WntCellCycleModel Class Reference

#include <WntCellCycleModel.hpp>

Inheritance diagram for WntCellCycleModel:

Collaboration diagram for WntCellCycleModel:

List of all members.

Public Member Functions

WntCellCycleModel (unsigned dimension)

WntCellCycleModel (const WntCellCycleModel &rOtherModel)

WntCellCycleModel (AbstractOdeSystem *pParentOdeSystem, const CellMutationState &rMutationState, double birthTime, double lastTime, bool inSG2MPhase, bool readyToDivide, double divideTime, unsigned dimension)

WntCellCycleModel (const std::vector< double > &rParentProteinConcentrations, const CellMutationState &rMutationState, const unsigned &rDimension)

AbstractCellCycleModel * CreateCellCycleModel ()

void Initialise ()

bool SolveOdeToTime (double currentTime)

Private Member Functions

template<class Archive>

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

void ChangeCellTypeDueToCurrentBetaCateninLevel ()

Friends

class boost::serialization::access

Detailed Description

Wnt-dependent cell cycle model. Needs to operate with a WntConcentration singleton object.

This model has a constant length M phase, runs ODEs to decide when to finish G1 phase then adds time for S and G2 phases. The CellType is updated dependent on the concentration of beta-catenin (given by one of the ODEs).

Note that this class uses C++'s default copying semantics, and so doesn't implement a copy constructor or operator=.

Definition at line 56 of file WntCellCycleModel.hpp.

Constructor & Destructor Documentation

WntCellCycleModel::WntCellCycleModel ( unsigned dimension ) [inline]

Default constructor.

Parameters:

dimension

the spatial dimension

Definition at line 91 of file WntCellCycleModel.hpp.

Referenced by CreateCellCycleModel().

WntCellCycleModel::WntCellCycleModel ( const WntCellCycleModel & rOtherModel )

Copy constructor.

Also copies our ODE system.

Parameters:

rOtherModel

the instance being copied.

Definition at line 30 of file WntCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::mpOdeSystem.

WntCellCycleModel::WntCellCycleModel	(	AbstractOdeSystem *	pParentOdeSystem,
		const CellMutationState &	rMutationState,
		double	birthTime,
		double	lastTime,
		bool	inSG2MPhase,
		bool	readyToDivide,
		double	divideTime,
		unsigned	dimension
	)

A private constructor for daughter cells called by the CreateDaughterCellCycleModel function (which can be called by TissueCell::CommonCopy() and isn't necessarily being born.

Parameters:

	pParentOdeSystem	to copy the state of
	rMutationState	the mutation state of the cell (used by ODEs)
	birthTime	the simulation time when the cell divided (birth time of parent cell)
	lastTime	last time the cell cycle model was evaluated
	inSG2MPhase	whether the cell is in S-G2-M (not evaluating ODEs and just waiting)
	readyToDivide	whether the cell is ready to divide
	divideTime	if in the future this is the time at which the cell is going to divide
	dimension	the spatial dimension

WntCellCycleModel::WntCellCycleModel	(	const std::vector< double > &	rParentProteinConcentrations,
		const CellMutationState &	rMutationState,
		const unsigned &	rDimension
	)

A private constructor for archiving.

Parameters:

	rParentProteinConcentrations	a std::vector of doubles of the protein concentrations (see WntCellCycleOdeSystem)
	rMutationState	the mutation state of the cell (used by ODEs)
	rDimension	the spatial dimension

Definition at line 41 of file WntCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::mpOdeSystem, and AbstractOdeSystem::rGetStateVariables().

Member Function Documentation

template<class Archive>

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

Archive the cell cycle model, never used directly - boost uses this.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractWntOdeBasedCellCycleModel.

Reimplemented in StochasticWntCellCycleModel.

Definition at line 62 of file WntCellCycleModel.hpp.

References AbstractOdeBasedCellCycleModel::mpOdeSystem.

void WntCellCycleModel::ChangeCellTypeDueToCurrentBetaCateninLevel ( ) [private, virtual]

Update the cell type according to the current beta catenin level as given by the WntCellCycleOdeSystem.

This method carries out the work for UpdateCellType(), but does not check the current time, so can also be called by Initialise().

Implements AbstractWntOdeBasedCellCycleModel.

Definition at line 59 of file WntCellCycleModel.cpp.

References AbstractCellCycleModel::mpCell, AbstractOdeBasedCellCycleModel::mpOdeSystem, AbstractOdeSystem::rGetStateVariables(), and TissueCell::SetCellType().

Referenced by Initialise().

AbstractCellCycleModel * WntCellCycleModel::CreateCellCycleModel ( ) [virtual]

Overridden builder method to create new copies of this cell cycle model.

Implements AbstractCellCycleModel.

Reimplemented in StochasticWntCellCycleModel.

Definition at line 53 of file WntCellCycleModel.cpp.

References WntCellCycleModel().

void WntCellCycleModel::Initialise ( void ) [virtual]

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

This overridden method sets up a new WntCellCycleOdeSystem and sets the cell type according to the current beta catenin level.

Reimplemented from AbstractCellCycleModel.

Reimplemented in StochasticWntCellCycleModel.

Definition at line 77 of file WntCellCycleModel.cpp.

References ChangeCellTypeDueToCurrentBetaCateninLevel(), AbstractOdeSystem::GetInitialConditions(), TissueCell::GetMutationState(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, AbstractOdeBasedCellCycleModel::mpOdeSystem, and AbstractOdeSystem::SetStateVariables().

Referenced by StochasticWntCellCycleModel::Initialise().

bool WntCellCycleModel::SolveOdeToTime ( double currentTime ) [virtual]

Solve the ODEs up to the current time and return whether a stopping event occurred.

Parameters:

currentTime

the current time

Returns:: whether a stopping event occured

Implements AbstractOdeBasedCellCycleModel.

Definition at line 91 of file WntCellCycleModel.cpp.

References TissueCell::GetMutationState(), SimulationTime::GetTimeStep(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), SimulationTime::Instance(), AbstractOdeBasedCellCycleModel::mLastTime, AbstractCellCycleModel::mpCell, AbstractOdeBasedCellCycleModel::mpOdeSystem, AbstractWntOdeBasedCellCycleModel::msSolver, AbstractOdeSystem::rGetStateVariables(), AbstractIvpOdeSolver::SolveAndUpdateStateVariable(), AbstractIvpOdeSolver::StoppingEventOccurred(), and AbstractWntOdeBasedCellCycleModel::UpdateCellType().

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractWntOdeBasedCellCycleModel.

Reimplemented in StochasticWntCellCycleModel.

Definition at line 60 of file WntCellCycleModel.hpp.

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

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


Public Member Functions
	WntCellCycleModel (unsigned dimension)
	WntCellCycleModel (const WntCellCycleModel &rOtherModel)
	WntCellCycleModel (AbstractOdeSystem *pParentOdeSystem, const CellMutationState &rMutationState, double birthTime, double lastTime, bool inSG2MPhase, bool readyToDivide, double divideTime, unsigned dimension)
	WntCellCycleModel (const std::vector< double > &rParentProteinConcentrations, const CellMutationState &rMutationState, const unsigned &rDimension)
AbstractCellCycleModel *	CreateCellCycleModel ()
void	Initialise ()
bool	SolveOdeToTime (double currentTime)
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
void	ChangeCellTypeDueToCurrentBetaCateninLevel ()
Friends
class	boost::serialization::access