COPASI API  4.40.278
CModelEntity Class Reference

#include <CModelValue.h>

Inheritance diagram for CModelEntity:
[legend]

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
 
CExpressiongetExpressionPtr ()
 
const CExpressiongetExpressionPtr () const
 
std::string getInitialExpression () const
 
CExpressiongetInitialExpressionPtr ()
 
const CExpressiongetInitialExpressionPtr () const
 
const C_FLOAT64getInitialValue () const
 
CDataObjectgetInitialValueReference () const
 
virtual const std::string & getKey () const override
 
CModelgetModel () const
 
std::string getNoiseExpression () const
 
CExpressiongetNoiseExpressionPtr ()
 
const CExpressiongetNoiseExpressionPtr () const
 
CDataObjectgetNoiseReference () const
 
const C_FLOAT64getRate () const
 
CDataObjectgetRateReference () const
 
const std::string & getSBMLId () const
 
const CModelEntity::StatusgetStatus () const
 
virtual const std::string & getUnitExpression () const
 
const C_FLOAT64getValue () const
 
virtual const CDataObjectgetValueObject () const override
 
virtual void * getValuePointer () const override
 
CDataObjectgetValueReference () 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 CObjectInterfacegetObject (const CCommonName &cn) const override
 
virtual objectMapgetObjects ()
 
virtual const objectMapgetObjects () const
 
virtual const std::string getUnits () const override
 
virtual CUndoObjectInterfaceinsert (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 CDataObjectgetDataObject () const override
 
CDataContainergetObjectAncestor (const std::string &type) const
 
CDataModelgetObjectDataModel () const
 
virtual std::string getObjectDisplayName () const override
 
const CObjectInterfacegetObjectFromCN (const CCommonName &cn) const
 
const std::string & getObjectName () const
 
CDataContainergetObjectParent () const
 
const std::string & getObjectType () const
 
virtual const CObjectInterface::ObjectSetgetPrerequisites () const override
 
virtual const CValiditygetValidity () 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
 
UnsupportedAnnotationgetUnsupportedAnnotations ()
 
const UnsupportedAnnotationgetUnsupportedAnnotations () 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 CModelEntityfromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataContainer
static CDataContainerfromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataObject
static CDataObjectfromData (const CData &data, CUndoObjectInterface *pParent)
 
static void sanitizeObjectName (std::string &name)
 
- Static Public Member Functions inherited from CObjectInterface
static const CDataObjectDataObject (const CObjectInterface *pInterface)
 
static CObjectInterfaceGetObjectFromCN (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 CMIRIAMInfoallocateMiriamInfo (CDataContainer *pParent)
 
static CAnnotationcastObject (CDataObject *pObject)
 
static const CAnnotationcastObject (const CDataObject *pObject)
 
static void freeMiriamInfo (CDataContainer *pParent)
 

Static Public Attributes

static const CEnumAnnotation< std::string, StatusStatusName
 
static const CEnumAnnotation< std::string, StatusXMLStatus
 
- 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
 
CExpressionmpExpression
 
CExpressionmpInitialExpression
 
CDataObjectReference< C_FLOAT64 > * mpIValueReference
 
CModelmpModel
 
CExpressionmpNoiseExpression
 
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 = CFlagsFlag >::None 
)

Default constructor

Parameters
conststd::string & name (default: "NoName")
constCDataContainer * 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 
)

◆ ~CModelEntity()

CModelEntity::~CModelEntity ( )

Destructor.

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

Member Function Documentation

◆ 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()

◆ createUndoData()

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

◆ fromData()

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

Static method to create a CDataObject based on the provided data

Parameters
constCData & 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()

◆ 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]

◆ getInitialExpression()

◆ 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]

◆ getInitialValue()

◆ getInitialValueReference()

◆ 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()

◆ getNoiseExpression()

◆ 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

◆ 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()

◆ getSBMLId()

◆ 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

◆ 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()

◆ hasNoise()

◆ initObjects()

◆ 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()

◆ 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()

◆ setInitialExpression()

◆ setInitialExpressionPtr()

bool CModelEntity::setInitialExpressionPtr ( CExpression pExpression)

◆ setInitialValue()

void CModelEntity::setInitialValue ( const C_FLOAT64 initialValue)
virtual

◆ setNoiseExpression()

bool CModelEntity::setNoiseExpression ( const std::string &  expression)

◆ 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
constCDataContainer * 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()

◆ setStatus()

◆ setUnitExpression()

◆ setUsed()

void CModelEntity::setUsed ( const bool &  used)

Set whether the model entity is used during simulation

Parameters
constbool & used

References mUsed.

Referenced by CModel::CModel().

◆ setValue()

void CModelEntity::setValue ( const C_FLOAT64 value)
virtual

Set the value

Parameters
constC_FLOAT64 & value

References mValue.

◆ 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

◆ 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

◆ mpIValueReference

◆ mpModel

◆ 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

◆ mpValueReference

◆ mRate

◆ 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

◆ mUnitExpression

std::string CModelEntity::mUnitExpression
protected

◆ 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

◆ XMLStatus


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