Bio::MAGE::Array::ArrayGroup - Class for the MAGE-OM API

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

       Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)

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

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

           •   width

               Sets the value of the "width" attribute

           •   numArrays

               Sets the value of the "numArrays" attribute

           •   arraySpacingY

               Sets the value of the "arraySpacingY" attribute

           •   orientationMarkPosition

               Sets the value of the "orientationMarkPosition" attribute

           •   arraySpacingX

               Sets the value of the "arraySpacingX" attribute

           •   name

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

           •   barcode

               Sets the value of the "barcode" attribute

           •   orientationMark

               Sets the value of the "orientationMark" attribute

           •   length

               Sets the value of the "length" attribute

           •   identifier

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

           •   arrays

               Sets the value of the "arrays" association

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

           •   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".

           •   substrateType

               Sets the value of the "substrateType" association

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

           •   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".

           •   fiducials

               Sets the value of the "fiducials" association

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

           •   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".

       $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.

           Returnvalue: It returns a reference to an object of the class.

           Sideeffects: 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.

           Returnvalue: A list of the names of all slots defined for this class.

           Sideeffects: 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.

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

       An array package is a physical platform that contains one or more arrays that are separately addressable
       (e.g. several arrays that can be hybridized on a single microscope slide) or a virtual grouping together
       of arrays.

       The array package that has been manufactured has information about where certain artifacts about the
       array are located for scanning and feature extraction purposes.

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

       •   Bio::MAGE::Identifiable

       $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.

           Returnvalue: It returns a reference to an object of the class.

           Sideeffects: 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.

           Returnvalue: none

           Sideeffects: 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.

           Returnvalue: a list of instance objects

           Sideeffects: none

       $val = $obj->set_slot($name,$val)
           The "set_slot()" method sets the slot $name to the value $val

           Returnvalue: the new value of the slot, i.e. $val

           Sideeffects: 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.

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

           Sideeffects: 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::ArrayGroup" has the following attribute accessor methods:

       width
           Methods for the "width" attribute.

           From the MAGE-OM documentation:

           The width of the platform

           $val = $arraygroup->setWidth($val)
               The restricted setter method for the "width" attribute.

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

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

               Side effects: none

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

           $val = $arraygroup->getWidth()
               The restricted getter method for the "width" attribute.

               Input parameters: none

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

               Side effects: none

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

       numArrays
           Methods for the "numArrays" attribute.

           From the MAGE-OM documentation:

           This attribute defines the number of arrays on a chip or a slide.

           $val = $arraygroup->setNumArrays($val)
               The restricted setter method for the "numArrays" attribute.

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

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

               Side effects: none

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

           $val = $arraygroup->getNumArrays()
               The restricted getter method for the "numArrays" attribute.

               Input parameters: none

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

               Side effects: none

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

       arraySpacingY
           Methods for the "arraySpacingY" attribute.

           From the MAGE-OM documentation:

           If there exist more than one array on a slide or a chip, then  the  spacing  between  the  arrays  is
           useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.

           $val = $arraygroup->setArraySpacingY($val)
               The restricted setter method for the "arraySpacingY" attribute.

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

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

               Side effects: none

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

           $val = $arraygroup->getArraySpacingY()
               The restricted getter method for the "arraySpacingY" attribute.

               Input parameters: none

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

               Side effects: none

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

       orientationMarkPosition
           Methods for the "orientationMarkPosition" attribute.

           From the MAGE-OM documentation:

           One of top, bottom, left or right.

           $val = $arraygroup->setOrientationMarkPosition($val)
               The restricted setter method for the "orientationMarkPosition" attribute.

               "orientationMarkPosition" is an enumerated attribute - it can only be set to "undef"  or  one  of
               the following values: top bottom left right

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

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

               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 one of the accepted enumeration  values:  top  bottom
               left right

           $val = $arraygroup->getOrientationMarkPosition()
               The restricted getter method for the "orientationMarkPosition" attribute.

               Input parameters: none

               Return  value: the current value of the "orientationMarkPosition" attribute : an instance of type
               "top bottom left right".

               Side effects: none

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

       arraySpacingX
           Methods for the "arraySpacingX" attribute.

           From the MAGE-OM documentation:

           If there exist more than one array on a slide or a chip, then  the  spacing  between  the  arrays  is
           useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.

           $val = $arraygroup->setArraySpacingX($val)
               The restricted setter method for the "arraySpacingX" attribute.

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

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

               Side effects: none

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

           $val = $arraygroup->getArraySpacingX()
               The restricted getter method for the "arraySpacingX" attribute.

               Input parameters: none

               Return value: the current value of the "arraySpacingX" 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 = $arraygroup->setName($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 = $arraygroup->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

       barcode
           Methods for the "barcode" attribute.

           From the MAGE-OM documentation:

           Identifier for the ArrayGroup.

           $val = $arraygroup->setBarcode($val)
               The restricted setter method for the "barcode" attribute.

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

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

               Side effects: none

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

           $val = $arraygroup->getBarcode()
               The restricted getter method for the "barcode" attribute.

               Input parameters: none

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

               Side effects: none

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

       orientationMark
           Methods for the "orientationMark" attribute.

           From the MAGE-OM documentation:

           For a human to determine where the top left side of the array is, such as a barcode or  frosted  side
           of the glass, etc.

           $val = $arraygroup->setOrientationMark($val)
               The restricted setter method for the "orientationMark" attribute.

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

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

               Side effects: none

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

           $val = $arraygroup->getOrientationMark()
               The restricted getter method for the "orientationMark" attribute.

               Input parameters: none

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

               Side effects: none

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

       length
           Methods for the "length" attribute.

           From the MAGE-OM documentation:

           The length of the platform.

           $val = $arraygroup->setLength($val)
               The restricted setter method for the "length" attribute.

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

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

               Side effects: none

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

           $val = $arraygroup->getLength()
               The restricted getter method for the "length" attribute.

               Input parameters: none

               Return value: the current value of the "length" 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 = $arraygroup->setIdentifier($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 = $arraygroup->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

   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::ArrayGroup has the following association accessor methods:

       arrays
           Methods for the "arrays" 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.

           $array_ref = $arraygroup->setArrays($array_ref)
               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"

               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::Array" instances

           $array_ref = $arraygroup->getArrays()
               The restricted getter method for the "arrays" association.

               Input parameters: none

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

               Side effects: none

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

           $val = $arraygroup->addArrays(@vals)
               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.

               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::Array"

       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 = $arraygroup->setAuditTrail($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 = $arraygroup->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 = $arraygroup->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"

       substrateType
           Methods for the "substrateType" association.

           From the MAGE-OM documentation:

           Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that  says  this
           must  be the case.  This association is for scanners to inform them on the possible different formats
           of slides that can contain arrays.

           $val = $arraygroup->setSubstrateType($val)
               The restricted setter method for the "substrateType" association.

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

               Return  value:  the  current  value  of  the  "substrateType"  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 = $arraygroup->getSubstrateType()
               The restricted getter method for the "substrateType" association.

               Input parameters: none

               Return value: the current value  of  the  "substrateType"  association  :  an  instance  of  type
               "Bio::MAGE::Description::OntologyEntry".

               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 = $arraygroup->setPropertySets($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 = $arraygroup->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 = $arraygroup->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"

       fiducials
           Methods for the "fiducials" association.

           From the MAGE-OM documentation:

           Association to the marks on the Array for alignment for the scanner.

           $array_ref = $arraygroup->setFiducials($array_ref)
               The restricted setter method for the "fiducials" association.

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

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

               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::Fiducial" instances

           $array_ref = $arraygroup->getFiducials()
               The restricted getter method for the "fiducials" association.

               Input parameters: none

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

               Side effects: none

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

           $val = $arraygroup->addFiducials(@vals)
               Because  the  fiducials  association has list cardinality, it may store more than one value. This
               method adds the current list of objects in the fiducials association.

               Input parameters: the list of values @vals to add to the fiducials 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::Fiducial"

       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 = $arraygroup->setDescriptions($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 = $arraygroup->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 = $arraygroup->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 unit of the measurement attributes.

           $val = $arraygroup->setDistanceUnit($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 = $arraygroup->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 = $arraygroup->setSecurity($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 = $arraygroup->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

           sub initialize {

             my $self = shift;
             return 1;

           }

       Bio::MAGE::Array::ArrayGroup - Class for the MAGE-OM API

       Hey! Theabovedocumenthadsomecodingerrors,whichareexplainedbelow:

       Around line 526:
           '=item' outside of any '=over'

       Around line 611:
           You forgot a '=back' before '=head2'

       Around line 1363:
           Expected '=item 2'

       Around line 1368:
           Expected '=item 3'

       Around line 1373:
           Expected '=item 4'

perl v5.32.0                                       2020-11-27                       MAGE::Array::ArrayGroup(3pm)

perl(1).

       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.

       DATACHECKING: No data type checking is made for these methods.

   ATTRIBUTESANDASSOCIATIONS
       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.

           DATACHECKING: 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.

           DATACHECKING:  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.

           DATACHECKING: Ensure that all arguments are of the correct MAGE-OM class.

   GENERICMETHODS
       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.

         use Bio::MAGE::Array::ArrayGroup

         # creating an empty instance
         my $arraygroup = Bio::MAGE::Array::ArrayGroup->new();

         # creating an instance with existing data
         my $arraygroup = Bio::MAGE::Array::ArrayGroup->new(
               width=>$width_val,
               numArrays=>$numarrays_val,
               arraySpacingY=>$arrayspacingy_val,
               orientationMarkPosition=>$orientationmarkposition_val,
               arraySpacingX=>$arrayspacingx_val,
               name=>$name_val,
               barcode=>$barcode_val,
               orientationMark=>$orientationmark_val,
               length=>$length_val,
               identifier=>$identifier_val,
               arrays=>\@array_list,
               substrateType=>$ontologyentry_ref,
               auditTrail=>\@audit_list,
               propertySets=>\@namevaluetype_list,
               fiducials=>\@fiducial_list,
               distanceUnit=>$distanceunit_ref,
               descriptions=>\@description_list,
               security=>$security_ref,
         );

         # 'width' attribute
         my $width_val = $arraygroup->width(); # getter
         $arraygroup->width($value); # setter

         # 'numArrays' attribute
         my $numArrays_val = $arraygroup->numArrays(); # getter
         $arraygroup->numArrays($value); # setter

         # 'arraySpacingY' attribute
         my $arraySpacingY_val = $arraygroup->arraySpacingY(); # getter
         $arraygroup->arraySpacingY($value); # setter

         # 'orientationMarkPosition' attribute
         my $orientationMarkPosition_val = $arraygroup->orientationMarkPosition(); # getter
         $arraygroup->orientationMarkPosition($value); # setter

         # 'arraySpacingX' attribute
         my $arraySpacingX_val = $arraygroup->arraySpacingX(); # getter
         $arraygroup->arraySpacingX($value); # setter

         # 'name' attribute
         my $name_val = $arraygroup->name(); # getter
         $arraygroup->name($value); # setter

         # 'barcode' attribute
         my $barcode_val = $arraygroup->barcode(); # getter
         $arraygroup->barcode($value); # setter

         # 'orientationMark' attribute
         my $orientationMark_val = $arraygroup->orientationMark(); # getter
         $arraygroup->orientationMark($value); # setter

         # 'length' attribute
         my $length_val = $arraygroup->length(); # getter
         $arraygroup->length($value); # setter

         # 'identifier' attribute
         my $identifier_val = $arraygroup->identifier(); # getter
         $arraygroup->identifier($value); # setter

         # 'arrays' association
         my $array_array_ref = $arraygroup->arrays(); # getter
         $arraygroup->arrays(\@array_list); # setter

         # 'substrateType' association
         my $ontologyentry_ref = $arraygroup->substrateType(); # getter
         $arraygroup->substrateType($ontologyentry_ref); # setter

         # 'auditTrail' association
         my $audit_array_ref = $arraygroup->auditTrail(); # getter
         $arraygroup->auditTrail(\@audit_list); # setter

         # 'propertySets' association
         my $namevaluetype_array_ref = $arraygroup->propertySets(); # getter
         $arraygroup->propertySets(\@namevaluetype_list); # setter

         # 'fiducials' association
         my $fiducial_array_ref = $arraygroup->fiducials(); # getter
         $arraygroup->fiducials(\@fiducial_list); # setter

         # 'distanceUnit' association
         my $distanceunit_ref = $arraygroup->distanceUnit(); # getter
         $arraygroup->distanceUnit($distanceunit_ref); # setter

         # 'descriptions' association
         my $description_array_ref = $arraygroup->descriptions(); # getter
         $arraygroup->descriptions(\@description_list); # setter

         # 'security' association
         my $security_ref = $arraygroup->security(); # getter
         $arraygroup->security($security_ref); # setter