Alarcon2004OxygenBasedCellCycleModel Class Reference

#include <Alarcon2004OxygenBasedCellCycleModel.hpp>

Inheritance diagram for Alarcon2004OxygenBasedCellCycleModel:

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List of all members.

Public Member Functions

 Alarcon2004OxygenBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())
virtual void ResetForDivision ()
AbstractCellCycleModelCreateCellCycleModel ()
void Initialise ()
virtual void OutputCellCycleModelParameters (out_stream &rParamsFile)

Private Member Functions

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

Friends

class boost::serialization::access


Detailed Description

Oxygen-dependent ODE-based cell-cycle model. Published by Alarcon et al. (doi:10.1016/j.jtbi.2004.04.016).

Definition at line 43 of file Alarcon2004OxygenBasedCellCycleModel.hpp.


Constructor & Destructor Documentation

Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel ( boost::shared_ptr< AbstractCellCycleModelOdeSolver pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>()  ) 

Default constructor.

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

Definition at line 35 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

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

Referenced by CreateCellCycleModel().


Member Function Documentation

template<class Archive>
void Alarcon2004OxygenBasedCellCycleModel::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Archive the cell-cycle model and ODE system.

Parameters:
archive the archive
version the archive version

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 56 of file Alarcon2004OxygenBasedCellCycleModel.hpp.

void Alarcon2004OxygenBasedCellCycleModel::AdjustOdeParameters ( double  currentTime  )  [private, virtual]

Adjust any ODE parameters needed before solving until currentTime.

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

Reimplemented from CellCycleModelOdeHandler.

Definition at line 159 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References CellwiseData< DIM >::GetValue(), CellwiseData< DIM >::Instance(), AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, NEVER_REACHED, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

void Alarcon2004OxygenBasedCellCycleModel::ResetForDivision (  )  [virtual]

Resets the oxygen-based model to the start of the cell cycle (this model does not cycle naturally). Cells are given a new birth time and cell cycle proteins are reset. Note that the oxygen concentration maintains its current value.

Should only be called by the Cell Divide() method.

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 46 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

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

AbstractCellCycleModel * Alarcon2004OxygenBasedCellCycleModel::CreateCellCycleModel (  )  [virtual]

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

Implements AbstractCellCycleModel.

Definition at line 60 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References Alarcon2004OxygenBasedCellCycleModel(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mCellProliferativeType, 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, NEVER_REACHED, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), AbstractOdeBasedCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetCellProliferativeType(), AbstractCellCycleModel::SetDimension(), AbstractOdeBasedCellCycleModel::SetDivideTime(), AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes(), AbstractCellCycleModel::SetG2Duration(), AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime(), CellCycleModelOdeHandler::SetLastTime(), AbstractCellCycleModel::SetMDuration(), AbstractCellCycleModel::SetMinimumGapDuration(), CellCycleModelOdeHandler::SetOdeSystem(), AbstractCellCycleModel::SetSDuration(), CellCycleModelOdeHandler::SetStateVariables(), AbstractCellCycleModel::SetStemCellG1Duration(), and AbstractCellCycleModel::SetTransitCellG1Duration().

void Alarcon2004OxygenBasedCellCycleModel::Initialise ( void   )  [virtual]

void Alarcon2004OxygenBasedCellCycleModel::OutputCellCycleModelParameters ( out_stream &  rParamsFile  )  [virtual]

Outputs cell cycle model parameters to files.

Parameters:
rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 191 of file Alarcon2004OxygenBasedCellCycleModel.cpp.

References AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters().


Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from AbstractOdeBasedCellCycleModel.

Definition at line 48 of file Alarcon2004OxygenBasedCellCycleModel.hpp.


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

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