Provided by: libbio-mage-perl_20030502.3-3_all 
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:
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::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
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 = $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
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 = $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
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::Hardware" instances
$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
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 = $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
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 = $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)
SEE ALSO
perl(1).
POD ERRORS
Hey! The above document had some coding errors, which are explained below:
Around line 456:
'=item' outside of any '=over'
Around line 541:
You forgot a '=back' before '=head2'
Around line 929:
Expected '=item 2'
Around line 934:
Expected '=item 3'
Around line 939:
Expected '=item 4'