Detailed Description

The ComponentDefinition class represents the structural entities of a biological design.

The primary usage of this class is to represent structural entities with designed sequences, such as DNA, RNA, and proteins, but it can also be used to represent any other entity that is part of a design, such as small molecules, proteins, and complexes

Public Attributes
URIProperty	types
	The types property is a REQUIRED set of URIs that specifies the category of biochemical or physical entity (for example DNA, protein, or small molecule) that a ComponentDefinition object abstracts for the purpose of engineering design. More...

URIProperty	roles
	The roles property is an OPTIONAL set of URIs that clarifies the potential function of the entity represented by a ComponentDefinition in a biochemical or physical context. More...

OwnedObject< Component >	components
	The components property is OPTIONAL and MAY specify a set of Component objects that are contained by the ComponentDefinition. The components properties of ComponentDefinition objects can be used to construct a hierarchy of Component and ComponentDefinition objects. If a ComponentDefinition in such a hierarchy refers to one or more Sequence objects, and there exist ComponentDefinition objects lower in the hierarchy that refer to Sequence objects with the same encoding, then the elements properties of these Sequence objects SHOULD be consistent with each other, such that well-defined mappings exist from the “lower level” elements to the “higher level” elements. This mapping is also subject to any restrictions on the positions of the Component objects in the hierarchy that are imposed by the SequenceAnnotation or SequenceConstraint objects contained by the ComponentDefinition objects in the hierarchy. The set of relations between Component and ComponentDefinition objects is strictly acyclic.

ReferencedObject	sequences
	The sequences property is OPTIONAL and MAY include a URI that refer to a Sequence object. The referenced object defines the primary structure of the ComponentDefinition.

OwnedObject< SequenceAnnotation >	sequenceAnnotations
	The sequenceAnnotations property is OPTIONAL and MAY contain a set of SequenceAnnotation objects. Each SequenceAnnotation specifies and describes a potentially discontiguous region on the Sequence objects referred to by the ComponentDefinition.

OwnedObject< SequenceConstraint >	sequenceConstraints
	The sequenceConstraints property is OPTIONAL and MAY contain a set of SequenceConstraint objects. These objects describe any restrictions on the relative, sequence-based positions and/or orientations of the Component objects contained by the ComponentDefinition. For example, the ComponentDefinition of a gene might specify that the position of its promoter Component precedes that of its CDS Component. This is particularly useful when a ComponentDefinition lacks a Sequence and therefore cannot specify the precise, sequence-based positions of its Component objects using SequenceAnnotation objects.

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
	ComponentDefinition (std::string uri="example", std::string type=BIOPAX_DNA, std::string version=VERSION_STRING)
	Construct a ComponentDefinition. More...

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

void	assemble (std::vector< ComponentDefinition *> &list_of_components, std::string assembly_standard="")
	Assembles ComponentDefinitions into an abstraction hierarchy. More...

void	assemble (std::vector< ComponentDefinition *> &list_of_components, Document &doc, std::string assembly_standard="")
	Assembles ComponentDefinitions into an abstraction hierarchy. More...

void	assemblePrimaryStructure (std::vector< std::string > &primary_structure, std::string assembly_standard="")
	Assembles ComponentDefinition into a linear primary structure. More...

void	assemblePrimaryStructure (std::vector< ComponentDefinition *> &primary_structure, std::string assembly_standard="")
	Assembles ComponentDefinition into a linear primary structure. More...

void	assemblePrimaryStructure (std::vector< ComponentDefinition *> &primary_structure, Document &doc, std::string assembly_standard="")
	Assembles ComponentDefinition into a linear primary structure. More...

void	assemble (std::vector< std::string > &list_of_uris, std::string assembly_standard="")
	Assembles ComponentDefinitions into an abstraction hierarchy. More...

std::string	compile ()
	Compiles an abstraction hierarchy of ComponentDefinitions into a nucleotide sequence. If no Sequence object is associated with this ComponentDefinition, one will be automatically instantiated.

std::string	updateSequence (std::string composite_sequence="")
	Assemble a parent ComponentDefinition's Sequence from its subcomponent Sequences. More...

std::vector< Component * >	getInSequentialOrder ()
	Orders this ComponentDefinition's member Components into a linear arrangement based on Sequence Constraints. More...

int	hasUpstreamComponent (Component &current_component)
	Checks if the specified Component has a Component upstream in linear arrangement on the DNA strand. More...

Component &	getUpstreamComponent (Component &current_component)
	Get the upstream Component. More...

int	hasDownstreamComponent (Component &current_component)
	Checks if the specified Component has a Component downstream in linear arrangement on the DNA strand. More...

Component &	getDownstreamComponent (Component &current_component)
	Get the downstream Component. More...

Component &	getFirstComponent ()
	Gets the first Component in a linear sequence. More...

Component &	getLastComponent ()
	Gets the last Component in a linear sequence. More...

std::vector< ComponentDefinition * >	applyToComponentHierarchy (void(callback_fn)(ComponentDefinition , void )=NULL, void user_data=NULL)
	Perform an operation on every Component in a structurally-linked hierarchy of Components by applying a callback function. More...

std::vector< ComponentDefinition * >	getPrimaryStructure ()
	Get the primary sequence of a design in terms of its sequentially ordered Components.

void	insertDownstreamComponent (Component &target, ComponentDefinition &insert)
	Insert a Component downstream of another in a primary sequence, shifting any adjacent Components dowstream as well. More...

void	insertUpstreamComponent (Component &target, ComponentDefinition &insert)
	Insert a Component upstream of another in a primary sequence, shifting any adjacent Components upstream as well. More...

void	addUpstreamFlank (Component &target, std::string elements)
	This may be a useful method when building up SBOL representations of natural DNA sequences. More...

void	addDownstreamFlank (Component &target, std::string elements)
	This may be a useful method when building up SBOL representations of natural DNA sequences. More...

bool	isRegular (std::string &msg)
	Use this diagnose an irregular design. More...

bool	isRegular ()
	Recursively checks if this ComponentDefinition defines a SequenceAnnotation and Range for every Sequence. More...

bool	isComplete (std::string &msg)
	Use this diagnose an incomplete design. More...

bool	isComplete ()
	Recursively verifies that the parent Document contains a ComponentDefinition and Sequence for each and every ComponentDefinition in the abstraction hierarchy. More...

void	disassemble (int range_start=1)
	Instantiates a Component for every SequenceAnnotation. When converting from a flat GenBank file to a flat SBOL file, the result is a ComponentDefinition with SequenceAnnotations. This method will convert the flat SBOL file into hierarchical SBOL.

void	participate (Participation &species)
	A convenience method that assigns a component to participate in a biochemical reaction. 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

◆ ComponentDefinition() [1/2]

ComponentDefinition	(	std::string	uri = `"example"`,
		std::string	type = `BIOPAX_DNA`,
		std::string	version = `VERSION_STRING`
	)

inline

Construct a ComponentDefinition.

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.
type	A BioPAX ontology term that indicates whether the ComponentDefinition is DNA, RNA, protein, or some other molecule type.
version	An arbitrary version string. If SBOLCompliance is enabled, this should be a Maven version string of the form "major.minor.patch".

◆ ComponentDefinition() [2/2]

ComponentDefinition	(	rdf_type	type,
		std::string	uri,
		std::string	component_type,
		std::string	version
	)

inline

Constructor used for defining extension classes.

Parameters

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

Member Function Documentation

◆ addDownstreamFlank()

void addDownstreamFlank	(	Component &	target,
		std::string	elements
	)

This may be a useful method when building up SBOL representations of natural DNA sequences.

For example it is often necessary to specify components that are assumed to have no meaningful role in the design, but are nevertheless important to fill in regions of sequence. This method autoconstructs a ComponentDefinition and Sequence object to create an arbitrary flanking sequence around design Components. The new ComponentDefinition will have Sequence Ontology type of flanking_sequence.

Parameters

target	The new flanking sequence will be placed downstream of the target
elements	The primary sequence elements will be assigned to the autoconstructed Sequence object. The encoding is inferred

◆ 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

◆ addUpstreamFlank()

void addUpstreamFlank	(	Component &	target,
		std::string	elements
	)

This may be a useful method when building up SBOL representations of natural DNA sequences.

For example it is often necessary to specify components that are assumed to have no meaningful role in the design, but are nevertheless important to fill in regions of sequence. This method autoconstructs a ComponentDefinition and Sequence object to create an arbitrary flanking sequence around design Components. The new ComponentDefinition will have Sequence Ontology type of flanking_region or SO:0000239

Parameters

target	The new flanking sequence will be placed upstream of the target
elements	The primary sequence elements will be assigned to the autoconstructed Sequence object. The encoding is inferred

◆ applyToComponentHierarchy()

vector< ComponentDefinition * > applyToComponentHierarchy	(	void()(ComponentDefinition , void *)	callback_fn = `NULL`,
		void *	user_data = `NULL`
	)

Perform an operation on every Component in a structurally-linked hierarchy of Components by applying a callback function.

If no callback is specified, the default behavior is to return a pointer list of each Component in the hierarchy.

Parameters

callback_fun	A pointer to a callback function with signature void callback_fn(ComponentDefinition , void ).
user_data	Arbitrary user data which can be passed in and out of the callback as an argument or return value.

Returns: Returns a flat list of pointers to all Components in the hierarchy.

◆ assemble() [1/3]

void assemble	(	std::vector< ComponentDefinition *> &	list_of_components,
		std::string	assembly_standard = `""`
	)

Assembles ComponentDefinitions into an abstraction hierarchy.

The resulting data structure is a partial design, still lacking a primary structure or explicit sequence. To form a primary structure out of the ComponentDefinitions, call linearize after calling assemble. To fully realize the target sequence, use Sequence::assemble().

Parameters

list_of_components	A list of subcomponents that will compose this ComponentDefinition
assembly_standard	An optional argument such as IGEM_STANDARD_ASSEMBLY that affects how components are composed and the final target sequence

◆ assemble() [2/3]

void assemble	(	std::vector< ComponentDefinition *> &	list_of_components,
		Document &	doc,
		std::string	assembly_standard = `""`
	)

Assembles ComponentDefinitions into an abstraction hierarchy.

The resulting data structure is a partial design, still lacking a primary structure or explicit sequence. To form a primary structure out of the ComponentDefinitions, call linearize after calling assemble. To fully realize the target sequence, use Sequence::assemble().

Parameters

list_of_components	A list of subcomponents that will compose this ComponentDefinition
doc	The Document to which the assembled ComponentDefinitions will be added
assembly_standard	An optional argument such as IGEM_STANDARD_ASSEMBLY that affects how components are composed and the final target sequence

◆ assemble() [3/3]

void assemble	(	std::vector< std::string > &	list_of_uris,
		std::string	assembly_standard = `""`
	)

Assembles ComponentDefinitions into an abstraction hierarchy.

The resulting data structure is a partial design, still lacking a primary structure or explicit sequence. To form a primary structure out of the ComponentDefinitions, call linearize after calling assemble. To fully realize the target sequence, use Sequence::assemble().

Parameters

list_of_uris	A list of URIs for the constituent ComponentDefinitions, or displayIds if using SBOL-compliant URIs
assembly_standard	An optional argument such as IGEM_STANDARD_ASSEMBLY that affects how components are composed and the final target sequence

◆ assemblePrimaryStructure() [1/3]

void assemblePrimaryStructure	(	std::vector< std::string > &	primary_structure,
		std::string	assembly_standard = `""`
	)

Assembles ComponentDefinition into a linear primary structure.

The resulting data structure is a partial design, still lacking an explicit sequence. To fully realize the target sequence, use Sequence::assemble().

Parameters

primary_structure	A list of URIs for the constituent ComponentDefinitions, or displayIds if using SBOL-compliant URIs
assembly_standard	An optional argument such as IGEM_STANDARD_ASSEMBLY that affects how components are composed and the final target sequence

◆ assemblePrimaryStructure() [2/3]

void assemblePrimaryStructure	(	std::vector< ComponentDefinition *> &	primary_structure,
		std::string	assembly_standard = `""`
	)

Assembles ComponentDefinition into a linear primary structure.

The resulting data structure is a partial design, still lacking an explicit sequence. To fully realize the target sequence, use Sequence::assemble().

Parameters

list_of_components	A list of subcomponents that will compose this ComponentDefinition
assembly_standard	An optional argument such as IGEM_STANDARD_ASSEMBLY that affects how components are composed and the final target sequence

◆ assemblePrimaryStructure() [3/3]

void assemblePrimaryStructure	(	std::vector< ComponentDefinition *> &	primary_structure,
		Document &	doc,
		std::string	assembly_standard = `""`
	)

Assembles ComponentDefinition into a linear primary structure.

The resulting data structure is a partial design, still lacking an explicit sequence. To fully realize the target sequence, use Sequence::assemble().

Parameters

list_of_components	A list of subcomponents that will compose this ComponentDefinition
doc	The Document to which the assembled ComponentDefinitions will be added
assembly_standard	An optional argument such as IGEM_STANDARD_ASSEMBLY that affects how components are composed and the final target sequence

◆ 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

◆ getDownstreamComponent()

Component & getDownstreamComponent ( Component & current_component )

Get the downstream Component.

Returns: The downstream component

◆ getFirstComponent()

Component & getFirstComponent ( )

Gets the first Component in a linear sequence.

Returns: The first component in sequential order

◆ getInSequentialOrder()

vector< Component * > getInSequentialOrder ( )

Orders this ComponentDefinition's member Components into a linear arrangement based on Sequence Constraints.

Returns: Primary sequence structure

◆ getLastComponent()

Component & getLastComponent ( )

Gets the last Component in a linear sequence.

Returns: The last component in sequential order

◆ 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

◆ getUpstreamComponent()

Component & getUpstreamComponent ( Component & current_component )

Get the upstream Component.

Returns: The upstream component

◆ hasDownstreamComponent()

int hasDownstreamComponent ( Component & current_component )

Checks if the specified Component has a Component downstream in linear arrangement on the DNA strand.

Checks that the appropriate SequenceConstraint exists.

Parameters

current_component A Component in this ComponentDefinition

Returns: 1 if found, 0 if not

◆ hasUpstreamComponent()

int hasUpstreamComponent ( Component & current_component )

Checks if the specified Component has a Component upstream in linear arrangement on the DNA strand.

Checks that the appropriate SequenceConstraint exists.

Parameters

current_component A Component in this ComponentDefinition

Returns: 1 if found, 0 if not

◆ insertDownstreamComponent()

void insertDownstreamComponent	(	Component &	target,
		ComponentDefinition &	insert
	)

Insert a Component downstream of another in a primary sequence, shifting any adjacent Components dowstream as well.

Parameters

target	The target Component will be upstream of the insert Component after this operation.
insert	The insert Component is inserted downstream of the target Component.

◆ insertUpstreamComponent()

void insertUpstreamComponent	(	Component &	target,
		ComponentDefinition &	insert
	)

Insert a Component upstream of another in a primary sequence, shifting any adjacent Components upstream as well.

Parameters

target	The target Component will be downstream of the insert Component after this operation.
insert	The insert Component is inserted upstream of the target Component.

◆ isComplete() [1/2]

bool isComplete ( std::string & msg )

Use this diagnose an incomplete design.

Recursively checks if this ComponentDefinition defines a SequenceAnnotation and Range for every Sequence. Completeness does not guarantee regularity

Parameters

msg	A message for diagnosing the irregularity, if any is found. The message is returned through an argument of type std::string&

Returns: true if the abstraction hierarchy is regular, false otherwise.

◆ isComplete() [2/2]

bool isComplete ( )

Recursively verifies that the parent Document contains a ComponentDefinition and Sequence for each and every ComponentDefinition in the abstraction hierarchy.

If a ComponentDefinition is not complete, some objects are missing from the Document or externally linked. Diagnose with isComplete(std::string &msg)

Returns: true if the abstraction hierarchy is complete, false otherwise.

◆ isRegular() [1/2]

bool isRegular ( std::string & msg )

Use this diagnose an irregular design.

Recursively checks if this ComponentDefinition defines a SequenceAnnotation and Range for every Sequence. Regularity is more stringent than completeness. A design must be complete to be regular.

Parameters

msg	A message for diagnosing the irregularity, if any is found. The message is returned through an argument of type std::string&

Returns: true if the abstraction hierarchy is regular, false otherwise.

◆ isRegular() [2/2]

bool isRegular ( )

Recursively checks if this ComponentDefinition defines a SequenceAnnotation and Range for every Sequence.

Regularity is more stringent than completeness. A design must be complete to be regular. If the Component is irregular, diagnose with isRegular(std::string &msg)

Returns: true if the abstraction hierarchy is regular, false otherwise.

◆ participate()

void participate ( Participation & species )

A convenience method that assigns a component to participate in a biochemical reaction.

Behind the scenes, it auto-constructs a FunctionalComponent for this ComponentDefinition and assigns it to a Participation

Parameters

species A Participation object (ie, participant species in a biochemical Interaction).

◆ 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

◆ updateSequence()

std::string updateSequence ( std::string composite_sequence = "" )

Assemble a parent ComponentDefinition's Sequence from its subcomponent Sequences.

Parameters

composite_sequence A recursive parameter, use default value

Returns: The assembled parent sequence

Member Data Documentation

◆ roles

URIProperty roles

The roles property is an OPTIONAL set of URIs that clarifies the potential function of the entity represented by a ComponentDefinition in a biochemical or physical context.

The roles property of a ComponentDefinition MAY contain one or more URIs that MUST identify terms from ontologies that are consistent with the types property of the ComponentDefinition. For example, the roles property of a DNA or RNA ComponentDefinition could contain URIs identifying terms from the Sequence Ontology (SO). See the table below for common examples

Role	URI for Sequence Ontology Term	LibSBOL symbol
Miscellaneous	http://identifiers.org/so/SO:0000001	SO_MISC
Promoter	http://identifiers.org/so/SO:0000167	SO_PROMOTER
RBS	http://identifiers.org/so/SO:0000139	SO_RBS
CDS	http://identifiers.org/so/SO:0000316	SO_CDS
Terminator	http://identifiers.org/so/SO:0000141	SO_TERMINATOR
Gene	http://identifiers.org/so/SO:0000704
Operator	http://identifiers.org/so/SO:0000057
Engineered Gene	http://identifiers.org/so/SO:0000280
mRNA	http://identifiers.org/so/SO:0000234
Effector	http://identifiers.org/chebi/CHEBI:35224

◆ types

URIProperty types

The types property is a REQUIRED set of URIs that specifies the category of biochemical or physical entity (for example DNA, protein, or small molecule) that a ComponentDefinition object abstracts for the purpose of engineering design.

The types property of every ComponentDefinition MUST contain one or more URIs that MUST identify terms from appropriate ontologies, such as the BioPAX ontology or the ontology of Chemical Entities of Biological Interest. See the table below for examples.

Type	URI for BioPAX Term	LibSBOL symbol
DNA	http://www.biopax.org/release/biopax-level3.owl#DnaRegion	BIOPAX_DNA
RNA	http://www.biopax.org/release/biopax-level3.owl#RnaRegion	BIOPAX_RNA
Protein	http://www.biopax.org/release/biopax-level3.owl#Protein	BIOPAX_PROTEIN
Small Molecule	http://www.biopax.org/release/biopax-level3.owl#SmallMolecule	BIOPAX_SMALL_MOLECULE
Complex	http://www.biopax.org/release/biopax-level3.owl#Complex	BIOPAX_COMPLEX

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

/Users/bbartley/Dev/git/libSBOL/source/componentdefinition.h
/Users/bbartley/Dev/git/libSBOL/source/assembly.cpp

Inheritance diagram for ComponentDefinition:

Detailed Description

Public Attributes

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

◆ ComponentDefinition() [1/2]

◆ ComponentDefinition() [2/2]

Member Function Documentation

◆ addDownstreamFlank()

◆ addPropertyValue()

◆ addUpstreamFlank()

◆ applyToComponentHierarchy()

◆ assemble() [1/3]

◆ assemble() [2/3]

◆ assemble() [3/3]

◆ assemblePrimaryStructure() [1/3]

◆ assemblePrimaryStructure() [2/3]

◆ assemblePrimaryStructure() [3/3]

◆ close()

◆ compare()

◆ copy()

◆ find()

◆ find_property()

◆ find_property_value()

◆ find_reference()

◆ generate() [1/2]

◆ generate() [2/2]

◆ getAnnotation()

◆ getClassName()

◆ getDownstreamComponent()

◆ getFirstComponent()

◆ getInSequentialOrder()

◆ getLastComponent()

◆ getProperties()

◆ getPropertyValue()

◆ getPropertyValues()

◆ getTypeURI()

◆ getUpstreamComponent()

◆ hasDownstreamComponent()

◆ hasUpstreamComponent()

◆ insertDownstreamComponent()

◆ insertUpstreamComponent()

◆ isComplete() [1/2]

◆ isComplete() [2/2]

◆ isRegular() [1/2]

◆ isRegular() [2/2]

◆ participate()

◆ register_extension_class()

◆ setAnnotation()

◆ setPropertyValue()

◆ simpleCopy()

◆ updateSequence()

Member Data Documentation

◆ roles

◆ types