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.\" ========================================================================
.\"
.IX Title "MAGE::ArrayDesign::PhysicalArrayDesign 3pm"
.TH MAGE::ArrayDesign::PhysicalArrayDesign 3pm "2003-11-12" "perl v5.34.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "Bio::MAGE::ArrayDesign::PhysicalArrayDesign"
.IX Header "Bio::MAGE::ArrayDesign::PhysicalArrayDesign"
.SS "\s-1SYNOPSIS\s0"
.IX Subsection "SYNOPSIS"
.Vb 1
\&  use Bio::MAGE::ArrayDesign::PhysicalArrayDesign;
\&
\&    # creating an empty instance
\&  my $physicalarraydesign = Bio::MAGE::ArrayDesign::PhysicalArrayDesign\->new();
\&
\&    # creating an already populated instance
\&  my $physicalarraydesign = Bio::MAGE::ArrayDesign::PhysicalArrayDesign\->new(surfaceType=>$surfaceType_value,
\&                        zoneGroups=>$zoneGroups_value);
\&
\&    # setting and retrieving object associations
\&  my $surfaceType_val = $physicalarraydesign\->surfaceType();
\&  $physicalarraydesign\->surfaceType($value);
\&
\&  my $zoneGroups_val = $physicalarraydesign\->zoneGroups();
\&  $physicalarraydesign\->zoneGroups($value);
.Ve
.SS "\s-1DESCRIPTION\s0"
.IX Subsection "DESCRIPTION"
From the MAGE-OM documentation for the \f(CW\*(C`PhysicalArrayDesign\*(C'\fR class:
.PP
A design that is expected to be used to manufacture physical arrays.
.SS "\s-1INHERITANCE\s0"
.IX Subsection "INHERITANCE"
Bio::MAGE::ArrayDesign::PhysicalArrayDesign has the following super classes
.IP "\(bu" 4
Bio::MAGE::ArrayDesign::ArrayDesign
.SS "\s-1CLASS METHODS\s0"
.IX Subsection "CLASS METHODS"
The following methods can all be called without first having an
instance of the class via the Bio::MAGE::ArrayDesign::PhysicalArrayDesign\->\fBmethodname()\fR syntax.
.IP "\fBnew()\fR" 4
.IX Item "new()"
.PD 0
.IP "new(%args)" 4
.IX Item "new(%args)"
.PD
The object constructor \f(CW\*(C`new()\*(C'\fR accepts the following optional
named-value style arguments:
.RS 4
.IP "\(bu" 4
surfaceType
.Sp
Sets the value of the surfaceType association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::ArrayDesign::PhysicalArrayDesign\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`OntologyEntry\*(C'\fR.
.IP "\(bu" 4
zoneGroups
.Sp
Sets the value of the zoneGroups association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::ArrayDesign::PhysicalArrayDesign\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`ZoneGroup\*(C'\fR.
.IP "\(bu" 4
version
.Sp
Sets the value of the version attribute (this attribute was inherited
from class \f(CW\*(C`Bio::MAGE::ArrayDesign::ArrayDesign\*(C'\fR).
.IP "\(bu" 4
numberOfFeatures
.Sp
Sets the value of the numberOfFeatures attribute (this attribute was inherited
from class \f(CW\*(C`Bio::MAGE::ArrayDesign::ArrayDesign\*(C'\fR).
.IP "\(bu" 4
reporterGroups
.Sp
Sets the value of the reporterGroups association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::ArrayDesign::ArrayDesign\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`ReporterGroup\*(C'\fR.
.IP "\(bu" 4
protocolApplications
.Sp
Sets the value of the protocolApplications association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::ArrayDesign::ArrayDesign\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`ProtocolApplication\*(C'\fR.
.IP "\(bu" 4
featureGroups
.Sp
Sets the value of the featureGroups association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::ArrayDesign::ArrayDesign\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`FeatureGroup\*(C'\fR.
.IP "\(bu" 4
designProviders
.Sp
Sets the value of the designProviders association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::ArrayDesign::ArrayDesign\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`Contact\*(C'\fR.
.IP "\(bu" 4
compositeGroups
.Sp
Sets the value of the compositeGroups association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::ArrayDesign::ArrayDesign\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`CompositeGroup\*(C'\fR.
.IP "\(bu" 4
identifier
.Sp
Sets the value of the identifier attribute (this attribute was inherited
from class \f(CW\*(C`Bio::MAGE::Identifiable\*(C'\fR).
.IP "\(bu" 4
name
.Sp
Sets the value of the name attribute (this attribute was inherited
from class \f(CW\*(C`Bio::MAGE::Identifiable\*(C'\fR).
.IP "\(bu" 4
descriptions
.Sp
Sets the value of the descriptions association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::Describable\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`Description\*(C'\fR.
.IP "\(bu" 4
security
.Sp
Sets the value of the security association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::Describable\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`Security\*(C'\fR.
.IP "\(bu" 4
auditTrail
.Sp
Sets the value of the auditTrail association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::Describable\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`Audit\*(C'\fR.
.IP "\(bu" 4
propertySets
.Sp
Sets the value of the propertySets association (this association was inherited
from class \f(CW\*(C`Bio::MAGE::Extendable\*(C'\fR).
.Sp
The value will be of type \f(CW\*(C`NameValueType\*(C'\fR.
.RE
.RS 4
.RE
.ie n .IP "$obj\->set_slots(%parameters)" 4
.el .IP "\f(CW$obj\fR\->set_slots(%parameters)" 4
.IX Item "$obj->set_slots(%parameters)"
.PD 0
.ie n .IP "$obj\->set_slots(\e@name_list, \e@value_list)" 4
.el .IP "\f(CW$obj\fR\->set_slots(\e@name_list, \e@value_list)" 4
.IX Item "$obj->set_slots(@name_list, @value_list)"
.PD
The \f(CW\*(C`set_slots()\*(C'\fR 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.
.Sp
\&\fBReturn value\fR: none
.Sp
\&\fBSide effects\fR: will call \f(CW\*(C`croak()\*(C'\fR if a slot_name is used that the class
does not define.
.ie n .IP "$obj\->get_slots(@name_list)" 4
.el .IP "\f(CW$obj\fR\->get_slots(@name_list)" 4
.IX Item "$obj->get_slots(@name_list)"
The \f(CW\*(C`get_slots()\*(C'\fR method is used to get the values of a number of
slots at the same time.
.Sp
\&\fBReturn value\fR: a list of instance objects
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $obj\->set_slot($name,$val)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->set_slot($name,$val)" 4
.IX Item "$val = $obj->set_slot($name,$val)"
The \f(CW\*(C`set_slot()\*(C'\fR method sets the slot \f(CW$name\fR to the value \f(CW$val\fR
.Sp
\&\fBReturn value\fR: the new value of the slot, i.e. \f(CW$val\fR
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$val = $obj\->get_slot($name)" 4
.el .IP "\f(CW$val\fR = \f(CW$obj\fR\->get_slot($name)" 4
.IX Item "$val = $obj->get_slot($name)"
The \f(CW\*(C`get_slot()\*(C'\fR method is used to get the values of a number of
slots at the same time.
.Sp
\&\fBReturn value\fR: a single slot value, or undef if the slot has not been
initialized.
.Sp
\&\fBSide effects\fR: none
.ie n .IP "@names = $obj\->\fBget_slot_names()\fR" 4
.el .IP "\f(CW@names\fR = \f(CW$obj\fR\->\fBget_slot_names()\fR" 4
.IX Item "@names = $obj->get_slot_names()"
The \f(CW\*(C`get_slot_names()\*(C'\fR method is used to retrieve the name of all
slots defined for a given object.
.Sp
\&\fBReturn value\fR: a single slot value, or undef if the slot has not been
initialized.
.Sp
\&\fBSide effects\fR: none
.ie n .IP "$name = \fBclass_name()\fR" 4
.el .IP "\f(CW$name\fR = \fBclass_name()\fR" 4
.IX Item "$name = class_name()"
Returns the full class name for this class, Bio::MAGE::ArrayDesign::PhysicalArrayDesign.
.ie n .IP "$package_name = \fBpackage()\fR" 4
.el .IP "\f(CW$package_name\fR = \fBpackage()\fR" 4
.IX Item "$package_name = package()"
Returns the unresolved package name (i.e. no 'Bio::MAGE::') of the
package that contains class, Bio::MAGE::ArrayDesign::PhysicalArrayDesign.
.ie n .IP "@classes = \fBsubclasses()\fR" 4
.el .IP "\f(CW@classes\fR = \fBsubclasses()\fR" 4
.IX Item "@classes = subclasses()"
returns the list of subclasses for this class.
.ie n .IP "@classes = \fBsuperclasses()\fR" 4
.el .IP "\f(CW@classes\fR = \fBsuperclasses()\fR" 4
.IX Item "@classes = superclasses()"
returns the list of superclasses for this class.
.ie n .IP "@methods = \fBattribute_methods()\fR" 4
.el .IP "\f(CW@methods\fR = \fBattribute_methods()\fR" 4
.IX Item "@methods = attribute_methods()"
returns the list of attribute accessor methods for this class.
.ie n .IP "@methods = \fBassociation_methods()\fR" 4
.el .IP "\f(CW@methods\fR = \fBassociation_methods()\fR" 4
.IX Item "@methods = association_methods()"
returns the list of association accessor methods for this class.
.ie n .IP "%assns = \fBassociations()\fR" 4
.el .IP "\f(CW%assns\fR = \fBassociations()\fR" 4
.IX Item "%assns = associations()"
returns the association meta-information in a hash where the keys are
the association names and the values are \f(CW\*(C`Bio::MAGE::Association\*(C'\fR
objects that provide the meta-information for the association.
.SS "\s-1ATTRIBUTES\s0"
.IX Subsection "ATTRIBUTES"
Attributes are simple data types that belong to a single instance of a
class. In the Perl implementation of the MAGE-OM classes, the
interface to attributes is implemented using separate setter and
getter methods for each attribute.
.PP
Bio::MAGE::ArrayDesign::PhysicalArrayDesign: has the following attribute accessor methods:
.Sp
.RS 4
Attributes Inherited from Bio::MAGE::ArrayDesign::ArrayDesign
.Sp
version
.Sp
From the MAGE-OM documentation for the \f(CW\*(C`version\*(C'\fR attribute:
.Sp
The version of this design.
.ie n .IP "$val = $arraydesign\->setVersion($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$arraydesign\fR\->setVersion($val)" 4
.IX Item "$val = $arraydesign->setVersion($val)"
The restricted setter method for the version attribute.
.Sp
Input parameters: the value to which the version attribute will be set
.Sp
Return value: the current value of the version attribute
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified
.ie n .IP "$val = $arraydesign\->\fBgetVersion()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$arraydesign\fR\->\fBgetVersion()\fR" 4
.IX Item "$val = $arraydesign->getVersion()"
The restricted getter method for the version attribute.
.Sp
Input parameters: none
.Sp
Return value: the current value of the version attribute
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.RE
.RS 4
.Sp
numberOfFeatures
.Sp
From the MAGE-OM documentation for the \f(CW\*(C`numberOfFeatures\*(C'\fR attribute:
.Sp
The number of features for this array
.ie n .IP "$val = $arraydesign\->setNumberOfFeatures($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$arraydesign\fR\->setNumberOfFeatures($val)" 4
.IX Item "$val = $arraydesign->setNumberOfFeatures($val)"
The restricted setter method for the numberOfFeatures attribute.
.Sp
Input parameters: the value to which the numberOfFeatures attribute will be set
.Sp
Return value: the current value of the numberOfFeatures attribute
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified
.ie n .IP "$val = $arraydesign\->\fBgetNumberOfFeatures()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$arraydesign\fR\->\fBgetNumberOfFeatures()\fR" 4
.IX Item "$val = $arraydesign->getNumberOfFeatures()"
The restricted getter method for the numberOfFeatures attribute.
.Sp
Input parameters: none
.Sp
Return value: the current value of the numberOfFeatures attribute
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.RE
.RS 4
.Sp
Attributes Inherited from Bio::MAGE::Identifiable
.Sp
identifier
.Sp
From the MAGE-OM documentation for the \f(CW\*(C`identifier\*(C'\fR attribute:
.Sp
An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
.ie n .IP "$val = $identifiable\->setIdentifier($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$identifiable\fR\->setIdentifier($val)" 4
.IX Item "$val = $identifiable->setIdentifier($val)"
The restricted setter method for the identifier attribute.
.Sp
Input parameters: the value to which the identifier attribute will be set
.Sp
Return value: the current value of the identifier attribute
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified
.ie n .IP "$val = $identifiable\->\fBgetIdentifier()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$identifiable\fR\->\fBgetIdentifier()\fR" 4
.IX Item "$val = $identifiable->getIdentifier()"
The restricted getter method for the identifier attribute.
.Sp
Input parameters: none
.Sp
Return value: the current value of the identifier attribute
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.RE
.RS 4
.Sp
name
.Sp
From the MAGE-OM documentation for the \f(CW\*(C`name\*(C'\fR attribute:
.Sp
The potentially ambiguous common identifier.
.ie n .IP "$val = $identifiable\->setName($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$identifiable\fR\->setName($val)" 4
.IX Item "$val = $identifiable->setName($val)"
The restricted setter method for the name attribute.
.Sp
Input parameters: the value to which the name attribute will be set
.Sp
Return value: the current value of the name attribute
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified
.ie n .IP "$val = $identifiable\->\fBgetName()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$identifiable\fR\->\fBgetName()\fR" 4
.IX Item "$val = $identifiable->getName()"
The restricted getter method for the name attribute.
.Sp
Input parameters: none
.Sp
Return value: the current value of the name attribute
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.RE
.RS 4
.RE
.SS "\s-1ASSOCIATIONS\s0"
.IX Subsection "ASSOCIATIONS"
Associations are references to other class objects which can be shared
by multiple class instances at the same time. In the Perl
implementation of MAGE-OM classes, associations are implemented using
three separate methods:
.IP "get*" 4
.IX Item "get*"
Retrieves the current value. If the association has list cardinality,
an array reference is returned.
.IP "set*" 4
.IX Item "set*"
Sets the current value \fBreplacing\fR any existing value. If the
association has list cardinality, the argument must be an array
reference. Unless you know what you are doing, you probably should be
using the add* methods.
.IP "add*" 4
.IX Item "add*"
This method exists only for associations with list cardinality. It
appends a list of objects to any values that may already be stored in
the association.
.PP
Bio::MAGE::ArrayDesign::PhysicalArrayDesign: has the following association accessor methods:
.IP "surfaceType" 4
.IX Item "surfaceType"
From the MAGE-OM documentation for the \f(CW\*(C`surfaceType\*(C'\fR association:
.Sp
The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.
.RS 4
.ie n .IP "$val = $physicalarraydesign\->setSurfaceType($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$physicalarraydesign\fR\->setSurfaceType($val)" 4
.IX Item "$val = $physicalarraydesign->setSurfaceType($val)"
The restricted setter method for the surfaceType association.
.Sp
Input parameters: the value to which the surfaceType association will be set : an instance of type \f(CW\*(C`Bio::MAGE::Description::OntologyEntry\*(C'\fR.
.Sp
Return value: the current value of the surfaceType association : an instance of type \f(CW\*(C`Bio::MAGE::Description::OntologyEntry\*(C'\fR.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$val\fR is not an instance of class \f(CW\*(C`Bio::MAGE::Description::OntologyEntry\*(C'\fR
.ie n .IP "$val = $physicalarraydesign\->\fBgetSurfaceType()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$physicalarraydesign\fR\->\fBgetSurfaceType()\fR" 4
.IX Item "$val = $physicalarraydesign->getSurfaceType()"
The restricted getter method for the surfaceType association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the surfaceType association : an instance of type \f(CW\*(C`Bio::MAGE::Description::OntologyEntry\*(C'\fR.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.RE
.RS 4
.RE
.IP "zoneGroups" 4
.IX Item "zoneGroups"
From the MAGE-OM documentation for the \f(CW\*(C`zoneGroups\*(C'\fR association:
.Sp
In the case where the array design is specified by one or more zones, allows specifying where those zones are located.
.RS 4
.ie n .IP "$array_ref = $physicalarraydesign\->setZoneGroups($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$physicalarraydesign\fR\->setZoneGroups($array_ref)" 4
.IX Item "$array_ref = $physicalarraydesign->setZoneGroups($array_ref)"
The restricted setter method for the zoneGroups association.
.Sp
Input parameters: the value to which the zoneGroups association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::ZoneGroup\*(C'\fR
.Sp
Return value: the current value of the zoneGroups association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::ZoneGroup\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::ArrayDesign::ZoneGroup\*(C'\fR instances
.ie n .IP "$array_ref = $physicalarraydesign\->\fBgetZoneGroups()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$physicalarraydesign\fR\->\fBgetZoneGroups()\fR" 4
.IX Item "$array_ref = $physicalarraydesign->getZoneGroups()"
The restricted getter method for the zoneGroups association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the zoneGroups association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::ZoneGroup\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$physicalarraydesign\->addZoneGroups(@vals)" 4
.el .IP "\f(CW$physicalarraydesign\fR\->addZoneGroups(@vals)" 4
.IX Item "$physicalarraydesign->addZoneGroups(@vals)"
Because the zoneGroups association has list cardinality, it may store more
than one value. This method adds the current list of objects in the zoneGroups
association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the zoneGroups
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::ArrayDesign::ZoneGroup\*(C'\fR
.RE
.RS 4
.Sp
Associations Inherited from Bio::MAGE::ArrayDesign::ArrayDesign
.RE
.IP "protocolApplications" 4
.IX Item "protocolApplications"
From the MAGE-OM documentation for the \f(CW\*(C`protocolApplications\*(C'\fR association:
.Sp
Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.
.RS 4
.ie n .IP "$array_ref = $arraydesign\->setProtocolApplications($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$arraydesign\fR\->setProtocolApplications($array_ref)" 4
.IX Item "$array_ref = $arraydesign->setProtocolApplications($array_ref)"
The restricted setter method for the protocolApplications association.
.Sp
Input parameters: the value to which the protocolApplications association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::Protocol::ProtocolApplication\*(C'\fR
.Sp
Return value: the current value of the protocolApplications association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::Protocol::ProtocolApplication\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::Protocol::ProtocolApplication\*(C'\fR instances
.ie n .IP "$array_ref = $arraydesign\->\fBgetProtocolApplications()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$arraydesign\fR\->\fBgetProtocolApplications()\fR" 4
.IX Item "$array_ref = $arraydesign->getProtocolApplications()"
The restricted getter method for the protocolApplications association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the protocolApplications association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::Protocol::ProtocolApplication\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$arraydesign\->addProtocolApplications(@vals)" 4
.el .IP "\f(CW$arraydesign\fR\->addProtocolApplications(@vals)" 4
.IX Item "$arraydesign->addProtocolApplications(@vals)"
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.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the protocolApplications
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::Protocol::ProtocolApplication\*(C'\fR
.RE
.RS 4
.RE
.IP "compositeGroups" 4
.IX Item "compositeGroups"
From the MAGE-OM documentation for the \f(CW\*(C`compositeGroups\*(C'\fR association:
.Sp
The grouping of like CompositeSequence together.  If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple CompositeGroups to segregate the technology types.
.RS 4
.ie n .IP "$array_ref = $arraydesign\->setCompositeGroups($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$arraydesign\fR\->setCompositeGroups($array_ref)" 4
.IX Item "$array_ref = $arraydesign->setCompositeGroups($array_ref)"
The restricted setter method for the compositeGroups association.
.Sp
Input parameters: the value to which the compositeGroups association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::CompositeGroup\*(C'\fR
.Sp
Return value: the current value of the compositeGroups association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::CompositeGroup\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::ArrayDesign::CompositeGroup\*(C'\fR instances
.ie n .IP "$array_ref = $arraydesign\->\fBgetCompositeGroups()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$arraydesign\fR\->\fBgetCompositeGroups()\fR" 4
.IX Item "$array_ref = $arraydesign->getCompositeGroups()"
The restricted getter method for the compositeGroups association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the compositeGroups association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::CompositeGroup\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$arraydesign\->addCompositeGroups(@vals)" 4
.el .IP "\f(CW$arraydesign\fR\->addCompositeGroups(@vals)" 4
.IX Item "$arraydesign->addCompositeGroups(@vals)"
Because the compositeGroups association has list cardinality, it may store more
than one value. This method adds the current list of objects in the compositeGroups
association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the compositeGroups
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::ArrayDesign::CompositeGroup\*(C'\fR
.RE
.RS 4
.RE
.IP "designProviders" 4
.IX Item "designProviders"
From the MAGE-OM documentation for the \f(CW\*(C`designProviders\*(C'\fR association:
.Sp
The primary contact for information on the array design
.RS 4
.ie n .IP "$array_ref = $arraydesign\->setDesignProviders($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$arraydesign\fR\->setDesignProviders($array_ref)" 4
.IX Item "$array_ref = $arraydesign->setDesignProviders($array_ref)"
The restricted setter method for the designProviders association.
.Sp
Input parameters: the value to which the designProviders association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Contact\*(C'\fR
.Sp
Return value: the current value of the designProviders association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Contact\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Contact\*(C'\fR instances
.ie n .IP "$array_ref = $arraydesign\->\fBgetDesignProviders()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$arraydesign\fR\->\fBgetDesignProviders()\fR" 4
.IX Item "$array_ref = $arraydesign->getDesignProviders()"
The restricted getter method for the designProviders association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the designProviders association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Contact\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$arraydesign\->addDesignProviders(@vals)" 4
.el .IP "\f(CW$arraydesign\fR\->addDesignProviders(@vals)" 4
.IX Item "$arraydesign->addDesignProviders(@vals)"
Because the designProviders association has list cardinality, it may store more
than one value. This method adds the current list of objects in the designProviders
association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the designProviders
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Contact\*(C'\fR
.RE
.RS 4
.RE
.IP "reporterGroups" 4
.IX Item "reporterGroups"
From the MAGE-OM documentation for the \f(CW\*(C`reporterGroups\*(C'\fR association:
.Sp
The grouping of like Reporter together.  If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple ReporterGroups to segregate the technology types.
.RS 4
.ie n .IP "$array_ref = $arraydesign\->setReporterGroups($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$arraydesign\fR\->setReporterGroups($array_ref)" 4
.IX Item "$array_ref = $arraydesign->setReporterGroups($array_ref)"
The restricted setter method for the reporterGroups association.
.Sp
Input parameters: the value to which the reporterGroups association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::ReporterGroup\*(C'\fR
.Sp
Return value: the current value of the reporterGroups association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::ReporterGroup\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::ArrayDesign::ReporterGroup\*(C'\fR instances
.ie n .IP "$array_ref = $arraydesign\->\fBgetReporterGroups()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$arraydesign\fR\->\fBgetReporterGroups()\fR" 4
.IX Item "$array_ref = $arraydesign->getReporterGroups()"
The restricted getter method for the reporterGroups association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the reporterGroups association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::ReporterGroup\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$arraydesign\->addReporterGroups(@vals)" 4
.el .IP "\f(CW$arraydesign\fR\->addReporterGroups(@vals)" 4
.IX Item "$arraydesign->addReporterGroups(@vals)"
Because the reporterGroups association has list cardinality, it may store more
than one value. This method adds the current list of objects in the reporterGroups
association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the reporterGroups
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::ArrayDesign::ReporterGroup\*(C'\fR
.RE
.RS 4
.RE
.IP "featureGroups" 4
.IX Item "featureGroups"
From the MAGE-OM documentation for the \f(CW\*(C`featureGroups\*(C'\fR association:
.Sp
The grouping of like Features together.  Typically for a physical array design, this will be a single grouping of features whose type might be \s-1PCR\s0 Product or Oligo.  If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple FeatureGroups to segregate the technology types.
.RS 4
.ie n .IP "$array_ref = $arraydesign\->setFeatureGroups($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$arraydesign\fR\->setFeatureGroups($array_ref)" 4
.IX Item "$array_ref = $arraydesign->setFeatureGroups($array_ref)"
The restricted setter method for the featureGroups association.
.Sp
Input parameters: the value to which the featureGroups association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::FeatureGroup\*(C'\fR
.Sp
Return value: the current value of the featureGroups association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::FeatureGroup\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::ArrayDesign::FeatureGroup\*(C'\fR instances
.ie n .IP "$array_ref = $arraydesign\->\fBgetFeatureGroups()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$arraydesign\fR\->\fBgetFeatureGroups()\fR" 4
.IX Item "$array_ref = $arraydesign->getFeatureGroups()"
The restricted getter method for the featureGroups association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the featureGroups association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::ArrayDesign::FeatureGroup\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$arraydesign\->addFeatureGroups(@vals)" 4
.el .IP "\f(CW$arraydesign\fR\->addFeatureGroups(@vals)" 4
.IX Item "$arraydesign->addFeatureGroups(@vals)"
Because the featureGroups association has list cardinality, it may store more
than one value. This method adds the current list of objects in the featureGroups
association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the featureGroups
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::ArrayDesign::FeatureGroup\*(C'\fR
.RE
.RS 4
.Sp
Associations Inherited from Bio::MAGE::Describable
.RE
.IP "security" 4
.IX Item "security"
From the MAGE-OM documentation for the \f(CW\*(C`security\*(C'\fR association:
.Sp
Information on the security for the instance of the class.
.RS 4
.ie n .IP "$val = $describable\->setSecurity($val)" 4
.el .IP "\f(CW$val\fR = \f(CW$describable\fR\->setSecurity($val)" 4
.IX Item "$val = $describable->setSecurity($val)"
The restricted setter method for the security association.
.Sp
Input parameters: the value to which the security association will be set : an instance of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Security\*(C'\fR.
.Sp
Return value: the current value of the security association : an instance of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Security\*(C'\fR.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$val\fR is not an instance of class \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Security\*(C'\fR
.ie n .IP "$val = $describable\->\fBgetSecurity()\fR" 4
.el .IP "\f(CW$val\fR = \f(CW$describable\fR\->\fBgetSecurity()\fR" 4
.IX Item "$val = $describable->getSecurity()"
The restricted getter method for the security association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the security association : an instance of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Security\*(C'\fR.
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.RE
.RS 4
.RE
.IP "auditTrail" 4
.IX Item "auditTrail"
From the MAGE-OM documentation for the \f(CW\*(C`auditTrail\*(C'\fR association:
.Sp
A list of Audit instances that track changes to the instance of Describable.
.RS 4
.ie n .IP "$array_ref = $describable\->setAuditTrail($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$describable\fR\->setAuditTrail($array_ref)" 4
.IX Item "$array_ref = $describable->setAuditTrail($array_ref)"
The restricted setter method for the auditTrail association.
.Sp
Input parameters: the value to which the auditTrail association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR
.Sp
Return value: the current value of the auditTrail association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR instances
.ie n .IP "$array_ref = $describable\->\fBgetAuditTrail()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$describable\fR\->\fBgetAuditTrail()\fR" 4
.IX Item "$array_ref = $describable->getAuditTrail()"
The restricted getter method for the auditTrail association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the auditTrail association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$describable\->addAuditTrail(@vals)" 4
.el .IP "\f(CW$describable\fR\->addAuditTrail(@vals)" 4
.IX Item "$describable->addAuditTrail(@vals)"
Because the auditTrail association has list cardinality, it may store more
than one value. This method adds the current list of objects in the auditTrail
association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the auditTrail
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::AuditAndSecurity::Audit\*(C'\fR
.RE
.RS 4
.RE
.IP "descriptions" 4
.IX Item "descriptions"
From the MAGE-OM documentation for the \f(CW\*(C`descriptions\*(C'\fR association:
.Sp
Free hand text descriptions.  Makes available the associations of Description to an instance of Describable.
.RS 4
.ie n .IP "$array_ref = $describable\->setDescriptions($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$describable\fR\->setDescriptions($array_ref)" 4
.IX Item "$array_ref = $describable->setDescriptions($array_ref)"
The restricted setter method for the descriptions association.
.Sp
Input parameters: the value to which the descriptions association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR
.Sp
Return value: the current value of the descriptions association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR instances
.ie n .IP "$array_ref = $describable\->\fBgetDescriptions()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$describable\fR\->\fBgetDescriptions()\fR" 4
.IX Item "$array_ref = $describable->getDescriptions()"
The restricted getter method for the descriptions association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the descriptions association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$describable\->addDescriptions(@vals)" 4
.el .IP "\f(CW$describable\fR\->addDescriptions(@vals)" 4
.IX Item "$describable->addDescriptions(@vals)"
Because the descriptions association has list cardinality, it may store more
than one value. This method adds the current list of objects in the descriptions
association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the descriptions
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::Description::Description\*(C'\fR
.RE
.RS 4
.Sp
Associations Inherited from Bio::MAGE::Extendable
.RE
.IP "propertySets" 4
.IX Item "propertySets"
From the MAGE-OM documentation for the \f(CW\*(C`propertySets\*(C'\fR association:
.Sp
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.
.RS 4
.ie n .IP "$array_ref = $extendable\->setPropertySets($array_ref)" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$extendable\fR\->setPropertySets($array_ref)" 4
.IX Item "$array_ref = $extendable->setPropertySets($array_ref)"
The restricted setter method for the propertySets association.
.Sp
Input parameters: the value to which the propertySets association will be set : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR
.Sp
Return value: the current value of the propertySets association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified, or
if too many input parameters are specified , or if \f(CW$array_ref\fR is not a reference to an array class \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR instances
.ie n .IP "$array_ref = $extendable\->\fBgetPropertySets()\fR" 4
.el .IP "\f(CW$array_ref\fR = \f(CW$extendable\fR\->\fBgetPropertySets()\fR" 4
.IX Item "$array_ref = $extendable->getPropertySets()"
The restricted getter method for the propertySets association.
.Sp
Input parameters: none
.Sp
Return value: the current value of the propertySets association : a reference to an array of objects of type \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if any input parameters are specified
.ie n .IP "$extendable\->addPropertySets(@vals)" 4
.el .IP "\f(CW$extendable\fR\->addPropertySets(@vals)" 4
.IX Item "$extendable->addPropertySets(@vals)"
Because the propertySets association has list cardinality, it may store more
than one value. This method adds the current list of objects in the propertySets
association.
.Sp
Input parameters: the list of values \f(CW@vals\fR to add to the propertySets
association. \fB\s-1NOTE\s0\fR: submitting a single value is permitted.
.Sp
Return value: none
.Sp
Side effects: none
.Sp
Exceptions: will call \f(CW\*(C`croak()\*(C'\fR if no input parameters are specified
, or if any of the objects in \f(CW@vals\fR is not an instance of class \f(CW\*(C`Bio::MAGE::NameValueType\*(C'\fR
.RE
.RS 4
.RE
.SH "BUGS"
.IX Header "BUGS"
Please send bug reports to mged\-mage@lists.sf.net
.SH "AUTHOR"
.IX Header "AUTHOR"
Jason E. Stewart (www.openinformatics.com)
.SH "SEE ALSO"
.IX Header "SEE ALSO"
\&\fBperl\fR\|(1).
.SH "POD ERRORS"
.IX Header "POD ERRORS"
Hey! \fBThe above document had some coding errors, which are explained below:\fR
.IP "Around line 105:" 4
.IX Item "Around line 105:"
\&'=item' outside of any '=over'
.IP "Around line 427:" 4
.IX Item "Around line 427:"
You forgot a '=back' before '=head2'
.IP "Around line 436:" 4
.IX Item "Around line 436:"
You can't have =items (as at line 441) unless the first thing after the =over is an =item