#include <ExponentialG1GenerationalCellCycleModel.hpp>

Inheritance diagram for ExponentialG1GenerationalCellCycleModel:

Collaboration diagram for ExponentialG1GenerationalCellCycleModel:

Public Member Functions
	ExponentialG1GenerationalCellCycleModel ()

AbstractCellCycleModel *	CreateCellCycleModel ()

virtual double	GetRate ()

virtual void	SetRate (double rate)

virtual void	SetStemCellG1Duration (double stemCellG1Duration)

virtual void	SetTransitCellG1Duration (double transitCellG1Duration)

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from AbstractSimpleGenerationalCellCycleModel
	AbstractSimpleGenerationalCellCycleModel ()

virtual	~AbstractSimpleGenerationalCellCycleModel ()

void	ResetForDivision ()

void	InitialiseDaughterCell ()

void	SetGeneration (unsigned generation)

unsigned	GetGeneration () const

void	SetMaxTransitGenerations (unsigned maxTransitGenerations)

unsigned	GetMaxTransitGenerations () const

Public Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
	AbstractSimplePhaseBasedCellCycleModel ()

virtual	~AbstractSimplePhaseBasedCellCycleModel ()

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

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
virtual void	SetG1Duration ()

	ExponentialG1GenerationalCellCycleModel (const ExponentialG1GenerationalCellCycleModel &rModel)

Protected Member Functions inherited from AbstractSimpleGenerationalCellCycleModel
	AbstractSimpleGenerationalCellCycleModel (const AbstractSimpleGenerationalCellCycleModel &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	mRate

Friends
class	TestSimpleCellCycleModels

class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractSimpleGenerationalCellCycleModel
unsigned	mGeneration

unsigned	mMaxTransitGenerations

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 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 ExponentialG1GenerationalCellCycleModel.hpp.

Constructor & Destructor Documentation

ExponentialG1GenerationalCellCycleModel::ExponentialG1GenerationalCellCycleModel ( const ExponentialG1GenerationalCellCycleModel & 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 ExponentialG1GenerationalCellCycleModel.cpp.

ExponentialG1GenerationalCellCycleModel::ExponentialG1GenerationalCellCycleModel ( )

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 ExponentialG1GenerationalCellCycleModel.cpp.

Referenced by CreateCellCycleModel(), and serialize().

Member Function Documentation

AbstractCellCycleModel * ExponentialG1GenerationalCellCycleModel::CreateCellCycleModel ( )

virtual

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

Returns: new cell-cycle model

Implements AbstractCellCycleModel.

Reimplemented in FixedSequenceCellCycleModel.

Definition at line 68 of file ExponentialG1GenerationalCellCycleModel.cpp.

References ExponentialG1GenerationalCellCycleModel().

Referenced by serialize().

double ExponentialG1GenerationalCellCycleModel::GetRate ( )

virtual

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

Returns: mRate, the rate parameter of the distribution

Reimplemented in FixedSequenceCellCycleModel.

Definition at line 93 of file ExponentialG1GenerationalCellCycleModel.cpp.

References mRate.

Referenced by serialize().

void ExponentialG1GenerationalCellCycleModel::OutputCellCycleModelParameters ( out_stream & rParamsFile )

virtual

Overridden OutputCellCycleModelParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractSimpleGenerationalCellCycleModel.

Reimplemented in FixedSequenceCellCycleModel.

Definition at line 123 of file ExponentialG1GenerationalCellCycleModel.cpp.

References CHASTE_CLASS_EXPORT, mRate, and AbstractSimpleGenerationalCellCycleModel::OutputCellCycleModelParameters().

Referenced by serialize().

template<class Archive >

void ExponentialG1GenerationalCellCycleModel::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 ExponentialG1GenerationalCellCycleModel.hpp.

References CHASTE_CLASS_EXPORT, CreateCellCycleModel(), ExponentialG1GenerationalCellCycleModel(), GetRate(), SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), RandomNumberGenerator::Instance(), mRate, OutputCellCycleModelParameters(), SetG1Duration(), SetRate(), SetStemCellG1Duration(), and SetTransitCellG1Duration().

void ExponentialG1GenerationalCellCycleModel::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 AbstractSimplePhaseBasedCellCycleModel.

Reimplemented in FixedSequenceCellCycleModel.

Definition at line 73 of file ExponentialG1GenerationalCellCycleModel.cpp.

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

Referenced by serialize().

void ExponentialG1GenerationalCellCycleModel::SetRate ( double rate )

virtual

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

Reimplemented in FixedSequenceCellCycleModel.

Definition at line 98 of file ExponentialG1GenerationalCellCycleModel.cpp.

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

Referenced by serialize().

void ExponentialG1GenerationalCellCycleModel::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 AbstractPhaseBasedCellCycleModel.

Reimplemented in FixedSequenceCellCycleModel.

Definition at line 107 of file ExponentialG1GenerationalCellCycleModel.cpp.

References mRate, and AbstractPhaseBasedCellCycleModel::mStemCellG1Duration.

Referenced by serialize(), and SetRate().

void ExponentialG1GenerationalCellCycleModel::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 AbstractPhaseBasedCellCycleModel.

Reimplemented in FixedSequenceCellCycleModel.

Definition at line 115 of file ExponentialG1GenerationalCellCycleModel.cpp.

References mRate, and AbstractPhaseBasedCellCycleModel::mTransitCellG1Duration.

Referenced by serialize(), and SetRate().

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 70 of file ExponentialG1GenerationalCellCycleModel.hpp.

Member Data Documentation

double ExponentialG1GenerationalCellCycleModel::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 ExponentialG1GenerationalCellCycleModel.hpp.

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

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

cell_based/src/cell/cycle/ExponentialG1GenerationalCellCycleModel.hpp
cell_based/src/cell/cycle/ExponentialG1GenerationalCellCycleModel.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