• Bio::MAGE::Protocol::ProtocolApplication
• SYNOPSIS
• DESCRIPTION
• INHERITANCE
• CLASS METHODS
• ATTRIBUTES
• ASSOCIATIONS
• BUGS
• AUTHOR
• SEE ALSO

Bio::MAGE::Protocol::ProtocolApplication

SYNOPSIS

  use Bio::MAGE::Protocol::ProtocolApplication;

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

    # creating an already populated instance
  my $protocolapplication = Bio::MAGE::Protocol::ProtocolApplication->new(activityDate=>$activityDate_value,
                        hardwareApplications=>$hardwareApplications_value,
                        protocol=>$protocol_value,
                        softwareApplications=>$softwareApplications_value,
                        performers=>$performers_value);

    # setting and retrieving object attributes
  my $activityDate_val = $protocolapplication->activityDate();
  $protocolapplication->activityDate($value);

    # setting and retrieving object associations
  my $hardwareApplications_val = $protocolapplication->hardwareApplications();
  $protocolapplication->hardwareApplications($value);

  my $protocol_val = $protocolapplication->protocol();
  $protocolapplication->protocol($value);

  my $softwareApplications_val = $protocolapplication->softwareApplications();
  $protocolapplication->softwareApplications($value);

  my $performers_val = $protocolapplication->performers();
  $protocolapplication->performers($value);

DESCRIPTION

From the MAGE-OM documentation for the ProtocolApplication class:

The use of a protocol with the requisite Parameters and ParameterValues.

INHERITANCE

Bio::MAGE::Protocol::ProtocolApplication has the following super classes

• Bio::MAGE::Protocol::ParameterizableApplication
  

CLASS METHODS

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

new()

new(%args)

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

• activityDate
  Sets the value of the activityDate attribute (from Bio::MAGE::Protocol::ProtocolApplication).

• hardwareApplications
  Sets the value of the hardwareApplications association (from Bio::MAGE::Protocol::ProtocolApplication).

• protocol
  Sets the value of the protocol association (from Bio::MAGE::Protocol::ProtocolApplication).

• softwareApplications
  Sets the value of the softwareApplications association (from Bio::MAGE::Protocol::ProtocolApplication).

• performers
  Sets the value of the performers association (from Bio::MAGE::Protocol::ProtocolApplication).

• parameterValues
  Sets the value of the parameterValues association (from Bio::MAGE::Protocol::ParameterizableApplication).

• security
  Sets the value of the security association (from Bio::MAGE::Describable).

• auditTrail
  Sets the value of the auditTrail association (from Bio::MAGE::Describable).

• descriptions
  Sets the value of the descriptions association (from Bio::MAGE::Describable).

• propertySets
  Sets the value of the propertySets association (from Bio::MAGE::Extendable).

$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

$name = class_name()

Returns the full class name for this class, Bio::MAGE::Protocol::ProtocolApplication.

$package_name = package()

Returns the unresolved package name (i.e. no 'Bio::MAGE::') of the package that contains class, Bio::MAGE::Protocol::ProtocolApplication.

@classes = subclasses()

returns the list of subclasses for this class.

@classes = superclasses()

returns the list of superclasses for this class.

@methods = attribute_methods()

returns the list of attribute accessor methods for this class.

@methods = association_methods()

returns the list of association accessor methods for this class.

%assns = associations()

returns the association meta-information in a hash where the keys are the association names and the values are Bio::MAGE::Association objects that provide the meta-information for the association.

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::ProtocolApplication: has the following attribute accessor methods:

activityDate

From the MAGE-OM documentation for the activityDate attribute:

When the protocol was applied.

$val = $protocolapplication->setActivityDate($val)

The restricted setter method for the activityDate attribute.

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

Return value: the current value of the activityDate attribute

Side effects: none

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

$val = $protocolapplication->getActivityDate()

The restricted getter method for the activityDate attribute.

Input parameters: none

Return value: the current value of the activityDate attribute

Side effects: none

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

ASSOCIATIONS

Associations are references to other class objects which can be shared by multiple class instances at the same time. In the Perl implementation of MAGE-OM classes, associations are implemented using three separate methods:

get*

Retrieves the current value. If the association has list cardinality, an array reference is returned.

set*

Sets the current value replacing any existing value. If the association has list cardinality, the argument must be an array reference. Unless you know what you are doing, you probably should be using the add* methods.

add*

This method exists only for associations with list cardinality. It appends a list of objects to any values that may already be stored in the association.

Bio::MAGE::Protocol::ProtocolApplication: has the following association accessor methods:

hardwareApplications

From the MAGE-OM documentation for the hardwareApplications association:

The use of hardware for the application of the protocol.

$array_ref = $protocolapplication->setHardwareApplications($array_ref)

The restricted setter method for the hardwareApplications association.

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

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

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::HardwareApplication instances

$array_ref = $protocolapplication->getHardwareApplications()

The restricted getter method for the hardwareApplications association.

Input parameters: none

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

Side effects: none

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

$protocolapplication->addHardwareApplications(@vals)

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

Input parameters: the list of values @vals to add to the hardwareApplications association. NOTE: submitting a single value is permitted.

Return value: none

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::HardwareApplication

protocol

From the MAGE-OM documentation for the protocol association:

The protocol that is being used.

$val = $protocolapplication->setProtocol($val)

The restricted setter method for the protocol association.

Input parameters: the value to which the protocol association will be set : an instance of type Bio::MAGE::Protocol::Protocol.

Return value: the current value of the protocol association : an instance of type Bio::MAGE::Protocol::Protocol.

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::Protocol::Protocol

$val = $protocolapplication->getProtocol()

The restricted getter method for the protocol association.

Input parameters: none

Return value: the current value of the protocol association : an instance of type Bio::MAGE::Protocol::Protocol.

Side effects: none

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

softwareApplications

From the MAGE-OM documentation for the softwareApplications association:

The use of software for the application of the protocol.

$array_ref = $protocolapplication->setSoftwareApplications($array_ref)

The restricted setter method for the softwareApplications association.

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

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

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::SoftwareApplication instances

$array_ref = $protocolapplication->getSoftwareApplications()

The restricted getter method for the softwareApplications association.

Input parameters: none

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

Side effects: none

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

$protocolapplication->addSoftwareApplications(@vals)

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

Input parameters: the list of values @vals to add to the softwareApplications association. NOTE: submitting a single value is permitted.

Return value: none

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::SoftwareApplication

performers

From the MAGE-OM documentation for the performers association:

The people who performed the protocol.

$array_ref = $protocolapplication->setPerformers($array_ref)

The restricted setter method for the performers association.

Input parameters: the value to which the performers association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Person

Return value: the current value of the performers association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Person

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::Person instances

$array_ref = $protocolapplication->getPerformers()

The restricted getter method for the performers association.

Input parameters: none

Return value: the current value of the performers association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Person

Side effects: none

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

$protocolapplication->addPerformers(@vals)

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

Input parameters: the list of values @vals to add to the performers association. NOTE: submitting a single value is permitted.

Return value: none

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::Person

Associations Inherited from Bio::MAGE::Protocol::ParameterizableApplication

parameterValues

From the MAGE-OM documentation for the parameterValues association:

The parameter values for this Parameterizable Application.

$array_ref = $parameterizableapplication->setParameterValues($array_ref)

The restricted setter method for the parameterValues association.

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

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

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::ParameterValue instances

$array_ref = $parameterizableapplication->getParameterValues()

The restricted getter method for the parameterValues association.

Input parameters: none

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

Side effects: none

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

$parameterizableapplication->addParameterValues(@vals)

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

Input parameters: the list of values @vals to add to the parameterValues association. NOTE: submitting a single value is permitted.

Return value: none

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::ParameterValue

Associations Inherited from Bio::MAGE::Describable

security

From the MAGE-OM documentation for the security association:

Information on the security for the instance of the class.

$val = $describable->setSecurity($val)

The restricted setter method for the security association.

Input parameters: the value to which the security association will be set : an instance of type Bio::MAGE::AuditAndSecurity::Security.

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 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 = $describable->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

auditTrail

From the MAGE-OM documentation for the auditTrail association:

A list of Audit instances that track changes to the instance of Describable.

$array_ref = $describable->setAuditTrail($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 = $describable->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

$describable->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: none

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

descriptions

From the MAGE-OM documentation for the descriptions association:

Free hand text descriptions. Makes available the associations of Description to an instance of Describable.

$array_ref = $describable->setDescriptions($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 = $describable->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

$describable->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: none

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

Associations Inherited from Bio::MAGE::Extendable

propertySets

From the MAGE-OM documentation for the propertySets association:

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 = $extendable->setPropertySets($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 = $extendable->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

$extendable->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: none

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

BUGS

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

AUTHOR

Jason E. Stewart (www.openinformatics.com)

SEE ALSO

perl(1).