Bio::MAGE::Array::ArrayManufacture - Class for the MAGE-OM API
use Bio::MAGE::Array::ArrayManufacture # creating an empty instance my $arraymanufacture = Bio::MAGE::Array::ArrayManufacture->new(); # creating an instance with existing data my $arraymanufacture = Bio::MAGE::Array::ArrayManufacture->new( name=>$name_val, identifier=>$identifier_val, tolerance=>$tolerance_val, manufacturingDate=>$manufacturingdate_val, arrayManufacturers=>\@contact_list, featureLIMSs=>\@manufacturelims_list, arrays=>\@array_list, auditTrail=>\@audit_list, propertySets=>\@namevaluetype_list, qualityControlStatistics=>\@namevaluetype_list, protocolApplications=>\@protocolapplication_list, descriptions=>\@description_list, security=>$security_ref, ); # 'name' attribute my $name_val = $arraymanufacture->name(); # getter $arraymanufacture->name($value); # setter # 'identifier' attribute my $identifier_val = $arraymanufacture->identifier(); # getter $arraymanufacture->identifier($value); # setter # 'tolerance' attribute my $tolerance_val = $arraymanufacture->tolerance(); # getter $arraymanufacture->tolerance($value); # setter # 'manufacturingDate' attribute my $manufacturingDate_val = $arraymanufacture->manufacturingDate(); # getter $arraymanufacture->manufacturingDate($value); # setter # 'arrayManufacturers' association my $contact_array_ref = $arraymanufacture->arrayManufacturers(); # getter $arraymanufacture->arrayManufacturers(\@contact_list); # setter # 'featureLIMSs' association my $manufacturelims_array_ref = $arraymanufacture->featureLIMSs(); # getter $arraymanufacture->featureLIMSs(\@manufacturelims_list); # setter # 'arrays' association my $array_array_ref = $arraymanufacture->arrays(); # getter $arraymanufacture->arrays(\@array_list); # setter # 'auditTrail' association my $audit_array_ref = $arraymanufacture->auditTrail(); # getter $arraymanufacture->auditTrail(\@audit_list); # setter # 'propertySets' association my $namevaluetype_array_ref = $arraymanufacture->propertySets(); # getter $arraymanufacture->propertySets(\@namevaluetype_list); # setter # 'qualityControlStatistics' association my $namevaluetype_array_ref = $arraymanufacture->qualityControlStatistics(); # getter $arraymanufacture->qualityControlStatistics(\@namevaluetype_list); # setter # 'protocolApplications' association my $protocolapplication_array_ref = $arraymanufacture->protocolApplications(); # getter $arraymanufacture->protocolApplications(\@protocolapplication_list); # setter # 'descriptions' association my $description_array_ref = $arraymanufacture->descriptions(); # getter $arraymanufacture->descriptions(\@description_list); # setter # 'security' association my $security_ref = $arraymanufacture->security(); # getter $arraymanufacture->security($security_ref); # setter
From the MAGE-OM documentation for the ArrayManufacture class:
ArrayManufacture
Describes the process by which arrays are produced.
Bio::MAGE::Array::ArrayManufacture has the following superclasses:
Bio::MAGE::Identifiable
The following methods can all be called without first having an instance of the class via the Bio::MAGE::Array::ArrayManufacture->methodname() syntax.
The object constructor new() accepts the following optional named-value style arguments:
new()
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).
tolerance
Sets the value of the tolerance attribute
manufacturingDate
Sets the value of the manufacturingDate attribute
arrayManufacturers
Sets the value of the arrayManufacturers association
The value must be of type: array of Bio::MAGE::AuditAndSecurity::Contact.
Bio::MAGE::AuditAndSecurity::Contact
featureLIMSs
Sets the value of the featureLIMSs association
The value must be of type: array of Bio::MAGE::Array::ManufactureLIMS.
Bio::MAGE::Array::ManufactureLIMS
arrays
Sets the value of the arrays association
The value must be of type: array of Bio::MAGE::Array::Array.
Bio::MAGE::Array::Array
auditTrail
Sets the value of the auditTrail association (this association was inherited from class Bio::MAGE::Describable).
Bio::MAGE::Describable
The value must be of type: array of Bio::MAGE::AuditAndSecurity::Audit.
Bio::MAGE::AuditAndSecurity::Audit
propertySets
Sets the value of the propertySets association (this association was inherited from class Bio::MAGE::Extendable).
Bio::MAGE::Extendable
The value must be of type: array of Bio::MAGE::NameValueType.
Bio::MAGE::NameValueType
qualityControlStatistics
Sets the value of the qualityControlStatistics association
protocolApplications
Sets the value of the protocolApplications association
The value must be of type: array of Bio::MAGE::Protocol::ProtocolApplication.
Bio::MAGE::Protocol::ProtocolApplication
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.
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.
Bio::MAGE::AuditAndSecurity::Security
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.
initialize()
The get_slot_names() method is used to retrieve the name of all slots defined in a given class.
get_slot_names()
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
returns the list of attribute data members for this class.
returns the list of association data members for this class.
returns the list of superclasses for this class.
returns the list of subclasses for this class.
Returns the full class name for this class.
Returns the base package name (i.e. no 'namespace::') of the package that contains this class.
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.
Association
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.
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.
set_slots()
Return value: none
Side effects: will call croak() if a slot_name is used that the class does not define.
croak()
The get_slots() method is used to get the values of a number of slots at the same time.
get_slots()
Return value: a list of instance objects
The set_slot() method sets the slot $name to the value $val
set_slot()
$name
$val
Return value: the new value of the slot, i.e. $val
The get_slot() method is used to get the values of a number of slots at the same time.
get_slot()
Return value: a single slot value, or undef if the slot has not been initialized.
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::Array::ArrayManufacture has the following attribute accessor methods:
Bio::MAGE::Array::ArrayManufacture
Methods for the name attribute.
From the MAGE-OM documentation:
The potentially ambiguous common identifier.
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
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified
The restricted getter method for the name attribute.
Input parameters: none
Exceptions: will call croak() if any input parameters are specified
Methods for the identifier attribute.
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.
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
The restricted getter method for the identifier attribute.
Methods for the tolerance attribute.
The allowable error of a feature printed to its intended position.
The restricted setter method for the tolerance attribute.
Input parameters: the value to which the tolerance attribute will be set
Return value: the current value of the tolerance attribute
The restricted getter method for the tolerance attribute.
Methods for the manufacturingDate attribute.
The date the arrays were manufactured
The restricted setter method for the manufacturingDate attribute.
Input parameters: the value to which the manufacturingDate attribute will be set
Return value: the current value of the manufacturingDate attribute
The restricted getter method for the manufacturingDate attribute.
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.
0..1
There may be one item in the association, i.e. this is an optional data field.
1..N
There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
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::Array::ArrayManufacture has the following association accessor methods:
Methods for the arrayManufacturers association.
The person or organization to contact for information concerning the ArrayManufacture.
The restricted setter method for the arrayManufacturers association.
Input parameters: the value to which the arrayManufacturers association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
Return value: the current value of the arrayManufacturers association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
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
The restricted getter method for the arrayManufacturers association.
Because the arrayManufacturers association has list cardinality, it may store more than one value. This method adds the current list of objects in the arrayManufacturers association.
Input parameters: the list of values @vals to add to the arrayManufacturers association. NOTE: submitting a single value is permitted.
@vals
Return value: the number of items stored in the slot after adding @vals
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
Methods for the featureLIMSs association.
Information on the manufacture of the features.
The restricted setter method for the featureLIMSs association.
Input parameters: the value to which the featureLIMSs association will be set : a reference to an array of objects of type Bio::MAGE::Array::ManufactureLIMS
Return value: the current value of the featureLIMSs association : a reference to an array of objects of type Bio::MAGE::Array::ManufactureLIMS
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::Array::ManufactureLIMS instances
The restricted getter method for the featureLIMSs association.
Because the featureLIMSs association has list cardinality, it may store more than one value. This method adds the current list of objects in the featureLIMSs association.
Input parameters: the list of values @vals to add to the featureLIMSs association. NOTE: submitting a single value is permitted.
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::Array::ManufactureLIMS
Methods for the arrays association.
Association between the manufactured array and the information on that manufacture.
The restricted setter method for the arrays association.
Input parameters: the value to which the arrays association will be set : a reference to an array of objects of type Bio::MAGE::Array::Array
Return value: the current value of the arrays association : a reference to an array of objects of type Bio::MAGE::Array::Array
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::Array::Array instances
The restricted getter method for the arrays association.
Because the arrays association has list cardinality, it may store more than one value. This method adds the current list of objects in the arrays association.
Input parameters: the list of values @vals to add to the arrays association. NOTE: submitting a single value is permitted.
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::Array::Array
Methods for the auditTrail association.
A list of Audit instances that track changes to the instance of Describable.
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
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
The restricted getter method for the auditTrail association.
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.
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
Methods 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.
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
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
The restricted getter method for the propertySets association.
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.
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
Methods for the qualityControlStatistics association.
Information on the quality of the ArrayManufacture.
The restricted setter method for the qualityControlStatistics association.
Input parameters: the value to which the qualityControlStatistics association will be set : a reference to an array of objects of type Bio::MAGE::NameValueType
Return value: the current value of the qualityControlStatistics association : a reference to an array of objects of type Bio::MAGE::NameValueType
The restricted getter method for the qualityControlStatistics association.
Because the qualityControlStatistics association has list cardinality, it may store more than one value. This method adds the current list of objects in the qualityControlStatistics association.
Input parameters: the list of values @vals to add to the qualityControlStatistics association. NOTE: submitting a single value is permitted.
Methods for the protocolApplications association.
The protocols followed in the manufacturing of the arrays.
The restricted setter method for the protocolApplications association.
Input parameters: the value to which the protocolApplications association will be set : a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication
Return value: the current value of the protocolApplications association : a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication
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::ProtocolApplication instances
The restricted getter method for the protocolApplications association.
Because the protocolApplications association has list cardinality, it may store more than one value. This method adds the current list of objects in the protocolApplications association.
Input parameters: the list of values @vals to add to the protocolApplications association. NOTE: submitting a single value is permitted.
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::ProtocolApplication
Methods for the descriptions association.
Free hand text descriptions. Makes available the associations of Description to an instance of Describable.
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
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
The restricted getter method for the descriptions association.
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.
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
Methods for the security association.
Information on the security for the instance of the class.
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.
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
The restricted getter method for the security association.
Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.
sub initialize {
my $self = shift; return 1;
}
In the Perl implementation of MAGE-OM classes, there are three types of class data members: slots, attributes, and associations.
slots
attributes
associations
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.
slot
Slots are implemented using unified getter/setter methods:
Retrieves the current value of the slot.
Store $new_var in the slot - the return value is also $new_var.
Returns the list of all slots in the class.
DATA CHECKING: No data type checking is made for these methods.
The terms attribute and association indicate data members of the class that were specified directly from the UML model.
attribute
association
In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:
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.
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.
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.
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:
Bio::MAGE::Base
See elsewhere in this page for a detailed description of these methods.
Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)
Jason E. Stewart (jasons 'at' cpan 'dot' org)
perl(1).
5 POD Errors
The following errors were encountered while parsing the POD:
'=item' outside of any '=over'
You forgot a '=back' before '=head2'
Expected '=item 2'
Expected '=item 3'
Expected '=item 4'
To install Bio::MAGE, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::MAGE
CPAN shell
perl -MCPAN -e shell install Bio::MAGE
For more information on module installation, please visit the detailed CPAN module installation guide.