IngeWntSwatCellCycleModel Class Reference

#include <IngeWntSwatCellCycleModel.hpp>

Inheritance diagram for IngeWntSwatCellCycleModel:

Collaboration diagram for IngeWntSwatCellCycleModel:

List of all members.

Public Member Functions

IngeWntSwatCellCycleModel (unsigned hypothesis)

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

IngeWntSwatCellCycleModel (const unsigned &rHypothesis, const std::vector< double > &rParentProteinConcentrations, const CellMutationState &rMutationState)

AbstractCellCycleModel * CreateDaughterCellCycleModel ()

void Initialise ()

bool SolveOdeToTime (double currentTime)

double GetMembraneBoundBetaCateninLevel ()

double GetCytoplasmicBetaCateninLevel ()

double GetNuclearBetaCateninLevel ()

unsigned GetHypothesis () const

Private Member Functions

template<class Archive>

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

void ChangeCellTypeDueToCurrentBetaCateninLevel ()

Private Attributes

unsigned mHypothesis

Friends

class boost::serialization::access

Detailed Description

Wnt-dependent cell cycle model.

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

Definition at line 52 of file IngeWntSwatCellCycleModel.hpp.

Constructor & Destructor Documentation

IngeWntSwatCellCycleModel::IngeWntSwatCellCycleModel ( unsigned hypothesis ) [inline]

Default constructor.

Parameters:

hypothesis

Hypothesis number (1 or 2), concerning the nature of the interactions modelled by the cell cycle ODE system.

Definition at line 99 of file IngeWntSwatCellCycleModel.hpp.

References mHypothesis.

Referenced by CreateDaughterCellCycleModel().

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

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:

	rHypothesis	which model hypothesis to use (1 or 2)
	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

Definition at line 32 of file IngeWntSwatCellCycleModel.cpp.

References SimulationTime::Instance(), AbstractCellCycleModel::mBirthTime, AbstractOdeBasedCellCycleModel::mDivideTime, AbstractOdeBasedCellCycleModel::mFinishedRunningOdes, mHypothesis, AbstractOdeBasedCellCycleModel::mpOdeSystem, AbstractCellCycleModel::mReadyToDivide, and AbstractOdeSystem::rGetStateVariables().

IngeWntSwatCellCycleModel::IngeWntSwatCellCycleModel	(	const unsigned &	rHypothesis,
		const std::vector< double > &	rParentProteinConcentrations,
		const CellMutationState &	rMutationState
	)

A 'private' constructor for archiving.

Parameters:

	rHypothesis	which model hypothesis to use (1 or 2)
	rParentProteinConcentrations	a std::vector of doubles of the protein concentrations (see IngeWntSwatCellCycleOdeSystem)
	rMutationState	the mutation state of the cell (used by ODEs)

Definition at line 69 of file IngeWntSwatCellCycleModel.cpp.

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

Member Function Documentation

template<class Archive>

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

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

Parameters:

	archive
	version

Reimplemented from AbstractWntOdeBasedCellCycleModel.

Definition at line 65 of file IngeWntSwatCellCycleModel.hpp.

References AbstractOdeBasedCellCycleModel::mpOdeSystem.

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

Called by Initialise() and UpdateCellType() only. Updates the mpCell::mCellType to match mpOdeSystem's beta-catenin levels

This carries out the work for UpdateCellType(); But does not check the current time so it can be used by the initialise method.

Implements AbstractWntOdeBasedCellCycleModel.

Definition at line 101 of file IngeWntSwatCellCycleModel.cpp.

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

Referenced by Initialise().

AbstractCellCycleModel * IngeWntSwatCellCycleModel::CreateDaughterCellCycleModel ( ) [virtual]

Returns a new IngeWntSwatCellCycleModel created with the correct initial conditions.

Should be called just after the parent cell cycle model has been Reset().

We call a cheeky version of the constructor which makes the new cell cycle model the same as the old one - not a dividing copy at this time, unless the parent cell has just divided.

Implements AbstractCellCycleModel.

Definition at line 81 of file IngeWntSwatCellCycleModel.cpp.

References TissueCell::GetMutationState(), IngeWntSwatCellCycleModel(), AbstractCellCycleModel::mBirthTime, AbstractOdeBasedCellCycleModel::mDivideTime, AbstractOdeBasedCellCycleModel::mFinishedRunningOdes, mHypothesis, AbstractOdeBasedCellCycleModel::mLastTime, AbstractCellCycleModel::mpCell, AbstractOdeBasedCellCycleModel::mpOdeSystem, and AbstractCellCycleModel::mReadyToDivide.

void IngeWntSwatCellCycleModel::Initialise ( void ) [virtual]

See AbstractCellCycleModel::Initialise()

In this case we set up a new ODE system for a daughter cell.

Reimplemented from AbstractCellCycleModel.

Definition at line 122 of file IngeWntSwatCellCycleModel.cpp.

References ChangeCellTypeDueToCurrentBetaCateninLevel(), AbstractOdeSystem::GetInitialConditions(), TissueCell::GetMutationState(), WntConcentration::Instance(), mHypothesis, AbstractCellCycleModel::mpCell, AbstractOdeBasedCellCycleModel::mpOdeSystem, and AbstractOdeSystem::SetStateVariables().

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

Solve the ODE to the current time.

Parameters:

currentTime

the current time

Returns:: Whether a stopping event occurred.

Implements AbstractOdeBasedCellCycleModel.

Definition at line 133 of file IngeWntSwatCellCycleModel.cpp.

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

double IngeWntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel ( )

Returns:: the level of membrane bound beta-catenin. To be used in cell-cell adhesion calculations.

Definition at line 156 of file IngeWntSwatCellCycleModel.cpp.

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

Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), and CryptSimulation2d::WriteBetaCatenin().

double IngeWntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel ( )

Returns:: the level of cytoplasmic beta-catenin (including ubiquitinated - awaiting degradation)

Definition at line 162 of file IngeWntSwatCellCycleModel.cpp.

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

Referenced by CryptSimulation2d::WriteBetaCatenin().

double IngeWntSwatCellCycleModel::GetNuclearBetaCateninLevel ( )

Returns:: the level of nuclear beta-catenin. To be used in transcription

Definition at line 170 of file IngeWntSwatCellCycleModel.cpp.

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

Referenced by CryptSimulation2d::WriteBetaCatenin().

unsigned IngeWntSwatCellCycleModel::GetHypothesis ( ) const

Returns:: mHypothesis.

Definition at line 179 of file IngeWntSwatCellCycleModel.cpp.

References mHypothesis.

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractWntOdeBasedCellCycleModel.

Definition at line 57 of file IngeWntSwatCellCycleModel.hpp.

Member Data Documentation

unsigned IngeWntSwatCellCycleModel::mHypothesis [private]

Hypothesis number (1 or 2), concerning the nature of the interactions modelled by the cell cycle ODE system.

Definition at line 89 of file IngeWntSwatCellCycleModel.hpp.

Referenced by CreateDaughterCellCycleModel(), GetHypothesis(), IngeWntSwatCellCycleModel(), and Initialise().

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

/tmp/release_1/cancer/src/tissue/cell/cycle/IngeWntSwatCellCycleModel.hpp
/tmp/release_1/cancer/src/tissue/cell/cycle/IngeWntSwatCellCycleModel.cpp


Public Member Functions
	IngeWntSwatCellCycleModel (unsigned hypothesis)
	IngeWntSwatCellCycleModel (const unsigned &rHypothesis, AbstractOdeSystem *pParentOdeSystem, const CellMutationState &rMutationState, double birthTime, double lastTime, bool inSG2MPhase, bool readyToDivide, double divideTime)
	IngeWntSwatCellCycleModel (const unsigned &rHypothesis, const std::vector< double > &rParentProteinConcentrations, const CellMutationState &rMutationState)
AbstractCellCycleModel *	CreateDaughterCellCycleModel ()
void	Initialise ()
bool	SolveOdeToTime (double currentTime)
double	GetMembraneBoundBetaCateninLevel ()
double	GetCytoplasmicBetaCateninLevel ()
double	GetNuclearBetaCateninLevel ()
unsigned	GetHypothesis () const
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
void	ChangeCellTypeDueToCurrentBetaCateninLevel ()
Private Attributes
unsigned	mHypothesis
Friends
class	boost::serialization::access