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Bio::MAGE::ArrayDesign::ArrayDesign - Class for the MAGE-OM API |
Bio::MAGE::ArrayDesign::ArrayDesign - Class for the MAGE-OM API
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
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.
Bio::MAGE::ArrayDesign::ArrayDesign has the following superclasses:
Bio::MAGE::ArrayDesign::ArrayDesign has the following subclasses:
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)new() accepts the following optional
named-value style arguments:
numberOfFeatures attribute
version attribute
name attribute (this attribute was inherited from class Bio::MAGE::Identifiable).
identifier attribute (this attribute was inherited from class Bio::MAGE::Identifiable).
auditTrail association (this association was inherited from class Bio::MAGE::Describable).
The value must be of type: array of Bio::MAGE::AuditAndSecurity::Audit.
propertySets association (this association was inherited from class Bio::MAGE::Extendable).
The value must be of type: array of Bio::MAGE::NameValueType.
designProviders association
The value must be of type: array of Bio::MAGE::AuditAndSecurity::Contact.
reporterGroups association
The value must be of type: array of Bio::MAGE::ArrayDesign::ReporterGroup.
protocolApplications association
The value must be of type: array of Bio::MAGE::Protocol::ProtocolApplication.
descriptions association (this association was inherited from class Bio::MAGE::Describable).
The value must be of type: array of Bio::MAGE::Description::Description.
featureGroups association
The value must be of type: array of Bio::MAGE::ArrayDesign::FeatureGroup.
security association (this association was inherited from class Bio::MAGE::Describable).
The value must be of type: instance of Bio::MAGE::AuditAndSecurity::Security.
compositeGroups association
The value must be of type: array of Bio::MAGE::ArrayDesign::CompositeGroup.
new(%parameters)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.
get_slot_names()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
get_attribute_names()get_association_names()get_superclasses()get_subclasses()class_name()package_name()associations()Association objects that
provide the meta-information for the association.
new()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.
set_slots(%parameters)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.
get_slots(@name_list)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
set_slot($name,$val)set_slot() method sets the slot $name to the value $val
Return value: the new value of the slot, i.e. $val
Side effects: none
get_slot($name)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 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 attribute.
From the MAGE-OM documentation:
The number of features for this array
setNumberOfFeatures($val)numberOfFeatures attribute.
Input parameters: the value to which the numberOfFeatures attribute will be set
Return value: the current value of the numberOfFeatures attribute
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or
if too many input parameters are specified
getNumberOfFeatures()numberOfFeatures attribute.
Input parameters: none
Return value: the current value of the numberOfFeatures attribute
Side effects: none
Exceptions: will call croak() if any input parameters are specified
version attribute.
From the MAGE-OM documentation:
The version of this design.
setVersion($val)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
getVersion()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 attribute.
From the MAGE-OM documentation:
The potentially ambiguous common identifier.
setName($val)name attribute.
Input parameters: the value to which the name attribute will be set
Return value: the current value of the name attribute
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or
if too many input parameters are specified
getName()name attribute.
Input parameters: none
Return value: the current value of the name attribute
Side effects: none
Exceptions: will call croak() if any input parameters are specified
identifier attribute.
From the MAGE-OM documentation:
An identifier is an unambiguous string that is unique within the scope (i.e. a document, a set of related documents, or a repository) of its use.
setIdentifier($val)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
getIdentifier()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 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:
Bio::MAGE::ArrayDesign::ArrayDesign has the following association accessor methods:
auditTrail association.
From the MAGE-OM documentation:
A list of Audit instances that track changes to the instance of Describable.
setAuditTrail($array_ref)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 $array_ref is not a reference to an array class Bio::MAGE::AuditAndSecurity::Audit instances
getAuditTrail()auditTrail association.
Input parameters: none
Return value: the current value of the auditTrail association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Audit
Side effects: none
Exceptions: will call croak() if any input parameters are specified
addAuditTrail(@vals)Input parameters: the list of values @vals to add to the auditTrail association. NOTE: submitting a single value is permitted.
Return value: the number of items stored in the slot after adding @vals
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Audit
propertySets association.
From the MAGE-OM documentation:
Allows specification of name/value pairs. Meant to primarily help in-house, pipeline processing of instances by providing a place for values that aren't part of the specification proper.
setPropertySets($array_ref)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 $array_ref is not a reference to an array class Bio::MAGE::NameValueType instances
getPropertySets()propertySets association.
Input parameters: none
Return value: the current value of the propertySets association : a reference to an array of objects of type Bio::MAGE::NameValueType
Side effects: none
Exceptions: will call croak() if any input parameters are specified
addPropertySets(@vals)Input parameters: the list of values @vals to add to the propertySets association. NOTE: submitting a single value is permitted.
Return value: the number of items stored in the slot after adding @vals
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::NameValueType
designProviders association.
From the MAGE-OM documentation:
The primary contact for information on the array design
setDesignProviders($array_ref)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 $array_ref is not a reference to an array class Bio::MAGE::AuditAndSecurity::Contact instances
getDesignProviders()designProviders association.
Input parameters: none
Return value: the current value of the designProviders association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
Side effects: none
Exceptions: will call croak() if any input parameters are specified
addDesignProviders(@vals)Input parameters: the list of values @vals to add to the designProviders association. NOTE: submitting a single value is permitted.
Return value: the number of items stored in the slot after adding @vals
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::AuditAndSecurity::Contact
reporterGroups association.
From the MAGE-OM documentation:
The grouping of like Reporter together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple ReporterGroups to segregate the technology types.
setReporterGroups($array_ref)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 $array_ref is not a reference to an array class Bio::MAGE::ArrayDesign::ReporterGroup instances
getReporterGroups()reporterGroups association.
Input parameters: none
Return value: the current value of the reporterGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::ReporterGroup
Side effects: none
Exceptions: will call croak() if any input parameters are specified
addReporterGroups(@vals)Input parameters: the list of values @vals to add to the reporterGroups association. NOTE: submitting a single value is permitted.
Return value: the number of items stored in the slot after adding @vals
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::ArrayDesign::ReporterGroup
protocolApplications association.
From the MAGE-OM documentation:
Describes the application of any protocols, such as the methodology used to pick oligos, in the design of the array.
setProtocolApplications($array_ref)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 $array_ref is not a reference to an array class Bio::MAGE::Protocol::ProtocolApplication instances
getProtocolApplications()protocolApplications association.
Input parameters: none
Return value: the current value of the protocolApplications association : a reference to an array of objects of type Bio::MAGE::Protocol::ProtocolApplication
Side effects: none
Exceptions: will call croak() if any input parameters are specified
addProtocolApplications(@vals)Input parameters: the list of values @vals to add to the protocolApplications association. NOTE: submitting a single value is permitted.
Return value: the number of items stored in the slot after adding @vals
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Protocol::ProtocolApplication
descriptions association.
From the MAGE-OM documentation:
Free hand text descriptions. Makes available the associations of Description to an instance of Describable.
setDescriptions($array_ref)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 $array_ref is not a reference to an array class Bio::MAGE::Description::Description instances
getDescriptions()descriptions association.
Input parameters: none
Return value: the current value of the descriptions association : a reference to an array of objects of type Bio::MAGE::Description::Description
Side effects: none
Exceptions: will call croak() if any input parameters are specified
addDescriptions(@vals)Input parameters: the list of values @vals to add to the descriptions association. NOTE: submitting a single value is permitted.
Return value: the number of items stored in the slot after adding @vals
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::Description::Description
featureGroups association.
From the MAGE-OM documentation:
The grouping of like Features together. Typically for a physical array design, this will be a single grouping of features whose type might be PCR Product or Oligo. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple FeatureGroups to segregate the technology types.
setFeatureGroups($array_ref)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 $array_ref is not a reference to an array class Bio::MAGE::ArrayDesign::FeatureGroup instances
getFeatureGroups()featureGroups association.
Input parameters: none
Return value: the current value of the featureGroups association : a reference to an array of objects of type Bio::MAGE::ArrayDesign::FeatureGroup
Side effects: none
Exceptions: will call croak() if any input parameters are specified
addFeatureGroups(@vals)Input parameters: the list of values @vals to add to the featureGroups association. NOTE: submitting a single value is permitted.
Return value: the number of items stored in the slot after adding @vals
Side effects: none
Exceptions: will call croak() if no input parameters are specified, or if any of the objects in @vals is not an instance of class Bio::MAGE::ArrayDesign::FeatureGroup
security association.
From the MAGE-OM documentation:
Information on the security for the instance of the class.
setSecurity($val)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 $val is not an instance of class Bio::MAGE::AuditAndSecurity::Security
getSecurity()security association.
Input parameters: none
Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.
Side effects: none
Exceptions: will call croak() if any input parameters are specified
compositeGroups association.
From the MAGE-OM documentation:
The grouping of like CompositeSequence together. If more than one technology type occurs on the array, such as the mixing of Cloned BioMaterial and Oligos, then there would be multiple CompositeGroups to segregate the technology types.
setCompositeGroups($array_ref)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
getCompositeGroups()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
addCompositeGroups(@vals)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 $self = shift; return 1;
}
In the Perl implementation of MAGE-OM classes, there are
three types of class data members: slots, attributes, and
associations.
This API uses the term slot to indicate a data member of the class
that was not present in the UML model and is used for mainly internal
purposes - use only if you understand the inner workings of the
API. Most often slots are used by generic methods such as those in the
XML writing and reading classes.
Slots are implemented using unified getter/setter methods:
get_slot_names()DATA CHECKING: No data type checking is made for these methods.
The terms attribute and association indicate data members of the
class that were specified directly from the UML model.
In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:
NOTE: For associations, if the association has list cardinality, an array reference is returned.
DATA CHECKING: Ensure that no argument is provided.
NOTE: For associations, if the association has list cardinality, the argument must be an array reference. Because of this, you probably should be using the add* methods.
DATA CHECKING: For attributes, ensure that a single value is provided as the argument. For associations, if the association has list cardinality, ensure that the argument is a reference to an array of instances of the correct MAGE-OM class, otherwise ensure that there is a single argument of the correct MAGE-OM class.
Appends a list of objects to any values that may already be stored in the association.
DATA CHECKING: Ensure that all arguments are of the correct MAGE-OM class.
The unified base class of all MAGE-OM classes, Bio::MAGE::Base, provides a set of generic methods that
will operate on slots, attributes, and associations:
get_slot($name)set_slot($name,$val)set_slots(%parameters)
Please send bug reports to the project mailing list: (mged-mage 'at' lists 'dot' sf 'dot' net)
Jason E. Stewart (jasons 'at' cpan 'dot' org)
perl(1).
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Bio::MAGE::ArrayDesign::ArrayDesign - Class for the MAGE-OM API |