NAME
Bio::MAGE::ArrayDesign::ArrayDesign - Class for the MAGE-OM API
SYNOPSIS
use Bio::MAGE::ArrayDesign::ArrayDesign
# creating an empty instance
my $arraydesign = Bio::MAGE::ArrayDesign::ArrayDesign->new();
# creating an instance with existing data
my $arraydesign = Bio::MAGE::ArrayDesign::ArrayDesign->new(
numberOfFeatures=>$numberoffeatures_val,
version=>$version_val,
name=>$name_val,
identifier=>$identifier_val,
auditTrail=>\@audit_list,
propertySets=>\@namevaluetype_list,
designProviders=>\@contact_list,
protocolApplications=>\@protocolapplication_list,
reporterGroups=>\@reportergroup_list,
featureGroups=>\@featuregroup_list,
descriptions=>\@description_list,
security=>$security_ref,
compositeGroups=>\@compositegroup_list,
);
# 'numberOfFeatures' attribute
my $numberOfFeatures_val = $arraydesign->numberOfFeatures(); # getter
$arraydesign->numberOfFeatures($value); # setter
# 'version' attribute
my $version_val = $arraydesign->version(); # getter
$arraydesign->version($value); # setter
# 'name' attribute
my $name_val = $arraydesign->name(); # getter
$arraydesign->name($value); # setter
# 'identifier' attribute
my $identifier_val = $arraydesign->identifier(); # getter
$arraydesign->identifier($value); # setter
# 'auditTrail' association
my $audit_array_ref = $arraydesign->auditTrail(); # getter
$arraydesign->auditTrail(\@audit_list); # setter
# 'propertySets' association
my $namevaluetype_array_ref = $arraydesign->propertySets(); # getter
$arraydesign->propertySets(\@namevaluetype_list); # setter
# 'designProviders' association
my $contact_array_ref = $arraydesign->designProviders(); # getter
$arraydesign->designProviders(\@contact_list); # setter
# 'protocolApplications' association
my $protocolapplication_array_ref = $arraydesign->protocolApplications(); # getter
$arraydesign->protocolApplications(\@protocolapplication_list); # setter
# 'reporterGroups' association
my $reportergroup_array_ref = $arraydesign->reporterGroups(); # getter
$arraydesign->reporterGroups(\@reportergroup_list); # setter
# 'featureGroups' association
my $featuregroup_array_ref = $arraydesign->featureGroups(); # getter
$arraydesign->featureGroups(\@featuregroup_list); # setter
# 'descriptions' association
my $description_array_ref = $arraydesign->descriptions(); # getter
$arraydesign->descriptions(\@description_list); # setter
# 'security' association
my $security_ref = $arraydesign->security(); # getter
$arraydesign->security($security_ref); # setter
# 'compositeGroups' association
my $compositegroup_array_ref = $arraydesign->compositeGroups(); # getter
$arraydesign->compositeGroups(\@compositegroup_list); # setter
DESCRIPTION
From the MAGE-OM documentation for the ArrayDesign class:
Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features.
INHERITANCE
Bio::MAGE::ArrayDesign::ArrayDesign has the following superclasses:
Bio::MAGE::Identifiable
Bio::MAGE::ArrayDesign::ArrayDesign has the following subclasses:
Bio::MAGE::ArrayDesign::PhysicalArrayDesign
CLASS METHODS
The following methods can all be called without first having an instance of the class via the Bio::MAGE::ArrayDesign::ArrayDesign->methodname() syntax.
- new()
- new(%args)
-
The object constructor
new()accepts the following optional named-value style arguments:numberOfFeatures
Sets the value of the
numberOfFeaturesattributeversion
Sets the value of the
versionattributename
Sets the value of the
nameattribute (this attribute was inherited from classBio::MAGE::Identifiable).identifier
Sets the value of the
identifierattribute (this attribute was inherited from classBio::MAGE::Identifiable).auditTrail
Sets the value of the
auditTrailassociation (this association was inherited from classBio::MAGE::Describable).The value must be of type: array of
Bio::MAGE::AuditAndSecurity::Audit.propertySets
Sets the value of the
propertySetsassociation (this association was inherited from classBio::MAGE::Extendable).The value must be of type: array of
Bio::MAGE::NameValueType.designProviders
Sets the value of the
designProvidersassociationThe value must be of type: array of
Bio::MAGE::AuditAndSecurity::Contact.reporterGroups
Sets the value of the
reporterGroupsassociationThe value must be of type: array of
Bio::MAGE::ArrayDesign::ReporterGroup.protocolApplications
Sets the value of the
protocolApplicationsassociationThe value must be of type: array of
Bio::MAGE::Protocol::ProtocolApplication.descriptions
Sets the value of the
descriptionsassociation (this association was inherited from classBio::MAGE::Describable).The value must be of type: array of
Bio::MAGE::Description::Description.featureGroups
Sets the value of the
featureGroupsassociationThe value must be of type: array of
Bio::MAGE::ArrayDesign::FeatureGroup.security
Sets the value of the
securityassociation (this association was inherited from classBio::MAGE::Describable).The value must be of type: instance of
Bio::MAGE::AuditAndSecurity::Security.compositeGroups
Sets the value of the
compositeGroupsassociationThe 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
Associationobjects 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,$val)
-
The
set_slot()method sets the slot$nameto the value$valReturn value: the new value of the slot, i.e.
$valSide 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::ArrayDesign has the following attribute accessor methods:
- numberOfFeatures
-
Methods for the
numberOfFeaturesattribute.From the MAGE-OM documentation:
The number of features for this array
- $val = $arraydesign->setNumberOfFeatures($val)
-
The restricted setter method for the
numberOfFeaturesattribute.Input parameters: the value to which the
numberOfFeaturesattribute will be setReturn value: the current value of the
numberOfFeaturesattributeSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified - $val = $arraydesign->getNumberOfFeatures()
-
The restricted getter method for the
numberOfFeaturesattribute.Input parameters: none
Return value: the current value of the
numberOfFeaturesattributeSide effects: none
Exceptions: will call
croak()if any input parameters are specified
- version
-
Methods for the
versionattribute.From the MAGE-OM documentation:
The version of this design.
- $val = $arraydesign->setVersion($val)
-
The restricted setter method for the
versionattribute.Input parameters: the value to which the
versionattribute will be setReturn value: the current value of the
versionattributeSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified - $val = $arraydesign->getVersion()
-
The restricted getter method for the
versionattribute.Input parameters: none
Return value: the current value of the
versionattributeSide effects: none
Exceptions: will call
croak()if any input parameters are specified
- name
-
Methods for the
nameattribute.From the MAGE-OM documentation:
The potentially ambiguous common identifier.
- $val = $arraydesign->setName($val)
-
The restricted setter method for the
nameattribute.Input parameters: the value to which the
nameattribute will be setReturn value: the current value of the
nameattributeSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified - $val = $arraydesign->getName()
-
The restricted getter method for the
nameattribute.Input parameters: none
Return value: the current value of the
nameattributeSide effects: none
Exceptions: will call
croak()if any input parameters are specified
- identifier
-
Methods for the
identifierattribute.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 = $arraydesign->setIdentifier($val)
-
The restricted setter method for the
identifierattribute.Input parameters: the value to which the
identifierattribute will be setReturn value: the current value of the
identifierattributeSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified - $val = $arraydesign->getIdentifier()
-
The restricted getter method for the
identifierattribute.Input parameters: none
Return value: the current value of the
identifierattributeSide 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:
There must be exactly one item in the association, i.e. this is a mandatory data field.
0..1
There may be one item in the association, i.e. this is an optional data field.
1..N
There must be one or more items in the association, i.e. this is a mandatory data field, with list cardinality.
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::ArrayDesign has the following association accessor methods:
- auditTrail
-
Methods for the
auditTrailassociation.From the MAGE-OM documentation:
A list of Audit instances that track changes to the instance of Describable.
- $array_ref = $arraydesign->setAuditTrail($array_ref)
-
The restricted setter method for the
auditTrailassociation.Input parameters: the value to which the
auditTrailassociation will be set : a reference to an array of objects of typeBio::MAGE::AuditAndSecurity::AuditReturn value: the current value of the
auditTrailassociation : a reference to an array of objects of typeBio::MAGE::AuditAndSecurity::AuditSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified, or if$array_refis not a reference to an array classBio::MAGE::AuditAndSecurity::Auditinstances - $array_ref = $arraydesign->getAuditTrail()
-
The restricted getter method for the
auditTrailassociation.Input parameters: none
Return value: the current value of the
auditTrailassociation : a reference to an array of objects of typeBio::MAGE::AuditAndSecurity::AuditSide effects: none
Exceptions: will call
croak()if any input parameters are specified - $val = $arraydesign->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
@valsto add to the auditTrail association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@valsSide 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 classBio::MAGE::AuditAndSecurity::Audit
- propertySets
-
Methods for the
propertySetsassociation.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 = $arraydesign->setPropertySets($array_ref)
-
The restricted setter method for the
propertySetsassociation.Input parameters: the value to which the
propertySetsassociation will be set : a reference to an array of objects of typeBio::MAGE::NameValueTypeReturn value: the current value of the
propertySetsassociation : a reference to an array of objects of typeBio::MAGE::NameValueTypeSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified, or if$array_refis not a reference to an array classBio::MAGE::NameValueTypeinstances - $array_ref = $arraydesign->getPropertySets()
-
The restricted getter method for the
propertySetsassociation.Input parameters: none
Return value: the current value of the
propertySetsassociation : a reference to an array of objects of typeBio::MAGE::NameValueTypeSide effects: none
Exceptions: will call
croak()if any input parameters are specified - $val = $arraydesign->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
@valsto add to the propertySets association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@valsSide 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 classBio::MAGE::NameValueType
- designProviders
-
Methods for the
designProvidersassociation.From the MAGE-OM documentation:
The primary contact for information on the array design
- $array_ref = $arraydesign->setDesignProviders($array_ref)
-
The restricted setter method for the
designProvidersassociation.Input parameters: the value to which the
designProvidersassociation will be set : a reference to an array of objects of typeBio::MAGE::AuditAndSecurity::ContactReturn value: the current value of the
designProvidersassociation : a reference to an array of objects of typeBio::MAGE::AuditAndSecurity::ContactSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified, or if$array_refis not a reference to an array classBio::MAGE::AuditAndSecurity::Contactinstances - $array_ref = $arraydesign->getDesignProviders()
-
The restricted getter method for the
designProvidersassociation.Input parameters: none
Return value: the current value of the
designProvidersassociation : a reference to an array of objects of typeBio::MAGE::AuditAndSecurity::ContactSide effects: none
Exceptions: will call
croak()if any input parameters are specified - $val = $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.
Input parameters: the list of values
@valsto add to the designProviders association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@valsSide 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 classBio::MAGE::AuditAndSecurity::Contact
- reporterGroups
-
Methods for the
reporterGroupsassociation.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 = $arraydesign->setReporterGroups($array_ref)
-
The restricted setter method for the
reporterGroupsassociation.Input parameters: the value to which the
reporterGroupsassociation will be set : a reference to an array of objects of typeBio::MAGE::ArrayDesign::ReporterGroupReturn value: the current value of the
reporterGroupsassociation : a reference to an array of objects of typeBio::MAGE::ArrayDesign::ReporterGroupSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified, or if$array_refis not a reference to an array classBio::MAGE::ArrayDesign::ReporterGroupinstances - $array_ref = $arraydesign->getReporterGroups()
-
The restricted getter method for the
reporterGroupsassociation.Input parameters: none
Return value: the current value of the
reporterGroupsassociation : a reference to an array of objects of typeBio::MAGE::ArrayDesign::ReporterGroupSide effects: none
Exceptions: will call
croak()if any input parameters are specified - $val = $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.
Input parameters: the list of values
@valsto add to the reporterGroups association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@valsSide 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 classBio::MAGE::ArrayDesign::ReporterGroup
- protocolApplications
-
Methods for the
protocolApplicationsassociation.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 = $arraydesign->setProtocolApplications($array_ref)
-
The restricted setter method for the
protocolApplicationsassociation.Input parameters: the value to which the
protocolApplicationsassociation will be set : a reference to an array of objects of typeBio::MAGE::Protocol::ProtocolApplicationReturn value: the current value of the
protocolApplicationsassociation : a reference to an array of objects of typeBio::MAGE::Protocol::ProtocolApplicationSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified, or if$array_refis not a reference to an array classBio::MAGE::Protocol::ProtocolApplicationinstances - $array_ref = $arraydesign->getProtocolApplications()
-
The restricted getter method for the
protocolApplicationsassociation.Input parameters: none
Return value: the current value of the
protocolApplicationsassociation : a reference to an array of objects of typeBio::MAGE::Protocol::ProtocolApplicationSide effects: none
Exceptions: will call
croak()if any input parameters are specified - $val = $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.
Input parameters: the list of values
@valsto add to the protocolApplications association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@valsSide 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 classBio::MAGE::Protocol::ProtocolApplication
- descriptions
-
Methods for the
descriptionsassociation.From the MAGE-OM documentation:
Free hand text descriptions. Makes available the associations of Description to an instance of Describable.
- $array_ref = $arraydesign->setDescriptions($array_ref)
-
The restricted setter method for the
descriptionsassociation.Input parameters: the value to which the
descriptionsassociation will be set : a reference to an array of objects of typeBio::MAGE::Description::DescriptionReturn value: the current value of the
descriptionsassociation : a reference to an array of objects of typeBio::MAGE::Description::DescriptionSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified, or if$array_refis not a reference to an array classBio::MAGE::Description::Descriptioninstances - $array_ref = $arraydesign->getDescriptions()
-
The restricted getter method for the
descriptionsassociation.Input parameters: none
Return value: the current value of the
descriptionsassociation : a reference to an array of objects of typeBio::MAGE::Description::DescriptionSide effects: none
Exceptions: will call
croak()if any input parameters are specified - $val = $arraydesign->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
@valsto add to the descriptions association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@valsSide 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 classBio::MAGE::Description::Description
- featureGroups
-
Methods for the
featureGroupsassociation.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 = $arraydesign->setFeatureGroups($array_ref)
-
The restricted setter method for the
featureGroupsassociation.Input parameters: the value to which the
featureGroupsassociation will be set : a reference to an array of objects of typeBio::MAGE::ArrayDesign::FeatureGroupReturn value: the current value of the
featureGroupsassociation : a reference to an array of objects of typeBio::MAGE::ArrayDesign::FeatureGroupSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified, or if$array_refis not a reference to an array classBio::MAGE::ArrayDesign::FeatureGroupinstances - $array_ref = $arraydesign->getFeatureGroups()
-
The restricted getter method for the
featureGroupsassociation.Input parameters: none
Return value: the current value of the
featureGroupsassociation : a reference to an array of objects of typeBio::MAGE::ArrayDesign::FeatureGroupSide effects: none
Exceptions: will call
croak()if any input parameters are specified - $val = $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.
Input parameters: the list of values
@valsto add to the featureGroups association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@valsSide 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 classBio::MAGE::ArrayDesign::FeatureGroup
- security
-
Methods for the
securityassociation.From the MAGE-OM documentation:
Information on the security for the instance of the class.
- $val = $arraydesign->setSecurity($val)
-
The restricted setter method for the
securityassociation.Input parameters: the value to which the
securityassociation will be set : one of the accepted enumerated values.Return value: the current value of the
securityassociation : 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$valis not an instance of classBio::MAGE::AuditAndSecurity::Security - $val = $arraydesign->getSecurity()
-
The restricted getter method for the
securityassociation.Input parameters: none
Return value: the current value of the
securityassociation : an instance of typeBio::MAGE::AuditAndSecurity::Security.Side effects: none
Exceptions: will call
croak()if any input parameters are specified
- compositeGroups
-
Methods for the
compositeGroupsassociation.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 = $arraydesign->setCompositeGroups($array_ref)
-
The restricted setter method for the
compositeGroupsassociation.Input parameters: the value to which the
compositeGroupsassociation will be set : a reference to an array of objects of typeBio::MAGE::ArrayDesign::CompositeGroupReturn value: the current value of the
compositeGroupsassociation : a reference to an array of objects of typeBio::MAGE::ArrayDesign::CompositeGroupSide effects: none
Exceptions: will call
croak()if no input parameters are specified, or if too many input parameters are specified, or if$array_refis not a reference to an array classBio::MAGE::ArrayDesign::CompositeGroupinstances - $array_ref = $arraydesign->getCompositeGroups()
-
The restricted getter method for the
compositeGroupsassociation.Input parameters: none
Return value: the current value of the
compositeGroupsassociation : a reference to an array of objects of typeBio::MAGE::ArrayDesign::CompositeGroupSide effects: none
Exceptions: will call
croak()if any input parameters are specified - $val = $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.
Input parameters: the list of values
@valsto add to the compositeGroups association. NOTE: submitting a single value is permitted.Return value: the number of items stored in the slot after adding
@valsSide 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 classBio::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).
5 POD Errors
The following errors were encountered while parsing the POD:
- Around line 510:
'=item' outside of any '=over'
- Around line 595:
You forgot a '=back' before '=head2'
- Around line 911:
Expected '=item 2'
- Around line 916:
Expected '=item 3'
- Around line 921:
Expected '=item 4'