NAME¶
Bio::MAGE::ArrayDesign::PhysicalArrayDesign - Class for the MAGE-OM API
SYNOPSIS¶
use Bio::MAGE::ArrayDesign::PhysicalArrayDesign
# creating an empty instance
my $physicalarraydesign = Bio::MAGE::ArrayDesign::PhysicalArrayDesign->new();
# creating an instance with existing data
my $physicalarraydesign = Bio::MAGE::ArrayDesign::PhysicalArrayDesign->new(
numberOfFeatures=>$numberoffeatures_val,
version=>$version_val,
name=>$name_val,
identifier=>$identifier_val,
auditTrail=>\@audit_list,
propertySets=>\@namevaluetype_list,
surfaceType=>$ontologyentry_ref,
designProviders=>\@contact_list,
protocolApplications=>\@protocolapplication_list,
reporterGroups=>\@reportergroup_list,
zoneGroups=>\@zonegroup_list,
featureGroups=>\@featuregroup_list,
descriptions=>\@description_list,
security=>$security_ref,
compositeGroups=>\@compositegroup_list,
);
# 'numberOfFeatures' attribute
my $numberOfFeatures_val = $physicalarraydesign->numberOfFeatures(); # getter
$physicalarraydesign->numberOfFeatures($value); # setter
# 'version' attribute
my $version_val = $physicalarraydesign->version(); # getter
$physicalarraydesign->version($value); # setter
# 'name' attribute
my $name_val = $physicalarraydesign->name(); # getter
$physicalarraydesign->name($value); # setter
# 'identifier' attribute
my $identifier_val = $physicalarraydesign->identifier(); # getter
$physicalarraydesign->identifier($value); # setter
# 'auditTrail' association
my $audit_array_ref = $physicalarraydesign->auditTrail(); # getter
$physicalarraydesign->auditTrail(\@audit_list); # setter
# 'propertySets' association
my $namevaluetype_array_ref = $physicalarraydesign->propertySets(); # getter
$physicalarraydesign->propertySets(\@namevaluetype_list); # setter
# 'surfaceType' association
my $ontologyentry_ref = $physicalarraydesign->surfaceType(); # getter
$physicalarraydesign->surfaceType($ontologyentry_ref); # setter
# 'designProviders' association
my $contact_array_ref = $physicalarraydesign->designProviders(); # getter
$physicalarraydesign->designProviders(\@contact_list); # setter
# 'protocolApplications' association
my $protocolapplication_array_ref = $physicalarraydesign->protocolApplications(); # getter
$physicalarraydesign->protocolApplications(\@protocolapplication_list); # setter
# 'reporterGroups' association
my $reportergroup_array_ref = $physicalarraydesign->reporterGroups(); # getter
$physicalarraydesign->reporterGroups(\@reportergroup_list); # setter
# 'zoneGroups' association
my $zonegroup_array_ref = $physicalarraydesign->zoneGroups(); # getter
$physicalarraydesign->zoneGroups(\@zonegroup_list); # setter
# 'featureGroups' association
my $featuregroup_array_ref = $physicalarraydesign->featureGroups(); # getter
$physicalarraydesign->featureGroups(\@featuregroup_list); # setter
# 'descriptions' association
my $description_array_ref = $physicalarraydesign->descriptions(); # getter
$physicalarraydesign->descriptions(\@description_list); # setter
# 'security' association
my $security_ref = $physicalarraydesign->security(); # getter
$physicalarraydesign->security($security_ref); # setter
# 'compositeGroups' association
my $compositegroup_array_ref = $physicalarraydesign->compositeGroups(); # getter
$physicalarraydesign->compositeGroups(\@compositegroup_list); # setter
DESCRIPTION¶
From the MAGE-OM documentation for the "PhysicalArrayDesign" class:
A design that is expected to be used to manufacture physical arrays.
INHERITANCE¶
Bio::MAGE::ArrayDesign::PhysicalArrayDesign has the following superclasses:
- •
- Bio::MAGE::ArrayDesign::ArrayDesign
CLASS METHODS¶
The following methods can all be called without first having an instance of the
class via the Bio::MAGE::ArrayDesign::PhysicalArrayDesign->
methodname() syntax.
- new()
- new(%args)
- The object constructor "new()" accepts the following optional
named-value style arguments:
- •
- numberOfFeatures
Sets the value of the "numberOfFeatures" attribute (this attribute
was inherited from class
"Bio::MAGE::ArrayDesign::ArrayDesign").
- •
- version
Sets the value of the "version" attribute (this attribute was
inherited from class
"Bio::MAGE::ArrayDesign::ArrayDesign").
- •
- name
Sets the value of the "name" attribute (this attribute was
inherited from class "Bio::MAGE::Identifiable").
- •
- identifier
Sets the value of the "identifier" attribute (this attribute was
inherited from class "Bio::MAGE::Identifiable").
- •
- 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".
- •
- 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".
- •
- surfaceType
Sets the value of the "surfaceType" association
The value must be of type: instance of
"Bio::MAGE::Description::OntologyEntry".
- •
- designProviders
Sets the value of the "designProviders" association (this
association was inherited from class
"Bio::MAGE::ArrayDesign::ArrayDesign").
The value must be of type: array of
"Bio::MAGE::AuditAndSecurity::Contact".
- •
- reporterGroups
Sets the value of the "reporterGroups" association (this
association was inherited from class
"Bio::MAGE::ArrayDesign::ArrayDesign").
The value must be of type: array of
"Bio::MAGE::ArrayDesign::ReporterGroup".
- •
- protocolApplications
Sets the value of the "protocolApplications" association (this
association was inherited from class
"Bio::MAGE::ArrayDesign::ArrayDesign").
The value must be of type: array of
"Bio::MAGE::Protocol::ProtocolApplication".
- •
- zoneGroups
Sets the value of the "zoneGroups" association
The value must be of type: array of
"Bio::MAGE::ArrayDesign::ZoneGroup".
- •
- 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".
- •
- featureGroups
Sets the value of the "featureGroups" association (this
association was inherited from class
"Bio::MAGE::ArrayDesign::ArrayDesign").
The value must be of type: array of
"Bio::MAGE::ArrayDesign::FeatureGroup".
- •
- 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".
- •
- compositeGroups
Sets the value of the "compositeGroups" association (this
association was inherited from class
"Bio::MAGE::ArrayDesign::ArrayDesign").
The value must be of type: array of
"Bio::MAGE::ArrayDesign::CompositeGroup".
- $obj = class->new(%parameters)
- The "new()" method is the class constructor.
Parameters: if given a list of name/value parameters the
corresponding slots, attributes, or associations will have their initial
values set by the constructor.
Return value: It returns a reference to an object of the class.
Side effects: It invokes the "initialize()" method if it
is defined by the class.
- @names = class->get_slot_names()
- The "get_slot_names()" method is used to retrieve the name of
all slots defined in a given class.
NOTE: the list of names does not include attribute or association
names.
Return value: A list of the names of all slots defined for this
class.
Side effects: none
- @name_list = get_attribute_names()
- returns the list of attribute data members for this class.
- @name_list = get_association_names()
- returns the list of association data members for this class.
- @class_list = get_superclasses()
- returns the list of superclasses for this class.
- @class_list = get_subclasses()
- returns the list of subclasses for this class.
- $name = class_name()
- Returns the full class name for this class.
- $package_name = package_name()
- Returns the base package name (i.e. no 'namespace::') of the package that
contains this class.
- %assns = associations()
- returns the association meta-information in a hash where the keys are the
association names and the values are "Association" objects that
provide the meta-information for the association.
INSTANCE METHODS¶
- $obj_copy = $obj->new()
- When invoked with an existing object reference and not a class name, the
"new()" method acts as a copy constructor - with the new
object's initial values set to be those of the existing object.
Parameters: No input parameters are used in the copy constructor,
the initial values are taken directly from the object to be copied.
Return value: It returns a reference to an object of the class.
Side effects: It invokes the "initialize()" method if it
is defined by the class.
- $obj->set_slots(%parameters)
- $obj->set_slots(\@name_list, \@value_list)
- The "set_slots()" method is used to set a number of slots at the
same time. It has two different invocation methods. The first takes a
named parameter list, and the second takes two array references.
Return value: none
Side effects: will call "croak()" if a slot_name is used
that the class does not define.
- @obj_list = $obj->get_slots(@name_list)
- The "get_slots()" method is used to get the values of a number
of slots at the same time.
Return value: a list of instance objects
Side effects: none
- $val = $obj->set_slot($name,$val)
- The "set_slot()" method sets the slot $name to the value $val
Return value: the new value of the slot, i.e. $val
Side effects: none
- $val = $obj->get_slot($name)
- The "get_slot()" method is used to get the values of a number of
slots at the same time.
Return value: a single slot value, or undef if the slot has not been
initialized.
Side effects: none
ATTRIBUTES¶
Attributes are simple data types that belong to a single instance of a class. In
the Perl implementation of the MAGE-OM classes, the interface to attributes is
implemented using separate setter and getter methods for each attribute.
"Bio::MAGE::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;
}
SLOTS, ATTRIBUTES, AND ASSOCIATIONS¶
In the Perl implementation of MAGE-OM classes, there are three types of class
data members: "slots", "attributes", and
"associations".
SLOTS¶
This API uses the term "slot" to indicate a data member of the class
that was not present in the UML model and is used for mainly internal purposes
- use only if you understand the inner workings of the API. Most often slots
are used by generic methods such as those in the XML writing and reading
classes.
Slots are implemented using unified getter/setter methods:
- $var = $obj->slot_name();
- Retrieves the current value of the slot.
- $new_var = $obj->slot_name($new_var);
- Store $new_var in the slot - the return value is also $new_var.
- @names = $obj->get_slot_names()
- Returns the list of all slots in the class.
DATA CHECKING: No data type checking is made for these methods.
ATTRIBUTES AND ASSOCIATIONS¶
The terms "attribute" and "association" indicate data
members of the class that were specified directly from the UML model.
In the Perl implementation of MAGE-OM classes, association and attribute
accessors are implemented using three separate methods:
- get*
- Retrieves the current value.
NOTE: For associations, if the association has list cardinality, an
array reference is returned.
DATA CHECKING: Ensure that no argument is provided.
- set*
- Sets the current value, replacing any existing value.
NOTE: For associations, if the association has list cardinality, the
argument must be an array reference. Because of this, you probably should
be using the add* methods.
DATA CHECKING: For attributes, ensure that a single value is
provided as the argument. For associations, if the association has list
cardinality, ensure that the argument is a reference to an array of
instances of the correct MAGE-OM class, otherwise ensure that there is a
single argument of the correct MAGE-OM class.
- add*
- NOTE: Only present in associations with list cardinality.
Appends a list of objects to any values that may already be stored in the
association.
DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM
class.
GENERIC METHODS¶
The unified base class of all MAGE-OM classes, "Bio::MAGE::Base",
provides a set of generic methods that will operate on slots, attributes, and
associations:
- $val = $obj->get_slot($name)
- \@list_ref = $obj->get_slots(@name_list);
- $val = $obj->set_slot($name,$val)
- $obj->set_slots(%parameters)
- $obj->set_slots(\@name_list, \@value_list)
- See elsewhere in this page for a detailed description of these
methods.
BUGS¶
Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot'
sf 'dot' net)
AUTHOR¶
Jason E. Stewart (jasons 'at' cpan 'dot' org)
SEE ALSO¶
perl(1).
POD ERRORS¶
Hey!
The above document had some coding errors, which are explained
below:
- Around line 467:
- '=item' outside of any '=over'
- Around line 552:
- You forgot a '=back' before '=head2'
- Around line 868:
- Expected '=item 2'
- Around line 873:
- Expected '=item 3'
- Around line 878:
- Expected '=item 4'