#include <CReference.h>

Inheritance diagram for CReference:

Public Member Functions
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)

void	clearInvalidEntries ()

virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const

	CReference (const CRDFTriplet &triplet, const std::string &objectName="", const CDataContainer *pParent=NO_PARENT)

	CReference (const CReference &src, const CDataContainer *pParent)

	CReference (const std::string &objectName, const CDataContainer *pParent=NO_PARENT)

virtual void	destruct ()

const std::string &	getDescription () const

const std::string &	getId () const

virtual const std::string &	getKey () const

const CMIRIAMResourceObject &	getMIRIAMResourceObject () const

std::string	getResource () const

const CRDFTriplet &	getTriplet () const

std::string	getURI () const

void	setDescription (const std::string &description)

void	setId (const std::string &id)

void	setResource (const std::string &resource)

virtual CData	toData () const

	~CReference ()

Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)

virtual bool	appendDeletedDependentData (CUndoData &undoData) const

	CDataContainer (const CDataContainer &src, const CDataContainer *pParent)

	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

virtual std::string	getChildObjectUnits (const CDataObject *pObject) const

void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const

virtual size_t	getIndex (const CDataObject *pObject) const

virtual const CObjectInterface *	getObject (const CCommonName &cn) const override

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

virtual CUndoObjectInterface *	insert (const CData &data) override

void	objectRenamed (CDataObject *pObject, const std::string &oldName)

virtual bool	remove (CDataObject *pObject)

virtual	~CDataContainer ()

Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)

void	addReference (const CDataContainer *pReference)

virtual void	calculateValue () override

	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)

virtual CCommonName	getCN () const override

virtual const CDataObject *	getDataObject () const override

CDataContainer *	getObjectAncestor (const std::string &type) const

CDataModel *	getObjectDataModel () const

virtual std::string	getObjectDisplayName () const override

const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const

const std::string &	getObjectName () const

CDataContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override

virtual const CValidity &	getValidity () const override

virtual void *	getValuePointer () const override

bool	hasFlag (const Flag &flag) const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override

bool	prerequisitsContains (const DataObjectSet &objects) const

virtual void	print (std::ostream *ostream) const override

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CDataContainer *pParent)

void	validityChanged (const CValidity &changedValidity) override

void	validityRemoved (const CValidity &changedValidity)

virtual	~CDataObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

	CObjectInterface (const CObjectInterface &src)

virtual	~CObjectInterface ()

Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()

	CUndoObjectInterface (const CUndoObjectInterface &src)

bool	generateUuid ()

const xg::Guid &	getUuid () const

bool	setUuid (const std::string &uuid)

bool	setUuid (const xg::Guid &uuid)

virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)

virtual	~CUndoObjectInterface ()

Static Public Member Functions
static CReference *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataContainer
static CDataContainer *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataObject
static CDataObject *	fromData (const CData &data, CUndoObjectInterface *pParent)

static void	sanitizeObjectName (std::string &name)

Static Public Member Functions inherited from CObjectInterface
static const CDataObject *	DataObject (const CObjectInterface *pInterface)

static CObjectInterface *	GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)

Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)

Private Attributes
CRDFTriplet	mIdTriplet

std::string	mKey

CRDFPredicate::Path	mNodePath

CMIRIAMResourceObject	mResource

CRDFTriplet	mTriplet

Additional Inherited Members
Public Types inherited from CDataContainer
typedef CDataObjectMap	objectMap

Public Types inherited from CDataObject
typedef std::set< const CDataObject * >	DataObjectSet

enum	Flag { Container , Vector , Matrix , NameVector , Reference , ValueBool , ValueInt , ValueInt64 , ValueDbl , NonUniqueName , StaticString , ValueString , Separator , DisplayName , ModelEntity , Array , DataModel , Root , Gui , __SIZE }

Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * >	ContainerList

typedef std::set< const CObjectInterface * >	ObjectSet

Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > *	addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataObjectReference< CType > *	addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataVectorReference< CType > *	addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

	CDataContainer (const CDataContainer &src)

void	initObjects ()

Protected Member Functions inherited from CDataObject
	CDataObject ()

	CDataObject (const std::string &name, const CDataContainer pParent=static_cast< CDataContainer >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

Protected Attributes inherited from CDataContainer
objectMap	mObjects

Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits

std::set< CDataContainer * >	mReferences

Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Detailed Description

CReferences: Stores publication details such as PubMed Id and DOI.

Constructor & Destructor Documentation

◆ CReference() [1/3]

CReference::CReference	(	const std::string &	objectName,
		const CDataContainer *	pParent = `NO_PARENT`
	)

Default constructor

Parameters

const	std::string & objectName
const	CDataContainer * pParent (default: NULL)

◆ CReference() [2/3]

CReference::CReference	(	const CRDFTriplet &	triplet,
		const std::string &	objectName = `""`,
		const CDataContainer *	pParent = `NO_PARENT`
	)

Specific constructor

Parameters

const	CRDFTriplet & triplet
const	std::string & objectName (default: "")
const	CDataContainer * pParent (default: NULL)

References CRDFPredicate::bqbiol_isDescribedBy, CRDFPredicate::bqmodel_isDescribedBy, CRDFPredicate::copasi_isDescribedBy, CRDFPredicate::end, CRDFNode::getDescendantsWithPredicate(), CRDFNode::getPath(), mIdTriplet, mNodePath, mResource, mTriplet, CRDFTriplet::pObject, and CMIRIAMResourceObject::setNode().

◆ CReference() [3/3]

CReference::CReference	(	const CReference &	src,
		const CDataContainer *	pParent
	)

Copy constructor

Parameters

const CReference &	src
const	CDataContainer * pParent (default: NULL)

◆ ~CReference()

CReference::~CReference ( )

Destructor

References CRootContainer::getKeyFactory(), mKey, and CKeyFactory::remove().

Member Function Documentation

◆ applyData()

bool CReference::applyData	(	const CData &	data,
		CUndoData::CChangeSet &	changes
	)

virtual

Apply the provided data to the object

Parameters

const CData & data

Returns: bool success

Reimplemented from CDataContainer.

References CDataContainer::applyData(), CDataObject::getObjectAncestor(), CData::getProperty(), CData::isSetProperty(), CData::MIRIAM_DESCRIPTION, CData::MIRIAM_ID, CData::MIRIAM_RESOURCE, CMIRIAMInfo::save(), setDescription(), setId(), setResource(), and CDataValue::toString().

◆ clearInvalidEntries()

void CReference::clearInvalidEntries ( )

Remove invalid combinations of resource and id

References CRDFPredicate::copasi_isDescribedBy, CMIRIAMResourceObject::isValid(), mIdTriplet, mNodePath, mResource, mTriplet, CRDFTriplet::pObject, CRDFNode::setFieldValue(), and CMIRIAMResourceObject::setURI().

◆ createUndoData()

void CReference::createUndoData	(	CUndoData &	undoData,
		const CUndoData::Type &	type,
		const CData &	oldData = `CData()`,
		const CCore::Framework &	framework = `CCore::Framework::ParticleNumbers`
	)		const

virtual

Create the undo data which represents the changes recording the differences between the provided oldData and the current data.

Parameters

CUndoData	& undoData
const	CUndoData::Type & type
const	CData & oldData (default: empty data)
const	CCore::Framework & framework (default: CCore::Framework::ParticleNumbers)

Returns: CUndoData undoData

Reimplemented from CDataContainer.

References CUndoData::addProperty(), CUndoData::CHANGE, CDataContainer::createUndoData(), CUndoData::empty(), getDescription(), getId(), CData::getProperty(), getResource(), CData::MIRIAM_DESCRIPTION, CData::MIRIAM_ID, CData::MIRIAM_RESOURCE, CData::OBJECT_HASH, CData::OBJECT_INDEX, CUndoData::removeProperty(), and toData().

◆ destruct()

void CReference::destruct ( )

virtual

Destruct the object

Reimplemented from CDataObject.

References CDataObject::destruct(), CDataObject::getObjectAncestor(), CMIRIAMInfo::removeReference(), and CMIRIAMInfo::save().

◆ fromData()

CReference * CReference::fromData	(	const CData &	data,
		CUndoObjectInterface *	pParent
	)

static

Static method to create a CDataObject based on the provided data

Parameters

const CData & data

Returns: CReference * pDataObject

References CMIRIAMInfo::createReference(), CDataObject::getObjectAncestor(), CData::getProperty(), CData::OBJECT_NAME, CDataContainer::remove(), and CDataValue::toString().

◆ getDescription()

const std::string & CReference::getDescription ( ) const

Retrieve the description for the reference.

Returns: std::string description

References CRDFPredicate::dcterms_description, CRDFNode::getFieldValue(), mTriplet, and CRDFTriplet::pObject.

Referenced by createUndoData(), and toData().

◆ getId()

const std::string & CReference::getId ( ) const

Retrieve the id of the reference in the MIRIAM resource.

Returns: const std::string & id

References CMIRIAMResourceObject::getId(), and mResource.

Referenced by createUndoData(), and toData().

◆ getKey()

const std::string & CReference::getKey ( ) const

virtual

Retrieve the key for the object

Returns: const std::string & key

Reimplemented from CDataObject.

References mKey.

◆ getMIRIAMResourceObject()

const CMIRIAMResourceObject & CReference::getMIRIAMResourceObject ( ) const

Retrieve the MIRIAM resource object for this reference

References mResource.

Referenced by CSBMLExporter::updateMIRIAMAnnotation().

◆ getResource()

std::string CReference::getResource ( ) const

Retrieve the MIRIAM resource for the reference.

Returns: std::string resource

References CMIRIAMResourceObject::getDisplayName(), and mResource.

Referenced by createUndoData(), and toData().

◆ getTriplet()

const CRDFTriplet & CReference::getTriplet ( ) const

Retrieve the RDF triplet holding the information for this reference.

Returns: const CRDFTriplet & triplet

References mTriplet.

Referenced by CMIRIAMInfo::removeReference(), and CSBMLExporter::updateMIRIAMAnnotation().

◆ getURI()

std::string CReference::getURI ( ) const

Retrieve the URI (comprised of resource an id) specifying this reference.

Returns: std::string uri

References CMIRIAMResourceObject::getURI(), and mResource.

◆ setDescription()

void CReference::setDescription ( const std::string & description )

Set the description for the reference.

Parameters

std::string description

References CRDFPredicate::dcterms_description, mNodePath, mTriplet, CRDFTriplet::pObject, and CRDFNode::setFieldValue().

Referenced by applyData().

◆ setId()

void CReference::setId ( const std::string & id )

Set the id of the reference in the MIRIAM resource.

Parameters

const std::string & id

References CRDFPredicate::copasi_isDescribedBy, CRDFNode::getDescendantsWithPredicate(), CRDFNode::getObject(), CMIRIAMResourceObject::getURI(), mIdTriplet, mNodePath, mResource, mTriplet, CRDFTriplet::pObject, CRDFNode::setFieldValue(), CMIRIAMResourceObject::setId(), CMIRIAMResourceObject::setNode(), and CRDFObject::setResource().

Referenced by applyData().

◆ setResource()

void CReference::setResource ( const std::string & resource )

Set the MIRIAM resource for the reference

Parameters

const std::string & resource

References CRDFPredicate::copasi_isDescribedBy, CRDFNode::getDescendantsWithPredicate(), CRDFNode::getObject(), CMIRIAMResourceObject::getURI(), mIdTriplet, mNodePath, mResource, mTriplet, CRDFTriplet::pObject, CMIRIAMResourceObject::setDisplayName(), CRDFNode::setFieldValue(), CMIRIAMResourceObject::setNode(), and CRDFObject::setResource().

Referenced by applyData().

◆ toData()

CData CReference::toData ( ) const

virtual

Retrieve the data describing the object

Returns: CData data

Reimplemented from CDataContainer.

References CData::addProperty(), getDescription(), getId(), getResource(), CData::hash(), CData::MIRIAM_DESCRIPTION, CData::MIRIAM_ID, CData::MIRIAM_RESOURCE, CData::OBJECT_HASH, CData::OBJECT_INDEX, CData::removeProperty(), and CDataContainer::toData().

Referenced by createUndoData().

Member Data Documentation

◆ mIdTriplet

CRDFTriplet CReference::mIdTriplet

private

Triplet in the RDF graph representing the reference.

Referenced by clearInvalidEntries(), CReference(), setId(), and setResource().

◆ mKey

std::string CReference::mKey

private

The key of the object needed for the COPASI tables.

Referenced by getKey(), and ~CReference().

◆ mNodePath

CRDFPredicate::Path CReference::mNodePath

private

The predicate path to the node.

Referenced by clearInvalidEntries(), CReference(), setDescription(), setId(), and setResource().

◆ mResource

CMIRIAMResourceObject CReference::mResource

private

MIRIAM resource for holding database and Id.

Referenced by clearInvalidEntries(), CReference(), getId(), getMIRIAMResourceObject(), getResource(), getURI(), setId(), and setResource().

◆ mTriplet

CRDFTriplet CReference::mTriplet

private

Triplet in the RDF graph representing the reference.

Referenced by clearInvalidEntries(), CReference(), getDescription(), getTriplet(), setDescription(), setId(), and setResource().

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

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CReference() [1/3]

◆ CReference() [2/3]

◆ CReference() [3/3]

◆ ~CReference()

Member Function Documentation

◆ applyData()

◆ clearInvalidEntries()

◆ createUndoData()

◆ destruct()

◆ fromData()

◆ getDescription()

◆ getId()

◆ getKey()

◆ getMIRIAMResourceObject()

◆ getResource()

◆ getTriplet()

◆ getURI()

◆ setDescription()

◆ setId()

◆ setResource()

◆ toData()

Member Data Documentation

◆ mIdTriplet

◆ mKey

◆ mNodePath

◆ mResource

◆ mTriplet