Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <DeltaNotchTrackingModifier.hpp>
Public Member Functions | |
DeltaNotchTrackingModifier () | |
virtual | ~DeltaNotchTrackingModifier () |
virtual void | UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation) |
virtual void | SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory) |
void | UpdateCellData (AbstractCellPopulation< DIM, DIM > &rCellPopulation) |
void | OutputSimulationModifierParameters (out_stream &rParamsFile) |
Public Member Functions inherited from AbstractCellBasedSimulationModifier< DIM, DIM > | |
AbstractCellBasedSimulationModifier () | |
virtual | ~AbstractCellBasedSimulationModifier () |
virtual void | UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)=0 |
virtual void | UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation) |
virtual void | SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0 |
virtual void | UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation) |
void | OutputSimulationModifierInfo (out_stream &rParamsFile) |
Public Member Functions inherited from Identifiable | |
virtual | ~Identifiable () |
std::string | GetIdentifier () const |
Private Member Functions | |
template<class Archive > | |
void | serialize (Archive &archive, const unsigned int version) |
Friends | |
class | boost::serialization::access |
A modifier class in which the mean levels of Delta in neighbouring cells are computed and stored in CellData. To be used in conjunction with Delta Notch cell cycle models.
Definition at line 50 of file DeltaNotchTrackingModifier.hpp.
DeltaNotchTrackingModifier< DIM >::DeltaNotchTrackingModifier | ( | ) |
Default constructor.
Definition at line 40 of file DeltaNotchTrackingModifier.cpp.
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virtual |
Destructor.
Definition at line 46 of file DeltaNotchTrackingModifier.cpp.
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virtual |
Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.
rParamsFile | the file stream to which the parameters are output |
Implements AbstractCellBasedSimulationModifier< DIM, DIM >.
Definition at line 117 of file DeltaNotchTrackingModifier.cpp.
References AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierParameters().
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inlineprivate |
Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.
archive | The boost archive. |
version | The current version of this class. |
Definition at line 62 of file DeltaNotchTrackingModifier.hpp.
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virtual |
Overridden SetupSolve() method.
Specifies what to do in the simulation before the start of the time loop.
rCellPopulation | reference to the cell population |
outputDirectory | the output directory, relative to where Chaste output is stored |
Definition at line 57 of file DeltaNotchTrackingModifier.cpp.
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virtual |
Overridden UpdateAtEndOfTimeStep() method.
Specifies what to do in the simulation at the end of each time step.
rCellPopulation | reference to the cell population |
Definition at line 51 of file DeltaNotchTrackingModifier.cpp.
void DeltaNotchTrackingModifier< DIM >::UpdateCellData | ( | AbstractCellPopulation< DIM, DIM > & | rCellPopulation | ) |
Helper method to compute the mean level of Delta in each cell's neighbours and store these in the CellData.
Note: If using a CaBasedCellPopulation, we assume a Moore neighbourhood and unit carrying capacity. If a cell has no neighbours (such as an isolated cell in a CaBasedCellPopulation), we store the value -1 in the CellData.
rCellPopulation | reference to the cell population |
Definition at line 67 of file DeltaNotchTrackingModifier.cpp.
References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), DeltaNotchSrnModel::GetDelta(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices(), DeltaNotchSrnModel::GetNotch(), and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().
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friend |
Needed for serialization.
Definition at line 53 of file DeltaNotchTrackingModifier.hpp.