#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)

Public Member Functions inherited from AbstractUntemplatedParameterisedSystem
	AbstractUntemplatedParameterisedSystem (unsigned numberOfStateVariables)

virtual	~AbstractUntemplatedParameterisedSystem ()

boost::shared_ptr< const AbstractOdeSystemInformation >	GetSystemInformation () const

std::string	GetSystemName () const

unsigned	GetNumberOfAttributes () const

bool	HasAttribute (const std::string &rName) const

double	GetAttribute (const std::string &rName) const

unsigned	GetNumberOfStateVariables () const

const std::vector< std::string > &	rGetStateVariableNames () const

const std::vector< std::string > &	rGetStateVariableUnits () const

unsigned	GetStateVariableIndex (const std::string &rName) const

bool	HasStateVariable (const std::string &rName) const

std::string	GetStateVariableUnits (unsigned index) const

unsigned	GetNumberOfParameters () const

const std::vector< std::string > &	rGetParameterNames () const

const std::vector< std::string > &	rGetParameterUnits () const

unsigned	GetParameterIndex (const std::string &rName) const

bool	HasParameter (const std::string &rName) const

std::string	GetParameterUnits (unsigned index) const

unsigned	GetNumberOfDerivedQuantities () const

const std::vector< std::string > &	rGetDerivedQuantityNames () const

const std::vector< std::string > &	rGetDerivedQuantityUnits () const

unsigned	GetDerivedQuantityIndex (const std::string &rName) const

bool	HasDerivedQuantity (const std::string &rName) const

std::string	GetDerivedQuantityUnits (unsigned index) const

unsigned	GetAnyVariableIndex (const std::string &rName) const

bool	HasAnyVariable (const std::string &rName) const

std::string	GetAnyVariableUnits (unsigned index) const

std::string	GetAnyVariableUnits (const std::string &rName) const

Protected Member Functions
std::string	DumpState (const std::string &rMessage)

std::string	DumpState (const std::string &rMessage, VECTOR Y)

std::string	DumpState (const std::string &rMessage, VECTOR Y, double time)

void	CheckParametersOnLoad (const std::vector< double > &rParameters, const std::vector< std::string > &rParameterNames)

Protected Attributes
VECTOR	mStateVariables

VECTOR	mParameters

Protected Attributes inherited from AbstractUntemplatedParameterisedSystem
unsigned	mNumberOfStateVariables

boost::shared_ptr < AbstractOdeSystemInformation >	mpSystemInfo

Private Member Functions
std::string	GetStateMessage (const std::string &rMessage, 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 97 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

Returns: a VECTOR of derived quantities

Definition at line 356 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

Returns: a VECTOR of derived quantities

Definition at line 363 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

Returns: an augmented message which includes the values of the internal state variables

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

Returns: an augmented message which includes the values of the state variables from Y

Definition at line 60 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR>

std::string AbstractParameterisedSystem< VECTOR >::DumpState	(	const std::string &	rMessage,
		VECTOR	Y,
		double	time
	)

protected

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

Parameters

rMessage	the exception message
Y	the values of the state variables
time	the independent variable (usually time).

Returns: an augmented message which includes the values of the state variables from Y and the time.

Definition at line 67 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR>

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

Returns: 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 284 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`
	)

Returns: 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 321 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR >

VECTOR AbstractParameterisedSystem< VECTOR >::GetInitialConditions ( ) const

Returns: 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 225 of file AbstractParameterisedSystem.cpp.

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

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

template<typename VECTOR >

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

Returns: the value of a given parameter.

Parameters

index the index of the parameter

Definition at line 248 of file AbstractParameterisedSystem.cpp.

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

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

template<typename VECTOR >

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

Returns: the value of a given parameter.

Parameters

rName the name of the parameter

Definition at line 274 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR>

std::string AbstractParameterisedSystem< VECTOR >::GetStateMessage	(	const std::string &	rMessage,
		VECTOR	Y
	)

private

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

Parameters

rMessage	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 78 of file AbstractParameterisedSystem.cpp.

References GetVectorComponent(), and GetVectorSize().

template<typename VECTOR >

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

Returns: the value of a given state variable.

Parameters

index the index of the state variable

Definition at line 164 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, and GetVectorComponent().

template<typename VECTOR >

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

Returns: the value of a given state variable.

Parameters

rName the name of the state variable

Definition at line 174 of file AbstractParameterisedSystem.cpp.

template<typename VECTOR >

VECTOR AbstractParameterisedSystem< VECTOR >::GetStateVariables ( )

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

Definition at line 142 of file AbstractParameterisedSystem.cpp.

References CopyVector().

template<typename VECTOR >

void AbstractParameterisedSystem< VECTOR >::ResetToInitialConditions ( )

virtual

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

Implements AbstractUntemplatedParameterisedSystem.

Definition at line 236 of file AbstractParameterisedSystem.cpp.

References DeleteVector().

template<typename VECTOR >

VECTOR & AbstractParameterisedSystem< VECTOR >::rGetStateVariables ( )

Returns: the values of the state variables in the ODE system.

Definition at line 136 of file AbstractParameterisedSystem.cpp.

Referenced by Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters(), AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters(), WntCellCycleModel::AdjustOdeParameters(), SingleOdeWntCellCycleModel::AdjustOdeParameters(), AbstractVanLeeuwen2009WntSwatCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), WntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), AbstractOdeSrnModel::CreateSrnModel(), SingleOdeWntCellCycleModel::GetBetaCateninConcentration(), Goldbeter1991SrnModel::GetC(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel(), DeltaNotchSrnModel::GetDelta(), Goldbeter1991SrnModel::GetM(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel(), DeltaNotchSrnModel::GetNotch(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetNuclearBetaCateninLevel(), AbstractOdeBasedCellCycleModel::GetProteinConcentrations(), AbstractOdeSrnModel::GetStateVariables(), Goldbeter1991SrnModel::GetX(), Alarcon2004OxygenBasedCellCycleModel::ResetForDivision(), TysonNovakCellCycleModel::ResetForDivision(), AbstractWntOdeBasedCellCycleModel::ResetForDivision(), AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly(), AbstractIvpOdeSolver::SolveAndUpdateStateVariable(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().

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 329 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 346 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 214 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 201 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

Definition at line 268 of file AbstractParameterisedSystem.cpp.

References SetVectorComponent().

Referenced by DeltaNotchSrnModel::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

Definition at line 258 of file AbstractParameterisedSystem.cpp.

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

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

Definition at line 180 of file AbstractParameterisedSystem.cpp.

References EXCEPTION, 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

Definition at line 190 of file AbstractParameterisedSystem.cpp.

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

Definition at line 148 of file AbstractParameterisedSystem.cpp.

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

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

template<typename VECTOR>

virtual void AbstractParameterisedSystem< VECTOR >::VerifyStateVariables ( )

inlinevirtual

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 198 of file AbstractParameterisedSystem.hpp.