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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <Alarcon2004OxygenBasedCellCycleModel.hpp>
Protected Member Functions | |
Alarcon2004OxygenBasedCellCycleModel (const Alarcon2004OxygenBasedCellCycleModel &rModel) | |
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AbstractOdeBasedPhaseBasedCellCycleModel (const AbstractOdeBasedPhaseBasedCellCycleModel &rModel) | |
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AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel) | |
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AbstractCellCycleModel (const AbstractCellCycleModel &rModel) | |
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CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler) | |
bool | SolveOdeToTime (double currentTime) |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
void | AdjustOdeParameters (double currentTime) |
Friends | |
class | boost::serialization::access |
Additional Inherited Members | |
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double | mDivideTime |
double | mG2PhaseStartTime |
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CellCyclePhase | mCurrentCellCyclePhase |
double | mG1Duration |
double | mMinimumGapDuration |
double | mStemCellG1Duration |
double | mTransitCellG1Duration |
double | mSDuration |
double | mG2Duration |
double | mMDuration |
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CellPtr | mpCell |
double | mBirthTime |
bool | mReadyToDivide |
unsigned | mDimension |
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double | mDt |
AbstractOdeSystem * | mpOdeSystem |
boost::shared_ptr< AbstractCellCycleModelOdeSolver > | mpOdeSolver |
double | mLastTime |
bool | mFinishedRunningOdes |
Oxygen-dependent ODE-based cell-cycle model.
Published by Alarcon et al. (doi:10.1016/j.jtbi.2004.04.016).
Definition at line 52 of file Alarcon2004OxygenBasedCellCycleModel.hpp.
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protected |
Protected copy-constructor for use by CreateCellCycleModel. The only way for external code to create a copy of a cell cycle model is by calling that method, to ensure that a model of the correct subclass is created. This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.
This method is called by child classes to set member variables for a daughter cell upon cell division. Note that the parent cell cycle model will have had ResetForDivision() called just before CreateCellCycleModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().
rModel | the cell cycle model to copy. |
Definition at line 51 of file Alarcon2004OxygenBasedCellCycleModel.cpp.
References CellCycleModelOdeHandler::GetOdeSystem(), AbstractCellCycleModel::mpCell, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), CellCycleModelOdeHandler::SetOdeSystem(), and CellCycleModelOdeHandler::SetStateVariables().
Alarcon2004OxygenBasedCellCycleModel::Alarcon2004OxygenBasedCellCycleModel | ( | boost::shared_ptr< AbstractCellCycleModelOdeSolver > | pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() | ) |
Default constructor.
pOdeSolver | An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers) |
Definition at line 40 of file Alarcon2004OxygenBasedCellCycleModel.cpp.
References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().
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privatevirtual |
Adjust any ODE parameters needed before solving until currentTime.
currentTime | the time up to which the system will be solved. |
Reimplemented from CellCycleModelOdeHandler.
Definition at line 105 of file Alarcon2004OxygenBasedCellCycleModel.cpp.
References AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
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virtual |
Overridden builder method to create new copies of this cell-cycle model.
Implements AbstractCellCycleModel.
Definition at line 74 of file Alarcon2004OxygenBasedCellCycleModel.cpp.
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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 93 of file Alarcon2004OxygenBasedCellCycleModel.cpp.
References AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractCellCycleModel::Initialise(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetStateVariables().
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virtual |
Overridden OutputCellCycleModelParameters() method.
rParamsFile | the file stream to which the parameters are output |
Reimplemented from AbstractOdeBasedPhaseBasedCellCycleModel.
Definition at line 115 of file Alarcon2004OxygenBasedCellCycleModel.cpp.
References AbstractOdeBasedPhaseBasedCellCycleModel::OutputCellCycleModelParameters().
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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 AbstractOdeBasedPhaseBasedCellCycleModel.
Definition at line 79 of file Alarcon2004OxygenBasedCellCycleModel.cpp.
References AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), CellCycleModelOdeHandler::mpOdeSystem, AbstractOdeBasedPhaseBasedCellCycleModel::ResetForDivision(), and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
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inlineprivate |
Archive the cell-cycle model and ODE system.
archive | the archive |
version | the archive version |
Definition at line 65 of file Alarcon2004OxygenBasedCellCycleModel.hpp.
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friend |
Needed for serialization.
Definition at line 57 of file Alarcon2004OxygenBasedCellCycleModel.hpp.