Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
SimpleWntCellCycleModel Class Reference

#include <SimpleWntCellCycleModel.hpp>

+ Inheritance diagram for SimpleWntCellCycleModel:
+ Collaboration diagram for SimpleWntCellCycleModel:

Public Member Functions

 SimpleWntCellCycleModel ()
 
virtual void UpdateCellCyclePhase ()
 
virtual void InitialiseDaughterCell ()
 
virtual AbstractCellCycleModelCreateCellCycleModel ()
 
bool GetUseCellProliferativeTypeDependentG1Duration () const
 
void SetUseCellProliferativeTypeDependentG1Duration (bool useCellProliferativeTypeDependentG1Duration=true)
 
virtual bool CanCellTerminallyDifferentiate ()
 
double GetWntStemThreshold () const
 
void SetWntStemThreshold (double wntStemThreshold)
 
double GetWntTransitThreshold () const
 
void SetWntTransitThreshold (double wntTransitThreshold)
 
double GetWntLabelledThreshold () const
 
void SetWntLabelledThreshold (double wntLabelledThreshold)
 
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from AbstractSimplePhaseBasedCellCycleModel
 AbstractSimplePhaseBasedCellCycleModel ()
 
virtual ~AbstractSimplePhaseBasedCellCycleModel ()
 
virtual void ResetForDivision ()
 
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 ()
 
void OutputCellCycleModelInfo (out_stream &rParamsFile)
 
- Public Member Functions inherited from Identifiable
virtual ~Identifiable ()
 
std::string GetIdentifier () const
 

Protected Member Functions

double GetWntLevel () const
 
WntConcentrationType GetWntType ()
 
void SetG1Duration ()
 
 SimpleWntCellCycleModel (const SimpleWntCellCycleModel &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)
 

Protected Attributes

bool mUseCellProliferativeTypeDependentG1Duration
 
double mWntStemThreshold
 
double mWntTransitThreshold
 
double mWntLabelledThreshold
 
- 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
 

Private Member Functions

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

Friends

class boost::serialization::access
 

Detailed Description

Simple Wnt-dependent cell-cycle model.

Definition at line 46 of file SimpleWntCellCycleModel.hpp.

Constructor & Destructor Documentation

◆ SimpleWntCellCycleModel() [1/2]

SimpleWntCellCycleModel::SimpleWntCellCycleModel ( const SimpleWntCellCycleModel 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 55 of file SimpleWntCellCycleModel.cpp.

◆ SimpleWntCellCycleModel() [2/2]

SimpleWntCellCycleModel::SimpleWntCellCycleModel ( )

Constructor - just a default, mBirthTime is now set in the AbstractPhaseBasedCellCycleModel class. mG1Duration is set very high, it is set for the individual cells when InitialiseDaughterCell is called.

Definition at line 47 of file SimpleWntCellCycleModel.cpp.

Referenced by CreateCellCycleModel().

Member Function Documentation

◆ CanCellTerminallyDifferentiate()

bool SimpleWntCellCycleModel::CanCellTerminallyDifferentiate ( )
virtual

Overridden CanCellTerminallyDifferentiate() method.

Returns
whether cell can terminally differentiate

Reimplemented from AbstractCellCycleModel.

Definition at line 285 of file SimpleWntCellCycleModel.cpp.

◆ CreateCellCycleModel()

AbstractCellCycleModel * SimpleWntCellCycleModel::CreateCellCycleModel ( )
virtual

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

Returns
the new cell-cycle model

Implements AbstractCellCycleModel.

Reimplemented in SingleOdeWntCellCycleModel.

Definition at line 79 of file SimpleWntCellCycleModel.cpp.

References SimpleWntCellCycleModel().

◆ GetUseCellProliferativeTypeDependentG1Duration()

bool SimpleWntCellCycleModel::GetUseCellProliferativeTypeDependentG1Duration ( ) const
Returns
mUseCellProliferativeTypeDependentG1Duration

Definition at line 84 of file SimpleWntCellCycleModel.cpp.

References mUseCellProliferativeTypeDependentG1Duration.

◆ GetWntLabelledThreshold()

double SimpleWntCellCycleModel::GetWntLabelledThreshold ( ) const
Returns
mWntLabelledThreshold

Definition at line 314 of file SimpleWntCellCycleModel.cpp.

References mWntLabelledThreshold.

◆ GetWntLevel()

◆ GetWntStemThreshold()

double SimpleWntCellCycleModel::GetWntStemThreshold ( ) const
Returns
mWntStemThreshold

Definition at line 290 of file SimpleWntCellCycleModel.cpp.

References mWntStemThreshold.

◆ GetWntTransitThreshold()

double SimpleWntCellCycleModel::GetWntTransitThreshold ( ) const
Returns
mWntTransitThreshold

Definition at line 302 of file SimpleWntCellCycleModel.cpp.

References mWntTransitThreshold.

◆ GetWntType()

WntConcentrationType SimpleWntCellCycleModel::GetWntType ( )
protected
Returns
the type of Wnt concentration (LINEAR, RADIAL, EXPONENTIAL or NONE). This affects how the cell cycle phase is updated.

Definition at line 163 of file SimpleWntCellCycleModel.cpp.

References WntConcentration< DIM >::GetType(), WntConcentration< DIM >::Instance(), AbstractCellCycleModel::mDimension, NEVER_REACHED, and UNSIGNED_UNSET.

Referenced by InitialiseDaughterCell(), and UpdateCellCyclePhase().

◆ InitialiseDaughterCell()

void SimpleWntCellCycleModel::InitialiseDaughterCell ( )
virtual

◆ OutputCellCycleModelParameters()

void SimpleWntCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual

◆ serialize()

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

Archive the cell-cycle model, never used directly - boost uses this.

Parameters
archivethe archive
versionthe current version of this class

Definition at line 59 of file SimpleWntCellCycleModel.hpp.

References RandomNumberGenerator::Instance(), mUseCellProliferativeTypeDependentG1Duration, mWntLabelledThreshold, mWntStemThreshold, and mWntTransitThreshold.

◆ SetG1Duration()

void SimpleWntCellCycleModel::SetG1Duration ( )
protectedvirtual

Stochastically set the G1 duration. The G1 duration is taken from a normal distribution whose mean is the G1 duration given in AbstractPhaseBasedCellCycleModel, for the cell type, and whose standard deviation is 1.

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

Reimplemented from AbstractSimplePhaseBasedCellCycleModel.

Definition at line 94 of file SimpleWntCellCycleModel.cpp.

References AbstractPhaseBasedCellCycleModel::GetStemCellG1Duration(), AbstractPhaseBasedCellCycleModel::GetTransitCellG1Duration(), RandomNumberGenerator::Instance(), AbstractPhaseBasedCellCycleModel::mG1Duration, AbstractPhaseBasedCellCycleModel::mMinimumGapDuration, AbstractCellCycleModel::mpCell, mUseCellProliferativeTypeDependentG1Duration, NEVER_REACHED, and RandomNumberGenerator::NormalRandomDeviate().

◆ SetUseCellProliferativeTypeDependentG1Duration()

void SimpleWntCellCycleModel::SetUseCellProliferativeTypeDependentG1Duration ( bool  useCellProliferativeTypeDependentG1Duration = true)

Set whether Whether the duration of the G1 phase is dependent on cell type

Parameters
useCellProliferativeTypeDependentG1Duration- boolean, defaults to true.

Definition at line 89 of file SimpleWntCellCycleModel.cpp.

References mUseCellProliferativeTypeDependentG1Duration.

◆ SetWntLabelledThreshold()

void SimpleWntCellCycleModel::SetWntLabelledThreshold ( double  wntLabelledThreshold)

Set mWntLabelledThreshold.

Parameters
wntLabelledThresholdthe value of mWntLabelledThreshold

Definition at line 319 of file SimpleWntCellCycleModel.cpp.

References mWntLabelledThreshold.

◆ SetWntStemThreshold()

void SimpleWntCellCycleModel::SetWntStemThreshold ( double  wntStemThreshold)

Set mWntStemThreshold.

Parameters
wntStemThresholdthe value of mWntStemThreshold

Definition at line 295 of file SimpleWntCellCycleModel.cpp.

References mWntStemThreshold.

◆ SetWntTransitThreshold()

void SimpleWntCellCycleModel::SetWntTransitThreshold ( double  wntTransitThreshold)

Set mWntTransitThreshold.

Parameters
wntTransitThresholdthe value of mWntTransitThreshold

Definition at line 307 of file SimpleWntCellCycleModel.cpp.

References mWntTransitThreshold.

◆ UpdateCellCyclePhase()

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 51 of file SimpleWntCellCycleModel.hpp.

Member Data Documentation

◆ mUseCellProliferativeTypeDependentG1Duration

bool SimpleWntCellCycleModel::mUseCellProliferativeTypeDependentG1Duration
protected

Whether to use different mean G1 durations for different cell types. For use in SetG1Duration().

Definition at line 78 of file SimpleWntCellCycleModel.hpp.

Referenced by GetUseCellProliferativeTypeDependentG1Duration(), OutputCellCycleModelParameters(), serialize(), SetG1Duration(), and SetUseCellProliferativeTypeDependentG1Duration().

◆ mWntLabelledThreshold

double SimpleWntCellCycleModel::mWntLabelledThreshold
protected

Non-dimensionalized Wnt threshold, above which labelled cells progress through the cell cycle.

Definition at line 93 of file SimpleWntCellCycleModel.hpp.

Referenced by GetWntLabelledThreshold(), OutputCellCycleModelParameters(), serialize(), SetWntLabelledThreshold(), and UpdateCellCyclePhase().

◆ mWntStemThreshold

double SimpleWntCellCycleModel::mWntStemThreshold
protected

Non-dimensionalized Wnt threshold, above which cells behave as stem cells.

Definition at line 83 of file SimpleWntCellCycleModel.hpp.

Referenced by GetWntStemThreshold(), OutputCellCycleModelParameters(), serialize(), SetWntStemThreshold(), and UpdateCellCyclePhase().

◆ mWntTransitThreshold

double SimpleWntCellCycleModel::mWntTransitThreshold
protected

Non-dimensionalized Wnt threshold, above which cells progress through the cell cycle.

Definition at line 88 of file SimpleWntCellCycleModel.hpp.

Referenced by GetWntTransitThreshold(), OutputCellCycleModelParameters(), serialize(), SetWntTransitThreshold(), and UpdateCellCyclePhase().


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