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StochasticDurationGenerationBasedCellCycleModel Class Reference

#include <StochasticDurationGenerationBasedCellCycleModel.hpp>

+ Inheritance diagram for StochasticDurationGenerationBasedCellCycleModel:
+ Collaboration diagram for StochasticDurationGenerationBasedCellCycleModel:

Public Member Functions

 StochasticDurationGenerationBasedCellCycleModel ()
 
AbstractCellCycleModel * CreateCellCycleModel ()
 
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from AbstractSimpleGenerationBasedCellCycleModel
 AbstractSimpleGenerationBasedCellCycleModel ()
 
virtual ~AbstractSimpleGenerationBasedCellCycleModel ()
 
void ResetForDivision ()
 
void InitialiseDaughterCell ()
 
void SetGeneration (unsigned generation)
 
unsigned GetGeneration () const
 
void SetMaxTransitGenerations (unsigned maxTransitGenerations)
 
unsigned GetMaxTransitGenerations () const
 
- Public Member Functions inherited from AbstractSimpleCellCycleModel
 AbstractSimpleCellCycleModel ()
 
virtual ~AbstractSimpleCellCycleModel ()
 
virtual void UpdateCellCyclePhase ()
 
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
 

Protected Member Functions

void SetG1Duration ()
 

Private Member Functions

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

Friends

class TestSimpleCellCycleModels
 
class boost::serialization::access
 

Additional Inherited Members

- Protected Attributes inherited from AbstractSimpleGenerationBasedCellCycleModel
unsigned mGeneration
 
unsigned mMaxTransitGenerations
 
- 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 employed by Meineke et al (2001) in their off-lattice model of the intestinal crypt (doi:10.1046/j.0960-7722.2001.00216.x).

Definition at line 46 of file StochasticDurationGenerationBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

StochasticDurationGenerationBasedCellCycleModel::StochasticDurationGenerationBasedCellCycleModel ( )

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 StochasticDurationGenerationBasedCellCycleModel.cpp.

Referenced by CreateCellCycleModel().

Member Function Documentation

AbstractCellCycleModel * StochasticDurationGenerationBasedCellCycleModel::CreateCellCycleModel ( )
virtual

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

Returns
new cell-cycle model

Implements AbstractCellCycleModel.

Definition at line 46 of file StochasticDurationGenerationBasedCellCycleModel.cpp.

References AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mG2Duration, AbstractSimpleGenerationBasedCellCycleModel::mGeneration, AbstractSimpleGenerationBasedCellCycleModel::mMaxTransitGenerations, AbstractCellCycleModel::mMDuration, AbstractCellCycleModel::mMinimumGapDuration, AbstractCellCycleModel::mSDuration, AbstractCellCycleModel::mStemCellG1Duration, AbstractCellCycleModel::mTransitCellG1Duration, AbstractCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetG2Duration(), AbstractSimpleGenerationBasedCellCycleModel::SetGeneration(), AbstractSimpleGenerationBasedCellCycleModel::SetMaxTransitGenerations(), AbstractCellCycleModel::SetMDuration(), AbstractCellCycleModel::SetMinimumGapDuration(), AbstractCellCycleModel::SetSDuration(), AbstractCellCycleModel::SetStemCellG1Duration(), AbstractCellCycleModel::SetTransitCellG1Duration(), and StochasticDurationGenerationBasedCellCycleModel().

void StochasticDurationGenerationBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual

Outputs cell cycle model parameters to file.

Parameters
rParamsFilethe file stream to which the parameters are output

Reimplemented from AbstractSimpleGenerationBasedCellCycleModel.

Definition at line 105 of file StochasticDurationGenerationBasedCellCycleModel.cpp.

References AbstractSimpleGenerationBasedCellCycleModel::OutputCellCycleModelParameters().

template<class Archive >
void StochasticDurationGenerationBasedCellCycleModel::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Archive the cell-cycle model and random number generator, never used directly - boost uses this.

Parameters
archivethe archive
versionthe current version of this class

Definition at line 61 of file StochasticDurationGenerationBasedCellCycleModel.hpp.

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

void StochasticDurationGenerationBasedCellCycleModel::SetG1Duration ( )
protectedvirtual

Stochastically set the G1 duration. 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 81 of file StochasticDurationGenerationBasedCellCycleModel.cpp.

References AbstractCellCycleModel::GetStemCellG1Duration(), AbstractCellCycleModel::GetTransitCellG1Duration(), RandomNumberGenerator::Instance(), AbstractCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, NEVER_REACHED, and RandomNumberGenerator::ranf().

Friends And Related Function Documentation

friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 53 of file StochasticDurationGenerationBasedCellCycleModel.hpp.

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