Detailed Description

A ComponentDeriviation specifies the composition of a combinatorial design or variant library for common use cases in synthetic biology, such as tuning the performance of a genetic circuit or biosynthetic pathway through combinatorial DNA assembly and screening.

Public Attributes
URIProperty	strategy
	The `strategy` property is OPTIONAL and has a data type of URI. More...

ReferencedObject	masterTemplate
	The `master` property is REQUIRED and MUST contain a URI that refers to a ComponentDefinition. This ComponentDefinition is expected to serve as a template for the derivation of new ComponentDefinition objects. Consequently, its components property SHOULD contain one or more Component objects that describe its substructure (referred to hereafter as template Component objects), and its sequenceConstraints property MAY also contain one or more SequenceConstraint objects that constrain this substructure.

OwnedObject< VariableComponent >	variableComponents
	VariableComponent objects denote the choices available when deriving the library of variants specified by a CombinatorialDerivation.

URIProperty	persistentIdentity
	The persistentIdentity property is OPTIONAL and has a data type of URI. This URI serves to uniquely refer to a set of SBOL objects that are different versions of each other. An Identified object MUST be referred to using either its identity URI or its persistentIdentity URI.

TextProperty	displayId
	The displayId property is an OPTIONAL identifier with a data type of String. This property is intended to be an intermediate between name and identity that is machine-readable, but more human-readable than the full URI of an identity. If the displayId property is used, then its String value SHOULD be locally unique (global uniqueness is not necessary) and MUST be composed of only alphanumeric or underscore characters and MUST NOT begin with a digit.

VersionProperty	version
	If the version property is used, then it is RECOMMENDED that version numbering follow the conventions of semantic versioning, particularly as implemented by Maven. This convention represents versions as sequences of numbers and qualifiers that are separated by the characters “.” and “-” and are compared in lexicographical order (for example, 1 < 1.3.1 < 2.0-beta). For a full explanation, see the linked resources.

URIProperty	wasDerivedFrom
	The wasDerivedFrom property is OPTIONAL and has a data type of URI. An SBOL object with this property refers to another SBOL object or non-SBOL resource from which this object was derived. If the wasDerivedFrom property of an SBOL object A that refers to an SBOL object B has an identical persistentIdentity, and both A and B have a version, then the version of B MUST precede that of A. In addition, an SBOL object MUST NOT refer to itself via its own wasDerivedFrom property or form a cyclical chain of references via its wasDerivedFrom property and those of other SBOL objects. For example, the reference chain “ A was derived from B and B was derived from A” is cyclical.

ReferencedObject	wasGeneratedBy
	An Activity which generated this ComponentDefinition, eg., a design process like codon-optimization or a construction process like Gibson Assembly.

TextProperty	name
	The name property is OPTIONAL and has a data type of String. This property is intended to be displayed to a human when visualizing an Identified object. If an Identified object lacks a name, then software tools SHOULD instead display the object’s displayId or identity. It is RECOMMENDED that software tools give users the ability to switch perspectives between name properties that are human-readable and displayId properties that are less human-readable, but are more likely to be unique.

TextProperty	description
	The description property is OPTIONAL and has a data type of String. This property is intended to contain a more thorough text description of an Identified object.

URIProperty	identity
	The identity property is REQUIRED by all Identified objects and has a data type of URI. A given Identified object’s identity URI MUST be globally unique among all other identity URIs. The identity of a compliant SBOL object MUST begin with a URI prefix that maps to a domain over which the user has control. Namely, the user can guarantee uniqueness of identities within this domain. For other best practices regarding URIs see Section 11.2 of the SBOL specification doucment.

Public Member Functions
	CombinatorialDerivation (std::string uri="example", std::string strategy="http://sbols.org/v2#enumerate", std::string version=VERSION_STRING)
	Constructor. More...

	CombinatorialDerivation (rdf_type type, std::string uri, std::string strategy, std::string version)
	Constructor used for defining extension classes. More...

template<class SBOLClass >
SBOLClass &	copy (Document *target_doc=NULL, std::string ns="", std::string version="")
	Recursively copies an object. More...

template<class SBOLClass >
SBOLClass &	simpleCopy (std::string uri)
	Copies an object. More...

template<class SBOLClass >
SBOLClass &	generate (std::string uri)

template<class SBOLClass >
SBOLClass &	generate (std::string uri, Agent &agent, Plan &plan, std::vector< Identified *> usages={})

virtual rdf_type	getTypeURI ()

std::string	getClassName (std::string type)

SBOLObject *	find (std::string uri)
	Search this object recursively to see if an object or any child object with URI already exists. More...

SBOLObject *	find_property (std::string uri)
	Search this object recursively to see if it contains a member property with the given RDF type. More...

std::vector< SBOLObject * >	find_property_value (std::string uri, std::string value, std::vector< SBOLObject *> matches={})
	Search this object recursively to see if it contains a member property with the given RDF type and indicated property value. More...

std::vector< SBOLObject * >	find_reference (std::string uri)
	Search this object recursively to see if it contains a member property with the given RDF type and indicated property value. More...

int	compare (SBOLObject *comparand)
	Compare two SBOL objects or Documents. More...

std::string	getPropertyValue (std::string property_uri)
	Get the value of a custom annotation property by its URI. More...

std::vector< std::string >	getPropertyValues (std::string property_uri)
	Get all values of a custom annotation property by its URI. More...

std::vector< std::string >	getProperties ()
	Gets URIs for all properties contained by this object. More...

void	setPropertyValue (std::string property_uri, std::string val)
	Set and overwrite the value for a user-defined annotation property. More...

void	addPropertyValue (std::string property_uri, std::string val)
	Append a value to a user-defined annotation property. More...

void	setAnnotation (std::string property_uri, std::string val)
	Set the value for a user-defined annotation property. More...

std::string	getAnnotation (std::string property_uri)
	Get the value of a custom annotation property by its URI. More...

virtual void	close ()
	Use this method to destroy an SBOL object that is not contained by a parent Document. More...

Protected Member Functions
template<class ExtensionClass >
void	register_extension_class (std::string ns, std::string ns_prefix, std::string class_name)
	Register an extension class and its namespace, so custom data can be embedded into and read from SBOL files. More...

Constructor & Destructor Documentation

◆ CombinatorialDerivation() [1/2]

CombinatorialDerivation	(	std::string	uri = `"example"`,
		std::string	strategy = `"http://sbols.org/v2#enumerate"`,
		std::string	version = `VERSION_STRING`
	)

inline

Constructor.

Parameters

uri	A full URI including a scheme, namespace, and identifier. If SBOLCompliance configuration is enabled, then this argument is simply the displayId for the new object and a full URI will automatically be constructed.
strategy	A URI indicating SBOL_ENUMERATE or SBOL_SAMPLE

◆ CombinatorialDerivation() [2/2]

CombinatorialDerivation	(	rdf_type	type,
		std::string	uri,
		std::string	strategy,
		std::string	version
	)

inline

Constructor used for defining extension classes.

Parameters

rdf_type The RDF type for an extension class derived from this one

Member Function Documentation

◆ addPropertyValue()

void addPropertyValue	(	std::string	property_uri,
		std::string	val
	)

inherited

Append a value to a user-defined annotation property.

Either a literal or URI value

◆ close()

void close ( )

virtualinherited

Use this method to destroy an SBOL object that is not contained by a parent Document.

If the object does have a parent Document, instead use doc.close() with the object's URI identity as an argument. Recurse through child objects and delete them.

◆ compare()

int compare ( SBOLObject * comparand )

inherited

Compare two SBOL objects or Documents.

The behavior is currently undefined for objects with custom annotations or extension classes.

Parameters

comparand A pointer to the object being compared to this one.

Returns: 1 if the objects are identical, 0 if they are different

◆ copy()

SBOLClass & copy	(	Document *	target_doc = `NULL`,
		std::string	ns = `""`,
		std::string	version = `""`
	)

inherited

Recursively copies an object.

Use this to copy an object to a new document, a new namespace, or to increment its version recursively. An object be recursively copied into a new document and a new namespace, assuming compliant URIs. If the optional version argument is specified, it will be used instead of incrementing the copied object's version (this can be used when using a custom versioning scheme other than libSBOL's default).

Template Parameters

SBOLClass The type of SBOL object being copied

Parameters

new_doc	The new copies will be attached to this Document. NULL by default.
ns	This namespace will be substituted for the current namespace (as configured by setHomespace) in all SBOL-compliant URIs.
version	A new version

Returns: The copied object.

◆ find()

SBOLObject * find ( std::string uri )

inherited

Search this object recursively to see if an object or any child object with URI already exists.

Parameters

uri	The URI to search for.

Returns: A pointer to theobject with this URI if it exists, NULL otherwise

◆ find_property()

SBOLObject * find_property ( std::string uri )

inherited

Search this object recursively to see if it contains a member property with the given RDF type.

Parameters

uri	The RDF type of the property to search for.

Returns: A pointer to the object that contains a member property with the specified RDF type, NULL otherwise

◆ find_property_value()

vector< SBOLObject * > find_property_value	(	std::string	uri,
		std::string	value,
		std::vector< SBOLObject *>	matches = `{}`
	)

inherited

Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.

Parameters

uri	The RDF type of the property to search for.
value	The property value to match

Returns: A vector containing all objects found that contain a member property with the specified RDF type

◆ find_reference()

vector< SBOLObject * > find_reference ( std::string uri )

inherited

Search this object recursively to see if it contains a member property with the given RDF type and indicated property value.

Parameters

uri	A URI, either an ontology term or an object reference, to search for

Returns: A vector containing all objects found that contain the URI in a property value

◆ generate() [1/2]

SBOLClass & generate ( std::string uri )

inherited

Parameters

uri	A URI for the new object, or a displayId if operating in SBOLCompliant mode

Template Parameters

The	type of SBOL object to generate

◆ generate() [2/2]

SBOLClass& generate	(	std::string	uri,
		Agent &	agent,
		Plan &	plan,
		std::vector< Identified *>	usages = `{}`
	)

inherited

Parameters

uri	A URI for the new object, or a displayId if operating in SBOLCompliant mode

Template Parameters

The	type of SBOL object to generate

◆ getAnnotation()

std::string getAnnotation ( std::string property_uri )

inherited

Get the value of a custom annotation property by its URI.

Synonymous with getPropertyValue

Parameters

property_uri The URI for the property

Returns: The value of the property or SBOL_ERROR_NOT_FOUND

◆ getClassName()

std::string getClassName ( std::string type )

inherited

Returns: Parses a local class name from the RDF-type of this SBOL Object

◆ getProperties()

std::vector< std::string > getProperties ( )

inherited

Gets URIs for all properties contained by this object.

This includes SBOL core properties as well as custom annotations. Use this to find custom extension data in an SBOL file.

Returns: A vector of URIs that identify the properties contained in this object

◆ getPropertyValue()

std::string getPropertyValue ( std::string property_uri )

inherited

Get the value of a custom annotation property by its URI.

Parameters

property_uri The URI for the property

Returns: The value of the property or SBOL_ERROR_NOT_FOUND

◆ getPropertyValues()

std::vector< std::string > getPropertyValues ( std::string property_uri )

inherited

Get all values of a custom annotation property by its URI.

Parameters

property_uri The URI for the property

Returns: A vector of property values or SBOL_ERROR_NOT_FOUND

◆ getTypeURI()

rdf_type getTypeURI ( )

virtualinherited

Returns: The uniform resource identifier that describes the RDF-type of this SBOL Object

◆ register_extension_class()

void register_extension_class	(	std::string	ns,
		std::string	ns_prefix,
		std::string	class_name
	)

protectedinherited

Register an extension class and its namespace, so custom data can be embedded into and read from SBOL files.

Template Parameters

ExtensionClass The new class

Parameters

ns	The extension namespace, eg, http://myhome.org/my_extension#. It's important that the namespace ends in a forward-slash or hash
ns_prefix	A shorthand symbol for the full namespace as it will appear in the output file, eg, my_extension

◆ setAnnotation()

void setAnnotation	(	std::string	property_uri,
		std::string	val
	)

inherited

Set the value for a user-defined annotation property.

Synonymous with setPropertyValue If the value is a URI, it should be surrounded by angle brackets, else it will be interpreted as a literal value

◆ setPropertyValue()

void setPropertyValue	(	std::string	property_uri,
		std::string	val
	)

inherited

Set and overwrite the value for a user-defined annotation property.

Either a literal or URI value

◆ simpleCopy()

SBOLClass & simpleCopy ( std::string uri )

inherited

Copies an object.

No child objects are copied.

Parameters

uri	A URI for the new object, or a displayId if operating in SBOLCompliant mode

Template Parameters

Usually the same type of SBOL object as this

Member Data Documentation

◆ strategy

URIProperty strategy

The strategy property is OPTIONAL and has a data type of URI.

Table 1 provides a list of REQUIRED strategy URIs. If the strategy property is not empty, then it MUST contain a URI from Table 1. This property recommends how many ComponentDefinition objects a user SHOULD derive from the template ComponentDefinition.

Strategy URI	Description
http://sbols.org/v2#enumerate	A user SHOULD derive all `ComponentDefinition` objects with a unique substructure as specified by the `Component` objects contained by the `template` `ComponentDefinition` and the `VariableComponent` objects contained by the `CombinatorialDerivation`.
http://sbols.org/v2#sample	A user SHOULD derive a subset of all `ComponentDefinition` objects with a unique substructure as specified by the `Component` objects contained by the `template` `ComponentDefinition` and the `VariableComponent` objects contained by the `CombinatorialDerivation`. The manner in which this subset is chosen is for the user to decide.

The documentation for this class was generated from the following file:

/Users/bbartley/Dev/git/libSBOL/source/combinatorialderivation.h

Inheritance diagram for CombinatorialDerivation:

Detailed Description

Public Attributes

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

◆ CombinatorialDerivation() [1/2]

◆ CombinatorialDerivation() [2/2]

Member Function Documentation

◆ addPropertyValue()

◆ close()

◆ compare()

◆ copy()

◆ find()

◆ find_property()

◆ find_property_value()

◆ find_reference()

◆ generate() [1/2]

◆ generate() [2/2]

◆ getAnnotation()

◆ getClassName()

◆ getProperties()

◆ getPropertyValue()

◆ getPropertyValues()

◆ getTypeURI()

◆ register_extension_class()

◆ setAnnotation()

◆ setPropertyValue()

◆ simpleCopy()

Member Data Documentation

◆ strategy