GammaDistributedStochasticDurationCellCycleModel Class Reference

#include <GammaDistributedStochasticDurationCellCycleModel.hpp>

Inheritance diagram for GammaDistributedStochasticDurationCellCycleModel:

Collaboration diagram for GammaDistributedStochasticDurationCellCycleModel:

Public Member Functions
	GammaDistributedStochasticDurationCellCycleModel ()
void	SetG1Duration ()
AbstractCellCycleModel *	CreateCellCycleModel ()
void	SetShape (double shape)
void	SetScale (double scale)
double	GetShape ()
double	GetScale ()
virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)
Public Member Functions inherited from AbstractSimpleCellCycleModel
	AbstractSimpleCellCycleModel ()
virtual	~AbstractSimpleCellCycleModel ()
virtual void	ResetForDivision ()
virtual void	UpdateCellCyclePhase ()
void	InitialiseDaughterCell ()
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 ()
virtual void	SetStemCellG1Duration (double stemCellG1Duration)
virtual void	SetTransitCellG1Duration (double transitCellG1Duration)
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

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

Private Attributes
double	mShape
double	mScale

Friends
class	TestSimpleCellCycleModels
class	boost::serialization::access

Additional Inherited Members
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 stochastic cell-cycle model where cells keep dividing with a stochastic G1 duration drawn from a gamma distribution with specified shape and scale parameters.

Definition at line 46 of file GammaDistributedStochasticDurationCellCycleModel.hpp.

Constructor & Destructor Documentation

GammaDistributedStochasticDurationCellCycleModel::GammaDistributedStochasticDurationCellCycleModel

(

)

Constructor.

Definition at line 42 of file GammaDistributedStochasticDurationCellCycleModel.cpp.

Referenced by CreateCellCycleModel().

Member Function Documentation

AbstractCellCycleModel * GammaDistributedStochasticDurationCellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns

a pointer to the GammaDistributedStochasticDurationCellCycleModel created.

Implements AbstractCellCycleModel.

Definition at line 49 of file GammaDistributedStochasticDurationCellCycleModel.cpp.

References GammaDistributedStochasticDurationCellCycleModel(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mG2Duration, AbstractCellCycleModel::mMDuration, AbstractCellCycleModel::mMinimumGapDuration, mScale, AbstractCellCycleModel::mSDuration, mShape, AbstractCellCycleModel::mStemCellG1Duration, AbstractCellCycleModel::mTransitCellG1Duration, AbstractCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetG2Duration(), AbstractCellCycleModel::SetMDuration(), AbstractCellCycleModel::SetMinimumGapDuration(), SetScale(), AbstractCellCycleModel::SetSDuration(), SetShape(), AbstractCellCycleModel::SetStemCellG1Duration(), and AbstractCellCycleModel::SetTransitCellG1Duration().

double GammaDistributedStochasticDurationCellCycleModel::GetScale

(

)

Returns

mScale.

Definition at line 117 of file GammaDistributedStochasticDurationCellCycleModel.cpp.

References mScale.

double GammaDistributedStochasticDurationCellCycleModel::GetShape

(

)

Returns

mShape.

Definition at line 112 of file GammaDistributedStochasticDurationCellCycleModel.cpp.

References mShape.

void GammaDistributedStochasticDurationCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile )

virtual

Overridden OutputCellCycleModelParameters() method.

Parameters

rParamsFile

the file stream to which the parameters are output

Reimplemented from AbstractSimpleCellCycleModel.

Definition at line 122 of file GammaDistributedStochasticDurationCellCycleModel.cpp.

References mScale, mShape, and AbstractSimpleCellCycleModel::OutputCellCycleModelParameters().

template<class Archive >

void GammaDistributedStochasticDurationCellCycleModel::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 67 of file GammaDistributedStochasticDurationCellCycleModel.hpp.

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

void GammaDistributedStochasticDurationCellCycleModel::SetG1Duration ( )

virtual

Overridden SetG1Duration().

Reimplemented from AbstractSimpleCellCycleModel.

Definition at line 84 of file GammaDistributedStochasticDurationCellCycleModel.cpp.

References RandomNumberGenerator::GammaRandomDeviate(), RandomNumberGenerator::Instance(), AbstractCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, mScale, mShape, and NEVER_REACHED.

void GammaDistributedStochasticDurationCellCycleModel::SetScale

(

double

scale

)

Returns

mScale.

Parameters

scale

the value of the scale parameter

Definition at line 107 of file GammaDistributedStochasticDurationCellCycleModel.cpp.

References mScale.

Referenced by CreateCellCycleModel().

void GammaDistributedStochasticDurationCellCycleModel::SetShape

(

double

shape

)

Set mShape.

Parameters

shape

the value of the shape parameter

Definition at line 102 of file GammaDistributedStochasticDurationCellCycleModel.cpp.

References mShape.

Referenced by CreateCellCycleModel().

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 59 of file GammaDistributedStochasticDurationCellCycleModel.hpp.

Member Data Documentation

double GammaDistributedStochasticDurationCellCycleModel::mScale

private

The scale parameter of the gamma distribution. This must be a positive real number.

Definition at line 56 of file GammaDistributedStochasticDurationCellCycleModel.hpp.

Referenced by CreateCellCycleModel(), GetScale(), OutputCellCycleModelParameters(), serialize(), SetG1Duration(), and SetScale().

double GammaDistributedStochasticDurationCellCycleModel::mShape

private

The shape parameter of the gamma distribution. This must be a positive real number.

Definition at line 53 of file GammaDistributedStochasticDurationCellCycleModel.hpp.

Referenced by CreateCellCycleModel(), GetShape(), OutputCellCycleModelParameters(), serialize(), SetG1Duration(), and SetShape().

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

• cell_based/src/cell/cycle/GammaDistributedStochasticDurationCellCycleModel.hpp
• cell_based/src/cell/cycle/GammaDistributedStochasticDurationCellCycleModel.cpp