Chaste  Release::2017.1
StochasticOxygenBasedCellCycleModel Class Reference

#include <StochasticOxygenBasedCellCycleModel.hpp>

+ Inheritance diagram for StochasticOxygenBasedCellCycleModel:
+ Collaboration diagram for StochasticOxygenBasedCellCycleModel:

Public Member Functions

 StochasticOxygenBasedCellCycleModel ()
 
void InitialiseDaughterCell ()
 
void Initialise ()
 
void ResetForDivision ()
 
double GetG2Duration () const
 
AbstractCellCycleModelCreateCellCycleModel ()
 
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from SimpleOxygenBasedCellCycleModel
 SimpleOxygenBasedCellCycleModel ()
 
void UpdateCellCyclePhase ()
 
void UpdateHypoxicDuration ()
 
double GetCurrentHypoxicDuration () const
 
double GetCurrentHypoxiaOnsetTime () const
 
double GetHypoxicConcentration () const
 
void SetHypoxicConcentration (double hypoxicConcentration)
 
double GetQuiescentConcentration () const
 
void SetQuiescentConcentration (double quiescentConcentration)
 
double GetCriticalHypoxicDuration () const
 
void SetCriticalHypoxicDuration (double criticalHypoxicDuration)
 
void SetCurrentHypoxiaOnsetTime (double currentHypoxiaOnsetTime)
 
- Public Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
 AbstractSimplePhaseBasedCellCycleModel ()
 
virtual ~AbstractSimplePhaseBasedCellCycleModel ()
 
- 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 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

 StochasticOxygenBasedCellCycleModel (const StochasticOxygenBasedCellCycleModel &rModel)
 
- Protected Member Functions inherited from SimpleOxygenBasedCellCycleModel
 SimpleOxygenBasedCellCycleModel (const SimpleOxygenBasedCellCycleModel &rModel)
 
- Protected Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
virtual void SetG1Duration ()
 
 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)
 
void GenerateStochasticG2Duration ()
 

Private Attributes

double mStochasticG2Duration
 

Friends

class TestSimpleCellCycleModels
 
class boost::serialization::access
 

Additional Inherited Members

- Protected Attributes inherited from SimpleOxygenBasedCellCycleModel
double mCurrentHypoxicDuration
 
double mCurrentHypoxiaOnsetTime
 
double mHypoxicConcentration
 
double mQuiescentConcentration
 
double mCriticalHypoxicDuration
 
- 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

Stochastic oxygen-based cell-cycle model.

A simple oxygen-dependent cell-cycle model that inherits from SimpleOxygenBasedCellCycleModel and in addition spends a random duration in G2 phase.

Definition at line 49 of file StochasticOxygenBasedCellCycleModel.hpp.

Constructor & Destructor Documentation

StochasticOxygenBasedCellCycleModel::StochasticOxygenBasedCellCycleModel ( const StochasticOxygenBasedCellCycleModel 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
rModelthe cell cycle model to copy.

Definition at line 43 of file StochasticOxygenBasedCellCycleModel.cpp.

StochasticOxygenBasedCellCycleModel::StochasticOxygenBasedCellCycleModel ( )

Constructor.

Definition at line 38 of file StochasticOxygenBasedCellCycleModel.cpp.

Referenced by CreateCellCycleModel().

Member Function Documentation

AbstractCellCycleModel * StochasticOxygenBasedCellCycleModel::CreateCellCycleModel ( )
virtual

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

Returns
new cell-cycle model

Reimplemented from SimpleOxygenBasedCellCycleModel.

Definition at line 106 of file StochasticOxygenBasedCellCycleModel.cpp.

References StochasticOxygenBasedCellCycleModel().

void StochasticOxygenBasedCellCycleModel::GenerateStochasticG2Duration ( )
private

Stochastically set the G2 duration. Called on cell creation at the start of a simulation, and for both parent and daughter cells at cell division.

Definition at line 67 of file StochasticOxygenBasedCellCycleModel.cpp.

References AbstractPhaseBasedCellCycleModel::GetG2Duration(), RandomNumberGenerator::Instance(), AbstractPhaseBasedCellCycleModel::mMinimumGapDuration, mStochasticG2Duration, and RandomNumberGenerator::NormalRandomDeviate().

Referenced by Initialise(), InitialiseDaughterCell(), and ResetForDivision().

double StochasticOxygenBasedCellCycleModel::GetG2Duration ( ) const
virtual
Returns
mStochasticG2Duration.

Reimplemented from AbstractPhaseBasedCellCycleModel.

Definition at line 101 of file StochasticOxygenBasedCellCycleModel.cpp.

References mStochasticG2Duration.

void StochasticOxygenBasedCellCycleModel::Initialise ( void  )
virtual

Initialise the cell-cycle model at the start of a simulation.

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Definition at line 89 of file StochasticOxygenBasedCellCycleModel.cpp.

References GenerateStochasticG2Duration(), and AbstractSimplePhaseBasedCellCycleModel::Initialise().

void StochasticOxygenBasedCellCycleModel::InitialiseDaughterCell ( )
virtual
void StochasticOxygenBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual

Overridden OutputCellCycleModelParameters() method.

Parameters
rParamsFilethe file stream to which the parameters are output

Reimplemented from SimpleOxygenBasedCellCycleModel.

Definition at line 111 of file StochasticOxygenBasedCellCycleModel.cpp.

References CHASTE_CLASS_EXPORT, and SimpleOxygenBasedCellCycleModel::OutputCellCycleModelParameters().

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

Boost Serialization method for archiving/checkpointing

Parameters
archiveThe boost archive.
versionThe current version of this class.

Definition at line 63 of file StochasticOxygenBasedCellCycleModel.hpp.

References SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), RandomNumberGenerator::Instance(), and mStochasticG2Duration.

Member Data Documentation

double StochasticOxygenBasedCellCycleModel::mStochasticG2Duration
private

The duration of the G2 phase, set stochastically.

Definition at line 77 of file StochasticOxygenBasedCellCycleModel.hpp.

Referenced by GenerateStochasticG2Duration(), GetG2Duration(), and serialize().


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