Chaste Release::3.1
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Friends
CellCycleModelOdeHandler Class Reference

#include <CellCycleModelOdeHandler.hpp>

Inheritance diagram for CellCycleModelOdeHandler:
Collaboration diagram for CellCycleModelOdeHandler:

List of all members.

Public Member Functions

 CellCycleModelOdeHandler (double lastTime=SimulationTime::Instance()->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
virtual ~CellCycleModelOdeHandler ()
AbstractOdeSystem * GetOdeSystem () 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)

Protected Member Functions

bool SolveOdeToTime (double currentTime)
virtual void AdjustOdeParameters (double currentTime)

Protected Attributes

double mDt
AbstractOdeSystem * mpOdeSystem
boost::shared_ptr
< AbstractCellCycleModelOdeSolver > 		mpOdeSolver
double mLastTime

Private Member Functions

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

Friends

class boost::serialization::access

Detailed Description

This class contains the functionality for running ODEs as part of a cell cycle model. It is designed to be used as an additional base class for models which require this functionality.

Definition at line 51 of file CellCycleModelOdeHandler.hpp.

Constructor & Destructor Documentation

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

Constructor.

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 38 of file CellCycleModelOdeHandler.cpp.

CellCycleModelOdeHandler::~CellCycleModelOdeHandler ( ) [virtual]

Destructor.

Definition at line 47 of file CellCycleModelOdeHandler.cpp.

References mpOdeSystem.

Member Function Documentation

void CellCycleModelOdeHandler::AdjustOdeParameters ( double  currentTime) [protected, virtual]

Adjust any ODE parameters needed before solving until currentTime. Defaults to do nothing.

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

Reimplemented in Alarcon2004OxygenBasedCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, SingleOdeWntCellCycleModel, and WntCellCycleModel.

Definition at line 113 of file CellCycleModelOdeHandler.cpp.

Referenced by SolveOdeToTime().

double CellCycleModelOdeHandler::GetDt ( )

Get method for mDt, which sets it to a default value if it hasn't been set by calling SetDt.

Definition at line 75 of file CellCycleModelOdeHandler.cpp.

References DOUBLE_UNSET, SimulationTime::GetTimeStep(), SimulationTime::Instance(), mDt, and mpOdeSolver.

Referenced by SolveOdeToTime().

const boost::shared_ptr< AbstractCellCycleModelOdeSolver > CellCycleModelOdeHandler::GetOdeSolver ( ) const
Returns:
mpOdeSolver

Definition at line 65 of file CellCycleModelOdeHandler.cpp.

References mpOdeSolver.

AbstractOdeSystem * CellCycleModelOdeHandler::GetOdeSystem ( ) const

Get mpOdeSystem.

Definition at line 60 of file CellCycleModelOdeHandler.cpp.

References mpOdeSystem.

Referenced by DeltaNotchCellCycleModel::CreateCellCycleModel().

template<class Archive >
void CellCycleModelOdeHandler::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Archive the object and its member variables.

Parameters:
archivethe archive
versionthe current version of this class

Reimplemented in AbstractOdeBasedCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, DeltaNotchCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, SingleOdeWntCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.

Definition at line 64 of file CellCycleModelOdeHandler.hpp.

References mDt, mLastTime, mpOdeSolver, and mpOdeSystem.

void CellCycleModelOdeHandler::SetDt ( double  timeStep)

Set the time step to use to solve the ODE system. For some adaptive solvers (e.g. CVODE) this is the maximum step to use.

Parameters:
timeSteptime step to use

Definition at line 70 of file CellCycleModelOdeHandler.cpp.

References mDt.

Referenced by Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel(), DeltaNotchCellCycleModel::DeltaNotchCellCycleModel(), SingleOdeWntCellCycleModel::SingleOdeWntCellCycleModel(), TysonNovakCellCycleModel::TysonNovakCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::VanLeeuwen2009WntSwatCellCycleModelHypothesisOne(), and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo().

void CellCycleModelOdeHandler::SetLastTime ( double  lastTime)

Set mLastTime.

Parameters:
lastTimethe new value of mLastTime

Definition at line 117 of file CellCycleModelOdeHandler.cpp.

References mLastTime.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::Initialise(), and DeltaNotchCellCycleModel::Initialise().

void CellCycleModelOdeHandler::SetOdeSystem ( AbstractOdeSystem *  pOdeSystem)

Set mpOdeSystem. Used in CreateCellCycleModel().

Parameters:
pOdeSystemthe ODE system

Definition at line 55 of file CellCycleModelOdeHandler.cpp.

References mpOdeSystem.

Referenced by WntCellCycleModel::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().

void CellCycleModelOdeHandler::SetStateVariables ( const std::vector< double > &  rStateVariables)

Set the values of the state variables in the cell-cycle model's ODE system.

Parameters:
rStateVariablesvector containing values for the state variables

Definition at line 122 of file CellCycleModelOdeHandler.cpp.

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

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::CreateCellCycleModel(), and Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel().

bool CellCycleModelOdeHandler::SolveOdeToTime ( double  currentTime) [protected]

Solves the ODE system to a given time.

Parameters:
currentTimethe current time
Returns:
whether a stopping event occurred.

Definition at line 91 of file CellCycleModelOdeHandler.cpp.

References AdjustOdeParameters(), GetDt(), mLastTime, mpOdeSolver, and mpOdeSystem.

Referenced by SingleOdeWntCellCycleModel::UpdateCellCyclePhase(), DeltaNotchCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented in AbstractOdeBasedCellCycleModel, Alarcon2004OxygenBasedCellCycleModel, DeltaNotchCellCycleModel, TysonNovakCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, AbstractWntOdeBasedCellCycleModel, SingleOdeWntCellCycleModel, StochasticWntCellCycleModel, VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo, and WntCellCycleModel.

Definition at line 56 of file CellCycleModelOdeHandler.hpp.

Member Data Documentation

double CellCycleModelOdeHandler::mDt [protected]

Timestep to use when solving the ODE system. For some adaptive solvers (e.g. CVODE) this is the maximum step to use.

Definition at line 78 of file CellCycleModelOdeHandler.hpp.

Referenced by GetDt(), serialize(), and SetDt().

double CellCycleModelOdeHandler::mLastTime [protected]

The last time the ODE system was evaluated.

Definition at line 87 of file CellCycleModelOdeHandler.hpp.

Referenced by WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), AbstractOdeBasedCellCycleModel::ResetForDivision(), serialize(), AbstractOdeBasedCellCycleModel::SetBirthTime(), SetLastTime(), AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly(), SolveOdeToTime(), AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase(), and AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase().

boost::shared_ptr<AbstractCellCycleModelOdeSolver> CellCycleModelOdeHandler::mpOdeSolver [protected]

A shared pointer to an ODE solver object.

Definition at line 84 of file CellCycleModelOdeHandler.hpp.

Referenced by Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel(), WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::DeltaNotchCellCycleModel(), GetDt(), GetOdeSolver(), AbstractOdeBasedCellCycleModel::GetOdeStopTime(), serialize(), SingleOdeWntCellCycleModel::SingleOdeWntCellCycleModel(), SolveOdeToTime(), StochasticWntCellCycleModel::StochasticWntCellCycleModel(), TysonNovakCellCycleModel::TysonNovakCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::VanLeeuwen2009WntSwatCellCycleModelHypothesisOne(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo(), and WntCellCycleModel::WntCellCycleModel().

AbstractOdeSystem* CellCycleModelOdeHandler::mpOdeSystem [protected]

A system of ODEs.

Definition at line 81 of file CellCycleModelOdeHandler.hpp.

Referenced by WntCellCycleModel::AdjustOdeParameters(), SingleOdeWntCellCycleModel::AdjustOdeParameters(), AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters(), Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters(), WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), SingleOdeWntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractVanLeeuwen2009WntSwatCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), WntCellCycleModel::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), DeltaNotchCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::GetBetaCateninConcentration(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel(), DeltaNotchCellCycleModel::GetDelta(), DeltaNotchCellCycleModel::GetMeanNeighbouringDelta(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel(), DeltaNotchCellCycleModel::GetNotch(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetNuclearBetaCateninLevel(), GetOdeSystem(), AbstractOdeBasedCellCycleModel::GetProteinConcentrations(), WntCellCycleModel::Initialise(), SingleOdeWntCellCycleModel::Initialise(), AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise(), TysonNovakCellCycleModel::Initialise(), DeltaNotchCellCycleModel::Initialise(), Alarcon2004OxygenBasedCellCycleModel::Initialise(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::InitialiseOdeSystem(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::InitialiseOdeSystem(), AbstractWntOdeBasedCellCycleModel::ResetForDivision(), TysonNovakCellCycleModel::ResetForDivision(), Alarcon2004OxygenBasedCellCycleModel::ResetForDivision(), serialize(), SetOdeSystem(), AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly(), SetStateVariables(), SolveOdeToTime(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), AbstractWntOdeBasedCellCycleModel::UpdateCellProliferativeType(), DeltaNotchCellCycleModel::UpdateDeltaNotch(), and ~CellCycleModelOdeHandler().

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