#include <CMoiety.h>

Inheritance diagram for CMoiety:

Public Member Functions
void	add (C_FLOAT64 value, CMetab *metabolite)

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

void	cleanup ()

	CMoiety (const CMoiety &src, const CDataContainer *pParent)

	CMoiety (const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT)

const C_FLOAT64 &	dependentNumber ()

const C_FLOAT64 &	getAmount () const

const C_FLOAT64 &	getDependentNumber () const

CDataObject *	getDependentNumberReference () const

std::string	getDescription (const CModel *model) const

const std::vector< std::pair< C_FLOAT64, CMetab * > > &	getEquation () const

std::string	getExpression () const

CDataObject *	getInitialTotalNumberReference () const

CDataObject *	getInitialValueReference () const

virtual const std::string &	getKey () const

C_FLOAT64	getNumber () const

CDataObject *	getTotalNumberReference () const

CDataObject *	getValueReference () const

void	refreshAmount ()

void	refreshDependentNumber ()

void	refreshInitialValue ()

void	refreshValue ()

virtual bool	setObjectParent (const CDataContainer *pParent)

virtual CData	toData () const

	~CMoiety ()

Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)

virtual bool	appendDeletedDependentData (CUndoData &undoData) const

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

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

virtual 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	~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

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)

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 CMoiety *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataContainer
static CDataContainer *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataObject
static CDataObject *	fromData (const CData &data, CUndoObjectInterface *pParent)

static void	sanitizeObjectName (std::string &name)

Static Public Member Functions inherited from CObjectInterface
static const CDataObject *	DataObject (const CObjectInterface *pInterface)

static CObjectInterface *	GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)

Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)

Private Member Functions
void	initConversionFactor ()

void	initObjects ()

Private Attributes
std::vector< std::pair< C_FLOAT64, CMetab * > >	mEquation

C_FLOAT64	mIAmount

C_FLOAT64	mINumber

std::string	mKey

C_FLOAT64	mNumber

const C_FLOAT64 *	mpConversionFactor

CDependentNumberReference *	mpDNumberReference

CTotalNumberReference *	mpINumberReference

CTotalNumberReference *	mpNumberReference

Static Private Attributes
static const C_FLOAT64	DefaultFactor

Additional Inherited Members
Public Types inherited from CDataContainer
typedef CDataObjectMap	objectMap

Public Types inherited from CDataObject
typedef std::set< const CDataObject * >	DataObjectSet

enum	Flag { Container , Vector , Matrix , NameVector , Reference , ValueBool , ValueInt , ValueInt64 , ValueDbl , NonUniqueName , StaticString , ValueString , Separator , DisplayName , ModelEntity , Array , DataModel , Root , Gui , __SIZE }

Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * >	ContainerList

typedef std::set< const CObjectInterface * >	ObjectSet

Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > *	addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataObjectReference< CType > *	addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataVectorReference< CType > *	addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

	CDataContainer (const CDataContainer &src)

void	initObjects ()

Protected Member Functions inherited from CDataObject
	CDataObject ()

	CDataObject (const std::string &name, const CDataContainer pParent=static_cast< CDataContainer >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

Protected Attributes inherited from CDataContainer
objectMap	mObjects

Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits

std::set< CDataContainer * >	mReferences

Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Constructor & Destructor Documentation

◆ CMoiety() [1/2]

CMoiety::CMoiety	(	const std::string &	name = `"NoName"`,
		const CDataContainer *	pParent = `NO_PARENT`
	)

Default constructor

Parameters

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

References CONSTRUCTOR_TRACE, and initObjects().

Referenced by fromData().

◆ CMoiety() [2/2]

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

Copy constructor

Parameters

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

References CONSTRUCTOR_TRACE, and initObjects().

◆ ~CMoiety()

CMoiety::~CMoiety ( )

Destructor

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

Member Function Documentation

◆ add()

void CMoiety::add	(	C_FLOAT64	value,
		CMetab *	metabolite
	)

Add a metabolite to a moiety

Parameters

C_FLOAT64	value
CMetab	* metabolite

References mEquation, and CMetab::setDependsOnMoiety().

Referenced by CModel::buildMoieties().

◆ applyData()

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

virtual

Apply the provided data to the object

Parameters

const CData & data

Returns: bool success

Reimplemented from CDataContainer.

References fatalError.

◆ cleanup()

void CMoiety::cleanup ( )

References mEquation.

◆ dependentNumber()

const C_FLOAT64 & CMoiety::dependentNumber ( )

Retrieve and refresh the dependent number;

Returns: const C_FLOAT64 & dependentNumber

References mNumber, and refreshDependentNumber().

◆ fromData()

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

static

Static method to create a CDataObject based on the provided data

Parameters

const CData & data

Returns: CMoiety * pDataObject

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

◆ getAmount()

const C_FLOAT64 & CMoiety::getAmount ( ) const

Retrieve the total amount

Returns: const C_FLOAT64 & amount

References mIAmount.

◆ getDependentNumber()

const C_FLOAT64 & CMoiety::getDependentNumber ( ) const

Retrieve the dependent number;

Returns: const C_FLOAT64 & dependentNumber

References mNumber.

Referenced by CMetab::calculate().

◆ getDependentNumberReference()

CDataObject * CMoiety::getDependentNumberReference ( ) const

Retrieve the object for the dependent particle number

Returns: CDataObject * dependentNumberReference

References mpDNumberReference.

Referenced by CMathObject::compileValue().

◆ getDescription()

std::string CMoiety::getDescription ( const CModel * model ) const

get the string representation of the moiety using the CMetabNameInterface

References CMetabNameInterface::getDisplayName(), and mEquation.

◆ getEquation()

const std::vector< std::pair< C_FLOAT64, CMetab * > > & CMoiety::getEquation ( ) const

Retrieve the components of the total mass equation

Returns: const std::vector<std::pair< C_FLOAT64, CMetab * > > & equation

References mEquation.

Referenced by CMathObject::compileDependentMass(), and CMathObject::compileTotalMass().

◆ getExpression()

std::string CMoiety::getExpression ( ) const

Retrieve the infix expression, which can be used to calculate the total amount.

Returns: std::string expression

References mEquation.

◆ getInitialTotalNumberReference()

CDataObject * CMoiety::getInitialTotalNumberReference ( ) const

Retrieve the object for the initial total particle number

Returns: CDataObject * initialTotalNumberReference

References mpINumberReference.

◆ getInitialValueReference()

CDataObject * CMoiety::getInitialValueReference ( ) const

Retrieve the object for the total particle number

Returns: CDataObject * initialValueReference

References mpINumberReference.

◆ getKey()

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

virtual

Returns a string with the name of this compartment.

Returns: std::string key

Reimplemented from CDataObject.

References mKey.

◆ getNumber()

C_FLOAT64 CMoiety::getNumber ( ) const

References mINumber.

◆ getTotalNumberReference()

CDataObject * CMoiety::getTotalNumberReference ( ) const

Retrieve the object for the total particle number

Returns: CDataObject * totalNumberReference

References mpNumberReference.

Referenced by CMathObject::compileDependentMass().

◆ getValueReference()

CDataObject * CMoiety::getValueReference ( ) const

Retrieve the object for the total particle number

Returns: CDataObject * valueReference

References mpNumberReference.

◆ initConversionFactor()

void CMoiety::initConversionFactor ( )

private

Initialize the number to amount conversion factor

References DefaultFactor, CModel::getNumber2QuantityFactor(), CDataObject::getObjectAncestor(), and mpConversionFactor.

Referenced by setObjectParent().

◆ initObjects()

void CMoiety::initObjects ( )

private

Initialize the contained CDataObjects

References CDataContainer::addObjectReference(), mIAmount, mINumber, mNumber, mpDNumberReference, mpINumberReference, mpNumberReference, and CDataObject::ValueDbl.

Referenced by CMoiety().

◆ refreshAmount()

void CMoiety::refreshAmount ( )

Refresh the total amount

References mIAmount, mINumber, and mpConversionFactor.

◆ refreshDependentNumber()

void CMoiety::refreshDependentNumber ( )

Refreshes the value of the dependent number

References mEquation, mINumber, and mNumber.

Referenced by dependentNumber().

◆ refreshInitialValue()

void CMoiety::refreshInitialValue ( )

Refresh the initial total particle number

References mEquation, and mINumber.

◆ refreshValue()

void CMoiety::refreshValue ( )

Refresh the total particle number

References mEquation, and mINumber.

◆ setObjectParent()

bool CMoiety::setObjectParent ( const CDataContainer * pParent )

virtual

Sets the parent of the moiety;

Parameters

const CDataContainer * pParent

Returns: bool success

Reimplemented from CDataObject.

References initConversionFactor(), and CDataObject::setObjectParent().

◆ toData()

CData CMoiety::toData ( ) const

virtual

Retrieve the data describing the object

Returns: CData data

Reimplemented from CDataContainer.

References fatalError.

Member Data Documentation

◆ DefaultFactor

const C_FLOAT64 CMoiety::DefaultFactor

staticprivate

The default conversion factor used if the moiety is not part of a model

Referenced by initConversionFactor().

◆ mEquation

std::vector<std::pair< C_FLOAT64, CMetab * > > CMoiety::mEquation

private

Vector of linear dependent CChemEqElement @supplierCardinality 0..*

Referenced by add(), cleanup(), getDescription(), getEquation(), getExpression(), refreshDependentNumber(), refreshInitialValue(), and refreshValue().

◆ mIAmount

C_FLOAT64 CMoiety::mIAmount

private

The total Amount of the Moiety.

Referenced by getAmount(), initObjects(), and refreshAmount().

◆ mINumber

C_FLOAT64 CMoiety::mINumber

private

Initial Number of Particles of Moiety.

Referenced by getNumber(), initObjects(), refreshAmount(), refreshDependentNumber(), refreshInitialValue(), and refreshValue().

◆ mKey

std::string CMoiety::mKey

private

The key of the moiety

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

◆ mNumber

C_FLOAT64 CMoiety::mNumber

private

Number of Particles of Moiety.

Referenced by dependentNumber(), getDependentNumber(), initObjects(), and refreshDependentNumber().

◆ mpConversionFactor

const C_FLOAT64* CMoiety::mpConversionFactor

private

A pointer to the conversion factor between the particle number and the amount.

Referenced by initConversionFactor(), and refreshAmount().

◆ mpDNumberReference

CDependentNumberReference* CMoiety::mpDNumberReference

private

A pointer to the object for the dependent particle number

Referenced by getDependentNumberReference(), and initObjects().

◆ mpINumberReference

CTotalNumberReference* CMoiety::mpINumberReference

private

A pointer to the object for the initial total particle number

Referenced by getInitialTotalNumberReference(), getInitialValueReference(), and initObjects().

◆ mpNumberReference

CTotalNumberReference* CMoiety::mpNumberReference

private

A pointer to the object for the total particle number This is used during events

Referenced by getTotalNumberReference(), getValueReference(), and initObjects().

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

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CMoiety() [1/2]

◆ CMoiety() [2/2]

◆ ~CMoiety()

Member Function Documentation

◆ add()

◆ applyData()

◆ cleanup()

◆ dependentNumber()

◆ fromData()

◆ getAmount()

◆ getDependentNumber()

◆ getDependentNumberReference()

◆ getDescription()

◆ getEquation()

◆ getExpression()

◆ getInitialTotalNumberReference()

◆ getInitialValueReference()

◆ getKey()

◆ getNumber()

◆ getTotalNumberReference()

◆ getValueReference()

◆ initConversionFactor()

◆ initObjects()

◆ refreshAmount()

◆ refreshDependentNumber()

◆ refreshInitialValue()

◆ refreshValue()

◆ setObjectParent()

◆ toData()

Member Data Documentation

◆ DefaultFactor

◆ mEquation

◆ mIAmount

◆ mINumber

◆ mKey

◆ mNumber

◆ mpConversionFactor

◆ mpDNumberReference

◆ mpINumberReference

◆ mpNumberReference