Bio::MAGE::Experiment::Experiment - Class for the MAGE-OM API
use Bio::MAGE::Experiment::Experiment # creating an empty instance my $experiment = Bio::MAGE::Experiment::Experiment->new(); # creating an instance with existing data my $experiment = Bio::MAGE::Experiment::Experiment->new( name=>$name_val, identifier=>$identifier_val, experimentDesigns=>\@experimentdesign_list, providers=>\@contact_list, auditTrail=>\@audit_list, propertySets=>\@namevaluetype_list, analysisResults=>\@bioassaydatacluster_list, bioAssays=>\@bioassay_list, descriptions=>\@description_list, bioAssayData=>\@bioassaydata_list, security=>$security_ref, ); # 'name' attribute my $name_val = $experiment->name(); # getter $experiment->name($value); # setter # 'identifier' attribute my $identifier_val = $experiment->identifier(); # getter $experiment->identifier($value); # setter # 'experimentDesigns' association my $experimentdesign_array_ref = $experiment->experimentDesigns(); # getter $experiment->experimentDesigns(\@experimentdesign_list); # setter # 'providers' association my $contact_array_ref = $experiment->providers(); # getter $experiment->providers(\@contact_list); # setter # 'auditTrail' association my $audit_array_ref = $experiment->auditTrail(); # getter $experiment->auditTrail(\@audit_list); # setter # 'propertySets' association my $namevaluetype_array_ref = $experiment->propertySets(); # getter $experiment->propertySets(\@namevaluetype_list); # setter # 'analysisResults' association my $bioassaydatacluster_array_ref = $experiment->analysisResults(); # getter $experiment->analysisResults(\@bioassaydatacluster_list); # setter # 'bioAssays' association my $bioassay_array_ref = $experiment->bioAssays(); # getter $experiment->bioAssays(\@bioassay_list); # setter # 'descriptions' association my $description_array_ref = $experiment->descriptions(); # getter $experiment->descriptions(\@description_list); # setter # 'bioAssayData' association my $bioassaydata_array_ref = $experiment->bioAssayData(); # getter $experiment->bioAssayData(\@bioassaydata_list); # setter # 'security' association my $security_ref = $experiment->security(); # getter $experiment->security($security_ref); # setter
From the MAGE-OM documentation for the Experiment class:
Experiment
The Experiment is the collection of all the BioAssays that are related by the ExperimentDesign.
Bio::MAGE::Experiment::Experiment has the following superclasses:
Bio::MAGE::Identifiable
The following methods can all be called without first having an instance of the class via the Bio::MAGE::Experiment::Experiment->methodname() syntax.
The object constructor new() accepts the following optional named-value style arguments:
new()
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).
experimentDesigns
Sets the value of the experimentDesigns association
The value must be of type: array of Bio::MAGE::Experiment::ExperimentDesign.
Bio::MAGE::Experiment::ExperimentDesign
providers
Sets the value of the providers association
The value must be of type: array of Bio::MAGE::AuditAndSecurity::Contact.
Bio::MAGE::AuditAndSecurity::Contact
auditTrail
Sets the value of the auditTrail association (this association was inherited from class Bio::MAGE::Describable).
Bio::MAGE::Describable
The value must be of type: array of Bio::MAGE::AuditAndSecurity::Audit.
Bio::MAGE::AuditAndSecurity::Audit
propertySets
Sets the value of the propertySets association (this association was inherited from class Bio::MAGE::Extendable).
Bio::MAGE::Extendable
The value must be of type: array of Bio::MAGE::NameValueType.
Bio::MAGE::NameValueType
analysisResults
Sets the value of the analysisResults association
The value must be of type: array of Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster.
Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster
bioAssays
Sets the value of the bioAssays association
The value must be of type: array of Bio::MAGE::BioAssay::BioAssay.
Bio::MAGE::BioAssay::BioAssay
bioAssayData
Sets the value of the bioAssayData association
The value must be of type: array of Bio::MAGE::BioAssayData::BioAssayData.
Bio::MAGE::BioAssayData::BioAssayData
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.
Bio::MAGE::Description::Description
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.
Bio::MAGE::AuditAndSecurity::Security
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.
initialize()
The get_slot_names() method is used to retrieve the name of all slots defined in a given class.
get_slot_names()
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
returns the list of attribute data members for this class.
returns the list of association data members for this class.
returns the list of superclasses for this class.
returns the list of subclasses for this class.
Returns the full class name for this class.
Returns the base package name (i.e. no 'namespace::') of the package that contains this class.
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.
Association
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.
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.
set_slots()
Return value: none
Side effects: will call croak() if a slot_name is used that the class does not define.
croak()
The get_slots() method is used to get the values of a number of slots at the same time.
get_slots()
Return value: a list of instance objects
The set_slot() method sets the slot $name to the value $val
set_slot()
$name
$val
Return value: the new value of the slot, i.e. $val
The get_slot() method is used to get the values of a number of slots at the same time.
get_slot()
Return value: a single slot value, or undef if the slot has not been initialized.
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::Experiment::Experiment has the following attribute accessor methods:
Bio::MAGE::Experiment::Experiment
Methods for the name attribute.
From the MAGE-OM documentation:
The potentially ambiguous common identifier.
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
Exceptions: will call croak() if no input parameters are specified, or if too many input parameters are specified
The restricted getter method for the name attribute.
Input parameters: none
Exceptions: will call croak() if any input parameters are specified
Methods for the identifier attribute.
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.
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
The restricted getter method for the identifier attribute.
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::Experiment::Experiment has the following association accessor methods:
Methods for the experimentDesigns association.
The association to the description and annotation of the Experiment, along with the grouping of the top-level BioAssays.
The restricted setter method for the experimentDesigns association.
Input parameters: the value to which the experimentDesigns association will be set : a reference to an array of objects of type Bio::MAGE::Experiment::ExperimentDesign
Return value: the current value of the experimentDesigns association : a reference to an array of objects of type Bio::MAGE::Experiment::ExperimentDesign
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::Experiment::ExperimentDesign instances
$array_ref
The restricted getter method for the experimentDesigns association.
Because the experimentDesigns association has list cardinality, it may store more than one value. This method adds the current list of objects in the experimentDesigns association.
Input parameters: the list of values @vals to add to the experimentDesigns association. NOTE: submitting a single value is permitted.
@vals
Return value: the number of items stored in the slot after adding @vals
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::Experiment::ExperimentDesign
Methods for the providers association.
The providers of the Experiment, its data and annotation.
The restricted setter method for the providers association.
Input parameters: the value to which the providers association will be set : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
Return value: the current value of the providers association : a reference to an array of objects of type Bio::MAGE::AuditAndSecurity::Contact
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
The restricted getter method for the providers association.
Because the providers association has list cardinality, it may store more than one value. This method adds the current list of objects in the providers association.
Input parameters: the list of values @vals to add to the providers association. NOTE: submitting a single value is permitted.
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
Methods for the auditTrail association.
A list of Audit instances that track changes to the instance of Describable.
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
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
The restricted getter method for the auditTrail association.
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.
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
Methods for the propertySets association.
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.
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
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
The restricted getter method for the propertySets association.
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.
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
Methods for the analysisResults association.
The results of analyzing the data, typically with a clustering algorithm.
The restricted setter method for the analysisResults association.
Input parameters: the value to which the analysisResults association will be set : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster
Return value: the current value of the analysisResults association : a reference to an array of objects of type Bio::MAGE::HigherLevelAnalysis::BioAssayDataCluster
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::HigherLevelAnalysis::BioAssayDataCluster instances
The restricted getter method for the analysisResults association.
Because the analysisResults association has list cardinality, it may store more than one value. This method adds the current list of objects in the analysisResults association.
Input parameters: the list of values @vals to add to the analysisResults association. NOTE: submitting a single value is permitted.
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::HigherLevelAnalysis::BioAssayDataCluster
Methods for the bioAssays association.
The collection of BioAssays for this Experiment.
The restricted setter method for the bioAssays association.
Input parameters: the value to which the bioAssays association will be set : a reference to an array of objects of type Bio::MAGE::BioAssay::BioAssay
Return value: the current value of the bioAssays association : a reference to an array of objects of type Bio::MAGE::BioAssay::BioAssay
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::BioAssay::BioAssay instances
The restricted getter method for the bioAssays association.
Because the bioAssays association has list cardinality, it may store more than one value. This method adds the current list of objects in the bioAssays association.
Input parameters: the list of values @vals to add to the bioAssays association. NOTE: submitting a single value is permitted.
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::BioAssay::BioAssay
Methods for the bioAssayData association.
The collection of BioAssayDatas for this Experiment.
The restricted setter method for the bioAssayData association.
Input parameters: the value to which the bioAssayData association will be set : a reference to an array of objects of type Bio::MAGE::BioAssayData::BioAssayData
Return value: the current value of the bioAssayData association : a reference to an array of objects of type Bio::MAGE::BioAssayData::BioAssayData
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::BioAssayData::BioAssayData instances
The restricted getter method for the bioAssayData association.
Because the bioAssayData association has list cardinality, it may store more than one value. This method adds the current list of objects in the bioAssayData association.
Input parameters: the list of values @vals to add to the bioAssayData association. NOTE: submitting a single value is permitted.
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::BioAssayData::BioAssayData
Methods for the descriptions association.
Free hand text descriptions. Makes available the associations of Description to an instance of Describable.
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
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
The restricted getter method for the descriptions association.
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.
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
Methods for the security association.
Information on the security for the instance of the class.
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.
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
The restricted getter method for the security association.
Return value: the current value of the security association : an instance of type Bio::MAGE::AuditAndSecurity::Security.
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.
slots
attributes
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.
slot
Slots are implemented using unified getter/setter methods:
Retrieves the current value of the slot.
Store $new_var in the slot - the return value is also $new_var.
Returns the list of all slots in the class.
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.
attribute
association
In the Perl implementation of MAGE-OM classes, association and attribute accessors are implemented using three separate methods:
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.
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.
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.
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:
Bio::MAGE::Base
See elsewhere in this page for a detailed description of these methods.
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).
5 POD Errors
The following errors were encountered while parsing the POD:
'=item' outside of any '=over'
You forgot a '=back' before '=head2'
Expected '=item 2'
Expected '=item 3'
Expected '=item 4'
To install Bio::MAGE, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::MAGE
CPAN shell
perl -MCPAN -e shell install Bio::MAGE
For more information on module installation, please visit the detailed CPAN module installation guide.