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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <WntCellCycleModel.hpp>
Protected Member Functions | |
WntCellCycleModel (const WntCellCycleModel &rModel) | |
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double | GetWntLevel () const |
void | UpdateCellCyclePhase () |
AbstractWntOdeBasedCellCycleModel (const AbstractWntOdeBasedCellCycleModel &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 | ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel () |
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 |
Wnt-dependent cell-cycle model. Needs to operate with a WntConcentration singleton object.
This model has a constant length M phase, runs ODEs to decide when to finish G1 phase then adds time for S and G2 phases. The CellProliferativeType is updated dependent on the concentration of beta-catenin (given by one of the ODEs).
Note that this class uses C++'s default copying semantics, and so doesn't implement a copy constructor or operator=.
Definition at line 60 of file WntCellCycleModel.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 61 of file WntCellCycleModel.cpp.
References CellCycleModelOdeHandler::GetOdeSystem(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), CellCycleModelOdeHandler::SetOdeSystem(), and CellCycleModelOdeHandler::SetStateVariables().
WntCellCycleModel::WntCellCycleModel | ( | 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 WntCellCycleModel.cpp.
References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), and CellCycleModelOdeHandler::mpOdeSolver.
WntCellCycleModel::~WntCellCycleModel | ( | ) |
Empty virtual destructor so archiving works with static libraries.
Definition at line 58 of file WntCellCycleModel.cpp.
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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 136 of file WntCellCycleModel.cpp.
References AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
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privatevirtual |
Update the cell type according to the current beta catenin level as given by the WntCellCycleOdeSystem.
This method carries out the work for UpdateCellProliferativeType(), but does not check the current time, so can also be called by Initialise().
Implements AbstractWntOdeBasedCellCycleModel.
Definition at line 93 of file WntCellCycleModel.cpp.
References AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by Initialise().
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virtual |
Overridden builder method to create new copies of this cell-cycle model.
Implements AbstractCellCycleModel.
Definition at line 87 of file WntCellCycleModel.cpp.
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virtual |
Initialise the cell-cycle model at the start of a simulation.
This overridden method sets up a new WntCellCycleOdeSystem and sets the cell type according to the current beta catenin level.
Reimplemented from AbstractCellCycleModel.
Definition at line 124 of file WntCellCycleModel.cpp.
References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetStateVariables().
Referenced by StochasticWntCellCycleModel::Initialise().
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virtual |
Overridden OutputCellCycleModelParameters() method.
rParamsFile | the file stream to which the parameters are output |
Reimplemented from AbstractWntOdeBasedCellCycleModel.
Reimplemented in StochasticWntCellCycleModel.
Definition at line 147 of file WntCellCycleModel.cpp.
References AbstractWntOdeBasedCellCycleModel::OutputCellCycleModelParameters().
Referenced by StochasticWntCellCycleModel::OutputCellCycleModelParameters().
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inlineprivate |
Archive the cell-cycle model and ODE system.
archive | the archive |
version | the archive version |
Definition at line 72 of file WntCellCycleModel.hpp.
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friend |
Needed for serialization.
Definition at line 64 of file WntCellCycleModel.hpp.