CBiologicalDescription Class Reference

#include <CBiologicalDescription.h>

Inheritance diagram for CBiologicalDescription:

Public Member Functions
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
	CBiologicalDescription (const CBiologicalDescription &src, const CDataContainer *pParent)
	CBiologicalDescription (const CRDFTriplet &triplet, const std::string &objectName="", const CDataContainer *pParent=NO_PARENT)
	CBiologicalDescription (const std::string &objectName, const CDataContainer *pParent=NO_PARENT)
void	clearInvalidEntries ()
virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
virtual void	destruct ()
const std::string &	getId () const
virtual const std::string &	getKey () const
const CMIRIAMResourceObject &	getMIRIAMResourceObject () const
std::string	getPredicate () const
std::string	getResource () const
const CRDFTriplet &	getTriplet () const
std::string	getURI () const
void	setId (const std::string &id)
void	setPredicate (const std::string &predicate)
void	setResource (const std::string &resource)
virtual CData	toData () const
	~CBiologicalDescription ()
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 CBiologicalDescription *	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
std::string	mKey
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

Constructor & Destructor Documentation

CBiologicalDescription() [1/3]

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

Default constructor

Parameters

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

CBiologicalDescription() [2/3]

CBiologicalDescription::CBiologicalDescription	(	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)

CBiologicalDescription() [3/3]

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

Copy constructor

Parameters

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

~CBiologicalDescription()

CBiologicalDescription::~CBiologicalDescription

(

)

Destructor

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

Member Function Documentation

applyData()

bool CBiologicalDescription::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_ID, CData::MIRIAM_PREDICATE, CData::MIRIAM_RESOURCE, CMIRIAMInfo::save(), setId(), setPredicate(), setResource(), and CDataValue::toString().

clearInvalidEntries()

void CBiologicalDescription::clearInvalidEntries

(

)

Convenience method removing invalid predicate, resource, and id combinations

References CRDFPredicate::getURI(), CMIRIAMResourceObject::isValid(), mResource, mTriplet, CRDFTriplet::pObject, CRDFTriplet::Predicate, CRDFTriplet::pSubject, CRDFNode::removeEdge(), and CRDFPredicate::unknown.

createUndoData()

void CBiologicalDescription::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(), getId(), getPredicate(), CData::getProperty(), getResource(), CData::MIRIAM_ID, CData::MIRIAM_PREDICATE, CData::MIRIAM_RESOURCE, CData::OBJECT_HASH, CData::OBJECT_INDEX, CUndoData::removeProperty(), and toData().

destruct()

void CBiologicalDescription::destruct ( )

virtual

Destruct the object

Reimplemented from CDataObject.

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

fromData()

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

static

Static method to create a CDataObject based on the provided data

Parameters

const

CData & data

Returns

CBiologicalDescription * pDataObject

References CMIRIAMInfo::createBiologicalDescription(), CDataObject::getObjectAncestor(), and CDataContainer::remove().

getId()

const std::string & CBiologicalDescription::getId

(

)

const

Retrieve the identifier of the subject in the MIRIAM resource.

Returns

const std::string id

References CMIRIAMResourceObject::getId(), and mResource.

Referenced by createUndoData(), toData(), and CSBMLExporter::updateMIRIAMAnnotation().

getKey()

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

virtual

Retrieve the key of the object.

Returns

const std::string & key

Reimplemented from CDataObject.

References mKey.

getMIRIAMResourceObject()

const CMIRIAMResourceObject & CBiologicalDescription::getMIRIAMResourceObject

(

)

const

Retrieve the MIRIAM resource object for this reference

References mResource.

Referenced by CSBMLExporter::updateMIRIAMAnnotation().

getPredicate()

std::string CBiologicalDescription::getPredicate

(

)

const

Retrieve the predicate, i.e. the relationship between the subject. and the MIRIAM resource.

Returns

std::string predicate

References CRDFPredicate::getDisplayName(), mTriplet, and CRDFTriplet::Predicate.

Referenced by createUndoData(), and toData().

getResource()

std::string CBiologicalDescription::getResource

(

)

const

Retrieve the MIRIAM resource (database) describing the subject.

Returns

std::string resource

References CMIRIAMResourceObject::getDisplayName(), and mResource.

Referenced by createUndoData(), toData(), and CSBMLExporter::updateMIRIAMAnnotation().

getTriplet()

const CRDFTriplet & CBiologicalDescription::getTriplet

(

)

const

Retrieve the RDF triplet holding the description.

Returns

const CRDFTriplet & triplet

References mTriplet.

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

getURI()

std::string CBiologicalDescription::getURI

(

)

const

Retrieve the URI comprised of MIRIAM resource and id.

Returns

std::string uri

References CMIRIAMResourceObject::getURI(), and mResource.

setId()

void CBiologicalDescription::setId

(

const std::string &

id

)

Set the identifier of the subject in the MIRIAM resource.

Parameters

const

std::string & id

References CRDFNode::getObject(), CMIRIAMResourceObject::getURI(), mResource, mTriplet, CRDFTriplet::pObject, CMIRIAMResourceObject::setId(), and CRDFObject::setResource().

Referenced by applyData(), and SBMLImporter::importMIRIAM().

setPredicate()

void CBiologicalDescription::setPredicate

(

const std::string &

predicate

)

Set the predicate, i.e., relationship between the subject and the MIRIAM resource.

Parameters

const

std::string & predicate

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

Referenced by applyData(), and SBMLImporter::importMIRIAM().

setResource()

void CBiologicalDescription::setResource

(

const std::string &

resource

)

Set the MIRIAM resource (database) describing the subject.

Parameters

const

std::string & predicate

References CRDFNode::getObject(), CMIRIAMResourceObject::getURI(), mResource, mTriplet, CRDFTriplet::pObject, CMIRIAMResourceObject::setDisplayName(), and CRDFObject::setResource().

Referenced by applyData(), and SBMLImporter::importMIRIAM().

toData()

CData CBiologicalDescription::toData ( ) const

virtual

Retrieve the data describing the object

Returns

CData data

Reimplemented from CDataContainer.

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

Referenced by createUndoData().

Member Data Documentation

mKey

std::string CBiologicalDescription::mKey

private

The key of the object needed for the COPASI tables.

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

mResource

CMIRIAMResourceObject CBiologicalDescription::mResource

private

MIRIAM resource for holding the database and Id.

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

mTriplet

CRDFTriplet CBiologicalDescription::mTriplet

private

Triplet in the RDF graph representing the description.

Referenced by clearInvalidEntries(), getPredicate(), getTriplet(), setId(), setPredicate(), and setResource().

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

• CBiologicalDescription.h
• CBiologicalDescription.cpp