Detailed Description

Read and write SBOL using a Document class. The Document is a container for Components, Modules, and all other SBOLObjects.

Classes
class	iterator
	Iterate through TopLevel objects in a Document. More...

Public Attributes
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
	Document ()
	Construct a Document. The Document is a container for Components, Modules, and all other SBOLObjects.

template<class SBOLClass >
void	add (SBOLClass &sbol_obj)
	Register an object in the Document. More...

template<class SBOLClass >
void	add (std::vector< SBOLClass * > sbol_objects)
	Register an object in the Document. More...

template<class SBOLClass >
SBOLClass &	get (std::string uri)
	Retrieve an object from the Document. More...

template<class SBOLClass >
std::vector< SBOLClass * >	getAll ()
	Retrieve a vector of objects from the Document. More...

std::string	write (std::string filename)
	Serialize all objects in this Document to an RDF/XML file. More...

void	read (std::string filename)
	Read an RDF/XML file and attach the SBOL objects to this Document. More...

void	readString (std::string &sbol)
	Convert text in SBOL into data objects. More...

std::string	writeString ()
	Convert data objects in this Document into textual SBOL.

void	append (std::string filename)
	Read an RDF/XML file and attach the SBOL objects to this Document. More...

std::string	request_comparison (Document &diff_file)
	Perform comparison on Documents using the online validation tool. More...

void	clear ()
	Delete all properties and objects in the Document.

void	generate (raptor_world world, raptor_serializer sbol_serializer, char *sbol_buffer, size_t sbol_buffer_len, raptor_iostream ios, raptor_uri base_uri)
	Generates rdf/xml. More...

std::string	validate ()
	Run validation on this Document via the online validation tool. More...

std::string	exportToFormat (std::string language="", std::string output_path="")
	Convert this SBOL Document to GenBank, FASTA, or GFF3.

std::string	importFromFormat (std::string language, std::string input_path)
	Import GenBank, FASTA, or GFF3 to an SBOL Document.

int	size ()
	Get the total number of objects in the Document, including SBOL core object and custom annotation objects.

std::string	summary ()
	Get a summary of objects in the Document, including SBOL core object and custom annotation objects.

SBOLObject *	find (std::string uri)
	Search recursively for an SBOLObject in this Document that matches the uri. More...

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

void	addNamespace (std::string ns, std::string prefix)
	Add a new namespace to this Document. More...

void	close (std::string uri="")
	Delete all objects in this Document and destroy the Document.

virtual rdf_type	getTypeURI ()

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

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
Identified &	copy (Document *target_doc=NULL, std::string ns="", std::string version="")
	Copy an object and automatically increment its version. More...

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...

Member Function Documentation

◆ add() [1/2]

void add ( SBOLClass & sbol_obj )

Register an object in the Document.

Parameters

sbol_obj The SBOL object you want to serialize

Template Parameters

SBOLClass The type of SBOL object

◆ add() [2/2]

void add ( std::vector< SBOLClass * > sbol_objects )

Register an object in the Document.

Parameters

sbol_objects A list of pointers to the SBOL objects you want to serialize

Template Parameters

SBOLClass The type of SBOL object

◆ addNamespace()

void addNamespace	(	std::string	ns,
		std::string	prefix
	)

Add a new namespace to this Document.

Parameters

ns	The namespace, eg. http://sbols.org/v2#
prefix	The namespace prefix, eg. sbol

◆ 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

◆ append()

void append ( std::string filename )

Read an RDF/XML file and attach the SBOL objects to this Document.

New objects will be added to the existing contents of the Document

Parameters

filename The full name of the file you want to read (including file extension)

◆ 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()

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

protectedinherited

Copy an object and automatically increment its version.

If the optional version argument is specified, it will be used instead of incrementing the copied object's version. An object may also be copied into a new document and a new namespace, assuming compliant URIs.

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-compliat URIs.
version	A new version

Returns: The full URI of the created object.

◆ find()

SBOLObject * find ( std::string uri )

Search recursively for an SBOLObject in this Document that matches the uri.

Parameters

uri	The identity of the object to search for

Returns: A pointer to the SBOLObject, or NULL if an object with this identity doesn't exist

◆ 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()

void generate	(	raptor_world **	world,
		raptor_serializer **	sbol_serializer,
		char **	sbol_buffer,
		size_t *	sbol_buffer_len,
		raptor_iostream **	ios,
		raptor_uri **	base_uri
	)

Generates rdf/xml.

Author: KC generates rdf/xml

◆ get()

SBOLClass & get ( std::string uri )

Retrieve an object from the Document.

Parameters

uri	The identity of the SBOL object you want to retrieve

Template Parameters

SBOLClass The type of SBOL object

◆ getAll()

std::vector<SBOLClass*> getAll ( )

Retrieve a vector of objects from the Document.

Template Parameters

SBOLClass The type of SBOL objects

◆ 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

◆ getNamespaces()

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

Returns: A vector of namespaces Get namespaces contained in this Document

◆ 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

◆ read()

void read ( std::string filename )

Read an RDF/XML file and attach the SBOL objects to this Document.

Existing contents of the Document will be wiped.

Parameters

filename The full name of the file you want to read (including file extension)

◆ readString()

void readString ( std::string & sbol )

Convert text in SBOL into data objects.

Parameters

sbol	A string formatted in SBOL

◆ 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

◆ request_comparison()

std::string request_comparison ( Document & diff_file )

Perform comparison on Documents using the online validation tool.

This is for cross-validation of SBOL documents with libSBOLj. Document comparison can also be performed using the built-in compare method.

Returns: The comparison results

◆ 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

◆ validate()

std::string validate ( )

Run validation on this Document via the online validation tool.

Returns: A string containing a message with the validation results

Author: KC

◆ write()

std::string write ( std::string filename )

Serialize all objects in this Document to an RDF/XML file.

Parameters

filename The full name of the file you want to write (including file extension)

Returns: A string with the validation results, or empty string if validation is disabled

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

/Users/bbartley/Dev/git/libSBOL/source/document.h
/Users/bbartley/Dev/git/libSBOL/source/dbtl.cpp
/Users/bbartley/Dev/git/libSBOL/source/document.cpp
/Users/bbartley/Dev/git/libSBOL/source/partshop.cpp

Inheritance diagram for Document:

Detailed Description

Classes

Public Attributes

Public Member Functions

Protected Member Functions

Member Function Documentation

◆ add() [1/2]

◆ add() [2/2]

◆ addNamespace()

◆ addPropertyValue()

◆ append()

◆ close()

◆ compare()

◆ copy()

◆ find()

◆ find_property()

◆ find_property_value()

◆ find_reference()

◆ generate()

◆ get()

◆ getAll()

◆ getAnnotation()

◆ getClassName()

◆ getNamespaces()

◆ getProperties()

◆ getPropertyValue()

◆ getPropertyValues()

◆ getTypeURI()

◆ read()

◆ readString()

◆ register_extension_class()

◆ request_comparison()

◆ setAnnotation()

◆ setPropertyValue()

◆ validate()

◆ write()