#include <CMetab.h>

Inheritance diagram for CMetab:

Public Member Functions
	CMetab (const std::string &name="NoName", const CCopasiContainer *pParent=NULL)
	CMetab (const CMetab &src, const CCopasiContainer *pParent=NULL)
	~CMetab ()
virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const
virtual const CCopasiObject *	getValueObject () const
virtual void *	getValuePointer () const
virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const
void	cleanup ()
void	initCompartment (const CCompartment *pCompartment=NULL)
CMetab &	operator= (const CMetabOld &rhs)
C_INT32	load (CReadConfig &configbuffer)
virtual bool	setObjectParent (const CCopasiContainer *pParent)
virtual void	setStatus (const CModelEntity::Status &status)
virtual bool	compile ()
bool	compileInitialValueDependencies (const bool &updateConcentration)
bool	isInitialConcentrationChangeAllowed ()
virtual void	calculate ()
virtual std::set< const CCopasiObject * >	getDeletedObjects () const
void	setConcentration (const C_FLOAT64 concentration)
const C_FLOAT64 &	getConcentration () const
void	setInitialConcentration (const C_FLOAT64 &initialConcentration)
const C_FLOAT64 &	getInitialConcentration () const
CCopasiObject *	getInitialConcentrationReference () const
CConcentrationReference *	getConcentrationReference () const
virtual void	refreshInitialValue ()
void	refreshInitialConcentration ()
void	refreshConcentration ()
void	refreshNumber ()
const CCompartment *	getCompartment () const
const CModel *	getModel () const
void	setTransitionTime (const C_FLOAT64 &transitionTime)
const C_FLOAT64 &	getTransitionTime () const
C_FLOAT64	getConcentrationRate () const
void	refreshConcentrationRate ()
void	refreshRate ()
void	refreshTransitionTime ()
void	setDependentOn (const CMoiety *pMoiety)
bool	isDependent () const
Static Public Member Functions
static C_FLOAT64	convertToNumber (const C_FLOAT64 &concentration, const CCompartment &compartment, const CModel &model)
static C_FLOAT64	convertToConcentration (const C_FLOAT64 &number, const CCompartment &compartment, const CModel &model)
Protected Attributes
CCopasiObjectReference < C_FLOAT64 > *	mpIConcReference
CConcentrationReference *	mpConcReference
CCopasiObjectReference < C_FLOAT64 > *	mpConcRateReference
CCopasiObjectReference < C_FLOAT64 > *	mpTTReference
Friends
void	CMoiety::add (C_FLOAT64 value, CMetab *pMetabolite)
std::ostream &	operator<< (std::ostream &os, const CMetab &d)

Constructor & Destructor Documentation

CMetab::CMetab	(	const std::string &	name = `"NoName"`,
		const CCopasiContainer *	pParent = `NULL`
	)

Default constructor

Parameters:

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

CMetab::CMetab	(	const CMetab &	src,
		const CCopasiContainer *	pParent = `NULL`
	)

Copy constructor

Parameters:

const	CMetab & src
const	CCopasiContainer * pParent (default: NULL)

CMetab::~CMetab ( )

Destructor.

Member Function Documentation

void CMetab::calculate ( void ) [virtual]

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

Reimplemented from CModelEntity.

void CMetab::cleanup ( )

Cleanup

bool CMetab::compile ( ) [virtual]

Compile the model value.

Returns:: bool success

Reimplemented from CModelEntity.

bool CMetab::compileInitialValueDependencies ( const bool & updateConcentration )

Compile the initial particle number and initial concentration dependencies.

Parameters:

const bool & updateConcentration

Returns:: bool success

C_FLOAT64 CMetab::convertToConcentration	(	const C_FLOAT64 &	number,
		const CCompartment &	compartment,
		const CModel &	model
	)		`[static]`

Converts the number to concentration

Parameters:

const	C_FLOAT64 & number
const	CCompartment & compartment
const	CModel & model

Returns:: C_FLOAT64 concentration

C_FLOAT64 CMetab::convertToNumber	(	const C_FLOAT64 &	concentration,
		const CCompartment &	compartment,
		const CModel &	model
	)		`[static]`

Converts the concentration to number

Parameters:

const	C_FLOAT64 & concentration
const	CCompartment & compartment
const	CModel & model

Returns:: C_FLOAT64 number

std::string CMetab::getChildObjectUnits ( const CCopasiObject * pObject ) const [virtual]

Retrieve the units of the child object.

Returns:: std::string units

Reimplemented from CCopasiContainer.

const CCompartment * CMetab::getCompartment ( ) const

const C_FLOAT64 & CMetab::getConcentration ( ) const

C_FLOAT64 CMetab::getConcentrationRate ( ) const

Return rate of production of this metaboLite

CConcentrationReference * CMetab::getConcentrationReference ( ) const

Retrieve object referencing the concentration

Returns:: CConcentrationReference * concentrationReference

std::set< const CCopasiObject * > CMetab::getDeletedObjects ( ) const [virtual]

Retrieve the list of deleted numeric child objects;

Returns:: std::set< const CCopasiObject * > deletedObjects

Reimplemented from CModelEntity.

const C_FLOAT64 & CMetab::getInitialConcentration ( ) const

CCopasiObject * CMetab::getInitialConcentrationReference ( ) const

Retrieve object referencing the initial concentration

Returns:: CCopasiObject * initialConcentrationReference

const CModel * CMetab::getModel ( ) const

std::string CMetab::getObjectDisplayName	(	bool	regular = `true`,
		bool	richtext = `false`
	)		const `[virtual]`

Reimplemented from CCopasiObject.

const C_FLOAT64 & CMetab::getTransitionTime ( ) const

Retrieves the transition time

Returns:: "const C_FLOAT64 &" transitionTime

const CCopasiObject * CMetab::getValueObject ( ) const [virtual]

Retrieve the object representing the value;

Reimplemented from CModelEntity.

void * CMetab::getValuePointer ( ) const [virtual]

Retrieve a pointer to the value;

Reimplemented from CModelEntity.

void CMetab::initCompartment ( const CCompartment * pCompartment = NULL )

bool CMetab::isDependent ( ) const

Retrieve whether the metabolite dependent

Returns:: bool dependent

bool CMetab::isInitialConcentrationChangeAllowed ( )

Check whether changing the initial concentration is allowed

Returns:: bool allowed

C_INT32 CMetab::load ( CReadConfig & configbuffer )

Loads an object with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters:

pconfigbuffer reference to a CReadConfig object.

Returns:: Fail

CMetab & CMetab::operator= ( const CMetabOld & rhs )

Assignment operator.

void CMetab::refreshConcentration ( )

void CMetab::refreshConcentrationRate ( )

Calculate the concentration rate.

void CMetab::refreshInitialConcentration ( )

void CMetab::refreshInitialValue ( ) [virtual]

Refresh the initial value

Reimplemented from CModelEntity.

void CMetab::refreshNumber ( )

void CMetab::refreshRate ( )

Calculate the particle rate.

void CMetab::refreshTransitionTime ( )

Calculate the transition time.

void CMetab::setConcentration ( const C_FLOAT64 concentration )

void CMetab::setDependentOn ( const CMoiety * pMoiety )

Set whether the metabolite is dependent, i.e., calculated by a moiety

Parameters:

const CMoiety * pMoiety

void CMetab::setInitialConcentration ( const C_FLOAT64 & initialConcentration )

bool CMetab::setObjectParent ( const CCopasiContainer * pParent ) [virtual]

Sets the parent of the metabolite;

Parameters:

const CCopasiContainer * pParent

Returns:: bool success

Reimplemented from CModelEntity.

void CMetab::setStatus ( const CModelEntity::Status & status ) [virtual]

Set the status

Parameters:

const CModelEntity::Status & status

Reimplemented from CModelEntity.

void CMetab::setTransitionTime ( const C_FLOAT64 & transitionTime )

Set transition time

Parameters:

const C_FLOAT64 & transitionTime

Friends And Related Function Documentation

void CMoiety::add	(	C_FLOAT64	value,
		CMetab *	pMetabolite
	)		`[friend]`

std::ostream& operator<<	(	std::ostream &	os,
		const CMetab &	d
	)		`[friend]`

ostream operator

Member Data Documentation

CCopasiObjectReference<C_FLOAT64>* CMetab::mpConcRateReference [protected]

CConcentrationReference* CMetab::mpConcReference [protected]

CCopasiObjectReference<C_FLOAT64>* CMetab::mpIConcReference [protected]

CCopasiObjectReference<C_FLOAT64>* CMetab::mpTTReference [protected]

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

copasi/model/CMetab.h
copasi/model/CMetab.cpp

Public Member Functions

Static Public Member Functions

Protected Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation