DeltaNotchCellCycleModel Class Reference
#include <DeltaNotchCellCycleModel.hpp>
Inherits StochasticDurationGenerationBasedCellCycleModel, and CellCycleModelOdeHandler.
Public Member Functions | |
| DeltaNotchCellCycleModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >()) | |
| AbstractCellCycleModel * | CreateCellCycleModel () |
| void | Initialise () |
| void | UpdateCellCyclePhase () |
| void | UpdateDeltaNotch () |
| double | GetNotch () |
| double | GetDelta () |
| double | GetMeanNeighbouringDelta () |
| virtual void | OutputCellCycleModelParameters (out_stream &rParamsFile) |
Private Member Functions | |
| template<class Archive > | |
| void | serialize (Archive &archive, const unsigned int version) |
Friends | |
| class | boost::serialization::access |
Detailed Description
A subclass of StochasticDurationGenerationBasedCellCycleModel that includes a Delta-Notch ODE system.
For another example of a cell cycle model that is not *based on* an ODE system, but that includes an ODE system, see SingleOdeWntCellCycleModel (in Crypt).
Definition at line 48 of file DeltaNotchCellCycleModel.hpp.
Constructor & Destructor Documentation
| DeltaNotchCellCycleModel::DeltaNotchCellCycleModel | ( | boost::shared_ptr< AbstractCellCycleModelOdeSolver > | pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() |
) |
Default constructor calls base class.
- Parameters:
-
pOdeSolver An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)
Definition at line 36 of file DeltaNotchCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().
Referenced by CreateCellCycleModel().
Member Function Documentation
| AbstractCellCycleModel * DeltaNotchCellCycleModel::CreateCellCycleModel | ( | ) | [virtual] |
Overridden builder method to create new copies of this cell-cycle model.
- Returns:
- Returns a copy of the current cell cycle model.
Reimplemented from StochasticDurationGenerationBasedCellCycleModel.
Definition at line 54 of file DeltaNotchCellCycleModel.cpp.
References DeltaNotchCellCycleModel(), GetMeanNeighbouringDelta(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mCellProliferativeType, AbstractCellCycleModel::mDimension, AbstractSimpleGenerationBasedCellCycleModel::mGeneration, CellCycleModelOdeHandler::mLastTime, AbstractSimpleGenerationBasedCellCycleModel::mMaxTransitGenerations, CellCycleModelOdeHandler::mpOdeSolver, CellCycleModelOdeHandler::mpOdeSystem, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), AbstractCellCycleModel::SetBirthTime(), AbstractCellCycleModel::SetCellProliferativeType(), AbstractCellCycleModel::SetDimension(), AbstractSimpleGenerationBasedCellCycleModel::SetGeneration(), CellCycleModelOdeHandler::SetLastTime(), AbstractSimpleGenerationBasedCellCycleModel::SetMaxTransitGenerations(), CellCycleModelOdeHandler::SetOdeSystem(), and CellCycleModelOdeHandler::SetStateVariables().
| double DeltaNotchCellCycleModel::GetDelta | ( | ) |
- Returns:
- Returns the current Delta level in this cell.
Definition at line 141 of file DeltaNotchCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
| double DeltaNotchCellCycleModel::GetMeanNeighbouringDelta | ( | ) |
- Returns:
- Get the current level of Delta neighbouring the cell.
Definition at line 148 of file DeltaNotchCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
Referenced by CreateCellCycleModel().
| double DeltaNotchCellCycleModel::GetNotch | ( | ) |
- Returns:
- Returns the current Notch level in this cell.
Definition at line 134 of file DeltaNotchCellCycleModel.cpp.
References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().
| void DeltaNotchCellCycleModel::Initialise | ( | void | ) | [virtual] |
Initialise the cell-cycle model at the start of a simulation.
This overridden method sets up a new Delta-Notch ODE system.
Reimplemented from AbstractSimpleCellCycleModel.
Definition at line 86 of file DeltaNotchCellCycleModel.cpp.
References AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractCellCycleModel::mBirthTime, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, CellCycleModelOdeHandler::SetLastTime(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().
| void DeltaNotchCellCycleModel::OutputCellCycleModelParameters | ( | out_stream & | rParamsFile | ) | [virtual] |
Outputs cell-cycle model parameters to file.
- Parameters:
-
rParamsFile the file stream to which the parameters are output
Reimplemented from StochasticDurationGenerationBasedCellCycleModel.
Definition at line 155 of file DeltaNotchCellCycleModel.cpp.
| void DeltaNotchCellCycleModel::serialize | ( | Archive & | archive, | |
| const unsigned int | version | |||
| ) | [inline, private] |
Archive the cell-cycle model and member variables.
- Parameters:
-
archive the archive version the current version of this class
Reimplemented from CellCycleModelOdeHandler.
Definition at line 61 of file DeltaNotchCellCycleModel.hpp.
| void DeltaNotchCellCycleModel::UpdateCellCyclePhase | ( | ) | [virtual] |
Overridden UpdateCellCyclePhase() method.
Reimplemented from AbstractSimpleCellCycleModel.
Definition at line 79 of file DeltaNotchCellCycleModel.cpp.
References SimulationTime::Instance(), and UpdateDeltaNotch().
| void DeltaNotchCellCycleModel::UpdateDeltaNotch | ( | ) |
Update the current levels of Delta and Notch in the cell.
Definition at line 99 of file DeltaNotchCellCycleModel.cpp.
References SimulationTime::Instance(), AbstractCellCycleModel::mDimension, AbstractCellCycleModel::mpCell, CellCycleModelOdeHandler::mpOdeSystem, NEVER_REACHED, AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and CellCycleModelOdeHandler::SolveOdeToTime().
Referenced by UpdateCellCyclePhase().
Friends And Related Function Documentation
friend class boost::serialization::access [friend] |
Needed for serialization.
Reimplemented from CellCycleModelOdeHandler.
Definition at line 53 of file DeltaNotchCellCycleModel.hpp.
The documentation for this class was generated from the following files:
- cell_based/src/population/cell/cycle/DeltaNotchCellCycleModel.hpp
- cell_based/src/population/cell/cycle/DeltaNotchCellCycleModel.cpp
