Detailed Description

The SequenceAnnotation class describes one or more regions of interest on the Sequence objects referred to by its parent ComponentDefinition. In addition, SequenceAnnotation objects can describe the substructure of their parent ComponentDefinition through association with the Component objects contained by this ComponentDefinition.

Public Attributes
ReferencedObject	component
	The component property is OPTIONAL and has a data type of URI. This URI MUST refer to a Component that is contained by the same parent ComponentDefinition that contains the SequenceAnnotation. In this way, the properties of the SequenceAnnotation, such as its description and locations, are associated with part of the substructure of its parent ComponentDefinition.

OwnedObject< Location >	locations
	The locations property is a REQUIRED set of one or more Location objects that indicate which elements of a Sequence are described by the SequenceAnnotation. More...

URIProperty	roles
	Alternatively to describing substructure, a SequenceAnnotation can be utilized to identify a feature, such as a GenBank feature, of a specified Sequence. 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
	SequenceAnnotation (std::string uri="example", std::string version=VERSION_STRING)
	Construct a ComponentDefinition. More...

bool	precedes (SequenceAnnotation &comparand)
	Tests if the comparand SequenceAnnotation precedes this one according to base coordinates. More...

bool	follows (SequenceAnnotation &comparand)
	Tests if the comparand SequenceAnnotation follows this one according to base coordinates. More...

bool	contains (SequenceAnnotation &comparand)
	Tests if the comparand SequenceAnnotation is contained within the same start and end base coordinates as this one. More...

bool	overlaps (SequenceAnnotation &comparand)
	Tests if the comparand SequenceAnnotation overlaps with this one in the primary sequence. More...

ComponentDefinition &	extract (int start_reference=1)
	Convert a SequenceAnnotation to a subcomponent. More...

int	length ()
	The length of a SequenceAnnotation in base coordinates.

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
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...

Constructor & Destructor Documentation

◆ SequenceAnnotation()

SequenceAnnotation	(	std::string	uri = `"example"`,
		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.
version	An arbitrary version string. If SBOLCompliance is enabled, this should be a Maven version string of the form "major.minor.patch".

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

◆ contains()

bool contains ( SequenceAnnotation & comparand )

Tests if the comparand SequenceAnnotation is contained within the same start and end base coordinates as this one.

This is mutually exclusive with overlaps.

Parameters

comparand Another SequenceAnnotation

Returns: true or false

◆ 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.

◆ extract()

ComponentDefinition & extract ( int start_reference = 1 )

Convert a SequenceAnnotation to a subcomponent.

Returns: A ComponentDefinition representing the subcomponent

◆ 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

◆ follows()

bool follows ( SequenceAnnotation & comparand )

Tests if the comparand SequenceAnnotation follows this one according to base coordinates.

Parameters

comparand Another SequenceAnnotation

Returns: true or false

◆ 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

◆ overlaps()

bool overlaps ( SequenceAnnotation & comparand )

Tests if the comparand SequenceAnnotation overlaps with this one in the primary sequence.

Parameters

comparand Another SequenceAnnotation

Returns: true or false

◆ precedes()

bool precedes ( SequenceAnnotation & comparand )

Tests if the comparand SequenceAnnotation precedes this one according to base coordinates.

Parameters

comparand Another SequenceAnnotation

Returns: true or false

◆ 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

Member Data Documentation

◆ locations

OwnedObject<Location> locations

The locations property is a REQUIRED set of one or more Location objects that indicate which elements of a Sequence are described by the SequenceAnnotation.

Allowing multiple Location objects on a single SequenceAnnotation is intended to enable representation of discontinuous regions (for example, a Component encoded across a set of exons with interspersed introns). As such, the Location objects of a single SequenceAnnotation SHOULD NOT specify overlapping regions, since it is not clear what this would mean. There is no such concern with different SequenceAnnotation objects, however, which can freely overlap in Location (for example, specifying overlapping linkers for sequence assembly).

◆ roles

URIProperty roles

Alternatively to describing substructure, a SequenceAnnotation can be utilized to identify a feature, such as a GenBank feature, of a specified Sequence.

In this use case, the SequenceAnnotation MUST NOT have a component property, but instead it would have a roles property. The roles property comprises an OPTIONAL set of zero or more URIs describing the specified sequence feature being annotated. If provided, these role URIs MUST identify terms from appropriate ontologies. Roles are not restricted to describing biological function; they may annotate Sequences’ function in any domain for which an ontology exists. It is RECOMMENDED that these role URIs identify terms that are compatible with the type properties of this SequenceAnnotation’s parent ComponentDefinition. For example, a role of a SequenceAnnotation which belongs to a ComponentDefinition of type DNA might refer to terms from the Sequence Ontology. See documentation for ComponentDefinition for a table of recommended ontology terms.

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

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

Inheritance diagram for SequenceAnnotation:

Detailed Description

Public Attributes

Public Member Functions

Protected Member Functions

Constructor & Destructor Documentation

◆ SequenceAnnotation()

Member Function Documentation

◆ addPropertyValue()

◆ close()

◆ compare()

◆ contains()

◆ copy()

◆ extract()

◆ find()

◆ find_property()

◆ find_property_value()

◆ find_reference()

◆ follows()

◆ getAnnotation()

◆ getClassName()

◆ getProperties()

◆ getPropertyValue()

◆ getPropertyValues()

◆ getTypeURI()

◆ overlaps()

◆ precedes()

◆ register_extension_class()

◆ setAnnotation()

◆ setPropertyValue()

Member Data Documentation

◆ locations

◆ roles