AbstractUntemplatedParameterisedSystem Class Reference

#include <AbstractParameterisedSystem.hpp>

Inherited by AbstractParameterisedSystem< VECTOR >, AbstractParameterisedSystem< N_Vector >, and AbstractParameterisedSystem< std::vector< double > >.

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List of all members.

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
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 46 of file AbstractParameterisedSystem.hpp.

Constructor & Destructor Documentation

AbstractUntemplatedParameterisedSystem::AbstractUntemplatedParameterisedSystem ( unsigned  numberOfStateVariables  ) 

Constructor.

Parameters:
numberOfStateVariables the number of state variables in the ODE system

Definition at line 38 of file AbstractParameterisedSystem.cpp.

AbstractUntemplatedParameterisedSystem::~AbstractUntemplatedParameterisedSystem (  )  [virtual]

Make this class polymorphic.

Definition at line 53 of file AbstractParameterisedSystem.cpp.

Member Function Documentation

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

Get 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 353 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by AbstractParameterisedSystem< VECTOR >::GetAnyVariable(), GetAnyVariableUnits(), AbstractParameterisedSystem< VECTOR >::SetAnyVariable(), and AbstractCardiacProblem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::WriteExtraVariablesOneStep().

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

Get 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 392 of file AbstractParameterisedSystem.cpp.

References GetAnyVariableIndex(), and GetAnyVariableUnits().

std::string AbstractUntemplatedParameterisedSystem::GetAnyVariableUnits ( unsigned  index  )  const

Get 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 387 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by GetAnyVariableUnits().

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

Get the value of a named attribute.

Parameters:
rName the attribute name.

Definition at line 456 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

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

Get the index of a derived quantity, given its name.

Parameters:
rName the name of a derived quantity.

Definition at line 430 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

std::string AbstractUntemplatedParameterisedSystem::GetDerivedQuantityUnits ( unsigned  index  )  const

Get the units of a derived quantity.

Parameters:
index an index from GetDerivedQuantityIndex.
Returns:
the units of the variable.

Definition at line 440 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

unsigned AbstractUntemplatedParameterisedSystem::GetNumberOfAttributes (  )  const

Return the number of named attributes that this system has.

Definition at line 446 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

unsigned AbstractUntemplatedParameterisedSystem::GetNumberOfDerivedQuantities (  )  const

Get the number of derived quantities.

Definition at line 401 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by AbstractParameterisedSystem< VECTOR >::GetAnyVariable(), and OdeSolution::rGetDerivedQuantities().

unsigned AbstractUntemplatedParameterisedSystem::GetNumberOfParameters (  )  const

Get the number of parameters.

Definition at line 240 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by OdeSolution::rGetParameters().

unsigned AbstractUntemplatedParameterisedSystem::GetNumberOfStateVariables (  )  const

Get the number of state variables in the ODE system.

Returns:
mNumberOfStateVariables

Definition at line 100 of file AbstractParameterisedSystem.cpp.

References mNumberOfStateVariables.

Referenced by RungeKuttaFehlbergIvpOdeSolver::CalculateNextYValue(), RungeKutta4IvpOdeSolver::CalculateNextYValue(), RungeKutta2IvpOdeSolver::CalculateNextYValue(), HeunIvpOdeSolver::CalculateNextYValue(), EulerIvpOdeSolver::CalculateNextYValue(), BackwardEulerIvpOdeSolver::CalculateNextYValue(), AbstractCardiacCell::CheckForArchiveFix(), RungeKuttaFehlbergIvpOdeSolver::InternalSolve(), AbstractCvodeSystem::RecordStoppingPoint(), CvodeAdaptor::SetupCvode(), AbstractCvodeSystem::SetupCvode(), RungeKuttaFehlbergIvpOdeSolver::Solve(), AbstractOneStepIvpOdeSolver::Solve(), AbstractIvpOdeSolver::SolveAndUpdateStateVariable(), AbstractCardiacTissue< ELEMENT_DIM, SPACE_DIM >::SolveCellSystems(), and AbstractOdeBasedCellCycleModel::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 288 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by AbstractParameterisedSystem< VECTOR >::GetParameter(), HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters(), and AbstractParameterisedSystem< VECTOR >::SetParameter().

std::string AbstractUntemplatedParameterisedSystem::GetParameterUnits ( unsigned  index  )  const

Get 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 298 of file AbstractParameterisedSystem.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 174 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by AbstractParameterisedSystem< VECTOR >::GetStateVariable(), and AbstractParameterisedSystem< VECTOR >::SetStateVariable().

std::string AbstractUntemplatedParameterisedSystem::GetStateVariableUnits ( unsigned  index  )  const

Get 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 184 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

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

Get the object which provides information about this ODE system.

Definition at line 58 of file AbstractParameterisedSystem.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(), CvodeAdaptor::Solve(), and AbstractOneStepIvpOdeSolver::Solve().

std::string AbstractUntemplatedParameterisedSystem::GetSystemName (  )  const

Get the name of this system.

Definition at line 65 of file AbstractParameterisedSystem.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 358 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

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

Test whether this system has a particular named attribute.

Parameters:
rName the attribute name.

Definition at line 451 of file AbstractParameterisedSystem.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 435 of file AbstractParameterisedSystem.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 293 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by HeartConfigRelatedCellFactory< SPACE_DIM >::SetCellParameters().

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 179 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

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

Get the vector of derived quantity names.

Definition at line 420 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

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

Get the vector of derived quantity units.

Definition at line 425 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

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

Get the names of the parameters in the ODE system.

Definition at line 278 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

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

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

Get the units of the parameters in the ODE system.

Definition at line 283 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

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

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

Definition at line 164 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

Referenced by AdaptiveBidomainProblem::AddCurrentSolutionToAdaptiveMesh(), AbstractParameterisedSystem< VECTOR >::GetStateMessage(), and AdaptiveBidomainProblem::InitializeSolutionOnAdaptedMesh().

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

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

Definition at line 169 of file AbstractParameterisedSystem.cpp.

References GetSystemInformation().

Member Data Documentation

unsigned AbstractUntemplatedParameterisedSystem::mNumberOfStateVariables [protected]

The number of state variables in the system.

Definition at line 281 of file AbstractParameterisedSystem.hpp.

Referenced by AbstractCardiacCell::AbstractCardiacCell(), CombinedOdeSystem::CombinedOdeSystem(), AbstractRushLarsenCardiacCell::Compute(), AbstractRushLarsenCardiacCell::ComputeExceptVoltage(), AbstractParameterisedSystem< VECTOR >::GetAnyVariable(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), GetNumberOfStateVariables(), AbstractParameterisedSystem< VECTOR >::GetStateVariable(), AbstractOdeSystem::load(), AbstractOdeSystem::save(), FakeBathCell::serialize(), AbstractParameterisedSystem< VECTOR >::SetAnyVariable(), AbstractParameterisedSystem< VECTOR >::SetDefaultInitialCondition(), AbstractParameterisedSystem< VECTOR >::SetDefaultInitialConditions(), AbstractParameterisedSystem< VECTOR >::SetStateVariable(), AbstractParameterisedSystem< VECTOR >::SetStateVariables(), 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 289 of file AbstractParameterisedSystem.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(), AbstractRushLarsenCardiacCell::Compute(), AbstractBackwardEulerCardiacCell< SIZE >::Compute(), CorriasBuistICCModified::CorriasBuistICCModified(), CorriasBuistSMCModified::CorriasBuistSMCModified(), DeltaNotchOdeSystem::DeltaNotchOdeSystem(), FakeBathCell::FakeBathCell(), FitzHughNagumo1961OdeSystem::FitzHughNagumo1961OdeSystem(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), GetSystemInformation(), Kerchoffs2003ContractionModel::Kerchoffs2003ContractionModel(), Mirams2010WntOdeSystem::Mirams2010WntOdeSystem(), Nash2004ContractionModel::Nash2004ContractionModel(), NhsContractionModel::NhsContractionModel(), OdeSystemForCoupledHeatEquation::OdeSystemForCoupledHeatEquation(), OdeSystemForCoupledHeatEquationWithSource::OdeSystemForCoupledHeatEquationWithSource(), AbstractParameterisedSystem< VECTOR >::SetDefaultInitialCondition(), AbstractParameterisedSystem< VECTOR >::SetDefaultInitialConditions(), AbstractCvodeSystem::Solve(), TysonNovak2001OdeSystem::TysonNovak2001OdeSystem(), VanLeeuwen2009WntSwatCellCycleOdeSystem::VanLeeuwen2009WntSwatCellCycleOdeSystem(), and WntCellCycleOdeSystem::WntCellCycleOdeSystem().

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