
The restricted getter method for the "security" association.
Input parameters: none
Return value: the current value of the "security" association : an instance of type
"Bio::MAGE::AuditAndSecurity::Security".
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
type
Methods for the "type" association.
From the MAGE-OM documentation:
The type of a piece of Hardware. Examples include: scanner, wash station...
$val = $hardware->setType($val)
The restricted setter method for the "type" association.
Input parameters: the value to which the "type" association will be set : one of the accepted
enumerated values.
Return value: the current value of the "type" 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 class
"Bio::MAGE::Description::OntologyEntry"
$val = $hardware->getType()
The restricted getter method for the "type" association.
Input parameters: none
Return value: the current value of the "type" association : an instance of type
"Bio::MAGE::Description::OntologyEntry".
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
sub initialize {
my $self = shift;
return 1;
}