AbstractCellCycleModel Class Reference

#include <AbstractCellCycleModel.hpp>

Inheritance diagram for AbstractCellCycleModel:

Collaboration diagram for AbstractCellCycleModel:

List of all members.

Public Member Functions

AbstractCellCycleModel ()

virtual ~AbstractCellCycleModel ()

void SetCell (TissueCell *pCell)

virtual void Initialise ()

virtual void InitialiseDaughterCell ()

TissueCell * GetCell ()

virtual void SetBirthTime (double birthTime)

double GetBirthTime () const

double GetAge ()

bool ReadyToDivide ()

virtual void UpdateCellCyclePhase ()=0

virtual void ResetForDivision ()

virtual AbstractCellCycleModel * CreateCellCycleModel ()=0

CellCyclePhase GetCurrentCellCyclePhase ()

virtual double GetG1Duration ()

virtual double GetSDuration ()

virtual double GetG2Duration ()

virtual double GetMDuration ()

Protected Attributes

TissueCell * mpCell

double mBirthTime

CellCyclePhase mCurrentCellCyclePhase

double mG1Duration

bool mReadyToDivide

Private Member Functions

template<class Archive>

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

AbstractCellCycleModel & operator= (const AbstractCellCycleModel &rOtherModel)

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 TissueCell.

Definition at line 54 of file AbstractCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractCellCycleModel::AbstractCellCycleModel ( )

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

Definition at line 31 of file AbstractCellCycleModel.cpp.

AbstractCellCycleModel::~AbstractCellCycleModel ( ) [virtual]

Base class with virtual methods needs a virtual destructor.

Definition at line 41 of file AbstractCellCycleModel.cpp.

Member Function Documentation

template<class Archive>

void AbstractCellCycleModel::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Archive the member variables.

Serialization of singleton objects must be done with care. Before the object is serialized via a pointer, it *MUST* be serialized directly, or an assertion will trip when a second instance of the class is created on de-serialization.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented in AbstractOdeBasedCellCycleModel, AbstractSimpleCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, AbstractWntOdeBasedCellCycleModel, FixedDurationGenerationBasedCellCycleModel, IngeWntSwatCellCycleModel, SimpleWntCellCycleModel, StochasticDurationGenerationBasedCellCycleModel, StochasticWntCellCycleModel, TysonNovakCellCycleModel, and WntCellCycleModel.

Definition at line 72 of file AbstractCellCycleModel.hpp.

References TissueConfig::Instance(), SimulationTime::Instance(), mBirthTime, mCurrentCellCyclePhase, mG1Duration, and mReadyToDivide.

AbstractCellCycleModel& AbstractCellCycleModel::operator= ( const AbstractCellCycleModel & rOtherModel ) [private]

Assignment operator has no definition and can't be called. This is to prevent running the default assignment operator.

Parameters:

rOtherModel

the cell cycle model being copied.

void AbstractCellCycleModel::SetCell ( TissueCell * pCell )

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

Some cell cycle models pass this pointer to other classes (e.g. WntConcentration), 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 49 of file AbstractCellCycleModel.cpp.

References mpCell.

Referenced by TissueCell::CommonCopy(), TissueCell::SetCellCycleModel(), and TissueCell::TissueCell().

virtual void AbstractCellCycleModel::Initialise ( void ) [inline, 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 tissue. It is not called on cell division; use ResetForDivision(), CreateCellCycleModel() and InitialiseDaughterCell() for that.

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

Reimplemented in AbstractSimpleCellCycleModel, IngeWntSwatCellCycleModel, StochasticWntCellCycleModel, and WntCellCycleModel.

Definition at line 158 of file AbstractCellCycleModel.hpp.

Referenced by TissueCell::InitialiseCellCycleModel().

virtual void AbstractCellCycleModel::InitialiseDaughterCell ( ) [inline, virtual]

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

This is called by TissueCell::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 AbstractSimpleCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, SimpleWntCellCycleModel, StochasticWntCellCycleModel, and TysonNovakCellCycleModel.

Definition at line 173 of file AbstractCellCycleModel.hpp.

Referenced by TissueCell::Divide(), and AbstractSimpleCellCycleModel::InitialiseDaughterCell().

TissueCell * AbstractCellCycleModel::GetCell ( )

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

Definition at line 55 of file AbstractCellCycleModel.cpp.

References mpCell.

Referenced by MeshBasedTissue< DIM >::CheckTissueCellPointers().

void AbstractCellCycleModel::SetBirthTime ( double birthTime ) [virtual]

Set the cell's time of birth (usually not required as it should be inside the indivdual 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 62 of file AbstractCellCycleModel.cpp.

References mBirthTime.

Referenced by AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel(), TissueCell::SetBirthTime(), and AbstractOdeBasedCellCycleModel::SetBirthTime().

double AbstractCellCycleModel::GetBirthTime ( ) const

Returns:: the time at which the cell was born.

Definition at line 68 of file AbstractCellCycleModel.cpp.

References mBirthTime.

Referenced by TissueCell::GetBirthTime().

double AbstractCellCycleModel::GetAge ( )

Returns the cell's age.

Definition at line 74 of file AbstractCellCycleModel.cpp.

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

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

bool AbstractCellCycleModel::ReadyToDivide ( )

Determine 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 118 of file AbstractCellCycleModel.cpp.

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

Referenced by TissueCell::ReadyToDivide().

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 AbstractOdeBasedCellCycleModel, AbstractSimpleCellCycleModel, and SimpleWntCellCycleModel.

Referenced by 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 TissueCell::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, AbstractSimpleCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, AbstractWntOdeBasedCellCycleModel, SimpleWntCellCycleModel, StochasticWntCellCycleModel, and TysonNovakCellCycleModel.

Definition at line 86 of file AbstractCellCycleModel.cpp.

References mCurrentCellCyclePhase, and mReadyToDivide.

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

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 the copy constructor and operator= of TissueCell to create a copy of the cell cycle model when copying a cell. It thus needs to create an instance of the right class which is an exact copy of this instance.

This method is also called by TissueCell::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().

It is suggested to implement this method using the copy constructor, for example: return new TysonNovakCellCycleModel(*this); If any special copying behaviour is required, a suitable copy constructor can then be written (which you should have done anyway, of course).

Note:: This base class does not define a copy constructor, despite the fact that it contains a pointer to a TissueCell. This is OK because the TissueCell is not deleted by our destructor, and in all cases where the copy constructor is used either the original object is immediately destroyed, or the copy is assigned to a new cell.

Implemented in FixedDurationGenerationBasedCellCycleModel, IngeWntSwatCellCycleModel, SimpleWntCellCycleModel, StochasticDurationGenerationBasedCellCycleModel, StochasticWntCellCycleModel, TysonNovakCellCycleModel, and WntCellCycleModel.

Referenced by TissueCell::CommonCopy(), and TissueCell::Divide().

CellCyclePhase AbstractCellCycleModel::GetCurrentCellCyclePhase ( )

Returns:: the current cell cycle phase

Definition at line 80 of file AbstractCellCycleModel.cpp.

References mCurrentCellCyclePhase.

Referenced by AbstractTissue< DIM >::GenerateCellResults().

double AbstractCellCycleModel::GetG1Duration ( ) [virtual]

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

Definition at line 100 of file AbstractCellCycleModel.cpp.

References mG1Duration.

Referenced by ReadyToDivide().

double AbstractCellCycleModel::GetSDuration ( ) [virtual]

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

Reimplemented in TysonNovakCellCycleModel.

Definition at line 94 of file AbstractCellCycleModel.cpp.

References TissueConfig::GetSDuration(), and TissueConfig::Instance().

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

double AbstractCellCycleModel::GetG2Duration ( ) [virtual]

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

Reimplemented in StochasticWntCellCycleModel, and TysonNovakCellCycleModel.

Definition at line 106 of file AbstractCellCycleModel.cpp.

References TissueConfig::GetG2Duration(), and TissueConfig::Instance().

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

double AbstractCellCycleModel::GetMDuration ( ) [virtual]

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

Reimplemented in TysonNovakCellCycleModel.

Definition at line 112 of file AbstractCellCycleModel.cpp.

References TissueConfig::GetMDuration(), and TissueConfig::Instance().

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

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented in AbstractOdeBasedCellCycleModel, AbstractSimpleCellCycleModel, AbstractSimpleGenerationBasedCellCycleModel, AbstractWntOdeBasedCellCycleModel, FixedDurationGenerationBasedCellCycleModel, IngeWntSwatCellCycleModel, SimpleWntCellCycleModel, StochasticDurationGenerationBasedCellCycleModel, StochasticWntCellCycleModel, TysonNovakCellCycleModel, and WntCellCycleModel.

Definition at line 59 of file AbstractCellCycleModel.hpp.

Member Data Documentation

TissueCell* AbstractCellCycleModel::mpCell [protected]

The cell that this model is associated with.

Definition at line 101 of file AbstractCellCycleModel.hpp.

Referenced by WntCellCycleModel::ChangeCellTypeDueToCurrentBetaCateninLevel(), IngeWntSwatCellCycleModel::ChangeCellTypeDueToCurrentBetaCateninLevel(), GetCell(), SimpleWntCellCycleModel::GetWntLevel(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), WntCellCycleModel::Initialise(), IngeWntSwatCellCycleModel::Initialise(), TysonNovakCellCycleModel::InitialiseDaughterCell(), SimpleWntCellCycleModel::InitialiseDaughterCell(), AbstractSimpleGenerationBasedCellCycleModel::InitialiseDaughterCell(), ReadyToDivide(), AbstractSimpleGenerationBasedCellCycleModel::ResetForDivision(), SetCell(), StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), SimpleWntCellCycleModel::SetG1Duration(), AbstractSimpleCellCycleModel::SetG1Duration(), WntCellCycleModel::SolveOdeToTime(), IngeWntSwatCellCycleModel::SolveOdeToTime(), SimpleWntCellCycleModel::UpdateCellCyclePhase(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), and AbstractWntOdeBasedCellCycleModel::UpdateCellType().

double AbstractCellCycleModel::mBirthTime [protected]

The time that the cell began to split from its parent (i.e. beginning of M phase NOT the end)

Definition at line 107 of file AbstractCellCycleModel.hpp.

Referenced by GetAge(), GetBirthTime(), AbstractSimpleCellCycleModel::ResetForDivision(), AbstractOdeBasedCellCycleModel::ResetForDivision(), serialize(), SetBirthTime(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().

CellCyclePhase AbstractCellCycleModel::mCurrentCellCyclePhase [protected]

The phase of the cell cycle that this model is in (specified in CellCyclePhases.hpp)

Definition at line 110 of file AbstractCellCycleModel.hpp.

Referenced by GetCurrentCellCyclePhase(), ReadyToDivide(), ResetForDivision(), serialize(), SimpleWntCellCycleModel::UpdateCellCyclePhase(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().

double AbstractCellCycleModel::mG1Duration [protected]

How long the G1 phase lasts for. Not necessarily a fixed value.

Definition at line 116 of file AbstractCellCycleModel.hpp.

Referenced by GetG1Duration(), AbstractOdeBasedCellCycleModel::ResetForDivision(), serialize(), StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), SimpleWntCellCycleModel::SetG1Duration(), AbstractSimpleCellCycleModel::SetG1Duration(), AbstractSimpleCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().

bool AbstractCellCycleModel::mReadyToDivide [protected]

Whether the cell is currently ready to undergo division.

Definition at line 121 of file AbstractCellCycleModel.hpp.

Referenced by ReadyToDivide(), ResetForDivision(), and serialize().

The documentation for this class was generated from the following files:

/tmp/release_1.1/cancer/src/tissue/cell/cycle/AbstractCellCycleModel.hpp
/tmp/release_1.1/cancer/src/tissue/cell/cycle/AbstractCellCycleModel.cpp


Public Member Functions
	AbstractCellCycleModel ()
virtual	~AbstractCellCycleModel ()
void	SetCell (TissueCell *pCell)
virtual void	Initialise ()
virtual void	InitialiseDaughterCell ()
TissueCell *	GetCell ()
virtual void	SetBirthTime (double birthTime)
double	GetBirthTime () const
double	GetAge ()
bool	ReadyToDivide ()
virtual void	UpdateCellCyclePhase ()=0
virtual void	ResetForDivision ()
virtual AbstractCellCycleModel *	CreateCellCycleModel ()=0
CellCyclePhase	GetCurrentCellCyclePhase ()
virtual double	GetG1Duration ()
virtual double	GetSDuration ()
virtual double	GetG2Duration ()
virtual double	GetMDuration ()
Protected Attributes
TissueCell *	mpCell
double	mBirthTime
CellCyclePhase	mCurrentCellCyclePhase
double	mG1Duration
bool	mReadyToDivide
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
AbstractCellCycleModel &	operator= (const AbstractCellCycleModel &rOtherModel)
Friends
class	boost::serialization::access