Chaste Commit::1fd4e48e3990e67db148bc1bc4cf6991a0049d0c
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#include <AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp>
Protected Member Functions | |
AbstractVanLeeuwen2009WntSwatCellCycleModel (const AbstractVanLeeuwen2009WntSwatCellCycleModel &rModel) | |
Protected Member Functions inherited from AbstractWntOdeBasedCellCycleModel | |
double | GetWntLevel () const |
void | UpdateCellCyclePhase () |
AbstractWntOdeBasedCellCycleModel (const AbstractWntOdeBasedCellCycleModel &rModel) | |
Protected Member Functions inherited from AbstractOdeBasedPhaseBasedCellCycleModel | |
AbstractOdeBasedPhaseBasedCellCycleModel (const AbstractOdeBasedPhaseBasedCellCycleModel &rModel) | |
Protected Member Functions inherited from AbstractPhaseBasedCellCycleModel | |
AbstractPhaseBasedCellCycleModel (const AbstractPhaseBasedCellCycleModel &rModel) | |
Protected Member Functions inherited from AbstractCellCycleModel | |
AbstractCellCycleModel (const AbstractCellCycleModel &rModel) | |
Protected Member Functions inherited from CellCycleModelOdeHandler | |
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 | |
Protected Attributes inherited from AbstractOdeBasedPhaseBasedCellCycleModel | |
double | mDivideTime |
double | mG2PhaseStartTime |
Protected Attributes inherited from AbstractPhaseBasedCellCycleModel | |
CellCyclePhase | mCurrentCellCyclePhase |
double | mG1Duration |
double | mMinimumGapDuration |
double | mStemCellG1Duration |
double | mTransitCellG1Duration |
double | mSDuration |
double | mG2Duration |
double | mMDuration |
Protected Attributes inherited from AbstractCellCycleModel | |
CellPtr | mpCell |
double | mBirthTime |
bool | mReadyToDivide |
unsigned | mDimension |
Protected Attributes inherited from CellCycleModelOdeHandler | |
double | mDt |
AbstractOdeSystem * | mpOdeSystem |
boost::shared_ptr< AbstractCellCycleModelOdeSolver > | mpOdeSolver |
double | mLastTime |
bool | mFinishedRunningOdes |
Wnt-dependent cell-cycle model.
Definition at line 53 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.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 46 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
AbstractVanLeeuwen2009WntSwatCellCycleModel::AbstractVanLeeuwen2009WntSwatCellCycleModel | ( | 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 41 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.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 111 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References AbstractWntOdeBasedCellCycleModel::GetWntLevel(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
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privatevirtual |
Called by Initialise() and UpdateCellProliferativeType() only. Updates mCellProliferativeType to match mpOdeSystem's beta-catenin levels
This carries out the work for UpdateCellProliferativeType(); But does not check the current time so it can be used by the initialise method.
Implements AbstractWntOdeBasedCellCycleModel.
Definition at line 64 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by Initialise().
double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetCytoplasmicBetaCateninLevel | ( | ) |
Definition at line 125 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput(), and CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().
double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetMembraneBoundBetaCateninLevel | ( | ) |
Definition at line 120 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), and CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().
double AbstractVanLeeuwen2009WntSwatCellCycleModel::GetNuclearBetaCateninLevel | ( | ) |
Definition at line 132 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().
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virtual |
See AbstractCellCycleModel::Initialise()
In this case we set up a new ODE system for a daughter cell.
Reimplemented from AbstractCellCycleModel.
Definition at line 97 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References ChangeCellProliferativeTypeDueToCurrentBetaCateninLevel(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractWntOdeBasedCellCycleModel::GetWntLevel(), InitialiseOdeSystem(), AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetStateVariables().
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pure virtual |
Allocate the mOdeSystem variable using the appropriate hypothesis (one or two).
As this method is pure virtual, it must be overridden in subclasses.
wntConcentration | Wnt concentration |
pMutationState | Mutation state |
Implemented in VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.
Referenced by Initialise().
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virtual |
Overridden OutputCellCycleModelParameters() method.
rParamsFile | the file stream to which the parameters are output |
Reimplemented from AbstractWntOdeBasedCellCycleModel.
Reimplemented in VanLeeuwen2009WntSwatCellCycleModelHypothesisOne, and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo.
Definition at line 140 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.cpp.
References AbstractWntOdeBasedCellCycleModel::OutputCellCycleModelParameters().
Referenced by VanLeeuwen2009WntSwatCellCycleModelHypothesisOne::OutputCellCycleModelParameters(), and VanLeeuwen2009WntSwatCellCycleModelHypothesisTwo::OutputCellCycleModelParameters().
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inlineprivate |
Archive the cell-cycle model, never used directly - boost uses this.
archive | the archive |
version | the current version of this class |
Definition at line 66 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp.
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friend |
Needed for serialization.
Definition at line 58 of file AbstractVanLeeuwen2009WntSwatCellCycleModel.hpp.