Chaste  Release::2017.1
CellwiseOdeSystemInformation< ODE_SYSTEM > Class Template Reference

#include <CellwiseOdeSystemInformation.hpp>

+ Inheritance diagram for CellwiseOdeSystemInformation< ODE_SYSTEM >:
+ Collaboration diagram for CellwiseOdeSystemInformation< ODE_SYSTEM >:

Public Member Functions

 CellwiseOdeSystemInformation ()
 
- Public Member Functions inherited from AbstractOdeSystemInformation
 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< doubleGetInitialConditions () 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

void Initialise ()
 
template<>
void Initialise ()
 
template<>
void Initialise ()
 
template<>
void Initialise ()
 
template<>
void Initialise ()
 
template<>
void Initialise ()
 
template<>
void Initialise ()
 

Additional Inherited Members

- Protected Attributes inherited from AbstractOdeSystemInformation
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, doublemAttributes
 
std::vector< doublemInitialConditions
 
bool mInitialised
 

Detailed Description

template<class ODE_SYSTEM>
class CellwiseOdeSystemInformation< ODE_SYSTEM >

Concrete implementation of AbstractOdeSystemInformation designed for use where some of the system information *can* vary across instances. As with OdeSystemInformation it is templated by ODE system class, to aid developers of ODE system classes - only a specialisation of the Initialise method is required.

Note: unexpected behaviour can occur if ODE system objects are copied (via copy constructor or operator=). The AbstractOdeSystem maintains a smart pointer (boost::shared_ptr) to the system information object. Hence both the original and the copy will share the same information object.

Definition at line 53 of file CellwiseOdeSystemInformation.hpp.

Constructor & Destructor Documentation

template<class ODE_SYSTEM >
CellwiseOdeSystemInformation< ODE_SYSTEM >::CellwiseOdeSystemInformation ( )

Default constructor; calls Initialise.

Designed to be used as follows by ODE system classes in their constructors: mpSystemInfo.reset(new CellwiseOdeSystemInformation<CLASS>);

Definition at line 86 of file CellwiseOdeSystemInformation.hpp.

References CellwiseOdeSystemInformation< ODE_SYSTEM >::Initialise().

Member Function Documentation

template<>
void CellwiseOdeSystemInformation< DeltaNotchOdeSystem >::Initialise ( )
protectedvirtual

Initialise the ODE system information.

This must be provided by subclasses.

Implements AbstractOdeSystemInformation.

Definition at line 81 of file DeltaNotchOdeSystem.cpp.

References CHASTE_CLASS_EXPORT.

template<class ODE_SYSTEM >
void CellwiseOdeSystemInformation< ODE_SYSTEM >::Initialise ( void  )
protectedvirtual

Generic implementation of Initialise, which does nothing.

Developers should specialise this method to their ODE system. For example,

template<> void CellwiseOdeSystemInformation<MyNewOdeSystem>::Initialise() { this->mVariableNames.push_back("Variable_1"); this->mVariableUnits.push_back("Units_1"); this->mInitialConditions.push_back(0.0);

this->mInitialised = true; }

Implements AbstractOdeSystemInformation.

Definition at line 92 of file CellwiseOdeSystemInformation.hpp.

Referenced by CellwiseOdeSystemInformation< ODE_SYSTEM >::CellwiseOdeSystemInformation().

template<>
void CellwiseOdeSystemInformation< Goldbeter1991OdeSystem >::Initialise ( )
protectedvirtual

Initialise the ODE system information.

This must be provided by subclasses.

Implements AbstractOdeSystemInformation.

Definition at line 97 of file Goldbeter1991OdeSystem.cpp.

References CHASTE_CLASS_EXPORT.

template<>
void CellwiseOdeSystemInformation< Mirams2010WntOdeSystem >::Initialise ( )
protectedvirtual

Initialise the ODE system information.

This must be provided by subclasses.

Implements AbstractOdeSystemInformation.

Definition at line 163 of file Mirams2010WntOdeSystem.cpp.

template<>
void CellwiseOdeSystemInformation< Alarcon2004OxygenBasedCellCycleOdeSystem >::Initialise ( )
protectedvirtual

Initialise the ODE system information.

This must be provided by subclasses.

Implements AbstractOdeSystemInformation.

Definition at line 164 of file Alarcon2004OxygenBasedCellCycleOdeSystem.cpp.

References NAN.

template<>
void CellwiseOdeSystemInformation< WntCellCycleOdeSystem >::Initialise ( )
protectedvirtual

Initialise the ODE system information.

This must be provided by subclasses.

Implements AbstractOdeSystemInformation.

Definition at line 311 of file WntCellCycleOdeSystem.cpp.

References NAN.

template<>
void CellwiseOdeSystemInformation< VanLeeuwen2009WntSwatCellCycleOdeSystem >::Initialise ( )
protectedvirtual

Initialise the ODE system information.

This must be provided by subclasses.

Implements AbstractOdeSystemInformation.

Definition at line 393 of file VanLeeuwen2009WntSwatCellCycleOdeSystem.cpp.

References NAN.


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