SYNOPSIS

use Bio::MAGE::Array::Fiducial
# creating an empty instance
my $fiducial = Bio::MAGE::Array::Fiducial->new();
# creating an instance with existing data
my $fiducial = Bio::MAGE::Array::Fiducial->new(
position=>$position_ref,
auditTrail=>\@audit_list,
propertySets=>\@namevaluetype_list,
distanceUnit=>$distanceunit_ref,
descriptions=>\@description_list,
security=>$security_ref,
fiducialType=>$ontologyentry_ref,
);
# 'position' association
my $position_ref = $fiducial->position(); # getter
$fiducial->position($position_ref); # setter
# 'auditTrail' association
my $audit_array_ref = $fiducial->auditTrail(); # getter
$fiducial->auditTrail(\@audit_list); # setter
# 'propertySets' association
my $namevaluetype_array_ref = $fiducial->propertySets(); # getter
$fiducial->propertySets(\@namevaluetype_list); # setter
# 'distanceUnit' association
my $distanceunit_ref = $fiducial->distanceUnit(); # getter
$fiducial->distanceUnit($distanceunit_ref); # setter
# 'descriptions' association
my $description_array_ref = $fiducial->descriptions(); # getter
$fiducial->descriptions(\@description_list); # setter
# 'security' association
my $security_ref = $fiducial->security(); # getter
$fiducial->security($security_ref); # setter
# 'fiducialType' association
my $ontologyentry_ref = $fiducial->fiducialType(); # getter
$fiducial->fiducialType($ontologyentry_ref); # setter

DESCRIPTION

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

A marking on the surface of the array that can be used to identify the array's origin, the coordinates of which are the fiducial's centroid.

INHERITANCE

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

• Bio::MAGE::Describable

CLASS METHODS

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

new()

new(%args)

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

• 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".

• position

  Sets the value of the "position" association

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

• 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".

• distanceUnit

  Sets the value of the "distanceUnit" association

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

• 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".

• fiducialType

  Sets the value of the "fiducialType" 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::Array::Fiducial" has the following attribute accessor methods:

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::Fiducial has the following association accessor methods:

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 = $fiducial->setAuditTrail($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 = $fiducial->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 = $fiducial->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"

position

Methods for the "position" association.

From the MAGE-OM documentation:

The position, relative to the upper left corner, of the fiducial

$val = $fiducial->setPosition($val)

The restricted setter method for the "position" association.

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

Return value: the current value of the "position" 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::DesignElement::Position"

$val = $fiducial->getPosition()

The restricted getter method for the "position" association.

Input parameters: none

Return value: the current value of the "position" association : an instance of type "Bio::MAGE::DesignElement::Position".

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 = $fiducial->setPropertySets($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 = $fiducial->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 = $fiducial->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 = $fiducial->setDescriptions($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 = $fiducial->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 = $fiducial->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"

distanceUnit

Methods for the "distanceUnit" association.

From the MAGE-OM documentation:

The units the fiducial is measured in.

$val = $fiducial->setDistanceUnit($val)

The restricted setter method for the "distanceUnit" association.

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

Return value: the current value of the "distanceUnit" 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::Measurement::DistanceUnit"

$val = $fiducial->getDistanceUnit()

The restricted getter method for the "distanceUnit" association.

Input parameters: none

Return value: the current value of the "distanceUnit" association : an instance of type "Bio::MAGE::Measurement::DistanceUnit".

Side effects: none

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

security

Methods for the "security" association.

From the MAGE-OM documentation:

Information on the security for the instance of the class.

$val = $fiducial->setSecurity($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 = $fiducial->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

fiducialType

Methods for the "fiducialType" association.

From the MAGE-OM documentation:

A descriptive string that indicates the type of a fiducial (e.g. the chrome border on an Affymetrix array, a laser ablation mark).

$val = $fiducial->setFiducialType($val)

The restricted setter method for the "fiducialType" association.

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

Return value: the current value of the "fiducialType" 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 = $fiducial->getFiducialType()

The restricted getter method for the "fiducialType" association.

Input parameters: none

Return value: the current value of the "fiducialType" 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.

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 395:

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Around line 480:

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

Around line 508:

Expected '=item 2'

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Expected '=item 3'

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