CChemEqElement Class Reference

#include <CChemEqElement.h>

Inheritance diagram for CChemEqElement:

Public Member Functions
void	addToMultiplicity (const C_FLOAT64 multiplicity=1.0)
	CChemEqElement (const CChemEqElement &src, const CDataContainer *pParent)
	CChemEqElement (const std::string &name="Chem Eq Element", const CDataContainer *pParent=NO_PARENT)
void	cleanup ()
const CMetab *	getMetabolite () const
const std::string &	getMetaboliteKey () const
const C_FLOAT64 &	getMultiplicity () const
void	setMetabolite (const std::string &key)
void	setMultiplicity (const C_FLOAT64 multiplicity)
	~CChemEqElement ()
Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)
virtual bool	appendDeletedDependentData (CUndoData &undoData) const
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes) override
	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 void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const override
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 CData	toData () const override
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 void	destruct () override
virtual CCommonName	getCN () const override
virtual const CDataObject *	getDataObject () const override
virtual const std::string &	getKey () const
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 CChemEqElement *	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 *)

Protected Member Functions
	CChemEqElement (const CChemEqElement &src)
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)

Private Member Functions
void	initObjects ()

Private Attributes
std::string	mMetaboliteKey
C_FLOAT64	mMultiplicity

Friends
std::ostream &	operator<< (std::ostream &os, const CChemEqElement &d)

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 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

CChemEqElement() [1/3]

CChemEqElement::CChemEqElement ( const CChemEqElement &  src )

protected

Referenced by fromData().

CChemEqElement() [2/3]

CChemEqElement::CChemEqElement	(	const std::string &	name = "Chem Eq Element",
		const CDataContainer *	pParent = NO_PARENT
	)

Default constructor

Parameters

const	std::string & name (default: "NoName")
const	CDataContainer * pParent (default: NULL)

References CONSTRUCTOR_TRACE, and initObjects().

CChemEqElement() [3/3]

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

Copy constructor

Parameters

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

References CONSTRUCTOR_TRACE, and initObjects().

~CChemEqElement()

CChemEqElement::~CChemEqElement

(

)

Destructor

References DESTRUCTOR_TRACE.

Member Function Documentation

addToMultiplicity()

void CChemEqElement::addToMultiplicity

(

const C_FLOAT64

multiplicity = 1.0

)

Add to the multiplicity of the element.

Parameters

const C_FLOAT64

multiplicity (default = 1.0)

References mMultiplicity.

cleanup()

void CChemEqElement::cleanup

(

)

cleanup

fromData()

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

static

Static method to create a CDataObject based on the provided data

Parameters

const

CData & data

Returns

CChemEqElement * pDataObject

References CChemEqElement(), CData::getProperty(), NO_PARENT, CData::OBJECT_NAME, and CDataValue::toString().

getMetabolite()

const CMetab * CChemEqElement::getMetabolite

(

)

const

Retrieves the metabolite of the element.

Returns

"CMetab *" metabolite

References CKeyFactory::get(), CRootContainer::getKeyFactory(), and mMetaboliteKey.

Referenced by SBMLImporter::applyStoichiometricExpressions(), CSBMLExporter::createReaction(), CModelExpansion::duplicateReaction(), CODEExporterC::KineticFunction2ODEmember(), CModelMerging::mergeMetabolites(), and CModelExpansion::replaceInReaction().

getMetaboliteKey()

const std::string & CChemEqElement::getMetaboliteKey

(

)

const

Retrieve the key of the species

Returns

const std::string & speciesKey

References mMetaboliteKey.

Referenced by CChemEq::addElement(), CModelAdd::addReactions(), SBMLImporter::applyStoichiometricExpressions(), CODEExporter::exportKineticFunction(), and SBMLImporter::isMassActionExpression().

getMultiplicity()

const C_FLOAT64 & CChemEqElement::getMultiplicity

(

)

const

Retrieves the multiplicity of the element.

Returns

const C_FLOAT64 & multiplicity

References mMultiplicity.

Referenced by CChemEq::addElement(), CModelAdd::addReactions(), SBMLImporter::applyStoichiometricExpressions(), CSBMLExporter::createReaction(), CModelExpansion::duplicateReaction(), CODEExporter::exportKineticFunction(), SBMLImporter::isMassActionExpression(), and CODEExporterC::KineticFunction2ODEmember().

initObjects()

void CChemEqElement::initObjects ( )

private

References CDataContainer::addObjectReference(), mMetaboliteKey, mMultiplicity, and CDataObject::ValueDbl.

Referenced by CChemEqElement().

setMetabolite()

void CChemEqElement::setMetabolite

(

const std::string &

key

)

Set the metabolite of the element.

Parameters

CMetab

* metabolite

References CKeyFactory::get(), CRootContainer::getKeyFactory(), CDataObject::getObjectName(), mMetaboliteKey, and CDataObject::setObjectName().

Referenced by CChemEq::addMetabolite(), CModelMerging::mergeMetabolites(), and CModelExpansion::replaceInReaction().

setMultiplicity()

void CChemEqElement::setMultiplicity

(

const C_FLOAT64

multiplicity

)

Set the multiplicity of the element.

Parameters

const C_FLOAT64

multiplicity

References mMultiplicity.

Referenced by CChemEq::addElement(), CChemEq::addMetabolite(), and CChemEq::setMultiplicity().

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  os, const CChemEqElement &  d  )

friend

Member Data Documentation

mMetaboliteKey

std::string CChemEqElement::mMetaboliteKey

private

The name of the metabolite the element

Referenced by getMetabolite(), getMetaboliteKey(), initObjects(), and setMetabolite().

mMultiplicity

C_FLOAT64 CChemEqElement::mMultiplicity

private

The multiplicity of the metabolite

Referenced by addToMultiplicity(), getMultiplicity(), initObjects(), and setMultiplicity().

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

• CChemEqElement.h
• CChemEqElement.cpp