#include <AbstractOdeSystemInformation.hpp>

Inheritance diagram for AbstractOdeSystemInformation:

Collaboration diagram for AbstractOdeSystemInformation:

Public Member Functions
	AbstractOdeSystemInformation ()

virtual	~AbstractOdeSystemInformation ()

std::string	GetSystemName () const

std::string	GetFreeVariableName () const

std::string	GetFreeVariableUnits () const

void	SetDefaultInitialConditions (const std::vector< double > &rInitialConditions)

void	SetDefaultInitialCondition (unsigned index, double initialCondition)

std::vector< double >	GetInitialConditions () 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

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	GetNumberOfParameters () const

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

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

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

unsigned	GetNumberOfAttributes () const

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

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

Protected Member Functions
virtual void	Initialise ()=0

Protected Attributes
std::string	mSystemName

std::string	mFreeVariableName

std::string	mFreeVariableUnits

std::vector< std::string >	mVariableNames

std::vector< std::string >	mVariableUnits

std::vector< std::string >	mParameterNames

std::vector< std::string >	mParameterUnits

std::vector< std::string >	mDerivedQuantityNames

std::vector< std::string >	mDerivedQuantityUnits

std::map< std::string, double >	mAttributes

std::vector< double >	mInitialConditions

bool	mInitialised

Friends
class	TestAbstractOdeSystem

Detailed Description

An abstract class which provides access to information about a particular ODE system *class* (as opposed to an instance).

The information available includes:

a name for the system
name & units of the free variable
names & units of state variables
suggested initial conditions
names & units of (settable) parameters
names & units of derived quantities

This class requires a subclass defining the Initialise method in order to set up the information. Developers may do this by defining their own subclass, but the most convenient method is likely to be to use the OdeSystemInformation class, which is a templated singleton subclass of this AbstractOdeSystemInformation class. See its documentation for details of how to use it.

Definition at line 62 of file AbstractOdeSystemInformation.hpp.

Constructor & Destructor Documentation

AbstractOdeSystemInformation::AbstractOdeSystemInformation ( )

Constructor.

Definition at line 43 of file AbstractOdeSystemInformation.cpp.

AbstractOdeSystemInformation::~AbstractOdeSystemInformation ( )

virtual

Virtual destructor since we have virtual methods.

Definition at line 48 of file AbstractOdeSystemInformation.cpp.

Member Function Documentation

unsigned AbstractOdeSystemInformation::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.

Indices go through Variables, Parameters then derived quantities.

Parameters

rName the name of a variable

Definition at line 171 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, GetDerivedQuantityIndex(), GetParameterIndex(), GetStateVariableIndex(), HasDerivedQuantity(), HasParameter(), HasStateVariable(), mInitialised, mParameterNames, and mVariableNames.

std::string AbstractOdeSystemInformation::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 199 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mDerivedQuantityUnits, mInitialised, mParameterUnits, and mVariableUnits.

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

Returns: the value of a named attribute.

Parameters

rName the attribute name.

Definition at line 287 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mAttributes, and mInitialised.

unsigned AbstractOdeSystemInformation::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 241 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mDerivedQuantityNames, and mInitialised.

Referenced by GetAnyVariableIndex().

std::string AbstractOdeSystemInformation::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 259 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mDerivedQuantityUnits, and mInitialised.

std::string AbstractOdeSystemInformation::GetFreeVariableName ( ) const

Returns: the name of the free variable in this system of ODEs.

Definition at line 57 of file AbstractOdeSystemInformation.cpp.

References mFreeVariableName.

std::string AbstractOdeSystemInformation::GetFreeVariableUnits ( ) const

Returns: the units of the free variable in this system of ODEs.

Definition at line 62 of file AbstractOdeSystemInformation.cpp.

References mFreeVariableUnits.

std::vector< double > AbstractOdeSystemInformation::GetInitialConditions ( ) const

Returns: a copy of the suggested initial conditions.

Definition at line 79 of file AbstractOdeSystemInformation.cpp.

References mInitialConditions, and mInitialised.

unsigned AbstractOdeSystemInformation::GetNumberOfAttributes ( ) const

Returns: the number of named attributes that this system has.

Definition at line 275 of file AbstractOdeSystemInformation.cpp.

References mAttributes, and mInitialised.

unsigned AbstractOdeSystemInformation::GetNumberOfDerivedQuantities ( ) const

Returns: the number of derived quantities in this system

Definition at line 269 of file AbstractOdeSystemInformation.cpp.

References mDerivedQuantityUnits, and mInitialised.

unsigned AbstractOdeSystemInformation::GetNumberOfParameters ( ) const

Returns: The number of parameters in this parameterised system.

Definition at line 165 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mParameterUnits.

unsigned AbstractOdeSystemInformation::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 method GetParameterUnits.

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 137 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mInitialised, and mParameterNames.

Referenced by GetAnyVariableIndex().

std::string AbstractOdeSystemInformation::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 155 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mInitialised, and mParameterUnits.

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

This method is used to establish a state varible's position within the vector of state variables of an ODE system. This number can then be used with the method 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 97 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mInitialised, and mVariableNames.

Referenced by GetAnyVariableIndex().

std::string AbstractOdeSystemInformation::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 115 of file AbstractOdeSystemInformation.cpp.

References EXCEPTION, mInitialised, and mVariableUnits.

std::string AbstractOdeSystemInformation::GetSystemName ( ) const

Returns: the name of this system of ODEs.

Definition at line 52 of file AbstractOdeSystemInformation.cpp.

References mSystemName.

bool AbstractOdeSystemInformation::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 193 of file AbstractOdeSystemInformation.cpp.

References HasDerivedQuantity(), HasParameter(), HasStateVariable(), and mInitialised.

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

Returns: true if this system has a particular named attribute.

Parameters

rName the attribute name.

Definition at line 281 of file AbstractOdeSystemInformation.cpp.

References mAttributes, and mInitialised.

bool AbstractOdeSystemInformation::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 252 of file AbstractOdeSystemInformation.cpp.

References mDerivedQuantityNames, and mInitialised.

Referenced by GetAnyVariableIndex(), and HasAnyVariable().

bool AbstractOdeSystemInformation::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 148 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mParameterNames.

Referenced by GetAnyVariableIndex(), and HasAnyVariable().

bool AbstractOdeSystemInformation::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 108 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mVariableNames.

Referenced by GetAnyVariableIndex(), and HasAnyVariable().

virtual void AbstractOdeSystemInformation::Initialise ( )

protectedpure virtual

Initialise the ODE system information.

This must be provided by subclasses.

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

Returns: the vector of derived quantity names.

Definition at line 229 of file AbstractOdeSystemInformation.cpp.

References mDerivedQuantityNames, and mInitialised.

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

Returns: the vector of derived quantity units.

Definition at line 235 of file AbstractOdeSystemInformation.cpp.

References mDerivedQuantityUnits, and mInitialised.

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

Returns: the vector of parameter names.

Definition at line 125 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mParameterNames.

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

Returns: the vector of parameter units.

Definition at line 131 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mParameterUnits.

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

Returns: the state variable names vector.

Definition at line 85 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mVariableNames.

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

Returns: the state variable units vector.

Definition at line 91 of file AbstractOdeSystemInformation.cpp.

References mInitialised, and mVariableUnits.

void AbstractOdeSystemInformation::SetDefaultInitialCondition	(	unsigned	index,
		double	initialCondition
	)

Set a single component of the default initial conditions for the ODE system. This method DOES NOT change the state variables of the ODE object on which it is called.

Parameters