CModelEntity Class Reference

#include <CModelValue.h>

Inheritance diagram for CModelEntity:

Public Types
enum class	Status {   FIXED = 0 , ASSIGNMENT , REACTIONS , ODE ,   TIME , __SIZE }
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
Public Types inherited from CAnnotation
typedef std::map< std::string, std::string >	UnsupportedAnnotation

Public Member Functions
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes) override
virtual void	calculate ()
	CModelEntity (const CModelEntity &src, const CDataContainer *pParent)
	CModelEntity (const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT, const std::string &type="ModelEntity", const CFlags< Flag > &flag=CFlags< Flag >::None)
virtual CIssue	compile ()
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 override
std::string	getDefaultNoiseExpression () const
std::string	getExpression () const
CExpression *	getExpressionPtr ()
const CExpression *	getExpressionPtr () const
std::string	getInitialExpression () const
CExpression *	getInitialExpressionPtr ()
const CExpression *	getInitialExpressionPtr () const
const C_FLOAT64 &	getInitialValue () const
CDataObject *	getInitialValueReference () const
virtual const std::string &	getKey () const override
CModel *	getModel () const
std::string	getNoiseExpression () const
CExpression *	getNoiseExpressionPtr ()
const CExpression *	getNoiseExpressionPtr () const
CDataObject *	getNoiseReference () const
const C_FLOAT64 &	getRate () const
CDataObject *	getRateReference () const
const std::string &	getSBMLId () const
const CModelEntity::Status &	getStatus () const
virtual const std::string &	getUnitExpression () const
const C_FLOAT64 &	getValue () const
virtual const CDataObject *	getValueObject () const override
virtual void *	getValuePointer () const override
CDataObject *	getValueReference () const
const bool &	hasNoise () const
bool	isFixed () const
const bool &	isUsed () const
CIssue	setExpression (const std::string &expression)
bool	setExpressionPtr (CExpression *pExpression)
void	setHasNoise (const bool &hasNoise)
CIssue	setInitialExpression (const std::string &expression)
bool	setInitialExpressionPtr (CExpression *pExpression)
virtual void	setInitialValue (const C_FLOAT64 &initialValue)
bool	setNoiseExpression (const std::string &expression)
bool	setNoiseExpressionPtr (CExpression *pExpression)
virtual bool	setObjectParent (const CDataContainer *pParent) override
void	setRate (const C_FLOAT64 &rate)
void	setSBMLId (const std::string &id) const
bool	setStatus (const CModelEntity::Status &status)
virtual CIssue	setUnitExpression (std::string unitExpression)
void	setUsed (const bool &used)
virtual void	setValue (const C_FLOAT64 &value)
virtual CData	toData () const override
	~CModelEntity ()
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)
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 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 void	destruct () override
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
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)
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 ()
Public Member Functions inherited from CAnnotation
bool	addUnsupportedAnnotation (const std::string &name, const std::string &xml)
bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
	CAnnotation ()
	CAnnotation (const CAnnotation &src)
void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
const std::string &	getMiriamAnnotation () const
const std::string &	getNotes () const
UnsupportedAnnotation &	getUnsupportedAnnotations ()
const UnsupportedAnnotation &	getUnsupportedAnnotations () const
void	initMiriamAnnotation (const std::string &newId)
bool	operator== (const CAnnotation &rhs) const
bool	removeUnsupportedAnnotation (const std::string &name)
bool	replaceUnsupportedAnnotation (const std::string &name, const std::string &xml)
void	setMiriamAnnotation (const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)
void	setNotes (const std::string &notes)
CData	toData () const
virtual	~CAnnotation ()

Static Public Member Functions
static CModelEntity *	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 *)
Static Public Member Functions inherited from CAnnotation
static CMIRIAMInfo *	allocateMiriamInfo (CDataContainer *pParent)
static CAnnotation *	castObject (CDataObject *pObject)
static const CAnnotation *	castObject (const CDataObject *pObject)
static void	freeMiriamInfo (CDataContainer *pParent)

Static Public Attributes
static const CEnumAnnotation< std::string, Status >	StatusName
static const CEnumAnnotation< std::string, Status >	XMLStatus
Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Protected Member Functions
	CModelEntity (const CModelEntity &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)

Protected Attributes
bool	mHasNoise
C_FLOAT64	mIValue
C_FLOAT64	mNoise
CExpression *	mpExpression
CExpression *	mpInitialExpression
CDataObjectReference< C_FLOAT64 > *	mpIValueReference
CModel *	mpModel
CExpression *	mpNoiseExpression
CDataObjectReference< C_FLOAT64 > *	mpNoiseReference
CDataObjectReference< C_FLOAT64 > *	mpRateReference
CDataObjectReference< C_FLOAT64 > *	mpValueReference
C_FLOAT64	mRate
std::string	mSBMLId
std::string	mUnitExpression
C_FLOAT64	mValue
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
Protected Attributes inherited from CAnnotation
std::string	mKey

Private Member Functions
void	initObjects ()

Private Attributes
Status	mStatus
bool	mUsed

Detailed Description

The base class for CCompartment, CMetab and CModelValue. CModelEntity is a base class for CCompartment, CMetab and CModelValue. These three classes have in common that (in the long run) they can each be model variables (subject to ODEs), constant, or subject to algebraic assignments. In addition, the CMetab objects can also be subject to reactions, and conservation rules.

Member Enumeration Documentation

Status

enum CModelEntity::Status

strong

The valid states for metabolites

Enumerator
FIXED
ASSIGNMENT
REACTIONS
ODE
TIME
__SIZE

Constructor & Destructor Documentation

CModelEntity() [1/3]

CModelEntity::CModelEntity ( const CModelEntity &  src )

protected

CModelEntity() [2/3]

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

Default constructor

Parameters

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

References CKeyFactory::add(), CONSTRUCTOR_TRACE, CRootContainer::getKeyFactory(), CDataObject::getObjectType(), CAnnotation::initMiriamAnnotation(), initObjects(), and CAnnotation::mKey.

CModelEntity() [3/3]

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

Copy constructor

Parameters

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

References CKeyFactory::add(), CRootContainer::getKeyFactory(), CAnnotation::getMiriamAnnotation(), CDataObject::getObjectType(), initObjects(), CAnnotation::mKey, mStatus, CAnnotation::setMiriamAnnotation(), and setStatus().

~CModelEntity()

CModelEntity::~CModelEntity

(

)

Destructor.

References DESTRUCTOR_TRACE, mpModel, and CModel::removeModelEntity().

Member Function Documentation

applyData()

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

overridevirtual

Apply the provided data to the object

Parameters

const

CData & data

Returns

bool success

Reimplemented from CDataContainer.

Reimplemented in CMetab, CModelValue, CModel, and CCompartment.

References CData::ADD_NOISE, CAnnotation::applyData(), CDataContainer::applyData(), CData::EXPRESSION, CData::getProperty(), CData::INITIAL_EXPRESSION, CData::INITIAL_VALUE, CData::isSetProperty(), mIValue, mpModel, CData::NOISE_EXPRESSION, CModel::setCompileFlag(), setExpression(), setHasNoise(), setInitialExpression(), setNoiseExpression(), setStatus(), CData::SIMULATION_TYPE, StatusName, CDataValue::toBool(), CDataValue::toDouble(), CEnumAnnotation< Type, Enum >::toEnum(), and CDataValue::toString().

Referenced by CCompartment::applyData(), CModel::applyData(), CModelValue::applyData(), and CMetab::applyData().

calculate()

void CModelEntity::calculate ( void  )

virtual

Calculate the value or the rate depending whether we have an ASIGNMENT or ODE

Reimplemented in CMetab.

References ASSIGNMENT, CExpression::calcValue(), mpExpression, mRate, mStatus, mValue, and ODE.

compile()

CIssue CModelEntity::compile ( )

virtual

Compile the model value. This is only needed for status ASIGNMENT and ODE.

Returns

CIssue issue

Reimplemented in CMetab, and CModel.

References CDataContainer::add(), CValidity::add(), ASSIGNMENT, CExpression::calcValue(), CValidity::clear(), CExpression::compile(), CExpression::createInitialExpression(), CIssue::ExpressionEmpty, getExpression(), CValidity::getFirstWorstIssue(), CEvaluationTree::getInfix(), getNoiseExpression(), CDataObject::getObjectDataModel(), CDataObject::getPrerequisites(), CDataObject::getValidity(), mHasNoise, mIValue, mpExpression, mpInitialExpression, mpModel, mpNoiseExpression, CDataObject::mPrerequisits, mStatus, CObjectInterface::mValidity, ODE, pdelete, CDataObject::setObjectName(), and CIssue::Warning.

Referenced by setExpression(), setExpressionPtr(), setInitialExpression(), setInitialExpressionPtr(), setNoiseExpression(), and setNoiseExpressionPtr().

createUndoData()

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

overridevirtual

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.

Reimplemented in CMetab, CModelValue, CModel, and CCompartment.

References CData::ADD_NOISE, CUndoData::addProperty(), CUndoData::CHANGE, CAnnotation::createUndoData(), CDataContainer::createUndoData(), CData::EXPRESSION, getExpression(), getInitialExpression(), getNoiseExpression(), CData::getProperty(), CData::INITIAL_EXPRESSION, CData::INITIAL_VALUE, mHasNoise, mIValue, mStatus, CData::NOISE_EXPRESSION, CData::SIMULATION_TYPE, and StatusName.

Referenced by CCompartment::createUndoData(), CModel::createUndoData(), CModelValue::createUndoData(), and CMetab::createUndoData().

fromData()

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

static

Static method to create a CDataObject based on the provided data

Parameters

const

CData & data

Returns

CModelEntity * pDataObject

getChildObjectUnits()

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

overridevirtual

Retrieve the units of the child object.

Returns

const & CUnit units

Reimplemented from CDataContainer.

Reimplemented in CMetab, and CModel.

References CModel::getTimeUnit(), CDataContainer::getUnits(), mpIValueReference, mpModel, mpRateReference, and mpValueReference.

Referenced by CModel::getChildObjectUnits(), CMetab::getChildObjectUnits(), and CModelParameter::getUnit().

getDefaultNoiseExpression()

std::string CModelEntity::getDefaultNoiseExpression

(

)

const

Retrieve the default expression for the noise.

Returns

std::string expression

References CDataObject::getCN(), and mpRateReference.

getExpression()

std::string CModelEntity::getExpression

(

)

const

Retrieve the expression for non FIXED model values.

Returns

std::string expression

References CEvaluationTree::getInfix(), isFixed(), mpExpression, and CExpression::updateInfix().

Referenced by compile(), CMetab::compile(), CMathObject::createExtensiveODERateExpression(), CSBMLExporter::createRule(), createUndoData(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CCopasiXML::saveModel(), CMetab::setObjectParent(), and toData().

getExpressionPtr() [1/2]

CExpression * CModelEntity::getExpressionPtr

(

)

Retrieve the pointer to the expression for non FIXED model values.

Returns

CExpression*

References mpExpression, and CExpression::updateInfix().

getExpressionPtr() [2/2]

const CExpression * CModelEntity::getExpressionPtr

(

)

const

Retrieve the pointer to the expression for non FIXED model values.

Returns

CExpression*

References mpExpression, and CExpression::updateInfix().

Referenced by CSBMLExporter::checkForPiecewiseFunctions(), CSBMLExporter::checkForUnsupportedFunctionCalls(), CSBMLExporter::checkForUnsupportedObjectReferences(), CMathObject::compileRate(), CMathObject::compileValue(), CModelAdd::copyExpression(), CSBMLExporter::createRule(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportModelValuesExpressions(), SBMLImporter::importRuleForModelEntity(), CModelMerging::mergeMetabolites(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInModelEntity(), and CMMLOutput::writeRHS_ModelEntity().

getInitialExpression()

std::string CModelEntity::getInitialExpression

(

)

const

Retrieve the expression for ODE or REACTION model values.

Returns

std::string expression

References ASSIGNMENT, CEvaluationTree::getInfix(), mpInitialExpression, mStatus, and CExpression::updateInfix().

Referenced by CModelAdd::addCompartmentsExpressions(), CModelAdd::addMetabolitesExpressions(), CModelAdd::addModelValuesExpressions(), CSBMLExporter::createCompartment(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), createUndoData(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CMathContainer::initializeMathObjects(), CModelMerging::mergeMetabolites(), CCopasiXML::saveModel(), and toData().

getInitialExpressionPtr() [1/2]

CExpression * CModelEntity::getInitialExpressionPtr

(

)

Retrieve the pointer to the expression for non FIXED model values.

Returns

CExpression*

References mpInitialExpression, and CExpression::updateInfix().

getInitialExpressionPtr() [2/2]

const CExpression * CModelEntity::getInitialExpressionPtr

(

)

const

Retrieve the pointer to the expression for non FIXED model values.

Returns

CExpression*

References mpInitialExpression, and CExpression::updateInfix().

Referenced by CSBMLExporter::checkForUnsupportedFunctionCalls(), CSBMLExporter::checkForUnsupportedObjectReferences(), CMathObject::compileInitialValue(), CModelAdd::copyInitialExpression(), CSBMLExporter::createInitialAssignment(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), SBMLImporter::importInitialAssignments(), CModelMerging::mergeMetabolites(), SBMLImporter::removeUnusedFunctions(), and CModelExpansion::replaceInModelEntity().

getInitialValue()

const C_FLOAT64 & CModelEntity::getInitialValue

(

)

const

Retrieve the initial value

References mIValue.

Referenced by CModelAdd::addCompartments(), CModelAdd::addModelValues(), addParticleNumberToInitialValueMap(), SBMLImporter::applyConversionFactors(), CFunctionAnalyzer::constructCallParametersActualValues(), CMetab::convertToConcentration(), CMetab::convertToNumber(), CSBMLExporter::createCompartment(), CModelParameterSet::createFromModel(), CSBMLExporter::createMetabolite(), CModel::createMetabolite(), CSBMLExporter::createParameter(), CCSPMethod::cspstep(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CODEExporter::exportCompartments(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportModelValues(), CModel::initializeAtolVector(), CReactionInterface::loadMappingAndValues(), CModelParameter::refreshFromModel(), and CModel::suitableForStochasticSimulation().

getInitialValueReference()

CDataObject * CModelEntity::getInitialValueReference

(

)

const

Retrieve object referencing the initial value

Returns

CDataObject * initialValueReference

References mpIValueReference.

Referenced by addParticleNumberToInitialValueMap(), CMathObject::compileInitialValue(), CMathObject::createExtensiveValueExpression(), CModelParameterSet::createFromModel(), CSBMLExporter::createInitialAssignment(), CExpression::createInitialExpression(), CDataModel::findObjectByDisplayName(), CMetab::getChildObjectUnits(), getInitialCNForSBase(), CModelParameter::getUnit(), SBMLImporter::importInitialAssignments(), CMathContainer::initializeAtolVector(), CMathContainer::initializeObjects(), CModelParameter::refreshFromModel(), SBMLImporter::replace_time_with_initial_time(), CModelParameterSet::saveToStream(), and SEDMLImporter::updateCopasiTaskForSimulation().

getKey()

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

overridevirtual

Retrieve the key

Returns

std::string key

Reimplemented from CAnnotation.

Reimplemented in CModel.

References CAnnotation::getKey().

Referenced by CModelAdd::addCompartments(), CModelAdd::addCompartmentsExpressions(), CModelAdd::addMetabolites(), CModelAdd::addMetabolitesExpressions(), CModelAdd::addModelValues(), CModelAdd::addModelValuesExpressions(), addParticleNumberToInitialValueMap(), CModelAdd::addReactions(), CLayoutInitializer::createCompartmentGlyph(), CCopasiSpringLayout::createLayout(), CLayoutInitializer::createMetabGlyph(), CChemEqInterface::createNonExistingMetabs(), CReactionInterface::createOtherObjects(), CSBMLExporter::createSBMLDocument(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateEvent(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CModelExpansion::duplicateReaction(), CODEExporter::exportExpression(), CODEExporter::exportKineticFunction(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportODEs(), CODEExporterBM::exportSingleCompartment(), CODEExporterC::exportSingleCompartment(), CODEExporterXPPAUT::exportSingleCompartment(), CODEExporterBM::exportSingleMetabolite(), CODEExporterC::exportSingleMetabolite(), CODEExporterXPPAUT::exportSingleMetabolite(), CODEExporterBM::exportSingleModelEntity(), CODEExporterC::exportSingleModelEntity(), CODEExporterXPPAUT::exportSingleModelEntity(), CODEExporterBM::exportSingleModVal(), CODEExporterC::exportSingleModVal(), CODEExporterXPPAUT::exportSingleModVal(), CODEExporterBM::exportSingleODE(), CODEExporterC::exportSingleODE(), CODEExporterXPPAUT::exportSingleODE(), CMetabNameInterface::getMetaboliteKey(), CEFMTask::getSpeciesChanges(), SBMLImporter::importMIRIAM(), CCopasiSpringLayout::initFromLayout(), CODEExporterC::KineticFunction2ODEmember(), CReaction::loadOneRole(), CModelMerging::mergeMetabolites(), CODEExporter::preprocess(), CODEExporterC::preprocess(), CompartmentHandler::processEnd(), MetaboliteHandler::processEnd(), ModelValueHandler::processEnd(), CompartmentGlyphHandler::processStart(), MetaboliteGlyphHandler::processStart(), ModifierHandler::processStart(), ProductHandler::processStart(), SubstrateHandler::processStart(), TextGlyphHandler::processStart(), CCopasiSpringLayout::randomize(), CModel::removeMetabolite(), CModelExpansion::replaceInReaction(), CCopasiXML::saveModel(), CChemEq::setMultiplicity(), CModelMerging::simpleCall(), and CMMLOutput::writeRHS().

getModel()

CModel * CModelEntity::getModel

(

)

const

Retrieve a pointer to the model the entity belongs too

Returns

CModel * pModel

References mpModel.

Referenced by CMetab::convertToConcentration(), CMetab::convertToNumber(), CSBMLExporter::createAreaUnit(), SBMLImporter::createCModelFromSBMLDocument(), CSBMLExporter::createCompartments(), CSBMLExporter::createLengthUnit(), CSBMLExporter::createMetabolites(), CSBMLExporter::createParameters(), CSBMLExporter::createReactions(), CSBMLExporter::createSubstanceUnit(), CSBMLExporter::createTimeUnit(), CSBMLExporter::createVolumeUnit(), CSBMLExporter::hasVolumeAssignment(), CDataModel::loadModelParameterSets(), and CILDMMethod::printResult().

getNoiseExpression()

std::string CModelEntity::getNoiseExpression

(

)

const

Retrieve the expression for non FIXED model values.

Returns

std::string expression

References CEvaluationTree::getInfix(), mpNoiseExpression, mStatus, ODE, and CExpression::updateInfix().

Referenced by compile(), CMetab::compile(), CMathObject::createExtensiveNoiseExpression(), createUndoData(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CCopasiXML::saveModel(), and toData().

getNoiseExpressionPtr() [1/2]

CExpression * CModelEntity::getNoiseExpressionPtr

(

)

Retrieve the pointer to the expression for ODE model values.

Returns

CExpression*

References mpNoiseExpression, and CExpression::updateInfix().

getNoiseExpressionPtr() [2/2]

const CExpression * CModelEntity::getNoiseExpressionPtr

(

)

const

Retrieve the pointer to the expression for ODE model values.

Returns

CExpression*

References mpNoiseExpression, and CExpression::updateInfix().

Referenced by CMathObject::compileNoise(), CMathObject::createIntensiveNoiseExpression(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), and CModelExpansion::replaceInModelEntity().

getNoiseReference()

CDataObject * CModelEntity::getNoiseReference

(

)

const

Retrieve object referencing the noise

Returns

CDataObject * rateReference

References mpNoiseReference.

getRate()

const C_FLOAT64 & CModelEntity::getRate

(

)

const

Return rate of production of this entity

References mRate.

getRateReference()

CDataObject * CModelEntity::getRateReference

(

)

const

Retrieve object referencing the rate

Returns

CDataObject * rateReference

References mpRateReference.

Referenced by CModel::appendAllDependents(), CMathObject::compileTransitionTime(), CMathObject::createIntensiveRateExpression(), CDataModel::findObjectByDisplayName(), CMathContainer::initializeObjects(), and SEDMLUtils::resolveVariable().

getSBMLId()

const std::string & CModelEntity::getSBMLId

(

)

const

Returns a reference to the SBML Id.

References mSBMLId.

Referenced by SBMLImporter::applyStoichiometricExpressions(), CSBMLExporter::collectIds(), CSBMLExporter::createCompartment(), SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createInitialAssignment(), CSBMLExporter::createKineticLaw(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CSBMLExporter::createReaction(), CSBMLExporter::createRule(), CSBMLExporter::createRules(), CSBMLExporter::createSBMLDocument(), CSBMLExporter::createTimesTree(), CSBMLExporter::exportEventAssignments(), SEDMLUtils::getSbmlId(), SBMLImporter::replaceObjectNames(), CCopasiXML::saveModel(), CEvaluationNodeObject::toAST(), and VariableInfo::VariableInfo().

getStatus()

const CModelEntity::Status & CModelEntity::getStatus

(

)

const

Retrieve the status of the entity.

Returns

const CModelEntity::Status & status

References mStatus.

Referenced by CModelAdd::addCompartments(), CModelAdd::addMetabolites(), CModelAdd::addModelValues(), CModel::appendAllDependents(), CMetab::calculate(), CSBMLExporter::checkForODESpeciesInNonfixedCompartment(), CSBMLExporter::checkForPiecewiseFunctions(), CMetab::compile(), CEventAssignment::compile(), CMathObject::compileTransitionTime(), CFunctionAnalyzer::constructCallParametersActualValues(), CSBMLExporter::createCompartment(), CMathObject::createIntensiveRateExpression(), CCopasiSpringLayout::createLayout(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), CSBMLExporter::createRule(), CMathEvent::createUpdateSequences(), CModelParameter::diff(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CODEExporter::exportCompartments(), CODEExporter::exportExpression(), CODEExporter::exportMetabolites(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportModelValues(), CODEExporter::exportModelValuesExpressions(), CODEExporter::exportODEs(), CODEExporterBM::exportSingleCompartment(), CODEExporterC::exportSingleCompartment(), CODEExporterXPPAUT::exportSingleCompartment(), CODEExporterBM::exportSingleMetabolite(), CODEExporterC::exportSingleMetabolite(), CODEExporterXPPAUT::exportSingleMetabolite(), CODEExporterBM::exportSingleModelEntity(), CODEExporterC::exportSingleModelEntity(), CODEExporterXPPAUT::exportSingleModelEntity(), CODEExporterBM::exportSingleModVal(), CODEExporterC::exportSingleModVal(), CODEExporterXPPAUT::exportSingleModVal(), SBMLImporter::importRuleForModelEntity(), CMathContainer::initializeObjects(), CSBMLExporter::isEventAssignmentSBMLCompatible(), CODEExporter::isModelEntityExpressionODEExporterCompatible(), CModelMerging::mergeMetabolites(), CODEExporter::preprocess(), CODEExporterC::preprocess(), SBMLImporter::removeUnusedFunctions(), CSBMLExporter::replaceSpeciesReferences(), CCopasiXML::saveModel(), CCopasiXML::saveModelParameterSets(), CMetab::setObjectParent(), CModelParameter::updateModel(), and CModelParameterSpecies::updateModel().

getUnitExpression()

const std::string & CModelEntity::getUnitExpression ( ) const

virtual

Get the unit.

Returns

CUnit &

References mUnitExpression.

Referenced by CSBMLExporter::createParameter(), CModelParameter::getUnit(), and CCopasiXML::saveModel().

getValue()

const C_FLOAT64 & CModelEntity::getValue

(

)

const

Retrieve the value

References mValue.

Referenced by CMetab::calculate(), and CSBMLExporter::replaceSpeciesReferences().

getValueObject()

const CDataObject * CModelEntity::getValueObject ( ) const

overridevirtual

Retrieve the object representing the value;

Reimplemented from CDataContainer.

Reimplemented in CMetab.

References mpValueReference.

Referenced by CEventAssignment::CEventAssignment(), and CEventAssignment::compile().

getValuePointer()

void * CModelEntity::getValuePointer ( ) const

overridevirtual

Retrieve a pointer to the value;

Reimplemented from CDataObject.

Reimplemented in CMetab.

References C_FLOAT64, and mValue.

getValueReference()

CDataObject * CModelEntity::getValueReference

(

)

const

Retrieve object referencing the value

Returns

CDataObject * valueReference

References mpValueReference.

Referenced by CMathObject::compile(), CTimeSeries::compile(), CMathEvent::CAssignment::compile(), CMathObject::compilePropensity(), CMathObject::compileTransitionTime(), CMathObject::compileValue(), SEDMLUtils::createAmountMV(), CPlotSpecification::createDefaultPlot(), CMathObject::createExtensiveValueExpression(), CExpression::createInitialExpression(), CSBMLExporter::createRule(), CSBMLExporter::exportEventAssignments(), CDataModel::findObjectByDisplayName(), CMathContainer::getCompartment(), CModel::getCorrespondingTransientObject(), CModelParameterGroup::getObjectUnit(), SBMLImporter::importEvent(), SBMLImporter::importRuleForModelEntity(), CMathReaction::initialize(), CMathContainer::initializeObjects(), CSBMLExporter::replaceSpeciesReferences(), SEDMLUtils::resolveVariable(), SBMLImporter::sbmlId2CopasiCN(), CTrajectoryMethodDsaLsodar::start(), and VariableInfo::VariableInfo().

hasNoise()

const bool & CModelEntity::hasNoise

(

)

const

Check whether noise is added to the ODE

Returns

const bool & hasNoise

References mHasNoise.

Referenced by CMathObject::compileNoise(), CMathObject::createExtensiveNoiseExpression(), CMathObject::createIntensiveNoiseExpression(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CCopasiXML::saveModel(), and setHasNoise().

initObjects()

void CModelEntity::initObjects ( )

private

Initialize the contained CDataObjects

References CModel::addModelEntity(), CDataContainer::addObjectReference(), CDataObject::getObjectAncestor(), mIValue, mNoise, mpIValueReference, mpModel, mpNoiseReference, mpRateReference, mpValueReference, mRate, mSBMLId, mValue, CDataObject::ValueDbl, and CDataObject::ValueString.

Referenced by CModelEntity().

isFixed()

bool CModelEntity::isFixed ( ) const

inline

Check whether the entity is FIXED or not.

Returns

bool isFixed

References FIXED, and mStatus.

Referenced by getExpression(), CMetab::setConcentration(), setExpression(), and setExpressionPtr().

isUsed()

const bool & CModelEntity::isUsed

(

)

const

Retrieve whether the model value is used during simulation

Returns

const bool & used

References mUsed.

Referenced by CModel::buildUserOrder().

setExpression()

CIssue CModelEntity::setExpression

(

const std::string &

expression

)

Set the expression for non FIXED model values

Parameters

const

std::string & expression

Returns

CIssue issue

References CValidity::add(), CFlags< Enum >::All, compile(), CIssue::Error, CEvaluationTree::getInfix(), isFixed(), mpExpression, mpModel, CObjectInterface::mValidity, CValidity::remove(), CModel::setCompileFlag(), CExpression::setInfix(), and CIssue::SettingFixedExpression.

Referenced by applyData(), CModelAdd::copyExpression(), SEDMLUtils::createAmountMV(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CompartmentHandler::processEnd(), MetaboliteHandler::processEnd(), ModelValueHandler::processEnd(), and CMetab::setObjectParent().

setExpressionPtr()

bool CModelEntity::setExpressionPtr

(

CExpression *

pExpression

)

Set the expression for non FIXED model values

Parameters

CExpression*

Returns

bool success

References CDataContainer::add(), compile(), isFixed(), mpExpression, mpModel, pdelete, CDataContainer::remove(), CModel::setCompileFlag(), CDataObject::setObjectName(), and CDataObject::setObjectParent().

Referenced by SBMLImporter::importRuleForModelEntity().

setHasNoise()

void CModelEntity::setHasNoise

(

const bool &

hasNoise

)

Set whether to add noise to the ODE

Parameters

const

bool & hasNoise

References hasNoise(), mHasNoise, mpModel, and CModel::setCompileFlag().

Referenced by applyData(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CompartmentHandler::processStart(), MetaboliteHandler::processStart(), and ModelValueHandler::processStart().

setInitialExpression()

CIssue CModelEntity::setInitialExpression

(

const std::string &

expression

)

Set the expression for ODE or REACTION model values

Parameters

const

std::string & expression

Returns

CIssue issue

References CValidity::add(), CFlags< Enum >::All, ASSIGNMENT, compile(), CIssue::Error, CEvaluationTree::getInfix(), CIssue::InitialExpressionWithAssignment, mpInitialExpression, mpModel, mStatus, CObjectInterface::mValidity, CValidity::remove(), CModel::setCompileFlag(), and CExpression::setInfix().

Referenced by applyData(), CModelAdd::copyInitialExpression(), SBMLImporter::createCReactionFromReaction(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CompartmentHandler::processEnd(), MetaboliteHandler::processEnd(), ModelHandler::processEnd(), ModelValueHandler::processEnd(), and CModelParameter::updateModel().

setInitialExpressionPtr()

bool CModelEntity::setInitialExpressionPtr

(

CExpression *

pExpression

)

Set the expression for non FIXED model values

Parameters

CExpression*

Returns

bool success

References CDataContainer::add(), ASSIGNMENT, compile(), mpInitialExpression, mpModel, mStatus, pdelete, CDataContainer::remove(), CModel::setCompileFlag(), CDataObject::setObjectName(), and CDataObject::setObjectParent().

Referenced by SBMLImporter::importInitialAssignments().

setInitialValue()

void CModelEntity::setInitialValue ( const C_FLOAT64 &  initialValue )

virtual

Set the initial value

Parameters

const

C_FLOAT64 & initialValue

References mIValue.

Referenced by CModel::createCompartment(), SBMLImporter::createHasOnlySubstanceUnitFactor(), CModel::createMetabolite(), CModel::createModelValue(), CReactionInterface::createUndoData(), CCompartment::load(), CMetab::operator=(), and CModelParameter::updateModel().

setNoiseExpression()

bool CModelEntity::setNoiseExpression

(

const std::string &

expression

)

Set the expression for non FIXED model values

Parameters

const

std::string & expression

Returns

bool success

References compile(), mpModel, mpNoiseExpression, mStatus, ODE, CModel::setCompileFlag(), and CExpression::setInfix().

Referenced by applyData(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), CModelExpansion::duplicateMetab(), CompartmentHandler::processEnd(), MetaboliteHandler::processEnd(), and ModelValueHandler::processEnd().

setNoiseExpressionPtr()

bool CModelEntity::setNoiseExpressionPtr

(

CExpression *

pExpression

)

Set the noise expression for ODE model values

Parameters

CExpression*

Returns

bool success

References CDataContainer::add(), compile(), mpModel, mpNoiseExpression, mStatus, ODE, pdelete, CDataContainer::remove(), CModel::setCompileFlag(), CDataObject::setObjectName(), and CDataObject::setObjectParent().

setObjectParent()

bool CModelEntity::setObjectParent ( const CDataContainer *  pParent )

overridevirtual

Set the object parent

Parameters

const

CDataContainer * pParent

Returns

bool success

Reimplemented from CDataObject.

Reimplemented in CMetab, and CModel.

References CModel::addModelEntity(), CDataObject::getObjectAncestor(), mpModel, CModel::removeModelEntity(), and CDataObject::setObjectParent().

Referenced by CMetab::setObjectParent().

setRate()

void CModelEntity::setRate

(

const C_FLOAT64 &

rate

)

Set the rate (dmValue/dt)

Parameters

const C_FLOAT64 &

rate

References mRate.

setSBMLId()

void CModelEntity::setSBMLId

(

const std::string &

id

)

const

Sets the SBMLId.

References mSBMLId.

Referenced by SBMLImporter::createCCompartmentFromCompartment(), SBMLImporter::createCMetabFromSpecies(), SBMLImporter::createCModelFromSBMLDocument(), SBMLImporter::createCModelValueFromParameter(), CSBMLExporter::createCompartment(), SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createMetabolite(), CSBMLExporter::createParameter(), and SBMLMapHandler::processStart().

setStatus()

bool CModelEntity::setStatus

(

const CModelEntity::Status &

status

)

Set the status

Parameters

const

CModelEntity::Status & status

References __SIZE, CDataContainer::add(), ASSIGNMENT, CExpression::createInitialExpression(), FIXED, CDataObject::getObjectDataModel(), CDataObject::getObjectType(), mpExpression, mpInitialExpression, mpModel, mRate, mStatus, mUsed, ODE, pdelete, REACTIONS, CModel::setCompileFlag(), CDataObject::setObjectName(), and TIME.

Referenced by CModelAdd::addCompartments(), CModelAdd::addMetabolites(), CModelAdd::addModelValues(), applyData(), CCompartment::CCompartment(), CMetab::CMetab(), CModel::CModel(), CModelEntity(), SEDMLUtils::createAmountMV(), SBMLImporter::createCMetabFromSpecies(), SBMLImporter::createCReactionFromReaction(), CModel::createMetabolite(), CModelExpansion::duplicateCompartment(), CModelExpansion::duplicateGlobalQuantity(), SBMLImporter::importRuleForModelEntity(), CMetab::load(), CMetab::operator=(), CompartmentHandler::processStart(), MetaboliteHandler::processStart(), ModelValueHandler::processStart(), and CMetab::setObjectParent().

setUnitExpression()

CIssue CModelEntity::setUnitExpression ( std::string  unitExpression )

virtual

Set the unit.

Parameters

const

CUnit & unit

Returns

CIssue issue

References CValidity::add(), CFlags< Enum >::All, mUnitExpression, CObjectInterface::mValidity, CValidity::remove(), CUnit::setExpression(), CIssue::UnitConflict, CIssue::UnitInvalid, CIssue::UnitUndefined, and CIssue::Warning.

Referenced by CModelValue::applyData(), SBMLImporter::createCModelValueFromParameter(), and ModelValueHandler::processEnd().

setUsed()

void CModelEntity::setUsed

(

const bool &

used

)

Set whether the model entity is used during simulation

Parameters

const

bool & used

References mUsed.

Referenced by CModel::CModel().

setValue()

void CModelEntity::setValue ( const C_FLOAT64 &  value )

virtual

Set the value

Parameters

const

C_FLOAT64 & value

References mValue.

toData()

CData CModelEntity::toData ( ) const

overridevirtual

Retrieve the data describing the object

Returns

CData data

Reimplemented from CDataContainer.

Reimplemented in CMetab, CModelValue, CModel, and CCompartment.

References CData::ADD_NOISE, CData::addProperty(), CData::appendData(), CData::EXPRESSION, getExpression(), getInitialExpression(), getNoiseExpression(), CData::INITIAL_EXPRESSION, CData::INITIAL_VALUE, mHasNoise, mIValue, mStatus, CData::NOISE_EXPRESSION, CData::SIMULATION_TYPE, StatusName, CAnnotation::toData(), and CDataContainer::toData().

Referenced by CCompartment::toData(), CModel::toData(), CModelValue::toData(), and CMetab::toData().

Member Data Documentation

mHasNoise

bool CModelEntity::mHasNoise

protected

A Boolean flag indicating whether to add noise to the reaction

Referenced by compile(), CMetab::compile(), createUndoData(), hasNoise(), setHasNoise(), and toData().

mIValue

C_FLOAT64 CModelEntity::mIValue

protected

Pointer to the initial value of the model entity.

Referenced by CCompartment::applyData(), applyData(), CCompartment::CCompartment(), CModel::CModel(), compile(), CMetab::compile(), CCompartment::createUndoData(), createUndoData(), CModel::getInitialTime(), getInitialValue(), initObjects(), CModel::load(), CModel::setInitialTime(), setInitialValue(), CCompartment::toData(), and toData().

mNoise

C_FLOAT64 CModelEntity::mNoise

protected

Noise

Referenced by initObjects().

mpExpression

CExpression* CModelEntity::mpExpression

protected

The infix expression for objects of type ASSIGNMENT or ODE

Referenced by calculate(), CMetab::calculate(), compile(), CMetab::compile(), getExpression(), getExpressionPtr(), setExpression(), setExpressionPtr(), and setStatus().

mpInitialExpression

CExpression* CModelEntity::mpInitialExpression

protected

Optional initial expression

Referenced by compile(), CMetab::compile(), getInitialExpression(), getInitialExpressionPtr(), setInitialExpression(), setInitialExpressionPtr(), and setStatus().

mpIValueReference

CDataObjectReference<C_FLOAT64>* CModelEntity::mpIValueReference

protected

Referenced by CMetab::compileIsInitialValueChangeAllowed(), getChildObjectUnits(), getInitialValueReference(), CCompartment::initObjects(), CMetab::initObjects(), CModel::initObjects(), and initObjects().

mpModel

CModel* CModelEntity::mpModel

mutableprotected

Referenced by CCompartment::applyData(), applyData(), CMetab::calculate(), compile(), CMetab::compileIsInitialValueChangeAllowed(), CModel::createMetabolite(), CMetab::getChildObjectUnits(), getChildObjectUnits(), CMetab::getCountOfDependentReactions(), getModel(), CCompartment::getUnits(), CModel::initObjects(), initObjects(), CMetab::setCompartment(), setExpression(), setExpressionPtr(), setHasNoise(), setInitialExpression(), setInitialExpressionPtr(), setNoiseExpression(), setNoiseExpressionPtr(), setObjectParent(), setStatus(), CModel::~CModel(), and ~CModelEntity().

mpNoiseExpression

CExpression* CModelEntity::mpNoiseExpression

protected

Optional noise term for entities of type ODE

Referenced by compile(), CMetab::compile(), getNoiseExpression(), getNoiseExpressionPtr(), setNoiseExpression(), and setNoiseExpressionPtr().

mpNoiseReference

CDataObjectReference<C_FLOAT64>* CModelEntity::mpNoiseReference

protected

Referenced by getNoiseReference(), and initObjects().

mpRateReference

CDataObjectReference<C_FLOAT64>* CModelEntity::mpRateReference

protected

Referenced by getChildObjectUnits(), getDefaultNoiseExpression(), getRateReference(), CMetab::initObjects(), and initObjects().

mpValueReference

CDataObjectReference<C_FLOAT64>* CModelEntity::mpValueReference

protected

Referenced by getChildObjectUnits(), getValueObject(), getValueReference(), CCompartment::initObjects(), CMetab::initObjects(), CModel::initObjects(), and initObjects().

mRate

C_FLOAT64 CModelEntity::mRate

protected

Rate of change/time.

Referenced by calculate(), CMetab::calculate(), CMetab::compile(), getRate(), CModel::initObjects(), initObjects(), CMetab::operator=(), setRate(), and setStatus().

mSBMLId

std::string CModelEntity::mSBMLId

mutableprotected

The id of the corresponding parameter in an SBML file. This value is either set upon importing an SBML file, or when the object is first exported to an SBML file.

Referenced by getSBMLId(), initObjects(), and setSBMLId().

mStatus

Status CModelEntity::mStatus

private

Status of the model entity.

Referenced by calculate(), CModelEntity(), compile(), createUndoData(), getInitialExpression(), getNoiseExpression(), getStatus(), isFixed(), setInitialExpression(), setInitialExpressionPtr(), setNoiseExpression(), setNoiseExpressionPtr(), setStatus(), and toData().

mUnitExpression

std::string CModelEntity::mUnitExpression

protected

Pointer to the Unit of the model entity.

Referenced by CModelValue::createUndoData(), getUnitExpression(), CModelValue::getUnits(), setUnitExpression(), and CModelValue::toData().

mUsed

bool CModelEntity::mUsed

private

Indicates whether the model value is used, i.e., must be calculated during the simulation

Referenced by isUsed(), setStatus(), and setUsed().

mValue

C_FLOAT64 CModelEntity::mValue

protected

Pointer to the value of the model entity.

Referenced by calculate(), CMetab::calculate(), CModel::getTime(), getValue(), getValuePointer(), initObjects(), CModel::setTime(), and setValue().

StatusName

const CEnumAnnotation< std::string, CModelEntity::Status > CModelEntity::StatusName

static

String representation of the states

Referenced by CModelParameter::applyData(), applyData(), CModelParameter::createUndoData(), createUndoData(), CODEExporter::exportCompartments(), CODEExporter::exportMetabolites(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelEntityExpression(), CODEExporter::exportModelValues(), CModelParameter::toData(), and toData().

XMLStatus

const CEnumAnnotation< std::string, CModelEntity::Status > CModelEntity::XMLStatus

static

XML representation of the states

Referenced by CompartmentHandler::processStart(), MetaboliteHandler::processStart(), ModelParameterHandler::processStart(), ModelValueHandler::processStart(), CCopasiXML::saveModel(), CCopasiXML::saveModelParameter(), and CCopasiXML::saveModelParameterSets().

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

• CModelValue.h
• CModelValue.cpp