Chaste  Release::3.4
DeltaNotchTrackingModifier< DIM > Class Template Reference

#include <DeltaNotchTrackingModifier.hpp>

+ Inheritance diagram for DeltaNotchTrackingModifier< DIM >:
+ Collaboration diagram for DeltaNotchTrackingModifier< DIM >:

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)
 
virtual void UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
 
virtual void SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)
 
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
 

Detailed Description

template<unsigned DIM>
class DeltaNotchTrackingModifier< DIM >

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.

Constructor & Destructor Documentation

template<unsigned DIM>
DeltaNotchTrackingModifier< DIM >::DeltaNotchTrackingModifier ( )

Default constructor.

Definition at line 40 of file DeltaNotchTrackingModifier.cpp.

template<unsigned DIM>
DeltaNotchTrackingModifier< DIM >::~DeltaNotchTrackingModifier ( )
virtual

Destructor.

Definition at line 46 of file DeltaNotchTrackingModifier.cpp.

Member Function Documentation

template<unsigned DIM>
void DeltaNotchTrackingModifier< DIM >::OutputSimulationModifierParameters ( out_stream &  rParamsFile)
virtual

Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.

Parameters
rParamsFilethe 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().

template<unsigned DIM>
template<class Archive >
void DeltaNotchTrackingModifier< DIM >::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters
archiveThe boost archive.
versionThe current version of this class.

Definition at line 62 of file DeltaNotchTrackingModifier.hpp.

template<unsigned DIM>
void DeltaNotchTrackingModifier< DIM >::SetupSolve ( AbstractCellPopulation< DIM, DIM > &  rCellPopulation,
std::string  outputDirectory 
)
virtual

Overridden SetupSolve() method.

Specifies what to do in the simulation before the start of the time loop.

Parameters
rCellPopulationreference to the cell population
outputDirectorythe output directory, relative to where Chaste output is stored

Definition at line 57 of file DeltaNotchTrackingModifier.cpp.

template<unsigned DIM>
void DeltaNotchTrackingModifier< DIM >::UpdateAtEndOfTimeStep ( AbstractCellPopulation< DIM, DIM > &  rCellPopulation)
virtual

Overridden UpdateAtEndOfTimeStep() method.

Specifies what to do in the simulation at the end of each time step.

Parameters
rCellPopulationreference to the cell population

Definition at line 51 of file DeltaNotchTrackingModifier.cpp.

template<unsigned DIM>
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.

Parameters
rCellPopulationreference 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().

Friends And Related Function Documentation

template<unsigned DIM>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 53 of file DeltaNotchTrackingModifier.hpp.


The documentation for this class was generated from the following files: