#include <CModelValue.h>

Inheritance diagram for CModelEntity:

Public Types
enum	Status { FIXED = 0, ASSIGNMENT, REACTIONS, ODE, TIME }
Public Member Functions
	CModelEntity (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="ModelEntity", const unsigned C_INT32 &flag=CCopasiObject::Container\|CCopasiObject::ValueDbl)
	CModelEntity (const CModelEntity &src, const CCopasiContainer *pParent=NULL)
	~CModelEntity ()
virtual const std::string &	getKey () const
const CModelEntity::Status &	getStatus () const
virtual bool	compile ()
virtual void	calculate ()
bool	isFixed () const
const C_FLOAT64 &	getValue () const
const C_FLOAT64 &	getInitialValue () const
virtual void	refreshInitialValue ()
const C_FLOAT64 &	getRate () const
virtual void	setStatus (const CModelEntity::Status &status)
virtual void	setValue (const C_FLOAT64 &value)
virtual void	setInitialValue (const C_FLOAT64 &initialValue)
void	setRate (const C_FLOAT64 &rate)
virtual const CCopasiObject *	getValueObject () const
virtual void *	getValuePointer () const
virtual bool	setObjectParent (const CCopasiContainer *pParent)
virtual std::set< const CCopasiObject * >	getDeletedObjects () const
void	setSBMLId (const std::string &id)
const std::string &	getSBMLId () const
void	setInitialValuePtr (C_FLOAT64 *pInitialValue)
void	setValuePtr (C_FLOAT64 *pValue)
bool	setExpressionPtr (CExpression *pExpression)
const CExpression *	getExpressionPtr () const
CExpression *	getExpressionPtr ()
bool	setInitialExpressionPtr (CExpression *pExpression)
const CExpression *	getInitialExpressionPtr () const
CExpression *	getInitialExpressionPtr ()
bool	setExpression (const std::string &expression)
std::string	getExpression () const
bool	setInitialExpression (const std::string &expression)
std::string	getInitialExpression () const
void	setUsed (const bool &used)
const bool &	isUsed () const
CCopasiObject *	getInitialValueReference () const
CCopasiObject *	getValueReference () const
CCopasiObject *	getRateReference () const
Static Public Attributes
static const std::string	StatusName []
static const char *	XMLStatus []
Protected Attributes
std::string	mKey
std::string	mSBMLId
C_FLOAT64 *	mpValue
C_FLOAT64 *	mpIValue
C_FLOAT64	mRate
CExpression *	mpExpression
CExpression *	mpInitialExpression
CCopasiObjectReference < C_FLOAT64 > *	mpIValueReference
CCopasiObjectReference < C_FLOAT64 > *	mpValueReference
CCopasiObjectReference < C_FLOAT64 > *	mpRateReference
CModel *	mpModel

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

enum CModelEntity::Status

The valid states for metabolites

Enumerator:

FIXED
ASSIGNMENT
REACTIONS
ODE
TIME

Constructor & Destructor Documentation

CModelEntity::CModelEntity	(	const std::string &	name = `"NoName"`,
		const CCopasiContainer *	pParent = `NULL`,
		const std::string &	type = `"ModelEntity"`,
		const unsigned C_INT32 &	flag = `CCopasiObject::Container \| CCopasiObject::ValueDbl`
	)

Default constructor

Parameters:

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

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

Copy constructor

Parameters:

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

CModelEntity::~CModelEntity ( )

Destructor.

Member Function Documentation

void CModelEntity::calculate ( void ) [virtual]

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

Reimplemented in CMetab.

bool CModelEntity::compile ( ) [virtual]

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

Returns:: bool success

Reimplemented in CMetab.

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

Retrieve the list of deleted numeric child objects;

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

Reimplemented in CMetab, and CCompartment.

std::string CModelEntity::getExpression ( ) const

Retrieve the expression for non FIXED model values.

Returns:: std::string expression

const CExpression * CModelEntity::getExpressionPtr ( ) const

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

Returns:: CExpression*

CExpression * CModelEntity::getExpressionPtr ( )

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

Returns:: CExpression*

std::string CModelEntity::getInitialExpression ( ) const

Retrieve the expression for ODE or REACTION model values.

Returns:: std::string expression

const CExpression * CModelEntity::getInitialExpressionPtr ( ) const

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

Returns:: CExpression*

CExpression * CModelEntity::getInitialExpressionPtr ( )

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

Returns:: CExpression*

const C_FLOAT64 & CModelEntity::getInitialValue ( ) const

Retrieve the initial value

CCopasiObject * CModelEntity::getInitialValueReference ( ) const

Retrieve object referencing the initial value

Returns:: CCopasiObject * initialValueReference

const std::string & CModelEntity::getKey ( ) const [virtual]

Retrieve the key

Returns:: std::string key

Reimplemented from CCopasiObject.

Reimplemented in CModel.

const C_FLOAT64 & CModelEntity::getRate ( ) const

Return rate of production of this entity

CCopasiObject * CModelEntity::getRateReference ( ) const

Retrieve object referencing the rate

Returns:: CCopasiObject * rateReference

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

Returns a reference to the SBML Id.

const CModelEntity::Status & CModelEntity::getStatus ( ) const

Retrieve the status of the entity.

Returns:: const CModelEntity::Status & status

const C_FLOAT64 & CModelEntity::getValue ( ) const

Retrieve the value

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

Retrieve the object representing the value;

Reimplemented from CCopasiContainer.

Reimplemented in CMetab.

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

Retrieve a pointer to the value;

Reimplemented from CCopasiObject.

Reimplemented in CMetab.

CCopasiObject * CModelEntity::getValueReference ( ) const

Retrieve object referencing the value

Returns:: CCopasiObject * valueReference

bool CModelEntity::isFixed ( ) const [inline]

Check whether the entity is FIXED or not.

Returns:: bool isFixed

const bool & CModelEntity::isUsed ( ) const

Retrieve whether the model value is used during simulation

Returns:: const bool & used

void CModelEntity::refreshInitialValue ( ) [virtual]

Refresh the initial value

Reimplemented in CMetab.

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

Set the expression for non FIXED model values

Parameters:

const std::string & expression

Returns:: bool success

bool CModelEntity::setExpressionPtr ( CExpression * pExpression )

Set the expression for non FIXED model values

Parameters:

CExpression*

Returns:: bool success

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

Set the expression for ODE or REACTION model values

Parameters:

const std::string & expression

Returns:: bool success

bool CModelEntity::setInitialExpressionPtr ( CExpression * pExpression )

Set the expression for non FIXED model values

Parameters:

CExpression*

Returns:: bool success

void CModelEntity::setInitialValue ( const C_FLOAT64 & initialValue ) [virtual]

Set the initial value

Parameters:

const C_FLOAT64 & initialValue

void CModelEntity::setInitialValuePtr ( C_FLOAT64 * pInitialValue )

Set the pointer to the initial value

Parameters:

C_FLOAT64 * pInitialValue

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

Set the object parent

Parameters:

const CCopasiContainer * pParent

Returns:: bool success

Reimplemented from CCopasiObject.

Reimplemented in CMetab.

void CModelEntity::setRate ( const C_FLOAT64 & rate )

Set the rate (dmValue/dt)

Parameters:

const C_FLOAT64 & rate

void CModelEntity::setSBMLId ( const std::string & id )

Sets the SBMLId.

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

Set the status

Parameters:

const CModelEntity::Status & status

Reimplemented in CMetab.

void CModelEntity::setUsed ( const bool & used )

Set whether the model entity is used during simulation

Parameters:

const bool & used

void CModelEntity::setValue ( const C_FLOAT64 & value ) [virtual]

Set the value

Parameters:

const C_FLOAT64 & value

void CModelEntity::setValuePtr ( C_FLOAT64 * pValue )

Set the pointer to the value

Parameters:

C_FLOAT64 * pValue

Member Data Documentation

std::string CModelEntity::mKey [protected]

Key of the model entity. It is stored here, but constructed in the derived classes.

CExpression* CModelEntity::mpExpression [protected]

The infix expression for objects of type ASSIGNMENT or ODE

CExpression* CModelEntity::mpInitialExpression [protected]

Optional initial expression

C_FLOAT64* CModelEntity::mpIValue [protected]

Pointer to the initial value of the model entity.

CCopasiObjectReference<C_FLOAT64>* CModelEntity::mpIValueReference [protected]

CModel* CModelEntity::mpModel [protected]

CCopasiObjectReference<C_FLOAT64>* CModelEntity::mpRateReference [protected]

C_FLOAT64* CModelEntity::mpValue [protected]

Pointer to the value of the model entity.

CCopasiObjectReference<C_FLOAT64>* CModelEntity::mpValueReference [protected]

C_FLOAT64 CModelEntity::mRate [protected]

Rate of change/time.

std::string CModelEntity::mSBMLId [protected]

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.

const std::string CModelEntity::StatusName [static]

Initial value:

{
  "fixed",
  "assignment",
  "reactions",
  "ode",
  "time",
  ""
}

String representation of the states

const char * CModelEntity::XMLStatus [static]

Initial value:

{
  "fixed",
  "assignment",
  "reactions",
  "ode",
  "time",
  NULL
}

XML representation of the states

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

copasi/model/CModelValue.h
copasi/model/CModelValue.cpp

Public Types

Public Member Functions

Static Public Attributes

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation