Bio::MAGE::Protocol::Protocol - Class for the MAGE-OM API

SLOTS, ATTRIBUTES, AND ASSOCIATIONS

SLOTS
ATTRIBUTES AND ASSOCIATIONS
GENERIC METHODS

BUGS
AUTHOR
SEE ALSO

NAME

Bio::MAGE::Protocol::Protocol - Class for the MAGE-OM API

SYNOPSIS

  use Bio::MAGE::Protocol::Protocol

  # creating an empty instance
  my $protocol = Bio::MAGE::Protocol::Protocol->new();

  # creating an instance with existing data
  my $protocol = Bio::MAGE::Protocol::Protocol->new(
        URI=>$uri_val,
        name=>$name_val,
        identifier=>$identifier_val,
        text=>$text_val,
        title=>$title_val,
        parameterTypes=>\@parameter_list,
        auditTrail=>\@audit_list,
        propertySets=>\@namevaluetype_list,
        hardwares=>\@hardware_list,
        descriptions=>\@description_list,
        softwares=>\@software_list,
        security=>$security_ref,
        type=>$ontologyentry_ref,
  );

  # 'URI' attribute
  my $URI_val = $protocol->URI(); # getter
  $protocol->URI($value); # setter

  # 'name' attribute
  my $name_val = $protocol->name(); # getter
  $protocol->name($value); # setter

  # 'identifier' attribute
  my $identifier_val = $protocol->identifier(); # getter
  $protocol->identifier($value); # setter

  # 'text' attribute
  my $text_val = $protocol->text(); # getter
  $protocol->text($value); # setter

  # 'title' attribute
  my $title_val = $protocol->title(); # getter
  $protocol->title($value); # setter

  # 'parameterTypes' association
  my $parameter_array_ref = $protocol->parameterTypes(); # getter
  $protocol->parameterTypes(\@parameter_list); # setter

  # 'auditTrail' association
  my $audit_array_ref = $protocol->auditTrail(); # getter
  $protocol->auditTrail(\@audit_list); # setter

  # 'propertySets' association
  my $namevaluetype_array_ref = $protocol->propertySets(); # getter
  $protocol->propertySets(\@namevaluetype_list); # setter

  # 'hardwares' association
  my $hardware_array_ref = $protocol->hardwares(); # getter
  $protocol->hardwares(\@hardware_list); # setter

  # 'descriptions' association
  my $description_array_ref = $protocol->descriptions(); # getter
  $protocol->descriptions(\@description_list); # setter

  # 'softwares' association
  my $software_array_ref = $protocol->softwares(); # getter
  $protocol->softwares(\@software_list); # setter

  # 'security' association
  my $security_ref = $protocol->security(); # getter
  $protocol->security($security_ref); # setter

  # 'type' association
  my $ontologyentry_ref = $protocol->type(); # getter
  $protocol->type($ontologyentry_ref); # setter

DESCRIPTION

From the MAGE-OM documentation for the Protocol class:

A Protocol is a parameterizable description of a method. ProtocolApplication is used to specify the ParameterValues of it's Protocol's Parameters.

INHERITANCE

Bio::MAGE::Protocol::Protocol has the following superclasses:

Bio::MAGE::Protocol::Parameterizable

CLASS METHODS

The following methods can all be called without first having an instance of the class via the Bio::MAGE::Protocol::Protocol->methodname() syntax.

new()

new(%args)

The object constructor new() accepts the following optional named-value style arguments:

URI
Sets the value of the URI attribute (this attribute was inherited from class Bio::MAGE::Protocol::Parameterizable).
name
Sets the value of the name attribute (this attribute was inherited from class Bio::MAGE::Identifiable).
identifier
Sets the value of the identifier attribute (this attribute was inherited from class Bio::MAGE::Identifiable).
text
Sets the value of the text attribute
title
Sets the value of the title attribute
parameterTypes
Sets the value of the parameterTypes association (this association was inherited from class Bio::MAGE::Protocol::Parameterizable).
The value must be of type: array of Bio::MAGE::Protocol::Parameter.
auditTrail
Sets the value of the auditTrail association (this association was inherited from class Bio::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 class Bio::MAGE::Extendable).
The value must be of type: array of Bio::MAGE::NameValueType.
hardwares
Sets the value of the hardwares association
The value must be of type: array of Bio::MAGE::Protocol::Hardware.
softwares
Sets the value of the softwares association
The value must be of type: array of Bio::MAGE::Protocol::Software.
descriptions
Sets the value of the descriptions association (this association was inherited from class Bio::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 class Bio::MAGE::Describable).
The value must be of type: instance of Bio::MAGE::AuditAndSecurity::Security.
type
Sets the value of the type association
The value must be of type: instance of Bio::MAGE::Description::OntologyEntry.

$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::Protocol::Protocol has the following attribute accessor methods:

URI

Methods for the URI attribute.

From the MAGE-OM documentation:

Where an instantiated Parameterizable is located.

$val = $protocol->setURI($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 = $protocol->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

name

Methods for the name attribute.

From the MAGE-OM documentation:

The potentially ambiguous common identifier.

$val = $protocol->setName($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 = $protocol->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

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 = $protocol->setIdentifier($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 = $protocol->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

text

Methods for the text attribute.

From the MAGE-OM documentation:

The text description of the Protocol.

$val = $protocol->setText($val)

The restricted setter method for the text attribute.

Input parameters: the value to which the text attribute will be set

Return value: the current value of the text attribute

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $protocol->getText()

The restricted getter method for the text attribute.

Input parameters: none

Return value: the current value of the text attribute

Side effects: none

Exceptions: will call croak() if any input parameters are specified

title

Methods for the title attribute.

From the MAGE-OM documentation:

The title of the Protocol

$val = $protocol->setTitle($val)

The restricted setter method for the title attribute.

Input parameters: the value to which the title attribute will be set

Return value: the current value of the title attribute

Side effects: none

Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified

$val = $protocol->getTitle()

The restricted getter method for the title attribute.

Input parameters: none

Return value: the current value of the title 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:

There must be exactly one item in the association, i.e. this is a mandatory data field.
.1
There may be one item in the association, i.e. this is an optional data field.
.N
There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
.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::Protocol 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 = $protocol->setParameterTypes($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 = $protocol->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 = $protocol->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 = $protocol->setAuditTrail($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

$array_ref = $protocol->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 = $protocol->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 = $protocol->setPropertySets($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

$array_ref = $protocol->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 = $protocol->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

hardwares

Methods for the hardwares association.

From the MAGE-OM documentation:

Hardware used by this protocol.

$array_ref = $protocol->setHardwares($array_ref)

The restricted setter method for the hardwares association.

Input parameters: the value to which the hardwares association will be set : a reference to an array of objects of type Bio::MAGE::Protocol::Hardware

Return value: the current value of the hardwares association : a reference to an array of objects of type Bio::MAGE::Protocol::Hardware

Side effects: none

$array_ref = $protocol->getHardwares()

The restricted getter method for the hardwares association.

Input parameters: none

Return value: the current value of the hardwares association : a reference to an array of objects of type Bio::MAGE::Protocol::Hardware

Side effects: none

Exceptions: will call croak() if any input parameters are specified

$val = $protocol->addHardwares(@vals)

Because the hardwares association has list cardinality, it may store more than one value. This method adds the current list of objects in the hardwares association.

Input parameters: the list of values @vals to add to the hardwares 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::Hardware

softwares

Methods for the softwares association.

From the MAGE-OM documentation:

Software used by this Protocol.

$array_ref = $protocol->setSoftwares($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

$array_ref = $protocol->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 = $protocol->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 = $protocol->setDescriptions($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

$array_ref = $protocol->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 = $protocol->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 = $protocol->setSecurity($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 = $protocol->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 Protocol, a user should provide/use a recommended vocabulary. Examples of types include: RNA extraction, array washing, etc...

$val = $protocol->setType($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 = $protocol->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;

}

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)