SYNOPSIS

use Bio::MAGE::Array::Array
# creating an empty instance
my $array = Bio::MAGE::Array::Array->new();
# creating an instance with existing data
my $array = Bio::MAGE::Array::Array->new(
arrayXOrigin=>$arrayxorigin_val,
name=>$name_val,
arrayYOrigin=>$arrayyorigin_val,
identifier=>$identifier_val,
arrayIdentifier=>$arrayidentifier_val,
originRelativeTo=>$originrelativeto_val,
arrayGroup=>$arraygroup_ref,
arrayDesign=>$arraydesign_ref,
information=>$arraymanufacture_ref,
auditTrail=>\@audit_list,
propertySets=>\@namevaluetype_list,
descriptions=>\@description_list,
security=>$security_ref,
arrayManufactureDeviations=>\@arraymanufacturedeviation_list,
);
# 'arrayXOrigin' attribute
my $arrayXOrigin_val = $array->arrayXOrigin(); # getter
$array->arrayXOrigin($value); # setter
# 'name' attribute
my $name_val = $array->name(); # getter
$array->name($value); # setter
# 'arrayYOrigin' attribute
my $arrayYOrigin_val = $array->arrayYOrigin(); # getter
$array->arrayYOrigin($value); # setter
# 'identifier' attribute
my $identifier_val = $array->identifier(); # getter
$array->identifier($value); # setter
# 'arrayIdentifier' attribute
my $arrayIdentifier_val = $array->arrayIdentifier(); # getter
$array->arrayIdentifier($value); # setter
# 'originRelativeTo' attribute
my $originRelativeTo_val = $array->originRelativeTo(); # getter
$array->originRelativeTo($value); # setter
# 'arrayGroup' association
my $arraygroup_ref = $array->arrayGroup(); # getter
$array->arrayGroup($arraygroup_ref); # setter
# 'arrayDesign' association
my $arraydesign_ref = $array->arrayDesign(); # getter
$array->arrayDesign($arraydesign_ref); # setter
# 'information' association
my $arraymanufacture_ref = $array->information(); # getter
$array->information($arraymanufacture_ref); # setter
# 'auditTrail' association
my $audit_array_ref = $array->auditTrail(); # getter
$array->auditTrail(\@audit_list); # setter
# 'propertySets' association
my $namevaluetype_array_ref = $array->propertySets(); # getter
$array->propertySets(\@namevaluetype_list); # setter
# 'descriptions' association
my $description_array_ref = $array->descriptions(); # getter
$array->descriptions(\@description_list); # setter
# 'security' association
my $security_ref = $array->security(); # getter
$array->security($security_ref); # setter
# 'arrayManufactureDeviations' association
my $arraymanufacturedeviation_array_ref = $array->arrayManufactureDeviations(); # getter
$array->arrayManufactureDeviations(\@arraymanufacturedeviation_list); # setter

DESCRIPTION

From the MAGE-OM documentation for the "Array" class:

The physical substrate along with its features and their annotation

INHERITANCE

Bio::MAGE::Array::Array has the following superclasses:

• Bio::MAGE::Identifiable

CLASS METHODS

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

new()

new(%args)

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

• arrayXOrigin

  Sets the value of the "arrayXOrigin" attribute

• name

  Sets the value of the "name" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").

• arrayYOrigin

  Sets the value of the "arrayYOrigin" attribute

• identifier

  Sets the value of the "identifier" attribute (this attribute was inherited from class "Bio::MAGE::Identifiable").

• arrayIdentifier

  Sets the value of the "arrayIdentifier" attribute

• originRelativeTo

  Sets the value of the "originRelativeTo" attribute

• arrayGroup

  Sets the value of the "arrayGroup" association

  The value must be of type: instance of "Bio::MAGE::Array::ArrayGroup".

• arrayDesign

  Sets the value of the "arrayDesign" association

  The value must be of type: instance of "Bio::MAGE::ArrayDesign::ArrayDesign".

• 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".

• information

  Sets the value of the "information" association

  The value must be of type: instance of "Bio::MAGE::Array::ArrayManufacture".

• 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".

• 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".

• arrayManufactureDeviations

  Sets the value of the "arrayManufactureDeviations" association

  The value must be of type: array of "Bio::MAGE::Array::ArrayManufactureDeviation".

$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::Array::Array" has the following attribute accessor methods:

arrayXOrigin

Methods for the "arrayXOrigin" attribute.

From the MAGE-OM documentation:

This can indicate the x position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.

$val = $array->setArrayXOrigin($val)

The restricted setter method for the "arrayXOrigin" attribute.

Input parameters: the value to which the "arrayXOrigin" attribute will be set

Return value: the current value of the "arrayXOrigin" attribute

Side effects: none

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

$val = $array->getArrayXOrigin()

The restricted getter method for the "arrayXOrigin" attribute.

Input parameters: none

Return value: the current value of the "arrayXOrigin" 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 = $array->setName($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 = $array->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

arrayYOrigin

Methods for the "arrayYOrigin" attribute.

From the MAGE-OM documentation:

This can indicate the y position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.

$val = $array->setArrayYOrigin($val)

The restricted setter method for the "arrayYOrigin" attribute.

Input parameters: the value to which the "arrayYOrigin" attribute will be set

Return value: the current value of the "arrayYOrigin" attribute

Side effects: none

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

$val = $array->getArrayYOrigin()

The restricted getter method for the "arrayYOrigin" attribute.

Input parameters: none

Return value: the current value of the "arrayYOrigin" 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 = $array->setIdentifier($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 = $array->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

arrayIdentifier

Methods for the "arrayIdentifier" attribute.

From the MAGE-OM documentation:

An identifying string, e.g. a barcode.

$val = $array->setArrayIdentifier($val)

The restricted setter method for the "arrayIdentifier" attribute.

Input parameters: the value to which the "arrayIdentifier" attribute will be set

Return value: the current value of the "arrayIdentifier" attribute

Side effects: none

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

$val = $array->getArrayIdentifier()

The restricted getter method for the "arrayIdentifier" attribute.

Input parameters: none

Return value: the current value of the "arrayIdentifier" attribute

Side effects: none

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

originRelativeTo

Methods for the "originRelativeTo" attribute.

From the MAGE-OM documentation:

What the array origin is relative to, e.g. upper left corner, fiducial, etc.

$val = $array->setOriginRelativeTo($val)

The restricted setter method for the "originRelativeTo" attribute.

Input parameters: the value to which the "originRelativeTo" attribute will be set

Return value: the current value of the "originRelativeTo" attribute

Side effects: none

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

$val = $array->getOriginRelativeTo()

The restricted getter method for the "originRelativeTo" attribute.

Input parameters: none

Return value: the current value of the "originRelativeTo" 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::Array::Array has the following association accessor methods:

arrayGroup

Methods for the "arrayGroup" association.

From the MAGE-OM documentation:

Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.

$val = $array->setArrayGroup($val)

The restricted setter method for the "arrayGroup" association.

Input parameters: the value to which the "arrayGroup" association will be set : one of the accepted enumerated values.

Return value: the current value of the "arrayGroup" 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::Array::ArrayGroup"

$val = $array->getArrayGroup()

The restricted getter method for the "arrayGroup" association.

Input parameters: none

Return value: the current value of the "arrayGroup" association : an instance of type "Bio::MAGE::Array::ArrayGroup".

Side effects: none

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

arrayDesign

Methods for the "arrayDesign" association.

From the MAGE-OM documentation:

The association of a physical array with its array design.

$val = $array->setArrayDesign($val)

The restricted setter method for the "arrayDesign" association.

Input parameters: the value to which the "arrayDesign" association will be set : one of the accepted enumerated values.

Return value: the current value of the "arrayDesign" 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::ArrayDesign::ArrayDesign"

$val = $array->getArrayDesign()

The restricted getter method for the "arrayDesign" association.

Input parameters: none

Return value: the current value of the "arrayDesign" association : an instance of type "Bio::MAGE::ArrayDesign::ArrayDesign".

Side effects: none

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

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 = $array->setAuditTrail($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 = $array->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 = $array->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"

information

Methods for the "information" association.

From the MAGE-OM documentation:

Association between the manufactured array and the information on that manufacture.

$val = $array->setInformation($val)

The restricted setter method for the "information" association.

Input parameters: the value to which the "information" association will be set : one of the accepted enumerated values.

Return value: the current value of the "information" 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::Array::ArrayManufacture"

$val = $array->getInformation()

The restricted getter method for the "information" association.

Input parameters: none

Return value: the current value of the "information" association : an instance of type "Bio::MAGE::Array::ArrayManufacture".

Side effects: none

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

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 = $array->setPropertySets($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 = $array->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 = $array->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"

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 = $array->setDescriptions($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 = $array->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 = $array->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 = $array->setSecurity($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 = $array->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

arrayManufactureDeviations

Methods for the "arrayManufactureDeviations" association.

From the MAGE-OM documentation:

Association to classes to describe deviations from the ArrayDesign.

$array_ref = $array->setArrayManufactureDeviations($array_ref)

The restricted setter method for the "arrayManufactureDeviations" association.

Input parameters: the value to which the "arrayManufactureDeviations" association will be set : a reference to an array of objects of type "Bio::MAGE::Array::ArrayManufactureDeviation"

Return value: the current value of the "arrayManufactureDeviations" association : a reference to an array of objects of type "Bio::MAGE::Array::ArrayManufactureDeviation"

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::Array::ArrayManufactureDeviation" instances

$array_ref = $array->getArrayManufactureDeviations()

The restricted getter method for the "arrayManufactureDeviations" association.

Input parameters: none

Return value: the current value of the "arrayManufactureDeviations" association : a reference to an array of objects of type "Bio::MAGE::Array::ArrayManufactureDeviation"

Side effects: none

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

$val = $array->addArrayManufactureDeviations(@vals)

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

Input parameters: the list of values @vals to add to the arrayManufactureDeviations 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::Array::ArrayManufactureDeviation"

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.

AUTHOR

Jason E. Stewart (jasons 'at' cpan 'dot' org)

POD ERRORS

Hey! The above document had some coding errors, which are explained below:

Around line 484:

'=item' outside of any '=over'

Around line 569:

You forgot a '=back' before '=head2'

Around line 1029:

Expected '=item 2'

Around line 1034:

Expected '=item 3'

Around line 1039:

Expected '=item 4'