Chaste  Release::3.4
VanLeeuwen2009WntSwatCellCycleModelHypothesisOne Class Reference

#include <VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp>

+ Inheritance diagram for VanLeeuwen2009WntSwatCellCycleModelHypothesisOne:
+ Collaboration diagram for VanLeeuwen2009WntSwatCellCycleModelHypothesisOne:

Public Member Functions

 VanLeeuwen2009WntSwatCellCycleModelHypothesisOne (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 AbstractOdeBasedCellCycleModel
 AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
 
virtual ~AbstractOdeBasedCellCycleModel ()
 
double GetOdeStopTime ()
 
void SetBirthTime (double birthTime)
 
std::vector< doubleGetProteinConcentrations () const
 
void SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)
 
void SetFinishedRunningOdes (bool finishedRunningOdes)
 
void SetDivideTime (double divideTime)
 
void SetG2PhaseStartTime (double g2PhaseStartTime)
 
- Public Member Functions inherited from AbstractCellCycleModel
 AbstractCellCycleModel ()
 
virtual ~AbstractCellCycleModel ()
 
void SetCell (CellPtr pCell)
 
virtual void InitialiseDaughterCell ()
 
CellPtr GetCell ()
 
void SetDimension (unsigned dimension)
 
unsigned GetDimension ()
 
double GetBirthTime () const
 
double GetAge ()
 
virtual bool ReadyToDivide ()
 
CellCyclePhase GetCurrentCellCyclePhase ()
 
virtual double GetG1Duration ()
 
double GetStemCellG1Duration ()
 
double GetTransitCellG1Duration ()
 
double GetSG2MDuration ()
 
virtual double GetSDuration ()
 
virtual double GetG2Duration ()
 
virtual double GetMDuration ()
 
virtual void SetStemCellG1Duration (double stemCellG1Duration)
 
virtual void SetTransitCellG1Duration (double transitCellG1Duration)
 
void SetSDuration (double sDuration)
 
void SetG2Duration (double g2Duration)
 
void SetMDuration (double mDuration)
 
double GetMinimumGapDuration ()
 
void SetMinimumGapDuration (double minimumGapDuration)
 
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)
 

Private Member Functions

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

Friends

class boost::serialization::access
 

Additional Inherited Members

- Protected Member Functions inherited from AbstractWntOdeBasedCellCycleModel
double GetWntLevel ()
 
void UpdateCellCyclePhase ()
 
- Protected Member Functions inherited from CellCycleModelOdeHandler
bool SolveOdeToTime (double currentTime)
 
- Protected Attributes inherited from AbstractOdeBasedCellCycleModel
double mDivideTime
 
bool mFinishedRunningOdes
 
double mG2PhaseStartTime
 
- Protected Attributes inherited from AbstractCellCycleModel
CellPtr mpCell
 
double mBirthTime
 
CellCyclePhase mCurrentCellCyclePhase
 
double mG1Duration
 
bool mReadyToDivide
 
unsigned mDimension
 
double mMinimumGapDuration
 
double mStemCellG1Duration
 
double mTransitCellG1Duration
 
double mSDuration
 
double mG2Duration
 
double mMDuration
 
- Protected Attributes inherited from CellCycleModelOdeHandler
double mDt
 
AbstractOdeSystemmpOdeSystem
 
boost::shared_ptr
< AbstractCellCycleModelOdeSolver
mpOdeSolver
 
double mLastTime
 

Detailed Description

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

Definition at line 44 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp.

Constructor & Destructor Documentation

VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::VanLeeuwen2009WntSwatCellCycleModelHypothesisOne ( 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 VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp.

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

Referenced by CreateCellCycleModel().

Member Function Documentation

AbstractCellCycleModel * VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::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 62 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp.

References AbstractWntOdeBasedCellCycleModel::GetWntLevel(), InitialiseOdeSystem(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mDimension, AbstractOdeBasedCellCycleModel::mDivideTime, AbstractOdeBasedCellCycleModel::mFinishedRunningOdes, AbstractCellCycleModel::mG2Duration, AbstractOdeBasedCellCycleModel::mG2PhaseStartTime, CellCycleModelOdeHandler::mLastTime, AbstractCellCycleModel::mMDuration, AbstractCellCycleModel::mMinimumGapDuration, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSolver, CellCycleModelOdeHandler::mpOdeSystem, AbstractCellCycleModel::mSDuration, AbstractCellCycleModel::mStemCellG1Duration, AbstractCellCycleModel::mTransitCellG1Duration, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), AbstractOdeBasedCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetDimension(), AbstractOdeBasedCellCycleModel::SetDivideTime(), AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes(), AbstractCellCycleModel::SetG2Duration(), AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime(), CellCycleModelOdeHandler::SetLastTime(), AbstractCellCycleModel::SetMDuration(), AbstractCellCycleModel::SetMinimumGapDuration(), AbstractCellCycleModel::SetSDuration(), CellCycleModelOdeHandler::SetStateVariables(), AbstractCellCycleModel::SetStemCellG1Duration(), AbstractCellCycleModel::SetTransitCellG1Duration(), and VanLeeuwen2009WntSwatCellCycleModelHypothesisOne().

void VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::InitialiseOdeSystem ( double  wntConcentration,
boost::shared_ptr< AbstractCellMutationState pMutationState 
)
virtual

Overloaded method which allocates the ODE system using HYPOTHESIS ONE.

Parameters
wntConcentrationWnt concentration
pMutationStateMutation state

Implements AbstractVanLeeuwen2009WntSwatCellCycleModel.

Definition at line 57 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp.

References CellCycleModelOdeHandler::mpOdeSystem.

Referenced by CreateCellCycleModel().

void VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::OutputCellCycleModelParameters ( out_stream &  rParamsFile)
virtual

Outputs cell-cycle model parameters to file.

Parameters
rParamsFilethe file stream to which the parameters are output

Reimplemented from AbstractVanLeeuwen2009WntSwatCellCycleModel.

Definition at line 104 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.cpp.

References AbstractVanLeeuwen2009WntSwatCellCycleModel::OutputCellCycleModelParameters().

template<class Archive >
void VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::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 57 of file VanLeeuwen2009WntSwatCellCycleModelHypothesisOne.hpp.


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