VanLeeuwen2009WntSwatCellCycleModelHypothesisOne Class Reference

#include <VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp>

Inheritance diagram for VanLeeuwen2009WntSwatCellCycleModelHypothesisOne:

Collaboration diagram for VanLeeuwen2009WntSwatCellCycleModelHypothesisOne:

Public Member Functions
	VanLeeuwen2009WntSwatCellCycleModelHypothesisOne (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
void	InitialiseOdeSystem (double wntConcentration, boost::shared_ptr< AbstractCellMutationState > pMutationState)
AbstractCellCycleModel *	CreateCellCycleModel ()
virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)
Public Member Functions inherited from AbstractVanLeeuwen2009WntSwatCellCycleModel
	AbstractVanLeeuwen2009WntSwatCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
void	Initialise ()
double	GetMembraneBoundBetaCateninLevel ()
double	GetCytoplasmicBetaCateninLevel ()
double	GetNuclearBetaCateninLevel ()
Public Member Functions inherited from AbstractWntOdeBasedCellCycleModel
	AbstractWntOdeBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
virtual	~AbstractWntOdeBasedCellCycleModel ()
void	ResetForDivision ()
void	UpdateCellProliferativeType ()
double	GetAverageTransitCellCycleTime ()
double	GetAverageStemCellCycleTime ()
virtual bool	CanCellTerminallyDifferentiate ()
Public Member Functions inherited from AbstractOdeBasedCellCycleModel
	AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
virtual	~AbstractOdeBasedCellCycleModel ()
double	GetOdeStopTime ()
void	SetBirthTime (double birthTime)
std::vector< double >	GetProteinConcentrations () const
void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)
void	SetFinishedRunningOdes (bool finishedRunningOdes)
void	SetDivideTime (double divideTime)
void	SetG2PhaseStartTime (double g2PhaseStartTime)
Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()
virtual	~AbstractCellCycleModel ()
void	SetCell (CellPtr pCell)
virtual void	InitialiseDaughterCell ()
CellPtr	GetCell ()
void	SetDimension (unsigned dimension)
unsigned	GetDimension ()
double	GetBirthTime () const
double	GetAge ()
virtual bool	ReadyToDivide ()
CellCyclePhase	GetCurrentCellCyclePhase ()
virtual double	GetG1Duration ()
double	GetStemCellG1Duration ()
double	GetTransitCellG1Duration ()
double	GetSG2MDuration ()
virtual double	GetSDuration ()
virtual double	GetG2Duration ()
virtual double	GetMDuration ()
virtual void	SetStemCellG1Duration (double stemCellG1Duration)
virtual void	SetTransitCellG1Duration (double transitCellG1Duration)
void	SetSDuration (double sDuration)
void	SetG2Duration (double g2Duration)
void	SetMDuration (double mDuration)
double	GetMinimumGapDuration ()
void	SetMinimumGapDuration (double minimumGapDuration)
void	OutputCellCycleModelInfo (out_stream &rParamsFile)
Public Member Functions inherited from Identifiable
virtual	~Identifiable ()
std::string	GetIdentifier () const
Public Member Functions inherited from CellCycleModelOdeHandler
	CellCycleModelOdeHandler (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
virtual	~CellCycleModelOdeHandler ()
AbstractOdeSystem *	GetOdeSystem () const
void	SetOdeSystem (AbstractOdeSystem *pOdeSystem)
const boost::shared_ptr < AbstractCellCycleModelOdeSolver >	GetOdeSolver () const
void	SetLastTime (double lastTime)
double	GetDt ()
void	SetDt (double timeStep)
void	SetStateVariables (const std::vector< double > &rStateVariables)

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

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from AbstractWntOdeBasedCellCycleModel
double	GetWntLevel ()
void	UpdateCellCyclePhase ()
Protected Member Functions inherited from CellCycleModelOdeHandler
bool	SolveOdeToTime (double currentTime)
Protected Attributes inherited from AbstractOdeBasedCellCycleModel
double	mDivideTime
bool	mFinishedRunningOdes
double	mG2PhaseStartTime
Protected Attributes inherited from AbstractCellCycleModel
CellPtr	mpCell
double	mBirthTime
CellCyclePhase	mCurrentCellCyclePhase
double	mG1Duration
bool	mReadyToDivide
unsigned	mDimension
double	mMinimumGapDuration
double	mStemCellG1Duration
double	mTransitCellG1Duration
double	mSDuration
double	mG2Duration
double	mMDuration
Protected Attributes inherited from CellCycleModelOdeHandler
double	mDt
AbstractOdeSystem *	mpOdeSystem
boost::shared_ptr < AbstractCellCycleModelOdeSolver >	mpOdeSolver
double	mLastTime

Detailed Description

Concrete Van Leeuwen 2009 cell-cycle model, using hypothesis one (see paper).

Definition at line 44 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp.

Constructor & Destructor Documentation

VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::VanLeeuwen2009WntSwatCellCycleModelHypothesisOne

(

boost::shared_ptr< AbstractCellCycleModelOdeSolver >

pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>()

)

Default constructor calls base class.

Parameters

pOdeSolver

An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 38 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp.

References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().

Referenced by CreateCellCycleModel().

Member Function Documentation

AbstractCellCycleModel * VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel ( )

virtual

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

Returns

the new cell-cycle model

Implements AbstractCellCycleModel.

Definition at line 62 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp.

References AbstractWntOdeBasedCellCycleModel::GetWntLevel(), InitialiseOdeSystem(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mDimension, AbstractOdeBasedCellCycleModel::mDivideTime, AbstractOdeBasedCellCycleModel::mFinishedRunningOdes, AbstractCellCycleModel::mG2Duration, AbstractOdeBasedCellCycleModel::mG2PhaseStartTime, CellCycleModelOdeHandler::mLastTime, AbstractCellCycleModel::mMDuration, AbstractCellCycleModel::mMinimumGapDuration, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSolver, CellCycleModelOdeHandler::mpOdeSystem, AbstractCellCycleModel::mSDuration, AbstractCellCycleModel::mStemCellG1Duration, AbstractCellCycleModel::mTransitCellG1Duration, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), AbstractOdeBasedCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetDimension(), AbstractOdeBasedCellCycleModel::SetDivideTime(), AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes(), AbstractCellCycleModel::SetG2Duration(), AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime(), CellCycleModelOdeHandler::SetLastTime(), AbstractCellCycleModel::SetMDuration(), AbstractCellCycleModel::SetMinimumGapDuration(), AbstractCellCycleModel::SetSDuration(), CellCycleModelOdeHandler::SetStateVariables(), AbstractCellCycleModel::SetStemCellG1Duration(), AbstractCellCycleModel::SetTransitCellG1Duration(), and VanLeeuwen2009WntSwatCellCycleModelHypothesisOne().

void VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::InitialiseOdeSystem ( double  wntConcentration, boost::shared_ptr< AbstractCellMutationState >  pMutationState  )

virtual

Overloaded method which allocates the ODE system using HYPOTHESIS ONE.

Parameters

wntConcentration	Wnt concentration
pMutationState	Mutation state

Implements AbstractVanLeeuwen2009WntSwatCellCycleModel.

Definition at line 57 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp.

References CellCycleModelOdeHandler::mpOdeSystem.

Referenced by CreateCellCycleModel().

void VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::OutputCellCycleModelParameters ( out_stream &  rParamsFile )

virtual

Outputs cell-cycle model parameters to file.

Parameters

rParamsFile

the file stream to which the parameters are output

Reimplemented from AbstractVanLeeuwen2009WntSwatCellCycleModel.

Definition at line 104 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp.

References AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters().

template<class Archive >

void VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::serialize ( Archive &  archive, const unsigned int  version  )

inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 57 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp.

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

• crypt/src/cell/cycle/VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp
• crypt/src/cell/cycle/VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp