Chaste  Release::2017.1
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
GammaG1CellCycleModel Class Reference

#include <GammaG1CellCycleModel.hpp>

+ Inheritance diagram for GammaG1CellCycleModel:
+ Collaboration diagram for GammaG1CellCycleModel:

Public Member Functions

 GammaG1CellCycleModel ()
 
void SetG1Duration ()
 
AbstractCellCycleModel * CreateCellCycleModel ()
 
void SetShape (double shape)
 
void SetScale (double scale)
 
double GetShape () const
 
double GetScale () const
 
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
 AbstractSimplePhaseBasedCellCycleModel ()
 
virtual ~AbstractSimplePhaseBasedCellCycleModel ()
 
virtual void ResetForDivision ()
 
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
 
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

 GammaG1CellCycleModel (const GammaG1CellCycleModel &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 mShape
 
double mScale
 

Friends

class TestSimpleCellCycleModels
 
class boost::serialization::access
 

Additional Inherited Members

- 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 stochastic cell-cycle model where cells keep dividing with a stochastic G1 duration drawn from a gamma distribution with specified shape and scale parameters.

Definition at line 46 of file GammaG1CellCycleModel.hpp.

Constructor & Destructor Documentation

GammaG1CellCycleModel::GammaG1CellCycleModel ( const GammaG1CellCycleModel &  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 48 of file GammaG1CellCycleModel.cpp.

GammaG1CellCycleModel::GammaG1CellCycleModel ( )

Constructor.

Definition at line 41 of file GammaG1CellCycleModel.cpp.

Referenced by CreateCellCycleModel(), and serialize().

Member Function Documentation

AbstractCellCycleModel * GammaG1CellCycleModel::CreateCellCycleModel ( )
virtual

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

Returns
a pointer to the GammaG1CellCycleModel created.

Implements AbstractCellCycleModel.

Definition at line 69 of file GammaG1CellCycleModel.cpp.

References GammaG1CellCycleModel().

Referenced by serialize().

double GammaG1CellCycleModel::GetScale ( ) const
Returns
mScale.

Definition at line 107 of file GammaG1CellCycleModel.cpp.

References mScale.

Referenced by serialize().

double GammaG1CellCycleModel::GetShape ( ) const
Returns
mShape.

Definition at line 102 of file GammaG1CellCycleModel.cpp.

References mShape.

Referenced by serialize().

void GammaG1CellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual

Overridden OutputCellCycleModelParameters() method.

Parameters
rParamsFilethe file stream to which the parameters are output

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Definition at line 112 of file GammaG1CellCycleModel.cpp.

References CHASTE_CLASS_EXPORT, mScale, mShape, and AbstractSimplePhaseBasedCellCycleModel::OutputCellCycleModelParameters().

Referenced by serialize().

template<class Archive >
void GammaG1CellCycleModel::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 67 of file GammaG1CellCycleModel.hpp.

References CHASTE_CLASS_EXPORT, CreateCellCycleModel(), GammaG1CellCycleModel(), GetScale(), SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), GetShape(), RandomNumberGenerator::Instance(), mScale, mShape, OutputCellCycleModelParameters(), SetG1Duration(), SetScale(), and SetShape().

void GammaG1CellCycleModel::SetG1Duration ( )
virtual

Overridden SetG1Duration().

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Definition at line 74 of file GammaG1CellCycleModel.cpp.

References RandomNumberGenerator::GammaRandomDeviate(), RandomNumberGenerator::Instance(), AbstractPhaseBasedCellCycleModel::mG1Duration, AbstractCellCycleModel::mpCell, mScale, mShape, and NEVER_REACHED.

Referenced by serialize().

void GammaG1CellCycleModel::SetScale ( double  scale)
Returns
mScale.
Parameters
scalethe value of the scale parameter

Definition at line 97 of file GammaG1CellCycleModel.cpp.

References mScale.

Referenced by serialize().

void GammaG1CellCycleModel::SetShape ( double  shape)

Set mShape.

Parameters
shapethe value of the shape parameter

Definition at line 92 of file GammaG1CellCycleModel.cpp.

References mShape.

Referenced by serialize().

Friends And Related Function Documentation

friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 59 of file GammaG1CellCycleModel.hpp.

Member Data Documentation

double GammaG1CellCycleModel::mScale
private

The scale parameter of the gamma distribution. This must be a positive real number.

Definition at line 56 of file GammaG1CellCycleModel.hpp.

Referenced by GetScale(), OutputCellCycleModelParameters(), serialize(), SetG1Duration(), and SetScale().

double GammaG1CellCycleModel::mShape
private

The shape parameter of the gamma distribution. This must be a positive real number.

Definition at line 53 of file GammaG1CellCycleModel.hpp.

Referenced by GetShape(), OutputCellCycleModelParameters(), serialize(), SetG1Duration(), and SetShape().

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