$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::ArrayDesign::PhysicalArrayDesign" has the following attribute accessor methods:
numberOfFeatures
Methods for the "numberOfFeatures" attribute.
From the MAGE-OM documentation:
The number of features for this array
$val = $physicalarraydesign->setNumberOfFeatures($val)
The restricted setter method for the "numberOfFeatures" attribute.
Input parameters: the value to which the "numberOfFeatures" attribute will be set
Return value: the current value of the "numberOfFeatures" attribute
Side effects: none
Exceptions: will call "croak()" if no input parameters are specified, or if too many input
parameters are specified
$val = $physicalarraydesign->getNumberOfFeatures()
The restricted getter method for the "numberOfFeatures" attribute.
Input parameters: none
Return value: the current value of the "numberOfFeatures" attribute
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
version
Methods for the "version" attribute.
From the MAGE-OM documentation:
The version of this design.
$val = $physicalarraydesign->setVersion($val)
The restricted setter method for the "version" attribute.
Input parameters: the value to which the "version" attribute will be set
Return value: the current value of the "version" attribute
Side effects: none
Exceptions: will call "croak()" if no input parameters are specified, or if too many input
parameters are specified
$val = $physicalarraydesign->getVersion()
The restricted getter method for the "version" attribute.
Input parameters: none
Return value: the current value of the "version" 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 = $physicalarraydesign->setName($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 = $physicalarraydesign->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
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 = $physicalarraydesign->setIdentifier($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 = $physicalarraydesign->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::ArrayDesign::PhysicalArrayDesign 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 = $physicalarraydesign->setAuditTrail($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 = $physicalarraydesign->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 = $physicalarraydesign->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"
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 = $physicalarraydesign->setPropertySets($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 = $physicalarraydesign->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 = $physicalarraydesign->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"
surfaceType
Methods for the "surfaceType" association.
From the MAGE-OM documentation:
The type of surface from a controlled vocabulary that would include terms such as non-absorptive,
absorptive, etc.
$val = $physicalarraydesign->setSurfaceType($val)
The restricted setter method for the "surfaceType" association.
Input parameters: the value to which the "surfaceType" association will be set : one of the
accepted enumerated values.
Return value: the current value of the "surfaceType" 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 = $physicalarraydesign->getSurfaceType()
The restricted getter method for the "surfaceType" association.
Input parameters: none
Return value: the current value of the "surfaceType" association : an instance of type
"Bio::MAGE::Description::OntologyEntry".
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
designProviders
Methods for the "designProviders" association.
From the MAGE-OM documentation:
The primary contact for information on the array design
$array_ref = $physicalarraydesign->setDesignProviders($array_ref)
The restricted setter method for the "designProviders" association.
Input parameters: the value to which the "designProviders" association will be set : a reference
to an array of objects of type "Bio::MAGE::AuditAndSecurity::Contact"
Return value: the current value of the "designProviders" association : a reference to an array of
objects of type "Bio::MAGE::AuditAndSecurity::Contact"
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::Contact" instances
$array_ref = $physicalarraydesign->getDesignProviders()
The restricted getter method for the "designProviders" association.
Input parameters: none
Return value: the current value of the "designProviders" association : a reference to an array of
objects of type "Bio::MAGE::AuditAndSecurity::Contact"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $physicalarraydesign->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.
Input parameters: the list of values @vals to add to the designProviders 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::Contact"
reporterGroups
Methods for the "reporterGroups" association.
From the MAGE-OM documentation:
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.
$array_ref = $physicalarraydesign->setReporterGroups($array_ref)
The restricted setter method for the "reporterGroups" association.
Input parameters: the value to which the "reporterGroups" association will be set : a reference
to an array of objects of type "Bio::MAGE::ArrayDesign::ReporterGroup"
Return value: the current value of the "reporterGroups" association : a reference to an array of
objects of type "Bio::MAGE::ArrayDesign::ReporterGroup"
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::ArrayDesign::ReporterGroup" instances
$array_ref = $physicalarraydesign->getReporterGroups()
The restricted getter method for the "reporterGroups" association.
Input parameters: none
Return value: the current value of the "reporterGroups" association : a reference to an array of
objects of type "Bio::MAGE::ArrayDesign::ReporterGroup"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $physicalarraydesign->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.
Input parameters: the list of values @vals to add to the reporterGroups 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::ArrayDesign::ReporterGroup"
protocolApplications
Methods for the "protocolApplications" association.
From the MAGE-OM documentation:
Describes the application of any protocols, such as the methodology used to pick oligos, in the
design of the array.
$array_ref = $physicalarraydesign->setProtocolApplications($array_ref)
The restricted setter method for the "protocolApplications" association.
Input parameters: the value to which the "protocolApplications" association will be set : a
reference to an array of objects of type "Bio::MAGE::Protocol::ProtocolApplication"
Return value: the current value of the "protocolApplications" association : a reference to an
array of objects of type "Bio::MAGE::Protocol::ProtocolApplication"
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::Protocol::ProtocolApplication" instances
$array_ref = $physicalarraydesign->getProtocolApplications()
The restricted getter method for the "protocolApplications" association.
Input parameters: none
Return value: the current value of the "protocolApplications" association : a reference to an
array of objects of type "Bio::MAGE::Protocol::ProtocolApplication"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $physicalarraydesign->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.
Input parameters: the list of values @vals to add to the protocolApplications 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::Protocol::ProtocolApplication"
zoneGroups
Methods for the "zoneGroups" association.
From the MAGE-OM documentation:
In the case where the array design is specified by one or more zones, allows specifying where those
zones are located.
$array_ref = $physicalarraydesign->setZoneGroups($array_ref)
The restricted setter method for the "zoneGroups" association.
Input parameters: the value to which the "zoneGroups" association will be set : a reference to an
array of objects of type "Bio::MAGE::ArrayDesign::ZoneGroup"
Return value: the current value of the "zoneGroups" association : a reference to an array of
objects of type "Bio::MAGE::ArrayDesign::ZoneGroup"
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::ArrayDesign::ZoneGroup" instances
$array_ref = $physicalarraydesign->getZoneGroups()
The restricted getter method for the "zoneGroups" association.
Input parameters: none
Return value: the current value of the "zoneGroups" association : a reference to an array of
objects of type "Bio::MAGE::ArrayDesign::ZoneGroup"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $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.
Input parameters: the list of values @vals to add to the zoneGroups 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::ArrayDesign::ZoneGroup"
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 = $physicalarraydesign->setDescriptions($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 = $physicalarraydesign->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 = $physicalarraydesign->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"
featureGroups
Methods for the "featureGroups" association.
From the MAGE-OM documentation:
The grouping of like Features together. Typically for a physical array design, this will be a single
grouping of features whose type might be PCR 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.
$array_ref = $physicalarraydesign->setFeatureGroups($array_ref)
The restricted setter method for the "featureGroups" association.
Input parameters: the value to which the "featureGroups" association will be set : a reference to
an array of objects of type "Bio::MAGE::ArrayDesign::FeatureGroup"
Return value: the current value of the "featureGroups" association : a reference to an array of
objects of type "Bio::MAGE::ArrayDesign::FeatureGroup"
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::ArrayDesign::FeatureGroup" instances
$array_ref = $physicalarraydesign->getFeatureGroups()
The restricted getter method for the "featureGroups" association.
Input parameters: none
Return value: the current value of the "featureGroups" association : a reference to an array of
objects of type "Bio::MAGE::ArrayDesign::FeatureGroup"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $physicalarraydesign->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.
Input parameters: the list of values @vals to add to the featureGroups 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::ArrayDesign::FeatureGroup"
security
Methods for the "security" association.
From the MAGE-OM documentation:
Information on the security for the instance of the class.
$val = $physicalarraydesign->setSecurity($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 = $physicalarraydesign->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
compositeGroups
Methods for the "compositeGroups" association.
From the MAGE-OM documentation:
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.
$array_ref = $physicalarraydesign->setCompositeGroups($array_ref)
The restricted setter method for the "compositeGroups" association.
Input parameters: the value to which the "compositeGroups" association will be set : a reference
to an array of objects of type "Bio::MAGE::ArrayDesign::CompositeGroup"
Return value: the current value of the "compositeGroups" association : a reference to an array of
objects of type "Bio::MAGE::ArrayDesign::CompositeGroup"
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::ArrayDesign::CompositeGroup" instances
$array_ref = $physicalarraydesign->getCompositeGroups()
The restricted getter method for the "compositeGroups" association.
Input parameters: none
Return value: the current value of the "compositeGroups" association : a reference to an array of
objects of type "Bio::MAGE::ArrayDesign::CompositeGroup"
Side effects: none
Exceptions: will call "croak()" if any input parameters are specified
$val = $physicalarraydesign->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.
Input parameters: the list of values @vals to add to the compositeGroups 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::ArrayDesign::CompositeGroup"
sub initialize {
my $self = shift;
return 1;
}
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