#include <SimpleWntCellCycleModel.hpp>

Inheritance diagram for SimpleWntCellCycleModel:

Collaboration diagram for SimpleWntCellCycleModel:

Public Member Functions
	SimpleWntCellCycleModel ()

virtual void	UpdateCellCyclePhase ()

virtual void	InitialiseDaughterCell ()

virtual AbstractCellCycleModel *	CreateCellCycleModel ()

bool	GetUseCellProliferativeTypeDependentG1Duration () const

void	SetUseCellProliferativeTypeDependentG1Duration (bool useCellProliferativeTypeDependentG1Duration=true)

virtual bool	CanCellTerminallyDifferentiate ()

double	GetWntStemThreshold () const

void	SetWntStemThreshold (double wntStemThreshold)

double	GetWntTransitThreshold () const

void	SetWntTransitThreshold (double wntTransitThreshold)

double	GetWntLabelledThreshold () const

void	SetWntLabelledThreshold (double wntLabelledThreshold)

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
	AbstractSimplePhaseBasedCellCycleModel ()

virtual	~AbstractSimplePhaseBasedCellCycleModel ()

virtual void	ResetForDivision ()

virtual void	Initialise ()

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)

virtual double	GetAverageTransitCellCycleTime ()

virtual double	GetAverageStemCellCycleTime ()

double	GetMinimumGapDuration () const

void	SetMinimumGapDuration (double minimumGapDuration)

Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()

virtual	~AbstractCellCycleModel ()

void	SetCell (CellPtr pCell)

CellPtr	GetCell ()

virtual void	SetBirthTime (double birthTime)

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

Protected Member Functions
double	GetWntLevel () const

WntConcentrationType	GetWntType ()

void	SetG1Duration ()

	SimpleWntCellCycleModel (const SimpleWntCellCycleModel &rModel)

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

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

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

Protected Attributes
bool	mUseCellProliferativeTypeDependentG1Duration

double	mWntStemThreshold

double	mWntTransitThreshold

double	mWntLabelledThreshold

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

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

Friends
class	boost::serialization::access

Detailed Description

Simple Wnt-dependent cell-cycle model.

Definition at line 46 of file SimpleWntCellCycleModel.hpp.

Constructor & Destructor Documentation

SimpleWntCellCycleModel::SimpleWntCellCycleModel ( const SimpleWntCellCycleModel & 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 55 of file SimpleWntCellCycleModel.cpp.

SimpleWntCellCycleModel::SimpleWntCellCycleModel ( )

Constructor - just a default, mBirthTime is now set in the AbstractPhaseBasedCellCycleModel class. mG1Duration is set very high, it is set for the individual cells when InitialiseDaughterCell is called.

Definition at line 47 of file SimpleWntCellCycleModel.cpp.

Referenced by CreateCellCycleModel().

Member Function Documentation

bool SimpleWntCellCycleModel::CanCellTerminallyDifferentiate ( )

virtual

Overridden CanCellTerminallyDifferentiate() method.

Returns: whether cell can terminally differentiate

Reimplemented from AbstractCellCycleModel.

Definition at line 285 of file SimpleWntCellCycleModel.cpp.

AbstractCellCycleModel * SimpleWntCellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns: the new cell-cycle model

Implements AbstractCellCycleModel.

Reimplemented in SingleOdeWntCellCycleModel.

Definition at line 79 of file SimpleWntCellCycleModel.cpp.

References SimpleWntCellCycleModel().

bool SimpleWntCellCycleModel::GetUseCellProliferativeTypeDependentG1Duration ( ) const

Returns: mUseCellProliferativeTypeDependentG1Duration

Definition at line 84 of file SimpleWntCellCycleModel.cpp.

References mUseCellProliferativeTypeDependentG1Duration.

double SimpleWntCellCycleModel::GetWntLabelledThreshold ( ) const

Returns: mWntLabelledThreshold

Definition at line 314 of file SimpleWntCellCycleModel.cpp.

References mWntLabelledThreshold.

double SimpleWntCellCycleModel::GetWntLevel ( ) const

protected

Returns: the Wnt level experienced by the cell.

Definition at line 132 of file SimpleWntCellCycleModel.cpp.

References WntConcentration< DIM >::GetWntLevel(), WntConcentration< DIM >::Instance(), AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mpCell, and NEVER_REACHED.

Referenced by SingleOdeWntCellCycleModel::AdjustOdeParameters(), SingleOdeWntCellCycleModel::Initialise(), SingleOdeWntCellCycleModel::SingleOdeWntCellCycleModel(), and UpdateCellCyclePhase().

double SimpleWntCellCycleModel::GetWntStemThreshold ( ) const

Returns: mWntStemThreshold

Definition at line 290 of file SimpleWntCellCycleModel.cpp.

References mWntStemThreshold.

double SimpleWntCellCycleModel::GetWntTransitThreshold ( ) const

Returns: mWntTransitThreshold

Definition at line 302 of file SimpleWntCellCycleModel.cpp.

References mWntTransitThreshold.

WntConcentrationType SimpleWntCellCycleModel::GetWntType ( )

protected

Returns: the type of Wnt concentration (LINEAR, RADIAL, EXPONENTIAL or NONE). This affects how the cell cycle phase is updated.

Definition at line 163 of file SimpleWntCellCycleModel.cpp.

References WntConcentration< DIM >::GetType(), WntConcentration< DIM >::Instance(), AbstractCellCycleModel::mDimension, NEVER_REACHED, and UNSIGNED_UNSET.

Referenced by InitialiseDaughterCell(), and UpdateCellCyclePhase().

void SimpleWntCellCycleModel::InitialiseDaughterCell ( )

virtual

Overridden InitialiseDaughterCell() method.

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Definition at line 271 of file SimpleWntCellCycleModel.cpp.

References GetWntType(), AbstractSimplePhaseBasedCellCycleModel::InitialiseDaughterCell(), and AbstractCellCycleModel::mpCell.

void SimpleWntCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Overridden OutputCellCycleModelParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Reimplemented in SingleOdeWntCellCycleModel.

Definition at line 326 of file SimpleWntCellCycleModel.cpp.

References CHASTE_CLASS_EXPORT, mUseCellProliferativeTypeDependentG1Duration, mWntLabelledThreshold, mWntStemThreshold, mWntTransitThreshold, and AbstractSimplePhaseBasedCellCycleModel::OutputCellCycleModelParameters().

Referenced by SingleOdeWntCellCycleModel::OutputCellCycleModelParameters().

template<class Archive >

void SimpleWntCellCycleModel::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the cell-cycle model, never used directly - boost uses this.

Parameters

archive	the archive
version	the current version of this class

Definition at line 59 of file SimpleWntCellCycleModel.hpp.

References RandomNumberGenerator::Instance(), mUseCellProliferativeTypeDependentG1Duration, mWntLabelledThreshold, mWntStemThreshold, and mWntTransitThreshold.

void SimpleWntCellCycleModel::SetG1Duration ( )

protectedvirtual

Stochastically set the G1 duration. The G1 duration is taken from a normal distribution whose mean is the G1 duration given in AbstractPhaseBasedCellCycleModel, for the cell type, and whose standard deviation is 1.

Called on cell creation at the start of a simulation, and for both parent and daughter cells at cell division.

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Definition at line 94 of file SimpleWntCellCycleModel.cpp.

References AbstractPhaseBasedCellCycleModel::GetStemCellG1Duration(), AbstractPhaseBasedCellCycleModel::GetTransitCellG1Duration(), RandomNumberGenerator::Instance(), AbstractPhaseBasedCellCycleModel::mG1Duration, AbstractPhaseBasedCellCycleModel::mMinimumGapDuration, AbstractCellCycleModel::mpCell, mUseCellProliferativeTypeDependentG1Duration, NEVER_REACHED, and RandomNumberGenerator::NormalRandomDeviate().