Chaste  Release::2017.1
VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo Class Reference

#include <VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.hpp>

+ Inheritance diagram for VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo:
+ Collaboration diagram for VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo:

Public Member Functions

 VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
void InitialiseOdeSystem (double wntConcentration, boost::shared_ptr< AbstractCellMutationState > pMutationState)
 
AbstractCellCycleModelCreateCellCycleModel ()
 
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from AbstractVanLeeuwen2009WntSwatCellCycleModel
 AbstractVanLeeuwen2009WntSwatCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
void Initialise ()
 
double GetMembraneBoundBetaCateninLevel ()
 
double GetCytoplasmicBetaCateninLevel ()
 
double GetNuclearBetaCateninLevel ()
 
- 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 ()
 
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< AbstractCellCycleModelOdeSolverGetOdeSolver () 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

 VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo (const VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo &rModel)
 
- Protected Member Functions inherited from AbstractVanLeeuwen2009WntSwatCellCycleModel
 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)
 

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< AbstractCellCycleModelOdeSolvermpOdeSolver
 
double mLastTime
 
bool mFinishedRunningOdes
 

Detailed Description

Concrete Van Leeuwen 2009 cell-cycle model, using hypothesis two (see paper).

Definition at line 44 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.hpp.

Constructor & Destructor Documentation

VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo ( const VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo 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 57 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.cpp.

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

Referenced by CreateCellCycleModel(), and serialize().

VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo ( boost::shared_ptr< AbstractCellCycleModelOdeSolver pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>())

Default constructor calls base class.

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

Definition at line 38 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.cpp.

References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().

Member Function Documentation

AbstractCellCycleModel * VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel ( )
virtual

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

Returns
the new cell-cycle model

Implements AbstractCellCycleModel.

Definition at line 88 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.cpp.

References VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo().

Referenced by serialize().

void VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::InitialiseOdeSystem ( double  wntConcentration,
boost::shared_ptr< AbstractCellMutationState pMutationState 
)
virtual

Overloaded method which allocates the ODE system using HYPOTHESIS TWO.

Parameters
wntConcentrationWnt concentration
pMutationStateMutation state

Implements AbstractVanLeeuwen2009WntSwatCellCycleModel.

Definition at line 83 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.cpp.

References CellCycleModelOdeHandler::mpOdeSystem.

Referenced by serialize(), and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo().

void VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual

Overridden OutputCellCycleModelParameters() method.

Parameters
rParamsFilethe file stream to which the parameters are output

Reimplemented from AbstractVanLeeuwen2009WntSwatCellCycleModel.

Definition at line 93 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.cpp.

References CHASTE_CLASS_EXPORT, and AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters().

Referenced by serialize().

template<class Archive >
void VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

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

Definition at line 58 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.hpp.

References CHASTE_CLASS_EXPORT, CreateCellCycleModel(), InitialiseOdeSystem(), OutputCellCycleModelParameters(), and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo().


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