#include <AbstractSimpleCellCycleModel.hpp>

Inheritance diagram for AbstractSimpleCellCycleModel:

Collaboration diagram for AbstractSimpleCellCycleModel:

Public Member Functions
	AbstractSimpleCellCycleModel ()

virtual	~AbstractSimpleCellCycleModel ()

virtual void	ResetForDivision ()

virtual void	UpdateCellCyclePhase ()

void	InitialiseDaughterCell ()

virtual void	Initialise ()

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

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 ()

double	GetBirthTime () const

double	GetAge ()

virtual bool	ReadyToDivide ()

virtual AbstractCellCycleModel *	CreateCellCycleModel ()=0

CellCyclePhase	GetCurrentCellCyclePhase ()

virtual double	GetG1Duration ()

double	GetStemCellG1Duration ()

double	GetTransitCellG1Duration ()

double	GetSG2MDuration ()

virtual double	GetSDuration ()

virtual double	GetG2Duration ()

virtual double	GetMDuration ()

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 ()

virtual bool	CanCellTerminallyDifferentiate ()

double	GetMinimumGapDuration ()

void	SetMinimumGapDuration (double minimumGapDuration)

void	OutputCellCycleModelInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Member Functions
virtual void	SetG1Duration ()

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 AbstractCellCycleModel
CellPtr	mpCell

double	mBirthTime

CellCyclePhase	mCurrentCellCyclePhase

double	mG1Duration

bool	mReadyToDivide

unsigned	mDimension

double	mMinimumGapDuration

double	mStemCellG1Duration

double	mTransitCellG1Duration

double	mSDuration

double	mG2Duration

double	mMDuration

Detailed Description

This class contains all the functionality shared by 'simple' cell-cycle models, where the duration of each cell cycle phase is determined when the cell-cycle model is created. Note that whether or not the cell should actually divide may still depend on further conditions in subclasses; for example, the cell may only divide if the local concentration of a signalling molecule is sufficiently high/

This class of cell-cycle models is distinct from 'ODE-based' cell-cycle models, where the duration of one or more cell cycle phases are evaluated 'on the fly' as the cell ages, according to a system of ordinary differential equations (ODEs) governing (for example) the concentrations of key intracellular proteins.

Definition at line 57 of file AbstractSimpleCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractSimpleCellCycleModel::AbstractSimpleCellCycleModel ( )

Default constructor - creates an AbstractSimpleCellCycleModel.

Definition at line 42 of file AbstractSimpleCellCycleModel.cpp.

AbstractSimpleCellCycleModel::~AbstractSimpleCellCycleModel ( )

virtual

Destructor.

Definition at line 46 of file AbstractSimpleCellCycleModel.cpp.

Member Function Documentation

void AbstractSimpleCellCycleModel::Initialise ( void )

virtual

See AbstractCellCycleModel::Initialise()

Reimplemented from AbstractCellCycleModel.

Reimplemented in SingleOdeWntCellCycleModel, and StochasticOxygenBasedCellCycleModel.

Definition at line 50 of file AbstractSimpleCellCycleModel.cpp.

References SetG1Duration().

Referenced by StochasticOxygenBasedCellCycleModel::Initialise(), and SingleOdeWntCellCycleModel::Initialise().

void AbstractSimpleCellCycleModel::InitialiseDaughterCell ( )

virtual

Set the new cell's G1 duration once it has been created after division. The duration will be based on cell type.

Reimplemented from AbstractCellCycleModel.

Reimplemented in SimpleWntCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, and StochasticOxygenBasedCellCycleModel.

Definition at line 55 of file AbstractSimpleCellCycleModel.cpp.

References AbstractCellCycleModel::InitialiseDaughterCell(), and SetG1Duration().

Referenced by StochasticOxygenBasedCellCycleModel::InitialiseDaughterCell(), AbstractSimpleGenerationBasedCellCycleModel::InitialiseDaughterCell(), and SimpleWntCellCycleModel::InitialiseDaughterCell().

void AbstractSimpleCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Outputs cell cycle model parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellCycleModel.

Reimplemented in SimpleWntCellCycleModel, SimpleOxygenBasedCellCycleModel, ContactInhibitionCellCycleModel, ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel, SingleOdeWntCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, GammaDistributedStochasticDurationCellCycleModel, StochasticOxygenBasedCellCycleModel, StochasticDurationCellCycleModel, StochasticDurationGenerationBasedCellCycleModel, and FixedDurationGenerationBasedCellCycleModel.

Definition at line 117 of file AbstractSimpleCellCycleModel.cpp.

References AbstractCellCycleModel::OutputCellCycleModelParameters().

Referenced by StochasticDurationCellCycleModel::OutputCellCycleModelParameters(), GammaDistributedStochasticDurationCellCycleModel::OutputCellCycleModelParameters(), AbstractSimpleGenerationBasedCellCycleModel::OutputCellCycleModelParameters(), ContactInhibitionCellCycleModel::OutputCellCycleModelParameters(), SimpleOxygenBasedCellCycleModel::OutputCellCycleModelParameters(), and SimpleWntCellCycleModel::OutputCellCycleModelParameters().

void AbstractSimpleCellCycleModel::ResetForDivision ( )

virtual

See AbstractCellCycleModel::ResetForDivision()

Reimplemented from AbstractCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel, and AbstractSimpleGenerationBasedCellCycleModel.

Definition at line 83 of file AbstractSimpleCellCycleModel.cpp.

References SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::ResetForDivision(), and SetG1Duration().

Referenced by AbstractSimpleGenerationBasedCellCycleModel::ResetForDivision(), and StochasticOxygenBasedCellCycleModel::ResetForDivision().

template<class Archive >

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

inlineprivate

Archive the cell-cycle model.

Parameters

archive	the archive
version	the current version of this class

Definition at line 70 of file AbstractSimpleCellCycleModel.hpp.

void AbstractSimpleCellCycleModel::SetG1Duration ( )

protectedvirtual

Subclasses can override this function if they wish, this just allocates the default values for each of the different cell types' G1 durations as defined in AbstractCellCycleModel.

Reimplemented in SimpleWntCellCycleModel, ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel, GammaDistributedStochasticDurationCellCycleModel, StochasticDurationCellCycleModel, and StochasticDurationGenerationBasedCellCycleModel.

Definition at line 61 of file AbstractSimpleCellCycleModel.cpp.

References AbstractCellCycleModel::GetStemCellG1Duration(), AbstractCellCycleModel::GetTransitCellG1Duration(), AbstractCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, and NEVER_REACHED.

Referenced by Initialise(), InitialiseDaughterCell(), and ResetForDivision().

void AbstractSimpleCellCycleModel::UpdateCellCyclePhase ( )

virtual

Default UpdateCellCyclePhase() method for a simple cell-cycle model.

Can be overridden if they should do something more subtle.

Implements AbstractCellCycleModel.

Reimplemented in SimpleWntCellCycleModel, SingleOdeWntCellCycleModel, SimpleOxygenBasedCellCycleModel, and ContactInhibitionCellCycleModel.

Definition at line 90 of file AbstractSimpleCellCycleModel.cpp.

References AbstractCellCycleModel::GetAge(), AbstractCellCycleModel::GetG2Duration(), AbstractCellCycleModel::GetMDuration(), AbstractCellCycleModel::GetSDuration(), AbstractCellCycleModel::mCurrentCellCyclePhase, AbstractCellCycleModel::mG1Duration, and AbstractCellCycleModel::mpCell.