Chaste Release::3.1
AbstractOdeBasedCellCycleModel Class Reference

#include <AbstractOdeBasedCellCycleModel.hpp>

Inheritance diagram for AbstractOdeBasedCellCycleModel:
Collaboration diagram for AbstractOdeBasedCellCycleModel:

List of all members.

Public Member Functions

 AbstractOdeBasedCellCycleModel (double lastTime=SimulationTime::Instance()->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
virtual ~AbstractOdeBasedCellCycleModel ()
virtual void UpdateCellCyclePhase ()
double GetOdeStopTime ()
void SetBirthTime (double birthTime)
std::vector< doubleGetProteinConcentrations () const
void SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)
virtual void ResetForDivision ()
void SetFinishedRunningOdes (bool finishedRunningOdes)
void SetDivideTime (double divideTime)
void SetG2PhaseStartTime (double g2PhaseStartTime)
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)

Protected Attributes

double mDivideTime
bool mFinishedRunningOdes
double mG2PhaseStartTime

Private Member Functions

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

Friends

class boost::serialization::access

Detailed Description

This class contains all the things common to standard cell cycle ODE models for intracellular protein concentrations (along the lines of Tyson & Novak), such as solving the ODEs until a stopping condition is met.

Definition at line 55 of file AbstractOdeBasedCellCycleModel.hpp.


Constructor & Destructor Documentation

AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel ( double  lastTime = SimulationTime::Instance()->GetTime(),
boost::shared_ptr< AbstractCellCycleModelOdeSolver pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() 
)

Creates an AbstractOdeBasedCellCycleModel, calls SetBirthTime on the AbstractCellCycleModel to make sure that can be set 'back in time' for cells which did not divide at the current time.

Parameters:
lastTimeThe birth time of the cell / last time model was evaluated (defaults to the current SimulationTime)
pOdeSolverAn optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 41 of file AbstractOdeBasedCellCycleModel.cpp.

References SetBirthTime().

AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel ( ) [virtual]

Destructor.

Definition at line 51 of file AbstractOdeBasedCellCycleModel.cpp.


Member Function Documentation

double AbstractOdeBasedCellCycleModel::GetOdeStopTime ( )

Get the time at which the ODE stopping event occurred. Only called in those subclasses for which stopping events are defined.

Returns:
the time at which the ODE system reached its stopping event

Definition at line 158 of file AbstractOdeBasedCellCycleModel.cpp.

References DOUBLE_UNSET, and CellCycleModelOdeHandler::mpOdeSolver.

Referenced by AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase(), and UpdateCellCyclePhase().

std::vector< double > AbstractOdeBasedCellCycleModel::GetProteinConcentrations ( ) const

Returns the protein concentrations at the current time (useful for tests)

NB: Will copy the vector - you can't use this to modify the concentrations.

Definition at line 62 of file AbstractOdeBasedCellCycleModel.cpp.

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

void AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile) [virtual]
void AbstractOdeBasedCellCycleModel::ResetForDivision ( ) [virtual]

For a naturally cycling model this does not need to be overridden in the subclasses. But most models should override this function and then call AbstractOdeBasedCellCycleModel::ResetForDivision() from inside their version.

Reimplemented from AbstractCellCycleModel.

Reimplemented in Alarcon2004OxygenBasedCellCycleModel, TysonNovakCellCycleModel, AbstractWntOdeBasedCellCycleModel, and StochasticWntCellCycleModel.

Definition at line 147 of file AbstractOdeBasedCellCycleModel.cpp.

References AbstractCellCycleModel::mBirthTime, mDivideTime, mFinishedRunningOdes, AbstractCellCycleModel::mG1Duration, and CellCycleModelOdeHandler::mLastTime.

template<class Archive >
void AbstractOdeBasedCellCycleModel::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]
void AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly ( double  lastTime,
std::vector< double proteinConcentrations 
)

Sets the protein concentrations and time when the model was last evaluated - should only be called by tests

Parameters:
lastTimethe SimulationTime at which the protein concentrations apply
proteinConcentrationsa standard vector of doubles of protein concentrations

Definition at line 68 of file AbstractOdeBasedCellCycleModel.cpp.

References CellCycleModelOdeHandler::mLastTime, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().


Friends And Related Function Documentation


Member Data Documentation


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