#include <FixedSequenceCellCycleModel.hpp>

Inheritance diagram for FixedSequenceCellCycleModel:

Collaboration diagram for FixedSequenceCellCycleModel:

Public Member Functions
	FixedSequenceCellCycleModel ()

AbstractCellCycleModel *	CreateCellCycleModel ()

void	SetRate (double rate)

double	GetRate ()

void	SetStemCellG1Duration (double stemCellG1Duration)

void	SetTransitCellG1Duration (double transitCellG1Duration)

virtual void	OutputCellCycleModelParameters (out_stream &rParamsFile)

Public Member Functions inherited from ExponentialG1GenerationalCellCycleModel
	ExponentialG1GenerationalCellCycleModel ()

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
void	SetG1Duration ()

	FixedSequenceCellCycleModel (const FixedSequenceCellCycleModel &rModel)

Protected Member Functions inherited from ExponentialG1GenerationalCellCycleModel
	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)

Friends
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

This FixedSequenceCellCycleModel generates a sequence of randomly distributed cell cycle times at the beginning of the simulation rather than drawing random numbers during the simulation. The random seed for the generation of these random numbers may be specified by the user and the cell cycle times are stored in a separate singleton, the CellCycleTimesGenerator. This gives the user control over the exact cell cycle times used in the simulation while not interfering with other random events implemented in the simulation algorithm.

This cell cycle model is an extended version of the ExponentialG1GenerationalCellCycleModel. Similar to ExponentialG1GenerationalCellCycleModel, the G1 duration is exponentially random distributed, and the interface to FixedSequenceCellCycleModel and ExponentialG1GenerationalCellCycleModel are similar. In contrast to ExponentialG1GenerationalCellCycleModel this cell cycle model does not treat stem cells and transit cells differently.

If using this cell cycle model, the following line must be called before starting the simulation:

CellCycleTimesGenerator::Instance()->GenerateCellCycleTimeSequence();

Further, the following line must be run at the end of the simulation:

CellCycleTimesGenerator::Destroy();

Definition at line 68 of file FixedSequenceCellCycleModel.hpp.

Constructor & Destructor Documentation

FixedSequenceCellCycleModel::FixedSequenceCellCycleModel ( const FixedSequenceCellCycleModel & 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 49 of file FixedSequenceCellCycleModel.cpp.

FixedSequenceCellCycleModel::FixedSequenceCellCycleModel ( )

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 43 of file FixedSequenceCellCycleModel.cpp.

References AbstractPhaseBasedCellCycleModel::mStemCellG1Duration, and AbstractPhaseBasedCellCycleModel::mTransitCellG1Duration.

Referenced by CreateCellCycleModel(), and serialize().

Member Function Documentation

AbstractCellCycleModel * FixedSequenceCellCycleModel::CreateCellCycleModel ( )

virtual

Overridden method to create new cell cycle models after division

Returns: new cell cycle model

Reimplemented from ExponentialG1GenerationalCellCycleModel.

Definition at line 69 of file FixedSequenceCellCycleModel.cpp.

References FixedSequenceCellCycleModel().

Referenced by serialize().

double FixedSequenceCellCycleModel::GetRate ( )

virtual

Overridden GetRate method.

Returns: rate the value of the rate parameter

Reimplemented from ExponentialG1GenerationalCellCycleModel.

Definition at line 102 of file FixedSequenceCellCycleModel.cpp.

References CellCycleTimesGenerator::GetRate(), and CellCycleTimesGenerator::Instance().

Referenced by serialize().

void FixedSequenceCellCycleModel::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 ExponentialG1GenerationalCellCycleModel.

Definition at line 118 of file FixedSequenceCellCycleModel.cpp.

References CHASTE_CLASS_EXPORT, CellCycleTimesGenerator::GetRate(), CellCycleTimesGenerator::Instance(), and AbstractSimpleGenerationalCellCycleModel::OutputCellCycleModelParameters().

Referenced by serialize().

template<class Archive >

void FixedSequenceCellCycleModel::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 82 of file FixedSequenceCellCycleModel.hpp.

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

void FixedSequenceCellCycleModel::SetG1Duration ( )

protectedvirtual

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

Reimplemented from ExponentialG1GenerationalCellCycleModel.

Definition at line 74 of file FixedSequenceCellCycleModel.cpp.

References CellCycleTimesGenerator::GetNextCellCycleTime(), CellCycleTimesGenerator::Instance(), AbstractPhaseBasedCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, and NEVER_REACHED.

Referenced by serialize().

void FixedSequenceCellCycleModel::SetRate ( double rate )

virtual

Overridden SetRate method.

Parameters