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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <DeltaNotchSrnModel.hpp>
Protected Member Functions | |
DeltaNotchSrnModel (const DeltaNotchSrnModel &rModel) | |
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void | Initialise (AbstractOdeSystem *pOdeSystem) |
AbstractOdeSrnModel (const AbstractOdeSrnModel &rModel) | |
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AbstractSrnModel (const AbstractSrnModel &rModel) | |
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CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler) | |
bool | SolveOdeToTime (double currentTime) |
virtual void | AdjustOdeParameters (double currentTime) |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Friends | |
class | boost::serialization::access |
Additional Inherited Members | |
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std::vector< double > | mInitialConditions |
unsigned | mStateSize |
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CellPtr | mpCell |
double | mSimulatedToTime |
unsigned | mEdgeLocalIndex = UNSIGNED_UNSET |
bool | mIsEdgeBasedModel = false |
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double | mDt |
AbstractOdeSystem * | mpOdeSystem |
boost::shared_ptr< AbstractCellCycleModelOdeSolver > | mpOdeSolver |
double | mLastTime |
bool | mFinishedRunningOdes |
A subclass of AbstractOdeSrnModel that includes a Delta-Notch ODE system in the sub-cellular reaction network.
Definition at line 49 of file DeltaNotchSrnModel.hpp.
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protected |
Protected copy-constructor for use by CreateSrnModel(). The only way for external code to create a copy of a SRN 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 SRN model will have had ResetForDivision() called just before CreateSrnModel() 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 SRN model to copy. |
Definition at line 56 of file DeltaNotchSrnModel.cpp.
References CellCycleModelOdeHandler::GetOdeSystem(), AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and CellCycleModelOdeHandler::SetOdeSystem().
DeltaNotchSrnModel::DeltaNotchSrnModel | ( | boost::shared_ptr< AbstractCellCycleModelOdeSolver > | pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() | ) |
Default constructor calls base class.
pOdeSolver | An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers) |
Definition at line 38 of file DeltaNotchSrnModel.cpp.
References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().
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virtual |
Overridden builder method to create new copies of this SRN model.
Implements AbstractSrnModel.
Definition at line 78 of file DeltaNotchSrnModel.cpp.
double DeltaNotchSrnModel::GetDelta | ( | ) |
Definition at line 113 of file DeltaNotchSrnModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by DeltaNotchTrackingModifier< DIM >::UpdateCellData().
double DeltaNotchSrnModel::GetMeanNeighbouringDelta | ( | ) |
N.B. This doesn't calculate anything, it just returns the parameter from the DeltaNotchOdeSystem.
Definition at line 120 of file DeltaNotchSrnModel.cpp.
References AbstractParameterisedSystem< VECTOR >::GetParameter(), and CellCycleModelOdeHandler::mpOdeSystem.
double DeltaNotchSrnModel::GetNotch | ( | ) |
Definition at line 106 of file DeltaNotchSrnModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by DeltaNotchTrackingModifier< DIM >::UpdateCellData().
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virtual |
Initialise the SRN model at the start of a simulation.
This overridden method sets up a new Delta-Notch ODE system.
Reimplemented from AbstractOdeSrnModel.
Definition at line 92 of file DeltaNotchSrnModel.cpp.
References AbstractOdeSrnModel::Initialise().
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virtual |
Output SRN model parameters to file.
rParamsFile | the file stream to which the parameters are output |
Reimplemented from AbstractOdeSrnModel.
Definition at line 127 of file DeltaNotchSrnModel.cpp.
References AbstractOdeSrnModel::OutputSrnModelParameters().
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inlineprivate |
Archive the SRN model and member variables.
archive | the archive |
version | the current version of this class |
Definition at line 62 of file DeltaNotchSrnModel.hpp.
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virtual |
Overridden SimulateToTime() method for custom behaviour.
Reimplemented from AbstractOdeSrnModel.
Definition at line 83 of file DeltaNotchSrnModel.cpp.
References AbstractOdeSrnModel::SimulateToCurrentTime(), and UpdateDeltaNotch().
void DeltaNotchSrnModel::UpdateDeltaNotch | ( | ) |
Update the current levels of Delta and Notch in the cell.
N.B. Despite the name, this doesn't update the levels of delta or notch, or compute mean levels. It just copies the current mean delta from the CellData (set by DeltaNotchTrackingModifier) to the DeltaNotchOdeSystem.
Definition at line 97 of file DeltaNotchSrnModel.cpp.
References AbstractSrnModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::SetParameter().
Referenced by SimulateToCurrentTime().
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friend |
Needed for serialization.
Definition at line 54 of file DeltaNotchSrnModel.hpp.