#include <AbstractParameterisedSystem.hpp>

Inheritance diagram for AbstractParameterisedSystem< VECTOR >:

Collaboration diagram for AbstractParameterisedSystem< VECTOR >:

Public Member Functions
	AbstractParameterisedSystem (unsigned numberOfStateVariables)
VECTOR &	rGetStateVariables ()
VECTOR	GetStateVariables ()
void	SetStateVariables (const VECTOR &rStateVariables)
double	GetStateVariable (unsigned index) const
double	GetStateVariable (const std::string &rName) const
void	SetStateVariable (unsigned index, double newValue)
void	SetStateVariable (const std::string &rName, double newValue)
virtual void	VerifyStateVariables ()
void	SetDefaultInitialConditions (const VECTOR &rInitialConditions)
void	SetDefaultInitialCondition (unsigned index, double initialCondition)
VECTOR	GetInitialConditions () const
void	ResetToInitialConditions ()
double	GetParameter (unsigned index) const
double	GetParameter (const std::string &rName) const
void	SetParameter (const std::string &rName, double value)
void	SetParameter (unsigned index, double value)
double	GetAnyVariable (unsigned index, double time=0.0, VECTOR *pDerivedQuantities=NULL)
double	GetAnyVariable (const std::string &rName, double time=0.0, VECTOR *pDerivedQuantities=NULL)
void	SetAnyVariable (unsigned index, double value)
void	SetAnyVariable (const std::string &rName, double value)
virtual VECTOR	ComputeDerivedQuantities (double time, const VECTOR &rState)
VECTOR	ComputeDerivedQuantitiesFromCurrentState (double time)
Protected Member Functions
std::string	DumpState (const std::string &rMessage)
std::string	DumpState (const std::string &rMessage, VECTOR Y)
void	CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)
Protected Attributes
VECTOR	mStateVariables
VECTOR	mParameters
Private Member Functions
std::string	GetStateMessage (const std::string &message, VECTOR Y)
Friends
class	TestAbstractCvodeSystem

Detailed Description

template<typename VECTOR>
class AbstractParameterisedSystem< VECTOR >

This class contains the state variable and parameter vectors for an ODE system, along with methods to access these.

Its main purpose is to be a common base class for both AbstractOdeSystem and AbstractCvodeSystem, which require similar functionality but use different vector types.

Definition at line 55 of file AbstractParameterisedSystem.hpp.

Constructor & Destructor Documentation

template<typename VECTOR >

AbstractParameterisedSystem< VECTOR >::AbstractParameterisedSystem ( unsigned numberOfStateVariables )

Constructor.

Parameters:

numberOfStateVariables the number of state variables in the ODE system

Definition at line 46 of file AbstractParameterisedSystem.cpp.

References InitialiseEmptyVector(), AbstractParameterisedSystem< VECTOR >::mParameters, and AbstractParameterisedSystem< VECTOR >::mStateVariables.

Member Function Documentation

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::CheckParametersOnLoad	(	const std::vector< double > &	rParameters,
		const std::vector< std::string > &	rParameterNames
	)		`[protected]`

This method is called by subclasses on completion of the load method of serialization.

It checks that the parameters that were loaded match those that should be in the class, and fills in with default values any that are missing. Hence this method updates mParameters.

Parameters:

rParameters	the parameters that were loaded.
rParameterNames	the parameter names that were loaded.

Definition at line 80 of file AbstractParameterisedSystem.cpp.

References CreateVectorIfEmpty(), EXCEPTION, GetVectorSize(), and SetVectorComponent().

template<typename VECTOR>

VECTOR AbstractParameterisedSystem< VECTOR >::ComputeDerivedQuantities	(	double	time,
		const VECTOR &	rState
	)		`[virtual]`

Compute the derived quantities from the given system state. Uses the current values for the parameters.

Parameters:

time	the time at which to compute the derived quantities
rState	values for the state variables

Definition at line 337 of file AbstractParameterisedSystem.cpp.

References EXCEPTION.

Referenced by OdeSolution::rGetDerivedQuantities().

template<typename VECTOR >

VECTOR AbstractParameterisedSystem< VECTOR >::ComputeDerivedQuantitiesFromCurrentState ( double time )

Compute the derived quantities based on the current system state.

Parameters:

time	the time at which to compute the derived quantities

Definition at line 344 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR >

std::string AbstractParameterisedSystem< VECTOR >::DumpState ( const std::string & rMessage ) [protected]

Used to include extra debugging information in exception messages. For example, EXCEPTION(DumpState("Gating variable out of range"));

Parameters:

rMessage the exception message

Definition at line 54 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR>

std::string AbstractParameterisedSystem< VECTOR >::DumpState	(	const std::string &	rMessage,
		VECTOR	Y
	)		`[protected]`

Used to include extra debugging information in exception messages. For example, EXCEPTION(DumpState("Gating variable out of range", state_variables));

Parameters:

rMessage	the exception message
Y	the values of the state variables

Definition at line 60 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR>

double AbstractParameterisedSystem< VECTOR >::GetAnyVariable	(	unsigned	index,
		double	time = `0.0`,
		VECTOR *	pDerivedQuantities = `NULL`
	)

Get the value of a variable, whether a state variable, parameter, or derived quantity.

Note that if the variable is a derived quantity, this method will compute all derived quantities, so may not be very efficient. To avoid this, pass a pre-computed vector of derived quantities as the optional third argument.

Parameters:

index	the index of the variable, as given by GetAnyVariableIndex.
time	the current simulation time, possibly needed if the variable is a derived quantity.
pDerivedQuantities	optional vector of pre-computed derived quantity values.

Definition at line 265 of file AbstractParameterisedSystem.cpp.

References DeleteVector(), EXCEPTION, GetVectorComponent(), and GetVectorSize().

template<typename VECTOR>

double AbstractParameterisedSystem< VECTOR >::GetAnyVariable	(	const std::string &	rName,
		double	time = `0.0`,
		VECTOR *	pDerivedQuantities = `NULL`
	)

Get the value of a variable, whether a state variable, parameter, or derived quantity.

Note that if the variable is a derived quantity, this method will compute all derived quantities, so may not be very efficient. To avoid this, pass a pre-computed vector of derived quantities as the optional third argument.

Parameters:

rName	the name of the variable, (this method is the same as doing GetAnyVariableIndex(rName) and then calling the method above).
time	the current simulation time, possibly needed if the variable is a derived quantity.
pDerivedQuantities	optional vector of pre-computed derived quantity values.

Definition at line 302 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR >

VECTOR AbstractParameterisedSystem< VECTOR >::GetInitialConditions ( ) const

Get the default initial conditions for this system.

Note:: Returns a fresh vector, which the caller should delete if appropriate for the type.

Definition at line 206 of file AbstractParameterisedSystem.cpp.

References CopyFromStdVector(), CreateVectorIfEmpty(), and InitialiseEmptyVector().

Referenced by WntCellCycleModel::Initialise(), SingleOdeWntCellCycleModel::Initialise(), AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise(), TysonNovakCellCycleModel::Initialise(), DeltaNotchCellCycleModel::Initialise(), AbstractWntOdeBasedCellCycleModel::ResetForDivision(), TysonNovakCellCycleModel::ResetForDivision(), and Alarcon2004OxygenBasedCellCycleModel::ResetForDivision().

template<typename VECTOR >

double AbstractParameterisedSystem< VECTOR >::GetParameter ( unsigned index ) const

Get the value of a given parameter.

Parameters:

index the index of the parameter

Definition at line 229 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, GetVectorComponent(), and GetVectorSize().

Referenced by DeltaNotchCellCycleModel::GetMeanNeighbouringDelta(), and OdeSolution::rGetParameters().

template<typename VECTOR >

double AbstractParameterisedSystem< VECTOR >::GetParameter ( const std::string & rName ) const

Get the value of a given parameter.

Parameters:

rName the name of the parameter

Definition at line 255 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR>

std::string AbstractParameterisedSystem< VECTOR >::GetStateMessage	(	const std::string &	message,
		VECTOR	Y
	)		`[private]`

Helper method to construct a string containing a dump of the vector

Parameters:

message	a string to prefix (e.g. an error or the name of the vector)
Y	a vector

Returns:: a string containing the contents of the vector.

Definition at line 67 of file AbstractParameterisedSystem.cpp.

References GetVectorComponent(), and GetVectorSize().

template<typename VECTOR >

double AbstractParameterisedSystem< VECTOR >::GetStateVariable ( unsigned index ) const

Get the value of a given state variable.

Parameters:

index the index of the state variable

Definition at line 145 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, and GetVectorComponent().

template<typename VECTOR >

double AbstractParameterisedSystem< VECTOR >::GetStateVariable ( const std::string & rName ) const

Get the value of a given state variable.

Parameters:

rName the name of the state variable

Definition at line 155 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR >

VECTOR AbstractParameterisedSystem< VECTOR >::GetStateVariables ( )

Get a copy of the state variable vector. Caller takes responsibility for deleting the returned vector (if required for the VECTOR type).

Definition at line 125 of file AbstractParameterisedSystem.cpp.

References CopyVector().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::ResetToInitialConditions ( )

Reset the system's state variables to the default initial conditions.

Definition at line 217 of file AbstractParameterisedSystem.cpp.

References DeleteVector().

template<typename VECTOR >

VECTOR & AbstractParameterisedSystem< VECTOR >::rGetStateVariables ( )

Get the values of the state variables in the ODE system.

Definition at line 119 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetAnyVariable	(	unsigned	index,
		double	value
	)

Set the value of a variable, whether a state variable or parameter. Attempting to set the value of a derived quantity will raise an exception.

Parameters:

index	the index of the variable, as given by GetAnyVariableIndex.
value	the value to give the variable.

Definition at line 310 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, GetVectorSize(), and SetVectorComponent().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetAnyVariable	(	const std::string &	rName,
		double	value
	)

Set the value of a variable, whether a state variable or parameter. Attempting to set the value of a derived quantity will raise an exception.

Parameters:

rName	the name of the variable.
value	the value to give the variable.

Definition at line 327 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetDefaultInitialCondition	(	unsigned	index,
		double	initialCondition
	)

Set a single component of the default initial conditions for the system.

Note:: The default initial conditions are shared among all instances of the particular concrete system class.; This method DOES NOT change the state variables of the object on which it is called.

Parameters:

index	the index of the state variable in the system
initialCondition	the initial value for the state variable

Definition at line 195 of file AbstractParameterisedSystem.cpp.

References EXCEPTION.

template<typename VECTOR>

void AbstractParameterisedSystem< VECTOR >::SetDefaultInitialConditions ( const VECTOR & rInitialConditions )

Set the default initial conditions for the system.

Note:: The default initial conditions are shared among all instances of the particular concrete system class.; This method DOES NOT change the state variables of the object on which it is called.

Parameters:

rInitialConditions vector containing initial values for the state variables

Definition at line 182 of file AbstractParameterisedSystem.cpp.

References CopyToStdVector(), EXCEPTION, and GetVectorSize().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetParameter	(	const std::string &	rName,
		double	value
	)

Set the value of a given parameter.

Parameters:

rName	the name of the parameter
value	the value

Reimplemented in AbstractCardiacCell, and AbstractCvodeCell.

Definition at line 249 of file AbstractParameterisedSystem.cpp.

References SetVectorComponent().

Referenced by DeltaNotchCellCycleModel::CreateCellCycleModel(), and DeltaNotchCellCycleModel::UpdateDeltaNotch().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetParameter	(	unsigned	index,
		double	value
	)

Set the value of a given parameter.

Parameters:

index	the index of the parameter
value	the value

Reimplemented in AbstractCardiacCell, and AbstractCvodeCell.

Definition at line 239 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, GetVectorSize(), and SetVectorComponent().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetStateVariable	(	const std::string &	rName,
		double	newValue
	)

Set the value of a single state variable in the ODE system.

Parameters:

rName	name of the state variable to be set
newValue	new value of the state variable

Reimplemented in AbstractCardiacCell, and AbstractCvodeCell.

Definition at line 171 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::SetStateVariable	(	unsigned	index,
		double	newValue
	)

Set the value of a single state variable in the ODE system.

Parameters:

index	index of the state variable to be set
newValue	new value of the state variable

Reimplemented in AbstractCardiacCell, and AbstractCvodeCell.

Definition at line 161 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, and SetVectorComponent().

template<typename VECTOR>

void AbstractParameterisedSystem< VECTOR >::SetStateVariables ( const VECTOR & rStateVariables )

Set the state variables equal to the values in the given vector, copying it. Caller thus maintains responsibility for deleting the input vector (if required for the VECTOR type).

Parameters:

rStateVariables new values for the state variables

Reimplemented in AbstractCardiacCell, and AbstractCvodeCell.

Definition at line 131 of file AbstractParameterisedSystem.cpp.

References CreateVectorIfEmpty(), EXCEPTION, GetVectorComponent(), GetVectorSize(), and SetVectorComponent().

Referenced by WntCellCycleModel::Initialise(), SingleOdeWntCellCycleModel::Initialise(), AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise(), TysonNovakCellCycleModel::Initialise(), DeltaNotchCellCycleModel::Initialise(), TysonNovakCellCycleModel::ResetForDivision(), AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly(), and CellCycleModelOdeHandler::SetStateVariables().

template<typename VECTOR>

virtual void AbstractParameterisedSystem< VECTOR >::VerifyStateVariables ( ) [inline, virtual]

Empty method which can be over-ridden and used in solvers to go through the current state vector and do range checking on the values (e.g. check that concentrations are positive and probabilities are between zero and one).

This method is overridden with a currently commented out method in AbstractCardiacCell which would be called by the ComputeExceptVoltage method (in heart).

This method is called by the AbstractCvodeSystem::Solve() method (in ode).

Reimplemented in CorriasBuistICCModified, and CorriasBuistSMCModified.

Definition at line 181 of file AbstractParameterisedSystem.hpp.