ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel Class Reference

#include <ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.hpp>

Inherits AbstractSimpleGenerationBasedCellCycleModel.

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)
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

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.

template<class Archive >

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

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

Reimplemented from AbstractSimpleGenerationBasedCellCycleModel.

Definition at line 78 of file ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel.hpp.

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

void ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel::SetG1Duration ( ) [protected, virtual]

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.

Reimplemented from AbstractSimpleGenerationBasedCellCycleModel.

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

ExponentiallyDistributedStochasticDurationGenerationBasedCellCycleModel Class Reference

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation