#include <AbstractSimplePhaseBasedCellCycleModel.hpp>

Inheritance diagram for AbstractSimplePhaseBasedCellCycleModel:

Collaboration diagram for AbstractSimplePhaseBasedCellCycleModel:

Public Member Functions
	AbstractSimplePhaseBasedCellCycleModel ()

virtual	~AbstractSimplePhaseBasedCellCycleModel ()

virtual void	ResetForDivision ()

virtual void	UpdateCellCyclePhase ()

void	InitialiseDaughterCell ()

virtual void	Initialise ()

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

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 ()

virtual AbstractCellCycleModel *	CreateCellCycleModel ()=0

virtual bool	CanCellTerminallyDifferentiate ()

void	OutputCellCycleModelInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Member Functions
virtual void	SetG1Duration ()

	AbstractSimplePhaseBasedCellCycleModel (const AbstractSimplePhaseBasedCellCycleModel &rModel)

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

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

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 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

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 AbstractSimplePhaseBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractSimplePhaseBasedCellCycleModel::AbstractSimplePhaseBasedCellCycleModel ( const AbstractSimplePhaseBasedCellCycleModel & 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 49 of file AbstractSimplePhaseBasedCellCycleModel.cpp.

AbstractSimplePhaseBasedCellCycleModel::AbstractSimplePhaseBasedCellCycleModel ( )

Default constructor - creates an AbstractSimplePhaseBasedCellCycleModel.

Definition at line 41 of file AbstractSimplePhaseBasedCellCycleModel.cpp.

Referenced by serialize().

AbstractSimplePhaseBasedCellCycleModel::~AbstractSimplePhaseBasedCellCycleModel ( )

virtual

Destructor.

Definition at line 45 of file AbstractSimplePhaseBasedCellCycleModel.cpp.

Referenced by serialize().

Member Function Documentation

void AbstractSimplePhaseBasedCellCycleModel::Initialise ( void )

virtual

See AbstractPhaseBasedCellCycleModel::Initialise()

Reimplemented from AbstractCellCycleModel.

Reimplemented in SingleOdeWntCellCycleModel, and StochasticOxygenBasedCellCycleModel.

Definition at line 66 of file AbstractSimplePhaseBasedCellCycleModel.cpp.

References SetG1Duration().

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

void AbstractSimplePhaseBasedCellCycleModel::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, and StochasticOxygenBasedCellCycleModel.

Definition at line 71 of file AbstractSimplePhaseBasedCellCycleModel.cpp.

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

Referenced by StochasticOxygenBasedCellCycleModel::InitialiseDaughterCell(), AbstractSimpleGenerationalCellCycleModel::InitialiseDaughterCell(), SimpleWntCellCycleModel::InitialiseDaughterCell(), and serialize().

void AbstractSimplePhaseBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Overridden OutputCellCycleModelParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractPhaseBasedCellCycleModel.

Reimplemented in SimpleWntCellCycleModel, SimpleOxygenBasedCellCycleModel, ContactInhibitionCellCycleModel, SingleOdeWntCellCycleModel, ExponentialG1GenerationalCellCycleModel, FixedSequenceCellCycleModel, AbstractSimpleGenerationalCellCycleModel, GammaG1CellCycleModel, StochasticOxygenBasedCellCycleModel, UniformG1GenerationalCellCycleModel, and FixedG1GenerationalCellCycleModel.

Definition at line 132 of file AbstractSimplePhaseBasedCellCycleModel.cpp.

References AbstractPhaseBasedCellCycleModel::OutputCellCycleModelParameters().

Referenced by GammaG1CellCycleModel::OutputCellCycleModelParameters(), AbstractSimpleGenerationalCellCycleModel::OutputCellCycleModelParameters(), ContactInhibitionCellCycleModel::OutputCellCycleModelParameters(), SimpleOxygenBasedCellCycleModel::OutputCellCycleModelParameters(), SimpleWntCellCycleModel::OutputCellCycleModelParameters(), and serialize().

void AbstractSimplePhaseBasedCellCycleModel::ResetForDivision ( )

virtual

See AbstractPhaseBasedCellCycleModel::ResetForDivision()

Reimplemented from AbstractPhaseBasedCellCycleModel.

Reimplemented in StochasticOxygenBasedCellCycleModel, and AbstractSimpleGenerationalCellCycleModel.

Definition at line 99 of file AbstractSimplePhaseBasedCellCycleModel.cpp.

References AbstractPhaseBasedCellCycleModel::ResetForDivision(), and SetG1Duration().

Referenced by AbstractSimpleGenerationalCellCycleModel::ResetForDivision(), StochasticOxygenBasedCellCycleModel::ResetForDivision(), and serialize().

template<class Archive >

void AbstractSimplePhaseBasedCellCycleModel::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 AbstractSimplePhaseBasedCellCycleModel.hpp.

References AbstractSimplePhaseBasedCellCycleModel(), CLASS_IS_ABSTRACT, Initialise(), InitialiseDaughterCell(), OutputCellCycleModelParameters(), ResetForDivision(), SetG1Duration(), UpdateCellCyclePhase(), and ~AbstractSimplePhaseBasedCellCycleModel().

void AbstractSimplePhaseBasedCellCycleModel::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 AbstractPhaseBasedCellCycleModel.

Reimplemented in SimpleWntCellCycleModel, GammaG1CellCycleModel, FixedSequenceCellCycleModel, ExponentialG1GenerationalCellCycleModel, and UniformG1GenerationalCellCycleModel.

Definition at line 77 of file AbstractSimplePhaseBasedCellCycleModel.cpp.

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

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

void AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase ( )

virtual

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

Can be overridden if they should do something more subtle.

Implements AbstractPhaseBasedCellCycleModel.

Reimplemented in SimpleWntCellCycleModel, SingleOdeWntCellCycleModel, SimpleOxygenBasedCellCycleModel, and ContactInhibitionCellCycleModel.

Definition at line 105 of file AbstractSimplePhaseBasedCellCycleModel.cpp.

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