IngeWntSwatCellCycleModel Class Reference

#include <IngeWntSwatCellCycleModel.hpp>

Inheritance diagram for IngeWntSwatCellCycleModel:

Collaboration diagram for IngeWntSwatCellCycleModel:

List of all members.

Public Member Functions

IngeWntSwatCellCycleModel (unsigned hypothesis, unsigned dimension)

IngeWntSwatCellCycleModel (const IngeWntSwatCellCycleModel &rOtherModel)

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

AbstractCellCycleModel * CreateCellCycleModel ()

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,
		unsigned	dimension
	)

Default constructor.

Parameters:

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

Definition at line 32 of file IngeWntSwatCellCycleModel.cpp.

References mHypothesis.

Referenced by CreateCellCycleModel().

IngeWntSwatCellCycleModel::IngeWntSwatCellCycleModel ( const IngeWntSwatCellCycleModel & rOtherModel )

Copy constructor.

Creates an appropriate copy of our ODE system too.

Parameters:

rOtherModel

the instance being copied.

Definition at line 43 of file IngeWntSwatCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::mpOdeSystem.

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

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)
	rDimension	the spatial dimension

Definition at line 54 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	the archive
	version	the current version of this class

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 74 of file IngeWntSwatCellCycleModel.cpp.

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

Referenced by Initialise().

AbstractCellCycleModel * IngeWntSwatCellCycleModel::CreateCellCycleModel ( ) [virtual]

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

Implements AbstractCellCycleModel.

Definition at line 68 of file IngeWntSwatCellCycleModel.cpp.

References IngeWntSwatCellCycleModel().

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 95 of file IngeWntSwatCellCycleModel.cpp.

References ChangeCellTypeDueToCurrentBetaCateninLevel(), AbstractOdeSystem::GetInitialConditions(), TissueCell::GetMutationState(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), 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 109 of file IngeWntSwatCellCycleModel.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().

double IngeWntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel ( )

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

Definition at line 132 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 138 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 146 of file IngeWntSwatCellCycleModel.cpp.

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

Referenced by CryptSimulation2d::WriteBetaCatenin().

unsigned IngeWntSwatCellCycleModel::GetHypothesis ( ) const

Returns:: mHypothesis.

Definition at line 155 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 GetHypothesis(), IngeWntSwatCellCycleModel(), and Initialise().

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

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


Public Member Functions
	IngeWntSwatCellCycleModel (unsigned hypothesis, unsigned dimension)
	IngeWntSwatCellCycleModel (const IngeWntSwatCellCycleModel &rOtherModel)
	IngeWntSwatCellCycleModel (const unsigned &rHypothesis, const std::vector< double > &rParentProteinConcentrations, const CellMutationState &rMutationState, const unsigned &rDimension)
AbstractCellCycleModel *	CreateCellCycleModel ()
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