NAME

Bio::MAGE::Protocol - Container module for classes in the MAGE Protocol package

SYNOPSIS

  use Bio::MAGE::Protocol;

DESCRIPTION

This is a package module that encapsulates a number of classes in the Bio::MAGE hierarchy. These classes belong to the Protocol package of the MAGE-OM object model.

CLASSES

The Bio::MAGE::Protocol module contains the following Bio::MAGE classes:

• Protocol

• Parameter

• ParameterValue

• ProtocolApplication

• Software

• Hardware

• HardwareApplication

• SoftwareApplication

• Parameterizable

• ParameterizableApplication

CLASS METHODS

@class_list = Bio::MAGE::Protocol::classes();

This method returns a list of non-fully qualified class names (i.e. they do not have 'Bio::MAGE::' as a prefix) in this package.

$obj_ref = Bio::MAGE::Protocol->new(%parameters)

$obj_ref_copy = $obj_ref->new()

The new() method is the class constructor. If invoked with an existing object instance, it is a copy constructor.

Return value: It returns a reference to an object of class Bio::MAGE::Protocol.

Side effects: It invokes the initialize() method if it is defined by the class.

INSTANCE METHODS

$array_ref = $protocol->getHardware_list()

This method handles the list for the Bio::MAGE::ARRAY(0x10496ed4)::Hardware class. It returns a reference to an array of the class objects of that type associated with this package object.

This is useful when retrieving data from parsed MAGE-ML file.

$array_ref = $protocol->getSoftware_list()

This method handles the list for the Bio::MAGE::ARRAY(0x10496ed4)::Software class. It returns a reference to an array of the class objects of that type associated with this package object.

This is useful when retrieving data from parsed MAGE-ML file.

$array_ref = $protocol->getProtocol_list()

This method handles the list for the Bio::MAGE::ARRAY(0x10496ed4)::Protocol class. It returns a reference to an array of the class objects of that type associated with this package object.

This is useful when retrieving data from parsed MAGE-ML file.

$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->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

@names = $obj->get_slot_names()

The get_slot_names() method is used to retrieve the name of all slots defined for a given object.

Return value: a single slot value, or undef if the slot has not been initialized.

Side effects: none

$val = $protocol->hardware_list()

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

This is the unified setter/getter method for the hardware_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the hardware_list slot

Side effects: none

Exceptions: none

$val = $protocol->software_list()

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

This is the unified setter/getter method for the software_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the software_list slot

Side effects: none

Exceptions: none

$val = $protocol->protocol_list()

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

This is the unified setter/getter method for the protocol_list slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the protocol_list slot

Side effects: none

Exceptions: none

$val = $protocol->mageml_lists()

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

This is the unified setter/getter method for the mageml_lists slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the mageml_lists slot

Side effects: none

Exceptions: none

$val = $protocol->tagname()

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

This is the unified setter/getter method for the tagname slot. If $val is specified, the setter method is invoked, with no parameters, the getter method is invoked.

Input parameters: the optional $val will invoke the setter method.

Return value: for both setter and getter the current value of the tagname slot

Side effects: none

Exceptions: none

BUGS

Please send bug reports to mged-mage@lists.sf.net

AUTHOR

Jason E. Stewart (jason@openinformatics.com)

SEE ALSO

perl(1).