#include <VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.hpp>

Inheritance diagram for VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo:

Collaboration diagram for VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo:

Public Member Functions
	VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

void	InitialiseOdeSystem (double wntConcentration, boost::shared_ptr< AbstractCellMutationState > pMutationState)

AbstractCellCycleModel *	CreateCellCycleModel ()

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractVanLeeuwen2009WntSwatCellCycleModel
	AbstractVanLeeuwen2009WntSwatCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

void	Initialise ()

double	GetMembraneBoundBetaCateninLevel ()

double	GetCytoplasmicBetaCateninLevel ()

double	GetNuclearBetaCateninLevel ()

Public Member Functions inherited from AbstractWntOdeBasedCellCycleModel
	AbstractWntOdeBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~AbstractWntOdeBasedCellCycleModel ()

void	ResetForDivision ()

void	UpdateCellProliferativeType ()

double	GetAverageTransitCellCycleTime ()

double	GetAverageStemCellCycleTime ()

virtual bool	CanCellTerminallyDifferentiate ()

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

virtual	~AbstractOdeBasedPhaseBasedCellCycleModel ()

double	GetOdeStopTime ()

void	SetBirthTime (double birthTime)

Public Member Functions inherited from AbstractPhaseBasedCellCycleModel
	AbstractPhaseBasedCellCycleModel ()

virtual	~AbstractPhaseBasedCellCycleModel ()

virtual bool	ReadyToDivide ()

CellCyclePhase	GetCurrentCellCyclePhase () const

virtual double	GetG1Duration () const

double	GetStemCellG1Duration () const

double	GetTransitCellG1Duration () const

double	GetSG2MDuration () const

virtual double	GetSDuration () const

virtual double	GetG2Duration () const

virtual double	GetMDuration () const

virtual void	SetStemCellG1Duration (double stemCellG1Duration)

virtual void	SetTransitCellG1Duration (double transitCellG1Duration)

void	SetSDuration (double sDuration)

void	SetG2Duration (double g2Duration)

void	SetMDuration (double mDuration)

double	GetMinimumGapDuration () const

void	SetMinimumGapDuration (double minimumGapDuration)

Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()

virtual	~AbstractCellCycleModel ()

void	SetCell (CellPtr pCell)

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetDimension (unsigned dimension)

unsigned	GetDimension () const

double	GetBirthTime () const

double	GetAge ()

void	OutputCellCycleModelInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Public Member Functions inherited from CellCycleModelOdeHandler
	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
	VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo (const VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo &rModel)

Protected Member Functions inherited from AbstractVanLeeuwen2009WntSwatCellCycleModel
	AbstractVanLeeuwen2009WntSwatCellCycleModel (const AbstractVanLeeuwen2009WntSwatCellCycleModel &rModel)

Protected Member Functions inherited from AbstractWntOdeBasedCellCycleModel
double	GetWntLevel () const

void	UpdateCellCyclePhase ()

	AbstractWntOdeBasedCellCycleModel (const AbstractWntOdeBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractOdeBasedPhaseBasedCellCycleModel
	AbstractOdeBasedPhaseBasedCellCycleModel (const AbstractOdeBasedPhaseBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractPhaseBasedCellCycleModel
	AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel)

Protected Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel (const AbstractCellCycleModel &rModel)

Protected Member Functions inherited from CellCycleModelOdeHandler
	CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler)

bool	SolveOdeToTime (double currentTime)

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

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractOdeBasedPhaseBasedCellCycleModel
double	mDivideTime

double	mG2PhaseStartTime

Protected Attributes inherited from AbstractPhaseBasedCellCycleModel
CellCyclePhase	mCurrentCellCyclePhase

double	mG1Duration

double	mMinimumGapDuration

double	mStemCellG1Duration

double	mTransitCellG1Duration

double	mSDuration

double	mG2Duration

double	mMDuration

Protected Attributes inherited from AbstractCellCycleModel
CellPtr	mpCell

double	mBirthTime

bool	mReadyToDivide

unsigned	mDimension

Protected Attributes inherited from CellCycleModelOdeHandler
double	mDt

AbstractOdeSystem *	mpOdeSystem

boost::shared_ptr< AbstractCellCycleModelOdeSolver >	mpOdeSolver

double	mLastTime

bool	mFinishedRunningOdes

Detailed Description

Concrete Van Leeuwen 2009 cell-cycle model, using hypothesis two (see paper).

Definition at line 44 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.hpp.

Constructor & Destructor Documentation

VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo ( const VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo & rModel )

protected

Protected copy-constructor for use by CreateCellCycleModel. The only way for external code to create a copy of a cell cycle model is by calling that method, to ensure that a model of the correct subclass is created. This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.

This method is called by child classes to set member variables for a daughter cell upon cell division. Note that the parent cell cycle model will have had ResetForDivision() called just before CreateCellCycleModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().

Parameters

rModel the cell cycle model to copy.

Definition at line 57 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.cpp.

References CellCycleModelOdeHandler::GetOdeSystem(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), InitialiseOdeSystem(), AbstractCellCycleModel::mpCell, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and CellCycleModelOdeHandler::SetStateVariables().

Referenced by CreateCellCycleModel(), and serialize().

VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo ( boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() )

Default constructor calls base class.

Parameters

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 VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.cpp.

References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().

Member Function Documentation

AbstractCellCycleModel * VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel ( )

virtual

Overridden builder method to create new copies of this cell-cycle model.

Returns: the new cell-cycle model

Implements AbstractCellCycleModel.

Definition at line 88 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.cpp.

References VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo().

Referenced by serialize().

void VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::InitialiseOdeSystem	(	double	wntConcentration,
		boost::shared_ptr< AbstractCellMutationState >	pMutationState
	)