#include <CRDFGraph.h>

Public Types
typedef std::set< CRDFTriplet >::const_iterator	const_iterator

typedef std::set< CRDFTriplet >::iterator	iterator

typedef std::multimap< CRDFNode *, CRDFTriplet >	Node2Triplet

typedef std::pair< Node2Triplet::const_iterator, Node2Triplet::const_iterator >	Node2TripletConstRange

typedef std::pair< Node2Triplet::iterator, Node2Triplet::iterator >	Node2TripletRange

typedef std::multimap< CRDFPredicate, CRDFTriplet >	Predicate2Triplet

typedef std::pair< Predicate2Triplet::const_iterator, Predicate2Triplet::const_iterator >	Predicate2TripletConstRange

typedef std::pair< Predicate2Triplet::iterator, Predicate2Triplet::iterator >	Predicate2TripletRange

Public Member Functions
bool	addNameSpace (const std::string &prefix, const std::string &uri)

CRDFTriplet	addTriplet (const CRDFSubject &subject, const CRDFPredicate &predicate, const CRDFObject &object)

void	clean ()

	CRDFGraph ()

CRDFNode *	createAboutNode (const std::string &key)

bool	destroyUnreferencedNode (CRDFNode *pNode)

bool	empty () const

std::string	generatedNodeId (const std::string &existingId="")

const CRDFNode *	getAboutNode () const

const std::map< std::string, CRDFNode * > &	getBlankNodeMap () const

std::set< CRDFTriplet >	getIncomingTriplets (const CRDFNode *pObject) const

const std::map< std::string, CRDFNode * > &	getLocalResourceNodeMap () const

const std::map< std::string, std::string > &	getNameSpaceMap () const

std::set< const CRDFNode * >	getParentSubjects (const CRDFNode *pObject) const

CRDFPredicate::Path	getPredicatePath (const CRDFNode *pNode)

const std::vector< CRDFNode * > &	getRemoteResourceNodes () const

const std::set< CRDFTriplet > &	getTriplets () const

std::set< CRDFTriplet >	getTriplets (const CRDFNode *pSubject) const

std::set< CRDFTriplet >	getTriplets (const CRDFNode *pSubject, const CRDFPredicate &predicate) const

std::set< CRDFTriplet >	getTriplets (const CRDFPredicate &predicate, const bool &expandBag=true) const

bool	guessGraphRoot (const std::string &about=" ")

CRDFTriplet	moveTriplet (CRDFNode *pNewSubject, const CRDFTriplet &triplet)

bool	removeTriplet (CRDFNode pSubject, const CRDFPredicate &predicate, CRDFNode pObject)

void	updateNamespaces ()

	~CRDFGraph ()

Private Member Functions
bool	addTriplet (const CRDFTriplet &triplet)

bool	removeEmptyNodes ()

bool	removeTriplet (const CRDFTriplet &triplet)

Private Attributes
std::map< std::string, CRDFNode * >	mBlankNodeId2Node

std::set< unsigned int >	mGeneratedIds

std::map< std::string, std::string >	mIdMap

std::vector< CRDFNode * >	mLiteralNodes

std::map< std::string, CRDFNode * >	mLocalResource2Node

Node2Triplet	mObject2Triplet

CRDFNode *	mpAbout

Predicate2Triplet	mPredicate2Triplet

std::map< std::string, std::string >	mPrefix2Namespace

std::vector< CRDFNode * >	mRemoteResourceNodes

Node2Triplet	mSubject2Triplet

std::set< CRDFTriplet >	mTriplets

Friends
bool	CRDFNode::addTripletToGraph (const CRDFTriplet &triplet) const

bool	CRDFNode::removeTripletFromGraph (const CRDFTriplet &triplet) const

Member Typedef Documentation

◆ const_iterator

typedef std::set< CRDFTriplet >::const_iterator CRDFGraph::const_iterator

◆ iterator

typedef std::set< CRDFTriplet >::iterator CRDFGraph::iterator

◆ Node2Triplet

typedef std::multimap< CRDFNode *, CRDFTriplet > CRDFGraph::Node2Triplet

◆ Node2TripletConstRange

typedef std::pair< Node2Triplet::const_iterator, Node2Triplet::const_iterator> CRDFGraph::Node2TripletConstRange

◆ Node2TripletRange

typedef std::pair< Node2Triplet::iterator, Node2Triplet::iterator> CRDFGraph::Node2TripletRange

◆ Predicate2Triplet

typedef std::multimap< CRDFPredicate, CRDFTriplet > CRDFGraph::Predicate2Triplet

◆ Predicate2TripletConstRange

typedef std::pair< Predicate2Triplet::const_iterator, Predicate2Triplet::const_iterator> CRDFGraph::Predicate2TripletConstRange

◆ Predicate2TripletRange

typedef std::pair< Predicate2Triplet::iterator, Predicate2Triplet::iterator> CRDFGraph::Predicate2TripletRange

Constructor & Destructor Documentation

◆ CRDFGraph()

CRDFGraph::CRDFGraph ( )

Default Constructor

◆ ~CRDFGraph()

CRDFGraph::~CRDFGraph ( )

Destructor

References mBlankNodeId2Node, mLiteralNodes, mLocalResource2Node, mObject2Triplet, mPredicate2Triplet, mRemoteResourceNodes, mSubject2Triplet, mTriplets, and pdelete.

Member Function Documentation

◆ addNameSpace()

bool CRDFGraph::addNameSpace	(	const std::string &	prefix,
		const std::string &	uri
	)

Add a name space including prefix to the graph. It returns false if the prefix was already used with another namespace

Parameters

const	std::string & prefix
const	std::string & namespace

Returns: bool success;

References CCopasiMessage::ERROR, MCAnnotation, and mPrefix2Namespace.

Referenced by updateNamespaces().

◆ addTriplet() [1/2]

CRDFTriplet CRDFGraph::addTriplet	(	const CRDFSubject &	subject,
		const CRDFPredicate &	predicate,
		const CRDFObject &	object
	)

Add a triplet to the graph

Parameters

const	CRDFSubject & subject
const	CRDFPredicate & predicate
const	CRDFObject & object

Returns: CRDFTriplet triplet

References CRDFNode::addEdge(), CRDFObject::BLANK_NODE, CRDFSubject::BLANK_NODE, CRDFSubject::getBlankNodeID(), CRDFNode::getObject(), CRDFPredicate::getPredicateFromURI(), CRDFObject::getResource(), CRDFSubject::getResource(), CRDFObject::getType(), CRDFSubject::getType(), CRDFPredicate::getURI(), CRDFSubject::isLocal(), CRDFNode::isObjectNode(), CRDFNode::isSubjectNode(), CRDFObject::LITERAL, mBlankNodeId2Node, mLiteralNodes, mLocalResource2Node, mRemoteResourceNodes, CRDFPredicate::rdf_li, CRDFPredicate::rdf_predicate, CRDFObject::RESOURCE, CRDFSubject::RESOURCE, CRDFNode::setObject(), CRDFObject::setResource(), and CRDFNode::setSubject().

Referenced by CRDFNode::addEdge(), CRDFNode::addTripletToGraph(), CRDFGraphConverter::convert(), CMIRIAMInfo::createBiologicalDescription(), CMIRIAMInfo::createCreator(), CRDFNode::createMissingAncestors(), CMIRIAMInfo::createModification(), CMIRIAMInfo::createReference(), CMIRIAMInfo::setCreatedDT(), and CRDFNode::setFieldValue().

◆ addTriplet() [2/2]

bool CRDFGraph::addTriplet ( const CRDFTriplet & triplet )

private

Add a triplet to the graph. This method should only be used by CRDFNode

Parameters

const CRDFTriplet & triplet

Returns: bool success

References mObject2Triplet, mPredicate2Triplet, mSubject2Triplet, mTriplets, CRDFTriplet::pObject, CRDFTriplet::Predicate, and CRDFTriplet::pSubject.

◆ clean()

void CRDFGraph::clean ( )

Removes empty blank nodes . This should be called before CRDFWriter::xmlFromGraph

References removeEmptyNodes().

Referenced by CMIRIAMInfo::save(), and CRDFGraphConverter::SBML2Copasi().

◆ createAboutNode()

CRDFNode * CRDFGraph::createAboutNode ( const std::string & key )

If no about node exists a node is created with the attribute: rdf:about="#key

Parameters

const std::string & key

Returns: CRDFNode * pAbout

References guessGraphRoot(), mLocalResource2Node, mpAbout, CRDFSubject::RESOURCE, CRDFSubject::setResource(), CRDFNode::setSubject(), and CRDFSubject::setType().

Referenced by CMIRIAMInfo::load().

◆ destroyUnreferencedNode()

bool CRDFGraph::destroyUnreferencedNode ( CRDFNode * pNode )

Destroy a CRDFNode

Parameters

CRDFNode * pNode

Returns: true, if an element was deleted, false otherwise

References CRDFObject::BLANK_NODE, CRDFObject::getBlankNodeID(), CRDFNode::getObject(), CRDFObject::getResource(), CRDFObject::getType(), CRDFObject::isLocal(), CRDFObject::LITERAL, mBlankNodeId2Node, mLiteralNodes, mLocalResource2Node, mObject2Triplet, mRemoteResourceNodes, mSubject2Triplet, and CRDFObject::RESOURCE.

Referenced by removeEmptyNodes(), and removeTriplet().

◆ empty()

bool CRDFGraph::empty ( ) const

Check whether the graph is empty bool empty

References mTriplets.

Referenced by CMIRIAMInfo::empty(), and CRDFWriter::write().

◆ generatedNodeId()

std::string CRDFGraph::generatedNodeId ( const std::string & existingId = "" )

Generate a unique blank node id.

Parameters

const std::string & existingId (default: "")

Returns: std::string blankNodeId

References mBlankNodeId2Node, mGeneratedIds, and mIdMap.

Referenced by CRDFGraphConverter::convert(), CMIRIAMInfo::createCreator(), CRDFNode::createMissingAncestors(), CMIRIAMInfo::createModification(), CMIRIAMInfo::createReference(), CMIRIAMInfo::setCreatedDT(), and CRDFNode::setFieldValue().

◆ getAboutNode()

const CRDFNode * CRDFGraph::getAboutNode ( ) const

Retrieve the about/top node of the graph.

Returns: const CRDFNode * pAboutNode

References mpAbout.

Referenced by CMIRIAMInfo::createBiologicalDescription(), CMIRIAMInfo::createCreator(), CMIRIAMInfo::createModification(), and CMIRIAMInfo::createReference().

◆ getBlankNodeMap()

const std::map< std::string, CRDFNode * > & CRDFGraph::getBlankNodeMap ( ) const

Retrieve the map of IDs to blank nodes

Returns: const std::map< std::string, CRDFNode * > & blankNodeMap

References mBlankNodeId2Node.

◆ getIncomingTriplets()

std::set< CRDFTriplet > CRDFGraph::getIncomingTriplets ( const CRDFNode * pObject ) const

Retrieve all triples pointing to the object

Parameters

const CRDFNode * pObject

Returns: std::set< CRDFTriplet > triplets

References mObject2Triplet.

Referenced by removeEmptyNodes().

◆ getLocalResourceNodeMap()

const std::map< std::string, CRDFNode * > & CRDFGraph::getLocalResourceNodeMap ( ) const

Retrieve the map of URIs to local resource nodes

Returns: const std::map< std::string, CRDFNode * > & localResourceNodeMap

References mLocalResource2Node.

◆ getNameSpaceMap()

const std::map< std::string, std::string > & CRDFGraph::getNameSpaceMap ( ) const

Retrieve the map of prefixes to namespaces

Returns: const std::map< std::string, std::string > & nameSpaceMap

References mPrefix2Namespace.

Referenced by CRDFWriter::initNamespaces().

◆ getParentSubjects()

std::set< const CRDFNode * > CRDFGraph::getParentSubjects ( const CRDFNode * pObject ) const

Retrieve all parent subjects of the object

Parameters

const CRDFNode * pObject

Returns: std::set< const CRDFNode * > nodes

References mObject2Triplet.

Referenced by CRDFNode::hasAncestor().

◆ getPredicatePath()

CRDFPredicate::Path CRDFGraph::getPredicatePath ( const CRDFNode * pNode )

Retrieve the predicate path to the ginve node.

Parameters

const CRDFNode * pNode

Returns: CRDFPredicate::Path

References CRDFPredicate::about, mObject2Triplet, mpAbout, and CRDFPredicate::rdf_li.

Referenced by CRDFNode::getDescendantsWithPredicate(), CRDFNode::getPath(), and CRDFNode::isReadOnly().

◆ getRemoteResourceNodes()

const std::vector< CRDFNode * > & CRDFGraph::getRemoteResourceNodes ( ) const

Retrieve the vector of remote resource nodes

Returns: const std::vector< CRDFNode * > & remoteResourceNodes

References mRemoteResourceNodes.

◆ getTriplets() [1/4]

const std::set< CRDFTriplet > & CRDFGraph::getTriplets ( ) const

Retrieve all triplets.

Returns: const std::set< CRDFTriplet > & triplets

References mTriplets.

Referenced by CRDFNode::addEdge(), CRDFGraphConverter::convert(), CRDFNode::getDescendantsWithPredicate(), getTriplets(), CRDFNode::isBagNode(), CRDFNode::removeEdge(), and CRDFWriter::write().

◆ getTriplets() [2/4]

std::set< CRDFTriplet > CRDFGraph::getTriplets ( const CRDFNode * pSubject ) const

Retrieve all triplets with the specified subject

Parameters

const CRDFNode * pSubject

Returns: std::set< CRDFTriplet > triplets

References mSubject2Triplet.

◆ getTriplets() [3/4]

std::set< CRDFTriplet > CRDFGraph::getTriplets	(	const CRDFNode *	pSubject,
		const CRDFPredicate &	predicate
	)		const

Retrieve all triplets with the specified subject and predicate

Parameters

const	CRDFNode * pSubject
const	CRDFPredicate & predicate

Returns: std::set< CRDFTriplet > triplets

References mPredicate2Triplet.

◆ getTriplets() [4/4]

std::set< CRDFTriplet > CRDFGraph::getTriplets	(	const CRDFPredicate &	predicate,
		const bool &	expandBag = `true`
	)		const

Retrieve all triplets with the specified predicate, this will collapse predicate.rdf:li to predicate.

Parameters

const	CRDFPredicate & predicate
const	bool & expandBag (default: true)

Returns: std::set< CRDFTriplet > triplets

References getTriplets(), mPredicate2Triplet, and CRDFPredicate::rdf_li.

◆ guessGraphRoot()

bool CRDFGraph::guessGraphRoot ( const std::string & about = " " )

Guess the graph root element. If a unique root element is found true is returned other wise falls

Parameters

const std::string & about (default: <space>)

Returns: bool success

References CRDFSubject::getResource(), CRDFNode::getSubject(), CRDFSubject::getType(), CRDFSubject::isLocal(), CRDFNode::isSubjectNode(), mLocalResource2Node, mpAbout, and CRDFSubject::RESOURCE.

Referenced by createAboutNode(), and CRDFParser::parse().

◆ moveTriplet()

CRDFTriplet CRDFGraph::moveTriplet	(	CRDFNode *	pNewSubject,
		const CRDFTriplet &	triplet
	)

Move a edge from one node to another

Parameters

CRDFNode	* pNewSubject
CRDFNode	* const CRDFTriplet & triplet

Returns: CRDFGraph::CRDFTriplet triplet

References CRDFNode::addEdge(), CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, and CRDFNode::removeEdge().

Referenced by CRDFGraphConverter::convert().

◆ removeEmptyNodes()

bool CRDFGraph::removeEmptyNodes ( )

private

Removes all empty blank nodes. It returns true if a node was removed

Returns: bool haveRemoved

References destroyUnreferencedNode(), getIncomingTriplets(), CRDFNode::isBagNode(), mBlankNodeId2Node, mSubject2Triplet, and CCopasiMessage::WARNING_FILTERED.

Referenced by clean().

◆ removeTriplet() [1/2]

bool CRDFGraph::removeTriplet ( const CRDFTriplet & triplet )

private

Remove triplet from the graph. This method should only be used by CRDFNode Please note, this will also remove all unreferenced local resources created by removing the edge.

Parameters

const CRDFTriplet & triplet

Returns: true, if an element was deleted, false otherwise

References destroyUnreferencedNode(), mObject2Triplet, mPredicate2Triplet, mSubject2Triplet, mTriplets, CRDFTriplet::pObject, CRDFTriplet::Predicate, and CRDFTriplet::pSubject.

◆ removeTriplet() [2/2]

bool CRDFGraph::removeTriplet	(	CRDFNode *	pSubject,
		const CRDFPredicate &	predicate,
		CRDFNode *	pObject
	)

Remove triplet from the graph. Please note, this will also remove all unreferenced local resources created by removing the edge.

Parameters

CRDFNode	* pSubject
const	CRDFPredicate & predicate
CRDFNode	* pObject

Returns: true, if an element was deleted, false otherwise

References CRDFNode::removeEdge().

Referenced by CRDFGraphConverter::convert(), CMIRIAMInfo::removeBiologicalDescription(), CMIRIAMInfo::removeCreator(), CMIRIAMInfo::removeModification(), CMIRIAMInfo::removeReference(), and CRDFNode::removeTripletFromGraph().

◆ updateNamespaces()

void CRDFGraph::updateNamespaces ( )

Removes all unused name spaces.

References addNameSpace(), mPrefix2Namespace, and mTriplets.

Referenced by CMIRIAMInfo::save(), and CRDFGraphConverter::SBML2Copasi().

Friends And Related Function Documentation

◆ CRDFNode::addTripletToGraph

bool CRDFNode::addTripletToGraph ( const CRDFTriplet & triplet ) const

friend

◆ CRDFNode::removeTripletFromGraph

bool CRDFNode::removeTripletFromGraph ( const CRDFTriplet & triplet ) const

friend

Member Data Documentation

◆ mBlankNodeId2Node

std::map< std::string, CRDFNode * > CRDFGraph::mBlankNodeId2Node

private

A map of blank node ids to nodes of the graph.

Referenced by addTriplet(), destroyUnreferencedNode(), generatedNodeId(), getBlankNodeMap(), removeEmptyNodes(), and ~CRDFGraph().

◆ mGeneratedIds

std::set< unsigned int > CRDFGraph::mGeneratedIds

private

Memory for generated Ids

Referenced by generatedNodeId().

◆ mIdMap

std::map< std::string, std::string > CRDFGraph::mIdMap

private

Mapping from existing Ids to newly created ones.

Referenced by generatedNodeId().

◆ mLiteralNodes

std::vector< CRDFNode * > CRDFGraph::mLiteralNodes

private

A vector of all literal nodes of the graph

Referenced by addTriplet(), destroyUnreferencedNode(), and ~CRDFGraph().

◆ mLocalResource2Node

std::map< std::string, CRDFNode * > CRDFGraph::mLocalResource2Node

private

A map of resource URIs to local resource nodes of the graph, i

Referenced by addTriplet(), createAboutNode(), destroyUnreferencedNode(), getLocalResourceNodeMap(), guessGraphRoot(), and ~CRDFGraph().

◆ mObject2Triplet

Node2Triplet CRDFGraph::mObject2Triplet

private

Referenced by addTriplet(), destroyUnreferencedNode(), getIncomingTriplets(), getParentSubjects(), getPredicatePath(), removeTriplet(), and ~CRDFGraph().

◆ mpAbout

CRDFNode* CRDFGraph::mpAbout

private

The subject node this RDF graph is about

Referenced by createAboutNode(), getAboutNode(), getPredicatePath(), and guessGraphRoot().

◆ mPredicate2Triplet

Predicate2Triplet CRDFGraph::mPredicate2Triplet

private

Referenced by addTriplet(), getTriplets(), removeTriplet(), and ~CRDFGraph().

◆ mPrefix2Namespace

std::map< std::string, std::string > CRDFGraph::mPrefix2Namespace

private

A map of prefixes to namespaces

Referenced by addNameSpace(), getNameSpaceMap(), and updateNamespaces().

◆ mRemoteResourceNodes

std::vector< CRDFNode * > CRDFGraph::mRemoteResourceNodes

private

A vector of all remote resource nodes of the graph

Referenced by addTriplet(), destroyUnreferencedNode(), getRemoteResourceNodes(), and ~CRDFGraph().

◆ mSubject2Triplet

Node2Triplet CRDFGraph::mSubject2Triplet

private

Referenced by addTriplet(), destroyUnreferencedNode(), getTriplets(), removeEmptyNodes(), removeTriplet(), and ~CRDFGraph().

◆ mTriplets

std::set< CRDFTriplet > CRDFGraph::mTriplets

private

All the triplets of the graph

Referenced by addTriplet(), empty(), getTriplets(), removeTriplet(), updateNamespaces(), and ~CRDFGraph().

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Member Typedef Documentation

◆ const_iterator

◆ iterator

◆ Node2Triplet

◆ Node2TripletConstRange

◆ Node2TripletRange

◆ Predicate2Triplet

◆ Predicate2TripletConstRange

◆ Predicate2TripletRange

Constructor & Destructor Documentation

◆ CRDFGraph()

◆ ~CRDFGraph()

Member Function Documentation

◆ addNameSpace()

◆ addTriplet() [1/2]

◆ addTriplet() [2/2]

◆ clean()

◆ createAboutNode()

◆ destroyUnreferencedNode()

◆ empty()

◆ generatedNodeId()

◆ getAboutNode()

◆ getBlankNodeMap()

◆ getIncomingTriplets()

◆ getLocalResourceNodeMap()

◆ getNameSpaceMap()

◆ getParentSubjects()

◆ getPredicatePath()

◆ getRemoteResourceNodes()

◆ getTriplets() [1/4]

◆ getTriplets() [2/4]

◆ getTriplets() [3/4]

◆ getTriplets() [4/4]

◆ guessGraphRoot()

◆ moveTriplet()

◆ removeEmptyNodes()

◆ removeTriplet() [1/2]

◆ removeTriplet() [2/2]

◆ updateNamespaces()

Friends And Related Function Documentation

◆ CRDFNode::addTripletToGraph

◆ CRDFNode::removeTripletFromGraph

Member Data Documentation

◆ mBlankNodeId2Node

◆ mGeneratedIds

◆ mIdMap

◆ mLiteralNodes

◆ mLocalResource2Node

◆ mObject2Triplet

◆ mpAbout

◆ mPredicate2Triplet

◆ mPrefix2Namespace

◆ mRemoteResourceNodes

◆ mSubject2Triplet

◆ mTriplets