#include <AbstractPhaseBasedCellCycleModel.hpp>

Inheritance diagram for AbstractPhaseBasedCellCycleModel:

Collaboration diagram for AbstractPhaseBasedCellCycleModel:

Public Member Functions
	AbstractPhaseBasedCellCycleModel ()

virtual	~AbstractPhaseBasedCellCycleModel ()

virtual bool	ReadyToDivide ()

virtual void	ResetForDivision ()

virtual void	UpdateCellCyclePhase ()=0

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)

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)=0

Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()

virtual	~AbstractCellCycleModel ()

void	SetCell (CellPtr pCell)

virtual void	Initialise ()

virtual void	InitialiseDaughterCell ()

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
	AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel)

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

Protected Attributes
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

The AbstractPhaseBasedCellCycleModel contains basic information to all phase based cell-cycle models. It handles assignment of aspects of cell cycle phase.

Definition at line 56 of file AbstractPhaseBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractPhaseBasedCellCycleModel::AbstractPhaseBasedCellCycleModel ( const AbstractPhaseBasedCellCycleModel & 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 56 of file AbstractPhaseBasedCellCycleModel.cpp.

AbstractPhaseBasedCellCycleModel::AbstractPhaseBasedCellCycleModel ( )

Default constructor - creates an AbstractPhaseBasedCellCycleModel.

Definition at line 38 of file AbstractPhaseBasedCellCycleModel.cpp.

AbstractPhaseBasedCellCycleModel::~AbstractPhaseBasedCellCycleModel ( )

virtual

Destructor.

Definition at line 52 of file AbstractPhaseBasedCellCycleModel.cpp.

Member Function Documentation

double AbstractPhaseBasedCellCycleModel::GetAverageStemCellCycleTime ( )

virtual

Returns: the typical cell cycle duration for a stem cell, in hours. This method is overridden in some subclasses.

Implements AbstractCellCycleModel.

Reimplemented in AbstractWntOdeBasedCellCycleModel.

Definition at line 142 of file AbstractPhaseBasedCellCycleModel.cpp.

References GetSG2MDuration(), and mStemCellG1Duration.

double AbstractPhaseBasedCellCycleModel::GetAverageTransitCellCycleTime ( )

virtual

Returns: the typical cell cycle duration for a transit cell, in hours. This method is overridden in some subclasses.

Implements AbstractCellCycleModel.

Reimplemented in AbstractWntOdeBasedCellCycleModel.

Definition at line 137 of file AbstractPhaseBasedCellCycleModel.cpp.

References GetSG2MDuration(), and mTransitCellG1Duration.

CellCyclePhase AbstractPhaseBasedCellCycleModel::GetCurrentCellCyclePhase ( ) const

Returns: the current cell cycle phase

Definition at line 132 of file AbstractPhaseBasedCellCycleModel.cpp.

References mCurrentCellCyclePhase.

double AbstractPhaseBasedCellCycleModel::GetG1Duration ( ) const

virtual

Returns: the duration of the G1 phase of the cell cycle

Definition at line 97 of file AbstractPhaseBasedCellCycleModel.cpp.

References mG1Duration.

Referenced by ReadyToDivide(), SimpleTargetAreaModifier< DIM >::UpdateTargetAreaOfCell(), and TargetAreaLinearGrowthModifier< DIM >::UpdateTargetAreaOfCell().

double AbstractPhaseBasedCellCycleModel::GetG2Duration ( ) const

virtual

Returns: the duration of the G2 phase of the cell cycle mG2Duration

Reimplemented in StochasticWntCellCycleModel, and StochasticOxygenBasedCellCycleModel.

Definition at line 122 of file AbstractPhaseBasedCellCycleModel.cpp.

References mG2Duration.

Referenced by StochasticOxygenBasedCellCycleModel::GenerateStochasticG2Duration(), StochasticWntCellCycleModel::GenerateStochasticG2Duration(), ReadyToDivide(), AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase(), and TargetAreaLinearGrowthModifier< DIM >::UpdateTargetAreaOfCell().

double AbstractPhaseBasedCellCycleModel::GetMDuration ( ) const

virtual

Returns: the duration of the M phase of the cell cycle mMDuration

Definition at line 127 of file AbstractPhaseBasedCellCycleModel.cpp.

References mMDuration.

Referenced by ReadyToDivide(), AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase(), and TargetAreaLinearGrowthModifier< DIM >::UpdateTargetAreaOfCell().

double AbstractPhaseBasedCellCycleModel::GetMinimumGapDuration ( ) const

Returns: mMinimumGapDuration

Definition at line 147 of file AbstractPhaseBasedCellCycleModel.cpp.

References mMinimumGapDuration.

double AbstractPhaseBasedCellCycleModel::GetSDuration ( ) const

virtual

Returns: the duration of the S phase of the cell cycle mSDuration

Definition at line 117 of file AbstractPhaseBasedCellCycleModel.cpp.

References mSDuration.

Referenced by ReadyToDivide(), AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase(), and TargetAreaLinearGrowthModifier< DIM >::UpdateTargetAreaOfCell().

double AbstractPhaseBasedCellCycleModel::GetSG2MDuration ( ) const

Returns: mSDuration + mG2Duration + mMDuration

Definition at line 112 of file AbstractPhaseBasedCellCycleModel.cpp.

References mG2Duration, mMDuration, and mSDuration.

Referenced by GetAverageStemCellCycleTime(), and GetAverageTransitCellCycleTime().

double AbstractPhaseBasedCellCycleModel::GetStemCellG1Duration ( ) const

Returns: mStemCellG1Duration

Definition at line 102 of file AbstractPhaseBasedCellCycleModel.cpp.

References mStemCellG1Duration.

Referenced by AbstractSimplePhaseBasedCellCycleModel::SetG1Duration(), UniformG1GenerationalCellCycleModel::SetG1Duration(), and SimpleWntCellCycleModel::SetG1Duration().

double AbstractPhaseBasedCellCycleModel::GetTransitCellG1Duration ( ) const

Returns: mTransitCellG1Duration

Definition at line 107 of file AbstractPhaseBasedCellCycleModel.cpp.

References mTransitCellG1Duration.

Referenced by AbstractSimplePhaseBasedCellCycleModel::SetG1Duration(), UniformG1GenerationalCellCycleModel::SetG1Duration(), SimpleWntCellCycleModel::SetG1Duration(), and SimpleTargetAreaModifier< DIM >::UpdateTargetAreaOfCell().

void AbstractPhaseBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

pure virtual

Outputs cell cycle model parameters to file.

As this method is pure virtual, it must be overridden in subclasses.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellCycleModel.

Implemented in SimpleWntCellCycleModel, SimpleOxygenBasedCellCycleModel, ContactInhibitionCellCycleModel, SingleOdeWntCellCycleModel, ExponentialG1GenerationalCellCycleModel, FixedSequenceCellCycleModel, AbstractWntOdeBasedCellCycleModel, AbstractOdeBasedPhaseBasedCellCycleModel, StochasticWntCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractSimpleGenerationalCellCycleModel, WntCellCycleModel, GammaG1CellCycleModel, StochasticOxygenBasedCellCycleModel, AbstractSimplePhaseBasedCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, UniformG1GenerationalCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, and FixedG1GenerationalCellCycleModel.

Definition at line 188 of file AbstractPhaseBasedCellCycleModel.cpp.

References mG2Duration, mMDuration, mSDuration, mStemCellG1Duration, mTransitCellG1Duration, and AbstractCellCycleModel::OutputCellCycleModelParameters().

Referenced by AbstractSimplePhaseBasedCellCycleModel::OutputCellCycleModelParameters(), and AbstractOdeBasedPhaseBasedCellCycleModel::OutputCellCycleModelParameters().

bool AbstractPhaseBasedCellCycleModel::ReadyToDivide ( )

virtual

See AbstractCellCycleModel::ResetForDivision()

Returns: whether the cell is ready to divide (enter M phase).

Implements AbstractCellCycleModel.

Definition at line 81 of file AbstractPhaseBasedCellCycleModel.cpp.

References AbstractCellCycleModel::GetAge(), GetG1Duration(), GetG2Duration(), GetMDuration(), GetSDuration(), mCurrentCellCyclePhase, AbstractCellCycleModel::mpCell, AbstractCellCycleModel::mReadyToDivide, and UpdateCellCyclePhase().

void AbstractPhaseBasedCellCycleModel::ResetForDivision ( )

virtual

See AbstractCellCycleModel::ResetForDivision()

Reimplemented from AbstractCellCycleModel.

Reimplemented in AbstractOdeBasedPhaseBasedCellCycleModel, StochasticWntCellCycleModel, AbstractWntOdeBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, AbstractSimplePhaseBasedCellCycleModel, AbstractSimpleGenerationalCellCycleModel, and Alarcon2004OxygenBasedCellCycleModel.

Definition at line 75 of file AbstractPhaseBasedCellCycleModel.cpp.

References mCurrentCellCyclePhase, and AbstractCellCycleModel::ResetForDivision().

Referenced by AbstractSimplePhaseBasedCellCycleModel::ResetForDivision(), and AbstractOdeBasedPhaseBasedCellCycleModel::ResetForDivision().

template<class Archive >

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

inlineprivate

Archive the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 69 of file AbstractPhaseBasedCellCycleModel.hpp.

References mCurrentCellCyclePhase, mG1Duration, mG2Duration, mMDuration, mMinimumGapDuration, mSDuration, mStemCellG1Duration, and mTransitCellG1Duration.

void AbstractPhaseBasedCellCycleModel::SetG2Duration ( double g2Duration )

Set mG2Duration.

Parameters

g2Duration the new value of mG2Duration

Definition at line 170 of file AbstractPhaseBasedCellCycleModel.cpp.

References mG2Duration.

void AbstractPhaseBasedCellCycleModel::SetMDuration ( double mDuration )

Set mMDuration.

Parameters

mDuration the new value of mMDuration

Definition at line 176 of file AbstractPhaseBasedCellCycleModel.cpp.

References mMDuration.

void AbstractPhaseBasedCellCycleModel::SetMinimumGapDuration ( double minimumGapDuration )

Set mMinimumGapDuration

Parameters

minimumGapDuration the new value of mMinimumGapDuration

Definition at line 182 of file AbstractPhaseBasedCellCycleModel.cpp.

References mMinimumGapDuration.

void AbstractPhaseBasedCellCycleModel::SetSDuration ( double sDuration )

Set mSDuration.

Parameters

sDuration the new value of mSDuration

Definition at line 164 of file AbstractPhaseBasedCellCycleModel.cpp.

References mSDuration.

void AbstractPhaseBasedCellCycleModel::SetStemCellG1Duration ( double stemCellG1Duration )

virtual

Set mStemCellG1Duration.

Parameters

stemCellG1Duration the new value of mStemCellG1Duration

Reimplemented in ExponentialG1GenerationalCellCycleModel, and FixedSequenceCellCycleModel.

Definition at line 152 of file AbstractPhaseBasedCellCycleModel.cpp.

References mStemCellG1Duration.

void AbstractPhaseBasedCellCycleModel::SetTransitCellG1Duration ( double transitCellG1Duration )

virtual

Set mTransitCellG1Duration.

Parameters

transitCellG1Duration the new value of mTransitCellG1Duration

Reimplemented in ExponentialG1GenerationalCellCycleModel, and FixedSequenceCellCycleModel.

Definition at line 158 of file AbstractPhaseBasedCellCycleModel.cpp.

References mTransitCellG1Duration.

virtual void AbstractPhaseBasedCellCycleModel::UpdateCellCyclePhase ( )

pure virtual

Set the phase the cell-cycle model is currently in. This method is called from ReadyToDivide() just prior to deciding whether to divide the cell, based on how far through the cell cycle it is, i.e. whether it has completed M, G1, S and G2 phases.

As this method is pure virtual, it must be overridden in subclasses.

Implemented in SimpleWntCellCycleModel, SingleOdeWntCellCycleModel, SimpleOxygenBasedCellCycleModel, AbstractOdeBasedPhaseBasedCellCycleModel, ContactInhibitionCellCycleModel, AbstractSimplePhaseBasedCellCycleModel, and AbstractWntOdeBasedCellCycleModel.

Referenced by ReadyToDivide().