AbstractUntemplatedParameterisedSystem Class Reference

#include <AbstractUntemplatedParameterisedSystem.hpp>

Inheritance diagram for AbstractUntemplatedParameterisedSystem:

Collaboration diagram for AbstractUntemplatedParameterisedSystem:

Public Member Functions
	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
virtual void	ResetToInitialConditions ()=0
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 Attributes
unsigned	mNumberOfStateVariables
boost::shared_ptr < AbstractOdeSystemInformation >	mpSystemInfo

Detailed Description

This class is an untemplated base class for AbstractParameterisedSystem, containing those methods which don't require knowledge of the vector type, in order to make it easier to move between templated and generic parts of the codebase. In particular it holds the AbstractOdeSystemInformation pointer, and methods to access this object to provide information about the ODE system, such as state variable/parameter names and units.

Definition at line 53 of file AbstractUntemplatedParameterisedSystem.hpp.

Constructor & Destructor Documentation

AbstractUntemplatedParameterisedSystem::AbstractUntemplatedParameterisedSystem

(

unsigned

numberOfStateVariables

)

Constructor.

Parameters

numberOfStateVariables

the number of state variables in the ODE system

Definition at line 43 of file AbstractUntemplatedParameterisedSystem.cpp.

AbstractUntemplatedParameterisedSystem::~AbstractUntemplatedParameterisedSystem ( )

virtual

Make this class polymorphic.

Definition at line 48 of file AbstractUntemplatedParameterisedSystem.cpp.

Member Function Documentation

unsigned AbstractUntemplatedParameterisedSystem::GetAnyVariableIndex

(

const std::string &

rName

)

const

Returns

the index of a variable, whether a state variable, parameter, or derived quantity, with the given name. The returned index is suitable for use with GetAnyVariableUnits, GetAnyVariable, etc.

Parameters

rName

the name of a variable

Definition at line 136 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by GetAnyVariableUnits().

std::string AbstractUntemplatedParameterisedSystem::GetAnyVariableUnits

(

unsigned

index

)

const

Returns

the units of a variable, whether a state variable, parameter, or derived quantity, given its index as returned by GetAnyVariableIndex.

Parameters

index

an index from GetAnyVariableIndex.

Returns

the units of the variable.

Definition at line 146 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by GetAnyVariableUnits().

std::string AbstractUntemplatedParameterisedSystem::GetAnyVariableUnits

(

const std::string &

rName

)

const

Returns

the units of a variable, whether a state variable, parameter, or derived quantity, given its index as returned by GetAnyVariableIndex.

Parameters

rName

the name of any variable in the model.

Returns

the units of the variable.

Definition at line 151 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetAnyVariableIndex(), and GetAnyVariableUnits().

double AbstractUntemplatedParameterisedSystem::GetAttribute

(

const std::string &

rName

)

const

Returns

the value of a named attribute.

Parameters

rName

the attribute name.

Definition at line 201 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

unsigned AbstractUntemplatedParameterisedSystem::GetDerivedQuantityIndex

(

const std::string &

rName

)

const

Returns

the index of a derived quantity, given its name.

Parameters

rName

the name of a derived quantity.

Definition at line 175 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

std::string AbstractUntemplatedParameterisedSystem::GetDerivedQuantityUnits

(

unsigned

index

)

const

Returns

the units of a derived quantity.

Parameters

index

an index from GetDerivedQuantityIndex.

Returns

the units of the variable.

Definition at line 185 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

unsigned AbstractUntemplatedParameterisedSystem::GetNumberOfAttributes

(

)

const

Returns

the number of named attributes that this system has.

Definition at line 191 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

unsigned AbstractUntemplatedParameterisedSystem::GetNumberOfDerivedQuantities

(

)

const

Returns

the number of derived quantities.

Definition at line 160 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by OdeSolution::rGetDerivedQuantities().

unsigned AbstractUntemplatedParameterisedSystem::GetNumberOfParameters

(

)

const

Returns

the number of parameters.

Definition at line 102 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by AbstractCvodeCell::GetNumberOfParameters(), AbstractCardiacCell::GetNumberOfParameters(), and OdeSolution::rGetParameters().

unsigned AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables

(

)

const

Returns

the number of state variables in the ODE system.

mNumberOfStateVariables

Definition at line 68 of file AbstractUntemplatedParameterisedSystem.cpp.

References mNumberOfStateVariables.

Referenced by HeunIvpOdeSolver::CalculateNextYValue(), RungeKutta2IvpOdeSolver::CalculateNextYValue(), RungeKutta4IvpOdeSolver::CalculateNextYValue(), RKC21IvpOdeSolver::CalculateNextYValue(), EulerIvpOdeSolver::CalculateNextYValue(), GRL1IvpOdeSolver::CalculateNextYValue(), GRL2IvpOdeSolver::CalculateNextYValue(), RungeKuttaFehlbergIvpOdeSolver::CalculateNextYValue(), BackwardEulerIvpOdeSolver::CalculateNextYValue(), AbstractCvodeCell::GetNumberOfStateVariables(), AbstractCardiacCell::GetNumberOfStateVariables(), RungeKuttaFehlbergIvpOdeSolver::InternalSolve(), AbstractOdeBasedCellCycleModel::ReadyToDivide(), AbstractCvodeSystem::RecordStoppingPoint(), CvodeAdaptor::SetupCvode(), AbstractCvodeSystem::SetupCvode(), AbstractOneStepIvpOdeSolver::Solve(), RungeKuttaFehlbergIvpOdeSolver::Solve(), AbstractIvpOdeSolver::SolveAndUpdateStateVariable(), and AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase().

unsigned AbstractUntemplatedParameterisedSystem::GetParameterIndex

(

const std::string &

rName

)

const

This method is used to establish a parameter's position within the vector of parameters of an ODE system. This number can then be used with the methods GetParameterUnits and GetParameter.

Parameters

rName

the name of a parameter

Returns

the parameter's position within the vector of parameters associated with the ODE system.

Definition at line 117 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

std::string AbstractUntemplatedParameterisedSystem::GetParameterUnits

(

unsigned

index

)

const

Returns

the units of a parameter given its index in the ODE system.

Parameters

index

a state variable's position within the vector of state variables associated with the ODE system.

Returns

the units of the state variable.

Definition at line 127 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

unsigned AbstractUntemplatedParameterisedSystem::GetStateVariableIndex

(

const std::string &

rName

)

const

This method is used to establish a state variable's position within the vector of state variables of an ODE system. This number can then be used with the methods GetStateVariable and GetStateVariableUnits.

Parameters

rName

the name of a state variable.

Returns

the state variable's position within the vector of state variables associated with the ODE system.

Definition at line 83 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

std::string AbstractUntemplatedParameterisedSystem::GetStateVariableUnits

(

unsigned

index

)

const

Returns

the units of a state variable given its index in the ODE system.

Parameters

index

a state variable's position within the vector of state variables associated with the ODE system.

Returns

the units of the state variable.

Definition at line 93 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

boost::shared_ptr< const AbstractOdeSystemInformation > AbstractUntemplatedParameterisedSystem::GetSystemInformation

(

)

const

Returns

the object which provides information about this ODE system.

Definition at line 52 of file AbstractUntemplatedParameterisedSystem.cpp.

References mpSystemInfo.

Referenced by OdeSolution::CalculateDerivedQuantitiesAndParameters(), GetAnyVariableIndex(), GetAnyVariableUnits(), GetAttribute(), GetDerivedQuantityIndex(), GetDerivedQuantityUnits(), GetNumberOfAttributes(), GetNumberOfDerivedQuantities(), GetNumberOfParameters(), GetParameterIndex(), GetParameterUnits(), GetStateVariableIndex(), GetStateVariableUnits(), GetSystemName(), HasAnyVariable(), HasAttribute(), HasDerivedQuantity(), HasParameter(), HasStateVariable(), rGetDerivedQuantityNames(), rGetDerivedQuantityUnits(), rGetParameterNames(), rGetParameterUnits(), rGetStateVariableNames(), rGetStateVariableUnits(), AbstractOneStepIvpOdeSolver::Solve(), and CvodeAdaptor::Solve().

std::string AbstractUntemplatedParameterisedSystem::GetSystemName

(

)

const

Returns

the name of this system.

Definition at line 59 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

bool AbstractUntemplatedParameterisedSystem::HasAnyVariable

(

const std::string &

rName

)

const

This method is used to establish whether a variable is in an ODE system's state vars, parameters or derived quantitites. You can then safely call GetAnyVariableIndex without a try...catch statement.

Parameters

rName

the name of a variable

Returns

whether the variable is in this ODE system

Definition at line 141 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

bool AbstractUntemplatedParameterisedSystem::HasAttribute

(

const std::string &

rName

)

const

Returns

true if this system has a particular named attribute.

Parameters

rName

the attribute name.

Definition at line 196 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

bool AbstractUntemplatedParameterisedSystem::HasDerivedQuantity

(

const std::string &

rName

)

const

This method is used to establish whether a derived quantity is in an ODE system. You can then safely call GetDerivedQuantityIndex without a try...catch statement.

Parameters

rName

the name of a derived quantity

Returns

whether the derived quantity is in this ODE system

Definition at line 180 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

bool AbstractUntemplatedParameterisedSystem::HasParameter

(

const std::string &

rName

)

const

This method is used to establish whether a parameter is in an ODE system. You can then safely call GetParameterIndex without a try...catch statement.

Parameters

rName

the name of a parameter

Returns

whether the parameter is in this ODE system

Definition at line 122 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

bool AbstractUntemplatedParameterisedSystem::HasStateVariable

(

const std::string &

rName

)

const

This method is used to establish whether a state variable is in an ODE system. You can then safely call GetStateVariableIndex without a try...catch statement.

Parameters

rName

the name of a state variable

Returns

whether the state variable is in this ODE system

Definition at line 88 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

virtual void AbstractUntemplatedParameterisedSystem::ResetToInitialConditions ( )

pure virtual

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

Implemented in AbstractParameterisedSystem< VECTOR >, AbstractParameterisedSystem< N_Vector >, and AbstractParameterisedSystem< std::vector< double > >.

const std::vector< std::string > & AbstractUntemplatedParameterisedSystem::rGetDerivedQuantityNames

(

)

const

Returns

the vector of derived quantity names.

Definition at line 165 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

const std::vector< std::string > & AbstractUntemplatedParameterisedSystem::rGetDerivedQuantityUnits

(

)

const

Returns

the vector of derived quantity units.

Definition at line 170 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

const std::vector< std::string > & AbstractUntemplatedParameterisedSystem::rGetParameterNames

(

)

const

Returns

the names of the parameters in the ODE system.

Definition at line 107 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by AbstractCardiacCell::Init(), AbstractCvodeSystem::Init(), AbstractOdeSystem::save(), AbstractCvodeSystem::save(), and AbstractCardiacCell::serialize().

const std::vector< std::string > & AbstractUntemplatedParameterisedSystem::rGetParameterUnits

(

)

const

Returns

the units of the parameters in the ODE system.

Definition at line 112 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

const std::vector< std::string > & AbstractUntemplatedParameterisedSystem::rGetStateVariableNames

(

)

const

Returns

the names of the state variables in the ODE system.

Definition at line 73 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by AbstractCvodeSystem::CvodeError(), AbstractCvodeCell::rGetStateVariableNames(), AbstractCardiacCell::rGetStateVariableNames(), and AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SolveCellSystems().

const std::vector< std::string > & AbstractUntemplatedParameterisedSystem::rGetStateVariableUnits

(

)

const

Returns

the units of the state variables in the ODE system.

Definition at line 78 of file AbstractUntemplatedParameterisedSystem.cpp.

References GetSystemInformation().

Member Data Documentation

unsigned AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables

protected

The number of state variables in the system.

Definition at line 293 of file AbstractUntemplatedParameterisedSystem.hpp.

Referenced by AbstractCardiacCell::AbstractCardiacCell(), CombinedOdeSystem::CombinedOdeSystem(), AbstractRushLarsenCardiacCell::Compute(), AbstractRushLarsenCardiacCell::ComputeExceptVoltage(), GetNumberOfStateVariables(), AbstractOdeSystem::load(), AbstractCvodeSystem::load(), AbstractOdeSystem::save(), AbstractCvodeSystem::save(), FakeBathCell::serialize(), and AbstractRushLarsenCardiacCell::SolveAndUpdateState().

boost::shared_ptr<AbstractOdeSystemInformation> AbstractUntemplatedParameterisedSystem::mpSystemInfo

protected

Information about the concrete ODE system class.

Subclasses need to set this in their constructor to point to an instance of a suitable class. See for example the OdeSystemInformation class.

Definition at line 301 of file AbstractUntemplatedParameterisedSystem.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleOdeSystem::Alarcon2004OxygenBasedCellCycleOdeSystem(), CML_noble_varghese_kohl_noble_1998_basic_with_sac::CML_noble_varghese_kohl_noble_1998_basic_with_sac(), CombinedOdeSystem::CombinedOdeSystem(), AbstractGeneralizedRushLarsenCardiacCell::Compute(), AbstractRushLarsenCardiacCell::Compute(), AbstractBackwardEulerCardiacCell< 0u >::Compute(), CorriasBuistICCModified::CorriasBuistICCModified(), CorriasBuistSMCModified::CorriasBuistSMCModified(), DeltaNotchOdeSystem::DeltaNotchOdeSystem(), FakeBathCell::FakeBathCell(), FitzHughNagumo1961OdeSystem::FitzHughNagumo1961OdeSystem(), GetSystemInformation(), Goldbeter1991OdeSystem::Goldbeter1991OdeSystem(), Kerchoffs2003ContractionModel::Kerchoffs2003ContractionModel(), Mirams2010WntOdeSystem::Mirams2010WntOdeSystem(), Nash2004ContractionModel::Nash2004ContractionModel(), NhsContractionModel::NhsContractionModel(), OdeSystemForCoupledHeatEquation::OdeSystemForCoupledHeatEquation(), OdeSystemForCoupledHeatEquationWithSource::OdeSystemForCoupledHeatEquationWithSource(), AbstractCvodeSystem::Solve(), TysonNovak2001OdeSystem::TysonNovak2001OdeSystem(), VanLeeuwen2009WntSwatCellCycleOdeSystem::VanLeeuwen2009WntSwatCellCycleOdeSystem(), and WntCellCycleOdeSystem::WntCellCycleOdeSystem().

---

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

• ode/src/common/AbstractUntemplatedParameterisedSystem.hpp
• ode/src/common/AbstractUntemplatedParameterisedSystem.cpp