#include <CellCycleModelOdeSolver.hpp>

Inheritance diagram for CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >:

Collaboration diagram for CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >:

Public Member Functions
bool	IsSetUp ()

void	Initialise ()

virtual bool	IsAdaptive ()

void	Reset ()

Public Member Functions inherited from AbstractCellCycleModelOdeSolver
	AbstractCellCycleModelOdeSolver ()

virtual	~AbstractCellCycleModelOdeSolver ()

void	SolveAndUpdateStateVariable (AbstractOdeSystem *pAbstractOdeSystem, double startTime, double endTime, double timeStep)

bool	StoppingEventOccurred ()

double	GetStoppingTime ()

void	SetSizeOfOdeSystem (unsigned sizeOfOdeSystem)

unsigned	GetSizeOfOdeSystem ()

void	CheckForStoppingEvents ()

void	SetMaxSteps (long int numSteps)

void	SetTolerances (double relTol=1e-4, double absTol=1e-6)

Static Public Member Functions
static boost::shared_ptr < CellCycleModelOdeSolver < CELL_CYCLE_MODEL, ODE_SOLVER > >	Instance ()

Private Member Functions
	CellCycleModelOdeSolver ()

template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Static Private Attributes
static boost::shared_ptr < CellCycleModelOdeSolver < CELL_CYCLE_MODEL, ODE_SOLVER > >	mpInstance

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractCellCycleModelOdeSolver
boost::shared_ptr < AbstractIvpOdeSolver >	mpOdeSolver

unsigned	mSizeOfOdeSystem

Detailed Description

template<class CELL_CYCLE_MODEL, class ODE_SOLVER>
class CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >

A concrete implementation of AbstractCellCycleModelOdeSolver, that uses templates to provide an implementation for any pair of cell-cycle model and ODE solver classes.

All ODE-based cell-cycle model developers need to do is set mpOdeSolver in their constructor: mpOdeSolver = CellCycleModelOdeSolver<CELL_CYCLE_MODEL, ODE_SOLVER>::Instance();

This class contains all the machinery to make it a singleton, hence providing exactly one instance per pair of values of the template parameters.

Definition at line 58 of file CellCycleModelOdeSolver.hpp.

Constructor & Destructor Documentation

template<class CELL_CYCLE_MODEL , class ODE_SOLVER >

CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::CellCycleModelOdeSolver ( )

private

Default constructor. Not user accessible; to obtain an instance of this class use the Instance method.

The semantics of shared_ptr are different from normal pointers; we don't care if a second instance is constructed when loading an archive, since archiving the shared_ptr will ensure that the 'singleton' is correctly serialized. Thus, here we do not require an assertion that mpInstance is NULL, as we do in the constructors of the SimulationTime singleton class.

Definition at line 111 of file CellCycleModelOdeSolver.hpp.

Member Function Documentation

template<class CELL_CYCLE_MODEL , class ODE_SOLVER >

void CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Initialise ( void )

virtual

Initialise the ODE solver.

Implements AbstractCellCycleModelOdeSolver.

Definition at line 140 of file CellCycleModelOdeSolver.hpp.

template<class CELL_CYCLE_MODEL , class ODE_SOLVER >

boost::shared_ptr< CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER > > CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance ( )

static

Returns: a pointer to the singleton instance, creating it if necessary.

Definition at line 124 of file CellCycleModelOdeSolver.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel(), DeltaNotchSrnModel::DeltaNotchSrnModel(), Goldbeter1991SrnModel::Goldbeter1991SrnModel(), SingleOdeWntCellCycleModel::SingleOdeWntCellCycleModel(), StochasticWntCellCycleModel::StochasticWntCellCycleModel(), TysonNovakCellCycleModel::TysonNovakCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::VanLeeuwen2009WntSwatCellCycleModelHypothesisOne(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo(), and WntCellCycleModel::WntCellCycleModel().

template<class CELL_CYCLE_MODEL , class ODE_SOLVER >

bool CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::IsAdaptive ( )

virtual

Returns: true iff this is an adaptive solver such as CVODE for which it is safe to set the 'timestep' to be the outer simulation timestep, because the ODE solver will use this as its maximum, not actual, timestep.

By default calls the base class version; it is defined here so that specializations can override it.

Reimplemented from AbstractCellCycleModelOdeSolver.

Definition at line 155 of file CellCycleModelOdeSolver.hpp.

References AbstractCellCycleModelOdeSolver::IsAdaptive().

template<class CELL_CYCLE_MODEL , class ODE_SOLVER >

bool CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::IsSetUp ( )

virtual