Alarcon2004OxygenBasedCellCycleModel Class Reference
#include <Alarcon2004OxygenBasedCellCycleModel.hpp>
Inherits AbstractOdeBasedCellCycleModel.
Public Member Functions | |
| Alarcon2004OxygenBasedCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >()) | |
| virtual void | ResetForDivision () |
| AbstractCellCycleModel * | CreateCellCycleModel () |
| 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 44 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 CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().
Referenced by CreateCellCycleModel().
Member Function Documentation
| 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 AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, NEVER_REACHED, 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] |
Initialise the cell-cycle model at the start of a simulation.
This overridden method sets up a new ODE system.
Reimplemented from AbstractCellCycleModel.
Definition at line 125 of file Alarcon2004OxygenBasedCellCycleModel.cpp.
References AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, NEVER_REACHED, and AbstractParameterisedSystem< VECTOR >::SetStateVariables().
| 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.
| 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, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
| 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 57 of file Alarcon2004OxygenBasedCellCycleModel.hpp.
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from AbstractOdeBasedCellCycleModel.
Definition at line 49 of file Alarcon2004OxygenBasedCellCycleModel.hpp.
The documentation for this class was generated from the following files:
- cell_based/src/population/cell/cycle/Alarcon2004OxygenBasedCellCycleModel.hpp
- cell_based/src/population/cell/cycle/Alarcon2004OxygenBasedCellCycleModel.cpp
