#include <AbstractCellCycleModel.hpp>

Inheritance diagram for AbstractCellCycleModel:

Collaboration diagram for AbstractCellCycleModel:

Public Member Functions
	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 ()

double	GetBirthTime () const

double	GetAge ()

virtual bool	ReadyToDivide ()

virtual void	UpdateCellCyclePhase ()=0

virtual void	ResetForDivision ()

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)

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)=0

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Attributes
CellPtr	mpCell

double	mBirthTime

CellCyclePhase	mCurrentCellCyclePhase

double	mG1Duration

bool	mReadyToDivide

unsigned	mDimension

double	mMinimumGapDuration

double	mStemCellG1Duration

double	mTransitCellG1Duration

double	mSDuration

double	mG2Duration

double	mMDuration

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

Friends
class	boost::serialization::access

Detailed Description

The AbstractCellCycleModel contains basic information to all cell-cycle models. It handles assignment of birth time, cell cycle phase and a Cell.

Cell-cycle models are noncopyable since cells are noncopyable.

Definition at line 61 of file AbstractCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractCellCycleModel::AbstractCellCycleModel ( )

Sets up a new AbstractCellCycleModel, gives it a birth time of the present simulation time (which is overwritten by some subclasses)

Definition at line 38 of file AbstractCellCycleModel.cpp.

AbstractCellCycleModel::~AbstractCellCycleModel ( )

virtual

Base class with virtual methods needs a virtual destructor. The destructor does not delete mpCell. Instead, the cell takes responsibility for deleting the cell-cycle model when it is destroyed.

Definition at line 54 of file AbstractCellCycleModel.cpp.

Member Function Documentation

bool AbstractCellCycleModel::CanCellTerminallyDifferentiate ( )

virtual

Returns: whether a cell with this cell-cycle model is able to fully (terminally) differentiate.

Reimplemented in SimpleWntCellCycleModel, TysonNovakCellCycleModel, and AbstractWntOdeBasedCellCycleModel.

Definition at line 213 of file AbstractCellCycleModel.cpp.

virtual AbstractCellCycleModel* AbstractCellCycleModel::CreateCellCycleModel ( )

pure virtual

Builder method to create new instances of the cell-cycle model. Each concrete subclass must implement this method to create an instance of that subclass.

This method is called by Cell::Divide() to create a cell cycle model for the daughter cell. 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().

Returns: new cell-cycle model

Implemented in SimpleWntCellCycleModel, SimpleOxygenBasedCellCycleModel, SingleOdeWntCellCycleModel, ContactInhibitionCellCycleModel, StochasticOxygenBasedCellCycleModel, ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel, WntCellCycleModel, TysonNovakCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, StochasticWntCellCycleModel, StochasticDurationCellCycleModel, GammaDistributedStochasticDurationCellCycleModel, StochasticDurationGenerationBasedCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, and FixedDurationGenerationBasedCellCycleModel.

Referenced by Cell::Divide().

double AbstractCellCycleModel::GetAge ( )

Returns: the cell's age.

Definition at line 87 of file AbstractCellCycleModel.cpp.

References SimulationTime::GetTime(), SimulationTime::Instance(), and mBirthTime.

Referenced by Cell::GetAge(), ReadyToDivide(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().

double AbstractCellCycleModel::GetAverageStemCellCycleTime ( )

virtual

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

Reimplemented in TysonNovakCellCycleModel, and AbstractWntOdeBasedCellCycleModel.

Definition at line 208 of file AbstractCellCycleModel.cpp.

References GetSG2MDuration(), and mStemCellG1Duration.

double AbstractCellCycleModel::GetAverageTransitCellCycleTime ( )

virtual

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

Reimplemented in TysonNovakCellCycleModel, and AbstractWntOdeBasedCellCycleModel.

Definition at line 203 of file AbstractCellCycleModel.cpp.

References GetSG2MDuration(), and mTransitCellG1Duration.

double AbstractCellCycleModel::GetBirthTime ( ) const

Returns: the time at which the cell was born.

Definition at line 82 of file AbstractCellCycleModel.cpp.

References mBirthTime.

Referenced by Cell::GetBirthTime().

CellPtr AbstractCellCycleModel::GetCell ( )

Returns: The cell which plays host to this cell-cycle model.

Definition at line 71 of file AbstractCellCycleModel.cpp.

References mpCell.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers().

CellCyclePhase AbstractCellCycleModel::GetCurrentCellCyclePhase ( )

Returns: the current cell cycle phase

Definition at line 92 of file AbstractCellCycleModel.cpp.

References mCurrentCellCyclePhase.

unsigned AbstractCellCycleModel::GetDimension ( )

Returns: the dimension this cell-cycle model thinks the simulation is in.

Definition at line 198 of file AbstractCellCycleModel.cpp.

References mDimension.

double AbstractCellCycleModel::GetG1Duration ( )

virtual

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

Definition at line 104 of file AbstractCellCycleModel.cpp.

References mG1Duration.

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

double AbstractCellCycleModel::GetG2Duration ( )

virtual

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

Reimplemented in StochasticWntCellCycleModel, TysonNovakCellCycleModel, and StochasticOxygenBasedCellCycleModel.

Definition at line 133 of file AbstractCellCycleModel.cpp.

References mG2Duration.

Referenced by StochasticOxygenBasedCellCycleModel::GenerateStochasticG2Duration(), StochasticWntCellCycleModel::GenerateStochasticG2Duration(), ReadyToDivide(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), and FarhadifarTypeModifier< DIM >::UpdateTargetAreaOfCell().

double AbstractCellCycleModel::GetMDuration ( )

virtual

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

Reimplemented in TysonNovakCellCycleModel.

Definition at line 138 of file AbstractCellCycleModel.cpp.

References mMDuration.

Referenced by ReadyToDivide(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), and FarhadifarTypeModifier< DIM >::UpdateTargetAreaOfCell().

double AbstractCellCycleModel::GetMinimumGapDuration ( )

Returns: mMinimumGapDuration

Definition at line 224 of file AbstractCellCycleModel.cpp.

References mMinimumGapDuration.

double AbstractCellCycleModel::GetSDuration ( )

virtual

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

Reimplemented in TysonNovakCellCycleModel.

Definition at line 128 of file AbstractCellCycleModel.cpp.

References mSDuration.

Referenced by ReadyToDivide(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), and FarhadifarTypeModifier< DIM >::UpdateTargetAreaOfCell().

double AbstractCellCycleModel::GetSG2MDuration ( )

Returns: mSDuration + mG2Duration + mMDuration

Definition at line 123 of file AbstractCellCycleModel.cpp.

References mG2Duration, mMDuration, and mSDuration.

Referenced by GetAverageStemCellCycleTime(), and GetAverageTransitCellCycleTime().

double AbstractCellCycleModel::GetStemCellG1Duration ( )

Returns: mStemCellG1Duration

Definition at line 113 of file AbstractCellCycleModel.cpp.

References mStemCellG1Duration.

Referenced by StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), AbstractSimpleCellCycleModel::SetG1Duration(), StochasticDurationCellCycleModel::SetG1Duration(), and SimpleWntCellCycleModel::SetG1Duration().

double AbstractCellCycleModel::GetTransitCellG1Duration ( )

Returns: mTransitCellG1Duration

Definition at line 118 of file AbstractCellCycleModel.cpp.

References mTransitCellG1Duration.

Referenced by StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), AbstractSimpleCellCycleModel::SetG1Duration(), StochasticDurationCellCycleModel::SetG1Duration(), and SimpleWntCellCycleModel::SetG1Duration().

void AbstractCellCycleModel::Initialise ( void )

virtual

Initialise the cell-cycle model at the start of a simulation.

This method will be called precisely once per cell set up in the initial cell population. It is not called on cell division; use ResetForDivision(), CreateCellCycleModel() and InitialiseDaughterCell() for that.

By the time this is called, a CellPopulation will have been set up, so the model can know where its cell is located in space. If relevant to the simulation, any singletons will also have been initialised.

Reimplemented in WntCellCycleModel, StochasticWntCellCycleModel, SingleOdeWntCellCycleModel, AbstractSimpleCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, and TysonNovakCellCycleModel.

Definition at line 58 of file AbstractCellCycleModel.cpp.

Referenced by TysonNovakCellCycleModel::Initialise(), and Cell::InitialiseCellCycleModel().

void AbstractCellCycleModel::InitialiseDaughterCell ( )

virtual

Initialise the new daughter cell's cycle model after a cell division.

This is called by Cell::Divide once the new cell object has been fully created, to perform any initialisation of the cell cycle which requires access to the cell.

Note that much initialisation can be performed using the combination of ResetForDivision() (called on the parent prior to division) and CreateCellCycleModel() (called on the reset parent to create the new cell-cycle model object).

Reimplemented in SimpleWntCellCycleModel, TysonNovakCellCycleModel, AbstractSimpleCellCycleModel, StochasticWntCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, and StochasticOxygenBasedCellCycleModel.

Definition at line 62 of file AbstractCellCycleModel.cpp.

Referenced by AbstractSimpleCellCycleModel::InitialiseDaughterCell(), and StochasticWntCellCycleModel::InitialiseDaughterCell().

void AbstractCellCycleModel::OutputCellCycleModelInfo ( out_stream & rParamsFile )

Outputs cell-cycle model used in the simulation to file and then calls OutputCellCyclemodelParameters to output all relevant parameters.

Parameters

rParamsFile the file stream to which the parameters are output

Definition at line 229 of file AbstractCellCycleModel.cpp.

References Identifiable::GetIdentifier(), and OutputCellCycleModelParameters().

void AbstractCellCycleModel::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

Definition at line 238 of file AbstractCellCycleModel.cpp.

References mG2Duration, mMDuration, mSDuration, mStemCellG1Duration, and mTransitCellG1Duration.

Referenced by OutputCellCycleModelInfo(), AbstractSimpleCellCycleModel::OutputCellCycleModelParameters(), and AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters().

bool AbstractCellCycleModel::ReadyToDivide ( )

virtual

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

The intention is that this method is called precisely once at each timestep of the simulation. However this does not appear to always be the case at present, and so it can cope with more unusual usage patterns.

Definition at line 173 of file AbstractCellCycleModel.cpp.

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

Referenced by Cell::ReadyToDivide().

void AbstractCellCycleModel::ResetForDivision ( )

virtual

Each cell-cycle model must be able to be reset 'after' a cell division.

Actually, this method is called from Cell::Divide() to reset the cell cycle just before the daughter cell is created. CreateCellCycleModel() can then clone our state to generate a cell-cycle model instance for the daughter cell.

Reimplemented in AbstractOdeBasedCellCycleModel, StochasticWntCellCycleModel, AbstractWntOdeBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractSimpleCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, and AbstractSimpleGenerationBasedCellCycleModel.

Definition at line 97 of file AbstractCellCycleModel.cpp.

References mCurrentCellCyclePhase, and mReadyToDivide.

Referenced by Cell::Divide(), AbstractSimpleCellCycleModel::ResetForDivision(), and AbstractOdeBasedCellCycleModel::ResetForDivision().

template<class Archive >

void AbstractCellCycleModel::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 74 of file AbstractCellCycleModel.hpp.

References SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), SimulationTime::Instance(), mBirthTime, mCurrentCellCyclePhase, mDimension, mG1Duration, mG2Duration, mMDuration, mMinimumGapDuration, mReadyToDivide, mSDuration, mStemCellG1Duration, and mTransitCellG1Duration.

void AbstractCellCycleModel::SetBirthTime ( double birthTime )

virtual

Set the cell's time of birth (usually not required as it should be inside the individual cell-cycle-model-constructor, but useful for tests).

Parameters

birthTime the simulation time at this cell's birth.

(This function is overridden in AbstractOdeBasedCellCycleModel).

Reimplemented in AbstractOdeBasedCellCycleModel.

Definition at line 77 of file AbstractCellCycleModel.cpp.

References mBirthTime.

void AbstractCellCycleModel::SetCell ( CellPtr pCell )

Gives the cell-cycle model a pointer to its host cell.

Some cell-cycle models pass this pointer to other classes, which use this information to determine other information based upon the location of the cell (e.g. the Wnt concentration at this location).

Parameters

pCell pointer to the cell

Definition at line 66 of file AbstractCellCycleModel.cpp.

References mpCell.

Referenced by Cell::Cell(), and Cell::SetCellCycleModel().

void AbstractCellCycleModel::SetDimension ( unsigned dimension )

Set the spatial dimension.

Parameters

dimension

Definition at line 189 of file AbstractCellCycleModel.cpp.

References EXCEPTION, and mDimension.

void AbstractCellCycleModel::SetG2Duration ( double g2Duration )

Set mG2Duration.

Parameters

g2Duration the new value of mG2Duration

Definition at line 162 of file AbstractCellCycleModel.cpp.

References mG2Duration.

void AbstractCellCycleModel::SetMDuration ( double mDuration )

Set mMDuration.

Parameters

mDuration the new value of mMDuration

Definition at line 167 of file AbstractCellCycleModel.cpp.

References mMDuration.

void AbstractCellCycleModel::SetMinimumGapDuration ( double minimumGapDuration )

Set mMinimumGapDuration.

Parameters

minimumGapDuration the new value of mMinimumGapDuration

Definition at line 218 of file AbstractCellCycleModel.cpp.

References mMinimumGapDuration.

void AbstractCellCycleModel::SetSDuration ( double sDuration )

Set mSDuration.

Parameters

sDuration the new value of mSDuration

Definition at line 157 of file AbstractCellCycleModel.cpp.

References mSDuration.

void AbstractCellCycleModel::SetStemCellG1Duration ( double stemCellG1Duration )

virtual

Set mStemCellG1Duration.

Parameters

stemCellG1Duration the new value of mStemCellG1Duration

Reimplemented in ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.

Definition at line 147 of file AbstractCellCycleModel.cpp.

References mStemCellG1Duration.

void AbstractCellCycleModel::SetTransitCellG1Duration ( double transitCellG1Duration )

virtual

Set mTransitCellG1Duration.

Parameters

transitCellG1Duration the new value of mTransitCellG1Duration

Reimplemented in ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.

Definition at line 152 of file AbstractCellCycleModel.cpp.

References mTransitCellG1Duration.

virtual void AbstractCellCycleModel::UpdateCellCyclePhase ( )

pure virtual

This method must be implemented by subclasses in order to set the phase the cell-cycle model is currently in. It 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.

Implemented in SimpleWntCellCycleModel, SingleOdeWntCellCycleModel, AbstractOdeBasedCellCycleModel, SimpleOxygenBasedCellCycleModel, ContactInhibitionCellCycleModel, AbstractSimpleCellCycleModel, and AbstractWntOdeBasedCellCycleModel.

Referenced by ReadyToDivide().