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CellCycleModelOdeHandler Class Reference

#include <CellCycleModelOdeHandler.hpp>

+ Inheritance diagram for CellCycleModelOdeHandler:
+ Collaboration diagram for CellCycleModelOdeHandler:

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)
protectedvirtual

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 SingleOdeWntCellCycleModel, WntCellCycleModel, AbstractVanLeeuwen2009WntSwatCellCycleModel, and Alarcon2004OxygenBasedCellCycleModel.

Definition at line 113 of file CellCycleModelOdeHandler.cpp.

Referenced by SolveOdeToTime().

double CellCycleModelOdeHandler::GetDt ( )
Returns
mDt. This 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
Returns
mpOdeSystem.

Definition at line 60 of file CellCycleModelOdeHandler.cpp.

References mpOdeSystem.

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

Archive the object and its member variables.

Parameters
archivethe archive
versionthe current version of this class

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(), DeltaNotchSrnModel::DeltaNotchSrnModel(), Goldbeter1991SrnModel::Goldbeter1991SrnModel(), 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 VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), WntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), AbstractOdeSrnModel::CreateSrnModel(), AbstractOdeSrnModel::Initialise(), and SingleOdeWntCellCycleModel::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 Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), WntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), DeltaNotchSrnModel::CreateSrnModel(), and Goldbeter1991SrnModel::CreateSrnModel().

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 VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), WntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), and AbstractOdeSrnModel::CreateSrnModel().

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 AbstractOdeSrnModel::SimulateToCurrentTime(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), and SingleOdeWntCellCycleModel::UpdateCellCyclePhase().

Friends And Related Function Documentation

friend class boost::serialization::access
friend

Needed for serialization.

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 VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), WntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), AbstractOdeSrnModel::ResetForDivision(), AbstractOdeBasedCellCycleModel::ResetForDivision(), serialize(), AbstractOdeBasedCellCycleModel::SetBirthTime(), SetLastTime(), AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly(), AbstractOdeSrnModel::SimulateToCurrentTime(), 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(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), WntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), DeltaNotchSrnModel::CreateSrnModel(), Goldbeter1991SrnModel::CreateSrnModel(), DeltaNotchSrnModel::DeltaNotchSrnModel(), GetDt(), GetOdeSolver(), AbstractOdeBasedCellCycleModel::GetOdeStopTime(), Goldbeter1991SrnModel::Goldbeter1991SrnModel(), 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 Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters(), AbstractVanLeeuwen2009WntSwatCellCycleModel::AdjustOdeParameters(), WntCellCycleModel::AdjustOdeParameters(), SingleOdeWntCellCycleModel::AdjustOdeParameters(), AbstractVanLeeuwen2009WntSwatCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), WntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), SingleOdeWntCellCycleModel::ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::CreateCellCycleModel(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::CreateCellCycleModel(), StochasticWntCellCycleModel::CreateCellCycleModel(), Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel(), TysonNovakCellCycleModel::CreateCellCycleModel(), WntCellCycleModel::CreateCellCycleModel(), SingleOdeWntCellCycleModel::CreateCellCycleModel(), AbstractOdeSrnModel::CreateSrnModel(), SingleOdeWntCellCycleModel::GetBetaCateninConcentration(), Goldbeter1991SrnModel::GetC(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel(), DeltaNotchSrnModel::GetDelta(), Goldbeter1991SrnModel::GetM(), DeltaNotchSrnModel::GetMeanNeighbouringDelta(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel(), DeltaNotchSrnModel::GetNotch(), AbstractVanLeeuwen2009WntSwatCellCycleModel::GetNuclearBetaCateninLevel(), GetOdeSystem(), AbstractOdeBasedCellCycleModel::GetProteinConcentrations(), AbstractOdeSrnModel::GetStateVariables(), Goldbeter1991SrnModel::GetX(), TysonNovakCellCycleModel::Initialise(), AbstractVanLeeuwen2009WntSwatCellCycleModel::Initialise(), AbstractOdeSrnModel::Initialise(), Alarcon2004OxygenBasedCellCycleModel::Initialise(), SingleOdeWntCellCycleModel::Initialise(), WntCellCycleModel::Initialise(), VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::InitialiseOdeSystem(), VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::InitialiseOdeSystem(), Alarcon2004OxygenBasedCellCycleModel::ResetForDivision(), TysonNovakCellCycleModel::ResetForDivision(), AbstractWntOdeBasedCellCycleModel::ResetForDivision(), serialize(), SetOdeSystem(), AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly(), SetStateVariables(), AbstractOdeSrnModel::SimulateToCurrentTime(), SolveOdeToTime(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), AbstractWntOdeBasedCellCycleModel::UpdateCellProliferativeType(), DeltaNotchSrnModel::UpdateDeltaNotch(), and ~CellCycleModelOdeHandler().

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