Detailed Description

The primary structure (eg, nucleotide or amino acid sequence) of a ComponentDefinition object.

Public Attributes
TextProperty	elements
	The elements property is a REQUIRED String of characters that represents the constituents of a biological or chemical molecule. For example, these characters could represent the nucleotide bases of a molecule of DNA, the amino acid residues of a protein, or the atoms and chemical bonds of a small molecule.

URIProperty	encoding
	The encoding property is REQUIRED and has a data type of URI. More...

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
	Sequence (std::string uri="example", std::string elements="", std::string encoding=SBOL_ENCODING_IUPAC, std::string version=VERSION_STRING)
	Construct a Seqiemce. More...

	Sequence (rdf_type type_uri, std::string uri, std::string elements, std::string encoding, std::string version)
	Constructor used for defining extension classes. More...

std::string	assemble (std::string composite_sequence="")
	Calculates the complete sequence of a high-level Component from the sequence of its subcomponents. More...

std::string	compile ()
	Synonomous with Sequence::assemble. Calculates the complete sequence of a high-level Component from the sequence of its subcomponents. Prior to assembling the the complete sequence, you must assemble a template design by calling ComponentDefinition::assemble for the ComponentDefinition that references this Sequence.

int	length ()

ComponentDefinition &	synthesize (std::string clone_id)

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

◆ Sequence() [1/2]

Sequence	(	std::string	uri = `"example"`,
		std::string	elements = `""`,
		std::string	encoding = `SBOL_ENCODING_IUPAC`,
		std::string	version = `VERSION_STRING`
	)

inline

Construct a Seqiemce.

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.
elements	A string representation of the primary structure of DNA, RNA, protein, or a SMILES string for small molecules.
encoding	A URI that describes the representation format used for the elements property. Set to SBOL_ENCODING_IUPAC by default
version	An arbitrary version string. If SBOLCompliance is enabled, this should be a Maven version string.

◆ Sequence() [2/2]

Sequence	(	rdf_type	type_uri,
		std::string	uri,
		std::string	elements,
		std::string	encoding,
		std::string	version
	)

inline

Constructor used for defining extension classes.

Parameters

type_uri 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

◆ assemble()

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

Calculates the complete sequence of a high-level Component from the sequence of its subcomponents.

Pior to assembling the the complete sequence, you must assemble a template design by calling ComponentDefinition::assemble for the ComponentDefinition that references this Sequence.

Parameters

composite_sequence Typically no value for the composite sequence should be specified by the user. This parameter is used to hold the composite sequence as it is passed to function calls at a higher-level of the recursion stack.

◆ 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

◆ length()

int length ( )

Returns: The length of the primary sequence in the elements property

◆ 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

◆ synthesize()

ComponentDefinition & synthesize ( std::string clone_id )

Parameters

clone_id A URI for the build, or displayId if working in SBOLCompliant mode.

Member Data Documentation

◆ encoding

URIProperty encoding

The encoding property is REQUIRED and has a data type of URI.

This property MUST indicate how the elements property of a Sequence MUST be formed and interpreted. For example, the elements property of a Sequence with an IUPAC DNA encoding property MUST contain characters that represent nucleotide bases, such as a, t, c, and g. The elements property of a Sequence with a Simplified Molecular-Input Line-Entry System (SMILES) encoding, on the other hand, MUST contain characters that represent atoms and chemical bonds, such as C, N, O, and =. It is RECOMMENDED that the encoding property contains a URI from the table below. The terms in the table are organized by the type of ComponentDefinition that typically refer to a Sequence with such an encoding. When the encoding of a Sequence is well described by one of the URIs in the table, it MUST contain that URI.

ComponentDefinition type	Encoding	libSBOL Symbol	URI
DNA, RNA	IUPAC DNA, RNA	SBOL_ENCODING_IUPAC	http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html
Protein	IUPAC Protein	SBOL_ENCODING_IUPAC_PROTEIN	http://www.chem.qmul.ac.uk/iupac/AminoAcid/
Small Molecule	SMILES	SBOL_ENCODING_SMILES	http://www.opensmiles.org/opensmiles.html

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

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

Inheritance diagram for Sequence:

Detailed Description

Public Attributes

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

◆ Sequence() [1/2]

◆ Sequence() [2/2]

Member Function Documentation

◆ addPropertyValue()

◆ assemble()

◆ close()

◆ compare()

◆ copy()

◆ find()

◆ find_property()

◆ find_property_value()

◆ find_reference()

◆ generate() [1/2]

◆ generate() [2/2]

◆ getAnnotation()

◆ getClassName()

◆ getProperties()

◆ getPropertyValue()

◆ getPropertyValues()

◆ getTypeURI()

◆ length()

◆ register_extension_class()

◆ setAnnotation()

◆ setPropertyValue()

◆ simpleCopy()

◆ synthesize()

Member Data Documentation

◆ encoding