#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 () const

double	GetBirthTime () const

double	GetAge ()

virtual bool	ReadyToDivide ()=0

virtual void	ResetForDivision ()

virtual AbstractCellCycleModel *	CreateCellCycleModel ()=0

virtual bool	CanCellTerminallyDifferentiate ()

virtual double	GetAverageTransitCellCycleTime ()=0

virtual double	GetAverageStemCellCycleTime ()=0

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 Member Functions
	AbstractCellCycleModel (const AbstractCellCycleModel &rModel)

Protected Attributes
CellPtr	mpCell

double	mBirthTime

bool	mReadyToDivide

unsigned	mDimension

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

AbstractCellCycleModel &	operator= (const AbstractCellCycleModel &)

Friends
class	boost::serialization::access

Detailed Description

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

Cell-cycle models are noncopyable since cells are noncopyable.

Definition at line 61 of file AbstractCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractCellCycleModel::AbstractCellCycleModel ( const AbstractCellCycleModel & 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 AbstractCellCycleModel.cpp.

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 45 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, AbstractWntOdeBasedCellCycleModel, and TysonNovakCellCycleModel.

Definition at line 111 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().

Copy constructors are used to set all the member variables in the appropriate classes.

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

Returns: new cell-cycle model

Implemented in SimpleWntCellCycleModel, SimpleOxygenBasedCellCycleModel, SingleOdeWntCellCycleModel, StochasticOxygenBasedCellCycleModel, ContactInhibitionCellCycleModel, WntCellCycleModel, FixedSequenceCellCycleModel, ExponentialG1GenerationalCellCycleModel, BernoulliTrialCellCycleModel, UniformCellCycleModel, UniformG1GenerationalCellCycleModel, StochasticWntCellCycleModel, TysonNovakCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, GammaG1CellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, FixedG1GenerationalCellCycleModel, and NoCellCycleModel.

Referenced by Cell::Divide().

double AbstractCellCycleModel::GetAge ( )

Returns: the cell's age.

Definition at line 85 of file AbstractCellCycleModel.cpp.

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

Referenced by Cell::GetAge(), AbstractSimpleCellCycleModel::ReadyToDivide(), BernoulliTrialCellCycleModel::ReadyToDivide(), AbstractPhaseBasedCellCycleModel::ReadyToDivide(), AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedPhaseBasedCellCycleModel::UpdateCellCyclePhase().

virtual double AbstractCellCycleModel::GetAverageStemCellCycleTime ( )

pure virtual

Returns: the typical cell cycle duration for a stem cell, in hours.

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

#2788 Consider merging this with GetAverageTransitCellCycleTime to GetAverageCellCycleDuration

Implemented in AbstractPhaseBasedCellCycleModel, BernoulliTrialCellCycleModel, UniformCellCycleModel, AbstractWntOdeBasedCellCycleModel, TysonNovakCellCycleModel, and NoCellCycleModel.

virtual double AbstractCellCycleModel::GetAverageTransitCellCycleTime ( )

pure virtual

Returns: the typical cell cycle duration for a transit cell, in hours.

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

#2788 Consider merging this with GetAverageStemCellCycleTime to GetAverageCellCycleDuration

Implemented in AbstractPhaseBasedCellCycleModel, BernoulliTrialCellCycleModel, UniformCellCycleModel, AbstractWntOdeBasedCellCycleModel, TysonNovakCellCycleModel, and NoCellCycleModel.

double AbstractCellCycleModel::GetBirthTime ( ) const

Returns: the time at which the cell was born.

Definition at line 80 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 69 of file AbstractCellCycleModel.cpp.

References mpCell.

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

unsigned AbstractCellCycleModel::GetDimension ( ) const

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

Definition at line 106 of file AbstractCellCycleModel.cpp.

References mDimension.

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 StochasticWntCellCycleModel, WntCellCycleModel, SingleOdeWntCellCycleModel, AbstractSimpleCellCycleModel, AbstractSimplePhaseBasedCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, and TysonNovakCellCycleModel.

Definition at line 56 of file AbstractCellCycleModel.cpp.

Referenced by TysonNovakCellCycleModel::Initialise(), Alarcon2004OxygenBasedCellCycleModel::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, StochasticWntCellCycleModel, TysonNovakCellCycleModel, AbstractSimpleCellCycleModel, AbstractSimplePhaseBasedCellCycleModel, AbstractSimpleGenerationalCellCycleModel, and StochasticOxygenBasedCellCycleModel.

Definition at line 60 of file AbstractCellCycleModel.cpp.

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

AbstractCellCycleModel& AbstractCellCycleModel::operator= ( const AbstractCellCycleModel & )

private

Prevent copy-assignment of this class, or its subclasses. Note that we do not define this method, therefore statements like "AbstractCellCycleModel new = old;" will not compile. We do not inherit from boost::noncopyable because we *do* define a protected copy-constructor, for use by CreateCellCycleModel.

Returns: the new cell cycle model.

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 116 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 125 of file AbstractCellCycleModel.cpp.

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

virtual bool AbstractCellCycleModel::ReadyToDivide ( )

pure virtual

Returns: whether the cell is ready to divide.

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

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.

Implemented in AbstractPhaseBasedCellCycleModel, AbstractOdeBasedCellCycleModel, BernoulliTrialCellCycleModel, AbstractSimpleCellCycleModel, and NoCellCycleModel.

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 AbstractPhaseBasedCellCycleModel, AbstractOdeBasedPhaseBasedCellCycleModel, AbstractOdeBasedCellCycleModel, StochasticWntCellCycleModel, AbstractWntOdeBasedCellCycleModel, StochasticOxygenBasedCellCycleModel, AbstractSimpleCellCycleModel, TysonNovakCellCycleModel, AbstractSimplePhaseBasedCellCycleModel, AbstractSimpleGenerationalCellCycleModel, and Alarcon2004OxygenBasedCellCycleModel.

Definition at line 90 of file AbstractCellCycleModel.cpp.

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

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

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 ODE Based Cell Cycle Models).

Reimplemented in AbstractOdeBasedPhaseBasedCellCycleModel, and AbstractOdeBasedCellCycleModel.

Definition at line 75 of file AbstractCellCycleModel.cpp.

References mBirthTime.

Referenced by AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel(), AbstractOdeBasedPhaseBasedCellCycleModel::AbstractOdeBasedPhaseBasedCellCycleModel(), AbstractOdeBasedCellCycleModel::SetBirthTime(), AbstractOdeBasedPhaseBasedCellCycleModel::SetBirthTime(), and Cell::SetBirthTime().

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 64 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 97 of file AbstractCellCycleModel.cpp.

References EXCEPTION, mDimension, and UNSIGNED_UNSET.