#include <ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.hpp>

Inheritance diagram for ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel:

Collaboration diagram for ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel:

Public Member Functions
	ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel ()

AbstractCellCycleModel *	CreateCellCycleModel ()

double	GetRate ()

void	SetRate (double rate)

void	SetStemCellG1Duration (double stemCellG1Duration)

void	SetTransitCellG1Duration (double transitCellG1Duration)

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractSimpleGenerationBasedCellCycleModel
	AbstractSimpleGenerationBasedCellCycleModel ()

virtual	~AbstractSimpleGenerationBasedCellCycleModel ()

void	ResetForDivision ()

void	InitialiseDaughterCell ()

void	SetGeneration (unsigned generation)

unsigned	GetGeneration () const

void	SetMaxTransitGenerations (unsigned maxTransitGenerations)

unsigned	GetMaxTransitGenerations () const

Public Member Functions inherited from AbstractSimpleCellCycleModel
	AbstractSimpleCellCycleModel ()

virtual	~AbstractSimpleCellCycleModel ()

virtual void	UpdateCellCyclePhase ()

virtual void	Initialise ()

Public Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel ()

virtual	~AbstractCellCycleModel ()

void	SetCell (CellPtr pCell)

CellPtr	GetCell ()

virtual void	SetBirthTime (double birthTime)

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 ()

void	SetSDuration (double sDuration)

void	SetG2Duration (double g2Duration)

void	SetMDuration (double mDuration)

virtual double	GetAverageTransitCellCycleTime ()

virtual double	GetAverageStemCellCycleTime ()

virtual bool	CanCellTerminallyDifferentiate ()

double	GetMinimumGapDuration ()

void	SetMinimumGapDuration (double minimumGapDuration)

void	OutputCellCycleModelInfo (out_stream &rParamsFile)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Member Functions
void	SetG1Duration ()

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

Private Attributes
double	mRate

Friends
class	TestSimpleCellCycleModels

class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractSimpleGenerationBasedCellCycleModel
unsigned	mGeneration

unsigned	mMaxTransitGenerations

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

Detailed Description

A cell cycle model where the G1 duration is drawn from an exponential random distribution. The rate parameter of this distribution is defined by the member variable mRate.

The default value of mRate is set to the inverse of the default value of mTransitCellG1Duration in the constructor.

mRate may be set using the method SetRate(), which also sets mTransitCellG1Duration and mStemCellG1Duration to take the inverse of mRate's new value. Similarly, the overridden methods SetTransitCellG1Duration() and SetStemCellG1Duration() also set mRate to take the inverse of the new value of mTransitCellG1Duration and mStemCellG1Duration, respectively.

Definition at line 56 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel ( )

Constructor - just a default, mBirthTime is now set in the AbstractCellCycleModel class. mG1Duration is set very high, it is set for the individual cells when InitialiseDaughterCell is called

Definition at line 42 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp.

Referenced by CreateCellCycleModel().

Member Function Documentation

AbstractCellCycleModel * ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns: new cell-cycle model

Implements AbstractCellCycleModel.

Definition at line 48 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp.

double ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::GetRate ( )

Return the rate parameter (lambda) of the exponential distribution.

Returns: mRate, the rate parameter of the distribution

Definition at line 104 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp.

References mRate.

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::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 AbstractSimpleGenerationBasedCellCycleModel.

Definition at line 134 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp.

References mRate, and AbstractSimpleGenerationBasedCellCycleModel::OutputCellCycleModelParameters().

template<class Archive >

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

inlineprivate

Archive the cell-cycle model and random number generator, never used directly - boost uses this.

Parameters

archive	the archive
version	the current version of this class

Definition at line 78 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.hpp.

References SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), RandomNumberGenerator::Instance(), and mRate.

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::SetG1Duration ( )

protectedvirtual

Stochastically set the G1 duration following an exponential distribution. Called on cell creation at the start of a simulation, and for both parent and daughter cells at cell division.

Reimplemented from AbstractSimpleCellCycleModel.

Definition at line 84 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp.

References RandomNumberGenerator::ExponentialRandomDeviate(), RandomNumberGenerator::Instance(), AbstractCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, mRate, and NEVER_REACHED.

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::SetRate ( double rate )

Set the rate parameter of the exponential distribution. For consistency, this function also resets the internal values for mTransitCellG1Duration and mStemCellG1Duration to the average value of the exponential random variable, i.e. 1.0/rate. This ensures that GetAverageTransitCellCycleTime and GetAverageStemCellCycleTime returns correct values.

Parameters

rate

Definition at line 109 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp.

References mRate, SetStemCellG1Duration(), and SetTransitCellG1Duration().

Referenced by CreateCellCycleModel().

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::SetStemCellG1Duration ( double stemCellG1Duration )

virtual

Overridden SetStemCellG1Duration() method.

Set mStemCellG1Duration to be a given value and also set mRate to be the inverse of this value

Parameters

stemCellG1Duration the new value of mStemCellG1Duration

Reimplemented from AbstractCellCycleModel.

Definition at line 118 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp.

References mRate, and AbstractCellCycleModel::mStemCellG1Duration.

Referenced by CreateCellCycleModel(), and SetRate().

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::SetTransitCellG1Duration ( double transitCellG1Duration )

virtual

Overridden SetTransitCellG1Duration() method.

Set mTransitCellG1Duration to be a given value and also set mRate to be the inverse of this value

Parameters

transitCellG1Duration the new value of mTransitCellG1Duration

Reimplemented from AbstractCellCycleModel.

Definition at line 126 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp.

References mRate, and AbstractCellCycleModel::mTransitCellG1Duration.

Referenced by CreateCellCycleModel(), and SetRate().

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 70 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.hpp.

Member Data Documentation

double ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::mRate

private

The rate parameter of the exponential distribution, often denoted by lambda. This parameter is initialised to 1.0/mTransitCellG1Duration. The latter variable is inherited from the abstract cell cycle model. This initialisation ensures that cells will have the standard G1 duration (as defined in the abstract cell cycle model classes) on average.

Definition at line 67 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.hpp.

Referenced by CreateCellCycleModel(), GetRate(), OutputCellCycleModelParameters(), serialize(), SetG1Duration(), SetRate(), SetStemCellG1Duration(), and SetTransitCellG1Duration().

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

cell_based/src/cell/cycle/ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.hpp
cell_based/src/cell/cycle/ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation