CModelParameterSpecies Class Reference

#include <CModelParameter.h>

Inheritance diagram for CModelParameterSpecies:

Public Member Functions
	CModelParameterSpecies (CModelParameterGroup *pParent, const CModelParameter::Type &type=CModelParameter::Type::Species)
	CModelParameterSpecies (const CModelParameterSpecies &src, CModelParameterGroup *pParent)
virtual void	compile ()
virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
virtual std::string	getName () const
virtual const C_FLOAT64 &	getValue (const CCore::Framework &framework) const
virtual void	setCN (const CCommonName &cn)
virtual void	setValue (const C_FLOAT64 &value, const CCore::Framework &framework, bool updateModelIfActive=true)
virtual CData	toData () const
virtual bool	updateModel ()
virtual	~CModelParameterSpecies ()
Public Member Functions inherited from CModelParameter
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)
	CModelParameter (CModelParameterGroup *pParent, const CModelParameter::Type &type)
	CModelParameter (const CModelParameter &src, CModelParameterGroup *pParent)
virtual void	destruct ()
virtual const CompareResult &	diff (const CModelParameter &other, const CCore::Framework &framework=CCore::Framework::ParticleNumbers, const bool &createMissing=false)
virtual const CModelParameter *	getChild (const size_t &index) const
const CCommonName &	getCN () const
const CompareResult &	getCompareResult () const
virtual size_t	getIndex () const
std::string	getInitialExpression () const
const CExpression *	getInitialExpressionPtr () const
CModel *	getModel () const
virtual size_t	getNumChildren () const
CDataObject *	getObject () const
CModelParameterGroup *	getParent () const
CModelParameterSet *	getSet () const
const CModelEntity::Status &	getSimulationType () const
const Type &	getType () const
CValidatedUnit	getUnit (const CCore::Framework &framework) const
bool	isInitialExpressionValid () const
bool	isReadOnly () const
bool	operator< (const CModelParameter &rhs) const
virtual bool	refreshFromModel (const bool &modifyExistence)
void	setCompareResult (const CompareResult &compareResult)
void	setInitialExpression (const std::string &initialExpression)
void	setParent (CModelParameterGroup *pParent)
bool	setSimulationType (const CModelEntity::Status &simulationType)
virtual CModelParameterSet *	toSet ()
virtual const CModelParameterSet *	toSet () const
virtual	~CModelParameter ()
Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()
	CUndoObjectInterface (const CUndoObjectInterface &src)
bool	generateUuid ()
const xg::Guid &	getUuid () const
virtual CUndoObjectInterface *	insert (const CData &data)
bool	setUuid (const std::string &uuid)
bool	setUuid (const xg::Guid &uuid)
virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)
virtual	~CUndoObjectInterface ()

Private Member Functions
friend	CModelParameterCompartment::~CModelParameterCompartment ()
CCommonName	getCompartmentCN () const

Private Attributes
CRegisteredCommonName	mCompartmentCN
C_FLOAT64	mConcentration
CModelParameterCompartment *	mpCompartment

Additional Inherited Members
Public Types inherited from CModelParameter
enum class	CompareResult {   Obsolete , Missing , Modified , Conflict ,   Identical , __SIZE }
enum class	Type {   Model , Compartment , Species , ModelValue ,   ReactionParameter , Reaction , Group , Set ,   unknown , __SIZE }
Static Public Member Functions inherited from CModelParameter
static CModelParameter *	fromData (const CData &data, CUndoObjectInterface *pParent)
Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)
Static Public Attributes inherited from CModelParameter
static const CEnumAnnotation< std::string, CompareResult >	CompareResultNames
static const CEnumAnnotation< std::string, Type >	TypeNames
Protected Attributes inherited from CModelParameter
CRegisteredCommonName	mCN
CompareResult	mCompareResult
bool	mIsInitialExpressionValid
CExpression *	mpInitialExpression
CDataObject *	mpObject
CModelParameterGroup *	mpParent
CModelEntity::Status	mSimulationType
Type	mType
double	mValue

Constructor & Destructor Documentation

CModelParameterCompartment::~CModelParameterCompartment()

CModelParameterSpecies::CModelParameterCompartment::~CModelParameterCompartment ( )

private

CModelParameterSpecies() [1/2]

CModelParameterSpecies::CModelParameterSpecies	(	CModelParameterGroup *	pParent,
		const CModelParameter::Type &	type = CModelParameter::Type::Species
	)

Constructor

CModelParameterSpecies() [2/2]

CModelParameterSpecies::CModelParameterSpecies	(	const CModelParameterSpecies &	src,
		CModelParameterGroup *	pParent
	)

Copy constructor

~CModelParameterSpecies()

CModelParameterSpecies::~CModelParameterSpecies ( )

virtual

Destructor

References mpCompartment, and CModelParameterCompartment::removeSpecies().

Member Function Documentation

compile()

void CModelParameterSpecies::compile ( )

virtual

Compile the parameter

Reimplemented from CModelParameter.

References CModelParameterCompartment::addSpecies(), CModelParameter::compile(), CModelParameterGroup::getModelParameter(), CModelParameter::getSet(), mCompartmentCN, mpCompartment, CModelParameter::mValue, CCore::ParticleNumbers, setValue(), and CModelParameterSet::toGroup().

createUndoData()

void CModelParameterSpecies::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 CModelParameter.

References CUndoData::addProperty(), CData::addProperty(), CUndoData::CHANGE, CCore::Concentration, CModelParameter::createUndoData(), CData::FRAMEWORK, CCore::FrameworkNames, CData::getProperty(), CData::INITIAL_INTENSIVE_VALUE, CData::INITIAL_VALUE, mConcentration, CModelParameter::mValue, CData::PARAMETER_VALUE, and CDataValue::toData().

getCompartmentCN()

CCommonName CModelParameterSpecies::getCompartmentCN ( ) const

private

Retrieve the CN of the compartment the species is contained in.

Returns

CCommonName compartmentCN

References mCompartmentCN.

getName()

std::string CModelParameterSpecies::getName ( ) const

virtual

Retrieve the name.

Returns

std::string name

Reimplemented from CModelParameter.

References CMetabNameInterface::getDisplayName(), CModelParameterSet::getModel(), CModelParameter::getSet(), CModelParameter::mCN, mCompartmentCN, CModelParameter::mpObject, and CCommonName::nameFromCN().

getValue()

const C_FLOAT64 & CModelParameterSpecies::getValue ( const CCore::Framework &  framework ) const

virtual

Retrieve the value of the parameter based on the current framework

Parameters

const

Framework & framework

Returns

const double & value

Reimplemented from CModelParameter.

References CCore::Concentration, mConcentration, and CModelParameter::mValue.

setCN()

void CModelParameterSpecies::setCN ( const CCommonName &  cn )

virtual

Set the CN of the object represented by the parameter

Parameters

const

CCommonName & cn

Reimplemented from CModelParameter.

References CModelParameter::mCN, mCompartmentCN, and CModelParameter::setCN().

setValue()

void CModelParameterSpecies::setValue ( const C_FLOAT64 &  value, const CCore::Framework &  framework, bool  updateModelIfActive = true  )

virtual

Set the value of the parameter based on the current framework

Parameters

const	double & value
const	Framework & framework
updateModelIfActive	if this is the active parameter set, write the changes back to the model

Reimplemented from CModelParameter.

References CModelParameterCompartment::addSpecies(), CCore::Concentration, CModelParameter::getModel(), CModelParameterGroup::getModelParameter(), CModel::getNumber2QuantityFactor(), CModel::getQuantity2NumberFactor(), CModelParameter::getSet(), CModelParameter::getValue(), CModelParameterSet::isActive(), mCompartmentCN, mConcentration, mpCompartment, CModelParameter::mValue, CCore::ParticleNumbers, CModelParameterSet::toGroup(), and updateModel().

Referenced by compile().

toData()

CData CModelParameterSpecies::toData ( ) const

virtual

Retrieve the data describing the object

Returns

CData data

Reimplemented from CModelParameter.

References CData::addProperty(), CData::getProperty(), CData::INITIAL_INTENSIVE_VALUE, mConcentration, CData::PARAMETER_VALUE, CModelParameter::toData(), and CDataValue::toData().

updateModel()

bool CModelParameterSpecies::updateModel ( )

virtual

Update the corresponding model object with the current parameter settings

Reimplemented from CModelParameter.

References CModelEntity::ASSIGNMENT, CModelEntity::getStatus(), mConcentration, CModelParameter::mpObject, CMetab::setInitialConcentration(), and CModelParameter::updateModel().

Referenced by setValue().

Member Data Documentation

mCompartmentCN

CRegisteredCommonName CModelParameterSpecies::mCompartmentCN

private

The CN of the compartment the species is contained in.

Referenced by compile(), getCompartmentCN(), getName(), setCN(), and setValue().

mConcentration

C_FLOAT64 CModelParameterSpecies::mConcentration

private

The concentration value of the species.

Referenced by createUndoData(), getValue(), setValue(), toData(), and updateModel().

mpCompartment

CModelParameterCompartment* CModelParameterSpecies::mpCompartment

private

A pointer to the parameter representing the compartment the species is contained in.

Referenced by compile(), setValue(), and ~CModelParameterSpecies().

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

• CModelParameter.h
• CModelParameter.cpp