#include <CellCycleModelOdeHandler.hpp>

Inheritance diagram for CellCycleModelOdeHandler:

Collaboration diagram for CellCycleModelOdeHandler:

Public Member Functions
	CellCycleModelOdeHandler (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~CellCycleModelOdeHandler ()

AbstractOdeSystem *	GetOdeSystem () const

void	SetOdeSystem (AbstractOdeSystem *pOdeSystem)

const boost::shared_ptr< AbstractCellCycleModelOdeSolver >	GetOdeSolver () const

void	SetLastTime (double lastTime)

double	GetDt ()

void	SetDt (double timeStep)

void	SetStateVariables (const std::vector< double > &rStateVariables)

std::vector< double >	GetProteinConcentrations () const

void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)

Protected Member Functions
	CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler)

bool	SolveOdeToTime (double currentTime)

virtual void	AdjustOdeParameters (double currentTime)

Protected Attributes
double	mDt

AbstractOdeSystem *	mpOdeSystem

boost::shared_ptr< AbstractCellCycleModelOdeSolver >	mpOdeSolver

double	mLastTime

bool	mFinishedRunningOdes

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

CellCycleModelOdeHandler &	operator= (const AbstractCellCycleModelOdeSolver &)

Friends
class	boost::serialization::access

Detailed Description

This class contains the functionality for running ODEs as part of a cell cycle or SRN model. It is designed to be used as an additional base class for models which require this functionality.

Definition at line 52 of file CellCycleModelOdeHandler.hpp.

Constructor & Destructor Documentation

CellCycleModelOdeHandler::CellCycleModelOdeHandler ( const CellCycleModelOdeHandler & rHandler )

protected

Protected copy-constructor for use by CreateCellCycleModel and CreateSrnModel.

Parameters

rHandler ODE handler to copy.

Definition at line 56 of file CellCycleModelOdeHandler.cpp.

Referenced by serialize().

CellCycleModelOdeHandler::CellCycleModelOdeHandler	(	double	lastTime = `SimulationTime::Instance()->GetTime()`,
		boost::shared_ptr< AbstractCellCycleModelOdeSolver >	pOdeSolver = `boost::shared_ptr<AbstractCellCycleModelOdeSolver>()`
	)

Constructor.

Parameters

lastTime	The birth time of the cell / last time model was evaluated (defaults to the current SimulationTime)
pOdeSolver	An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 38 of file CellCycleModelOdeHandler.cpp.

CellCycleModelOdeHandler::~CellCycleModelOdeHandler ( )

virtual

Destructor.

Definition at line 48 of file CellCycleModelOdeHandler.cpp.

References mpOdeSystem.

Member Function Documentation

void CellCycleModelOdeHandler::AdjustOdeParameters ( double currentTime )

protectedvirtual

Adjust any ODE parameters needed before solving until currentTime. Defaults to do nothing.

Parameters

currentTime the time up to which the system will be solved.

Reimplemented in SingleOdeWntCellCycleModel, WntCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, and Alarcon2004OxygenBasedCellCycleModel.

Definition at line 123 of file CellCycleModelOdeHandler.cpp.

Referenced by SolveOdeToTime().

double CellCycleModelOdeHandler::GetDt ( )

Returns: mDt. This sets it to a default value if it hasn't been set by calling SetDt.

Definition at line 85 of file CellCycleModelOdeHandler.cpp.

References DOUBLE_UNSET, SimulationTime::GetTimeStep(), SimulationTime::Instance(), mDt, and mpOdeSolver.

Referenced by SolveOdeToTime().

const boost::shared_ptr< AbstractCellCycleModelOdeSolver > CellCycleModelOdeHandler::GetOdeSolver ( ) const

Returns: mpOdeSolver

Definition at line 75 of file CellCycleModelOdeHandler.cpp.

References mpOdeSolver.

AbstractOdeSystem * CellCycleModelOdeHandler::GetOdeSystem ( ) const

Returns: mpOdeSystem.

Definition at line 70 of file CellCycleModelOdeHandler.cpp.

References mpOdeSystem.

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

std::vector< double > CellCycleModelOdeHandler::GetProteinConcentrations ( ) const

Returns: the protein concentrations at the current time (useful for tests)

NB: Will copy the vector - you can't use this to modify the concentrations.

Definition at line 138 of file CellCycleModelOdeHandler.cpp.

References mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

Referenced by CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().

CellCycleModelOdeHandler& CellCycleModelOdeHandler::operator= ( const AbstractCellCycleModelOdeSolver & )

private

Prevent copy-assignment of this class, or its subclasses. Note that we do not define this method, therefore statements like "CellCycleModelOdeHandler new = old;" will not compile. We do not inherit from boost::noncopyable because we *do* define a protected copy-constructor, for use by CreateCellCycleModel and CreateSrnModel.