Chaste  Release::2018.1
AbstractVanLeeuwen2009WntSwatCellCycleModel Class Referenceabstract

#include <AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp>

+ Inheritance diagram for AbstractVanLeeuwen2009WntSwatCellCycleModel:
+ Collaboration diagram for AbstractVanLeeuwen2009WntSwatCellCycleModel:

Public Member Functions

 AbstractVanLeeuwen2009WntSwatCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
void Initialise ()
 
double GetMembraneBoundBetaCateninLevel ()
 
double GetCytoplasmicBetaCateninLevel ()
 
double GetNuclearBetaCateninLevel ()
 
virtual void InitialiseOdeSystem (double wntConcentration, boost::shared_ptr< AbstractCellMutationState > pMutationState)=0
 
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from AbstractWntOdeBasedCellCycleModel
 AbstractWntOdeBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
virtual ~AbstractWntOdeBasedCellCycleModel ()
 
void ResetForDivision ()
 
void UpdateCellProliferativeType ()
 
double GetAverageTransitCellCycleTime ()
 
double GetAverageStemCellCycleTime ()
 
virtual bool CanCellTerminallyDifferentiate ()
 
- Public Member Functions inherited from AbstractOdeBasedPhaseBasedCellCycleModel
 AbstractOdeBasedPhaseBasedCellCycleModel (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
virtual ~AbstractOdeBasedPhaseBasedCellCycleModel ()
 
double GetOdeStopTime ()
 
void SetBirthTime (double birthTime)
 
- 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)
 
double GetMinimumGapDuration () const
 
void SetMinimumGapDuration (double minimumGapDuration)
 
- Public Member Functions inherited from AbstractCellCycleModel
 AbstractCellCycleModel ()
 
virtual ~AbstractCellCycleModel ()
 
void SetCell (CellPtr pCell)
 
virtual void InitialiseDaughterCell ()
 
CellPtr GetCell ()
 
void SetDimension (unsigned dimension)
 
unsigned GetDimension () const
 
double GetBirthTime () const
 
double GetAge ()
 
virtual AbstractCellCycleModelCreateCellCycleModel ()=0
 
void OutputCellCycleModelInfo (out_stream &rParamsFile)
 
- Public Member Functions inherited from Identifiable
virtual ~Identifiable ()
 
std::string GetIdentifier () const
 
- Public Member Functions inherited from CellCycleModelOdeHandler
 CellCycleModelOdeHandler (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
virtual ~CellCycleModelOdeHandler ()
 
AbstractOdeSystemGetOdeSystem () const
 
void SetOdeSystem (AbstractOdeSystem *pOdeSystem)
 
const boost::shared_ptr
< AbstractCellCycleModelOdeSolver
GetOdeSolver () const
 
void SetLastTime (double lastTime)
 
double GetDt ()
 
void SetDt (double timeStep)
 
void SetStateVariables (const std::vector< double > &rStateVariables)
 
std::vector< doubleGetProteinConcentrations () const
 
void SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)
 

Protected Member Functions

 AbstractVanLeeuwen2009WntSwatCellCycleModel (const AbstractVanLeeuwen2009WntSwatCellCycleModel &rModel)
 
- Protected Member Functions inherited from AbstractWntOdeBasedCellCycleModel
double GetWntLevel () const
 
void UpdateCellCyclePhase ()
 
 AbstractWntOdeBasedCellCycleModel (const AbstractWntOdeBasedCellCycleModel &rModel)
 
- Protected Member Functions inherited from AbstractOdeBasedPhaseBasedCellCycleModel
 AbstractOdeBasedPhaseBasedCellCycleModel (const AbstractOdeBasedPhaseBasedCellCycleModel &rModel)
 
- Protected Member Functions inherited from AbstractPhaseBasedCellCycleModel
 AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel)
 
- Protected Member Functions inherited from AbstractCellCycleModel
 AbstractCellCycleModel (const AbstractCellCycleModel &rModel)
 
- Protected Member Functions inherited from CellCycleModelOdeHandler
 CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler)
 
bool SolveOdeToTime (double currentTime)
 

Private Member Functions

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

Friends

class boost::serialization::access
 

Additional Inherited Members

- Protected Attributes inherited from AbstractOdeBasedPhaseBasedCellCycleModel
double mDivideTime
 
double mG2PhaseStartTime
 
- 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
 
- Protected Attributes inherited from CellCycleModelOdeHandler
double mDt
 
AbstractOdeSystemmpOdeSystem
 
boost::shared_ptr
< AbstractCellCycleModelOdeSolver
mpOdeSolver
 
double mLastTime
 
bool mFinishedRunningOdes
 

Detailed Description

Wnt-dependent cell-cycle model.

Definition at line 53 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp.

Constructor & Destructor Documentation

AbstractVanLeeuwen2009WntSwatCellCycleModel::AbstractVanLeeuwen2009WntSwatCellCycleModel ( const AbstractVanLeeuwen2009WntSwatCellCycleModel 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 46 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

AbstractVanLeeuwen2009WntSwatCellCycleModel::AbstractVanLeeuwen2009WntSwatCellCycleModel ( boost::shared_ptr< AbstractCellCycleModelOdeSolver pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>())

Default constructor.

Parameters
pOdeSolverAn optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 41 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

Member Function Documentation

void AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters ( double  currentTime)
privatevirtual

Adjust any ODE parameters needed before solving until currentTime.

Parameters
currentTimethe time up to which the system will be solved.

Reimplemented from CellCycleModelOdeHandler.

Definition at line 111 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

References AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

void AbstractVanLeeuwen2009WntSwatCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel ( )
privatevirtual

Called by Initialise() and UpdateCellProliferativeType() only. Updates mCellProliferativeType to match mpOdeSystem's beta-catenin levels

This carries out the work for UpdateCellProliferativeType(); But does not check the current time so it can be used by the initialise method.

Implements AbstractWntOdeBasedCellCycleModel.

Definition at line 64 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.

References AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

Referenced by Initialise().

double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel ( )
double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel ( )
double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetNuclearBetaCateninLevel ( )
virtual void AbstractVanLeeuwen2009WntSwatCellCycleModel::InitialiseOdeSystem ( double  wntConcentration,
boost::shared_ptr< AbstractCellMutationState pMutationState 
)
pure virtual

Allocate the mOdeSystem variable using the appropriate hypothesis (one or two).

As this method is pure virtual, it must be overridden in subclasses.

Parameters
wntConcentrationWnt concentration
pMutationStateMutation state

Implemented in VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.

Referenced by Initialise().

void AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual
template<class Archive >
void AbstractVanLeeuwen2009WntSwatCellCycleModel::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 66 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp.

Friends And Related Function Documentation

friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 58 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp.


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