GammaG1CellCycleModel Class Reference

#include <GammaG1CellCycleModel.hpp>

Inheritance diagram for GammaG1CellCycleModel:

Collaboration diagram for GammaG1CellCycleModel:

Public Member Functions
	GammaG1CellCycleModel ()
void	SetG1Duration ()
AbstractCellCycleModel *	CreateCellCycleModel ()
void	SetShape (double shape)
void	SetScale (double scale)
double	GetShape () const
double	GetScale () const
virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)
Public Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
	AbstractSimplePhaseBasedCellCycleModel ()
virtual	~AbstractSimplePhaseBasedCellCycleModel ()
virtual void	ResetForDivision ()
virtual void	UpdateCellCyclePhase ()
void	InitialiseDaughterCell ()
virtual void	Initialise ()
Public Member Functions inherited from AbstractPhaseBasedCellCycleModel
	AbstractPhaseBasedCellCycleModel ()
virtual	~AbstractPhaseBasedCellCycleModel ()
virtual bool	ReadyToDivide ()
CellCyclePhase	GetCurrentCellCyclePhase () const
virtual double	GetG1Duration () const
double	GetStemCellG1Duration () const
double	GetTransitCellG1Duration () const
double	GetSG2MDuration () const
virtual double	GetSDuration () const
virtual double	GetG2Duration () const
virtual double	GetMDuration () const
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 ()
double	GetMinimumGapDuration () const
void	SetMinimumGapDuration (double minimumGapDuration)
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 () const
double	GetBirthTime () const
double	GetAge ()
virtual bool	CanCellTerminallyDifferentiate ()
void	OutputCellCycleModelInfo (out_stream &rParamsFile)
Public Member Functions inherited from Identifiable
virtual	~Identifiable ()
std::string	GetIdentifier () const

Protected Member Functions
	GammaG1CellCycleModel (const GammaG1CellCycleModel &rModel)
Protected Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
	AbstractSimplePhaseBasedCellCycleModel (const AbstractSimplePhaseBasedCellCycleModel &rModel)
Protected Member Functions inherited from AbstractPhaseBasedCellCycleModel
	AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel)
Protected Member Functions inherited from AbstractCellCycleModel
	AbstractCellCycleModel (const AbstractCellCycleModel &rModel)

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 AbstractPhaseBasedCellCycleModel
CellCyclePhase	mCurrentCellCyclePhase
double	mG1Duration
double	mMinimumGapDuration
double	mStemCellG1Duration
double	mTransitCellG1Duration
double	mSDuration
double	mG2Duration
double	mMDuration
Protected Attributes inherited from AbstractCellCycleModel
CellPtr	mpCell
double	mBirthTime
bool	mReadyToDivide
unsigned	mDimension

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 GammaG1CellCycleModel.hpp.

Constructor & Destructor Documentation

GammaG1CellCycleModel() [1/2]

GammaG1CellCycleModel::GammaG1CellCycleModel ( const GammaG1CellCycleModel &  rModel )

protected

Protected copy-constructor for use by CreateCellCycleModel. The only way for external code to create a copy of a cell cycle model is by calling that method, to ensure that a model of the correct subclass is created. This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.

This method is called by child classes to set member variables for a daughter cell upon cell division. Note that the parent cell cycle model will have had ResetForDivision() called just before CreateCellCycleModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().

Parameters

rModel

the cell cycle model to copy.

Definition at line 48 of file GammaG1CellCycleModel.cpp.

GammaG1CellCycleModel() [2/2]

GammaG1CellCycleModel::GammaG1CellCycleModel

(

)

Constructor.

Definition at line 41 of file GammaG1CellCycleModel.cpp.

Referenced by CreateCellCycleModel().

Member Function Documentation

CreateCellCycleModel()

AbstractCellCycleModel * GammaG1CellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns

a pointer to the GammaG1CellCycleModel created.

Implements AbstractCellCycleModel.

Definition at line 69 of file GammaG1CellCycleModel.cpp.

References GammaG1CellCycleModel().

GetScale()

double GammaG1CellCycleModel::GetScale

(

)

const

Returns

mScale.

Definition at line 107 of file GammaG1CellCycleModel.cpp.

References mScale.

GetShape()

double GammaG1CellCycleModel::GetShape

(

)

const

Returns

mShape.

Definition at line 102 of file GammaG1CellCycleModel.cpp.

References mShape.

OutputCellCycleModelParameters()

void GammaG1CellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile )

virtual

Overridden OutputCellCycleModelParameters() method.

Parameters

rParamsFile

the file stream to which the parameters are output

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Definition at line 112 of file GammaG1CellCycleModel.cpp.

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

serialize()

template<class Archive >

void GammaG1CellCycleModel::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 GammaG1CellCycleModel.hpp.

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

SetG1Duration()

void GammaG1CellCycleModel::SetG1Duration ( )

virtual

Overridden SetG1Duration().

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Definition at line 74 of file GammaG1CellCycleModel.cpp.

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

SetScale()

void GammaG1CellCycleModel::SetScale

(

double

scale

)

Parameters

scale

the value of the scale parameter

Definition at line 97 of file GammaG1CellCycleModel.cpp.

References mScale.

SetShape()

void GammaG1CellCycleModel::SetShape

(

double

shape

)

Set mShape.

Parameters

shape

the value of the shape parameter

Definition at line 92 of file GammaG1CellCycleModel.cpp.

References mShape.

Friends And Related Symbol Documentation

boost::serialization::access

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 59 of file GammaG1CellCycleModel.hpp.

TestSimpleCellCycleModels

friend class TestSimpleCellCycleModels

friend

Definition at line 48 of file GammaG1CellCycleModel.hpp.

Member Data Documentation

mScale

double GammaG1CellCycleModel::mScale

private

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

Definition at line 56 of file GammaG1CellCycleModel.hpp.

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

mShape

double GammaG1CellCycleModel::mShape

private

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

Definition at line 53 of file GammaG1CellCycleModel.hpp.

Referenced by 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/GammaG1CellCycleModel.hpp
• cell_based/src/cell/cycle/GammaG1CellCycleModel.cpp