Chaste  Release::3.4
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CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <CellCycleModelProteinConcentrationsWriter.hpp>

+ Inheritance diagram for CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >:
+ Collaboration diagram for CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions

 CellCycleModelProteinConcentrationsWriter ()
 
double GetCellDataForVtkOutput (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)
 
virtual void VisitCell (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)
 
- Public Member Functions inherited from AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >
 AbstractCellWriter (const std::string &rFileName)
 
void SetVtkCellDataName (std::string vtkCellDataName)
 
std::string GetVtkCellDataName ()
 
- Public Member Functions inherited from AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >
 AbstractCellBasedWriter (const std::string &rFileName)
 
virtual ~AbstractCellBasedWriter ()
 
void CloseFile ()
 
virtual void OpenOutputFile (OutputFileHandler &rOutputFileHandler)
 
void OpenOutputFileForAppend (OutputFileHandler &rOutputFileHandler)
 
virtual void WriteTimeStamp ()
 
virtual void WriteNewline ()
 
void SetFileName (std::string fileName)
 
std::string GetFileName ()
 
- 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
 

Additional Inherited Members

- Protected Attributes inherited from AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >
std::string mVtkCellDataName
 
- Protected Attributes inherited from AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >
std::string mFileName
 
out_stream mpOutStream
 

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >

A class written using the visitor pattern for writing cell-cycle model protein concentrations to file.

The output file is called proteinconcentrations.dat by default. If VTK is switched on, then the writer also specifies the VTK output for each cell, which is stored in the VTK cell data "Protein concentrations" by default.

Definition at line 51 of file CellCycleModelProteinConcentrationsWriter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::CellCycleModelProteinConcentrationsWriter ( )

Default constructor.

Definition at line 41 of file CellCycleModelProteinConcentrationsWriter.cpp.

References AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mVtkCellDataName.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
double CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput ( CellPtr  pCell,
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *  pCellPopulation 
)
virtual

Overridden GetCellDataForVtkOutput() method.

Get a double associated with a cell. This method reduces duplication of code between the methods VisitCell() and AddVtkData().

Parameters
pCella cell
pCellPopulationa pointer to the cell population owning the cell
Returns
data associated with the cell

Implements AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 48 of file CellCycleModelProteinConcentrationsWriter.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
template<class Archive >
void CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Serialize the object and its member variables.

Parameters
archivethe archive
versionthe current version of this class

Definition at line 63 of file CellCycleModelProteinConcentrationsWriter.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell ( CellPtr  pCell,
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *  pCellPopulation 
)
virtual

Overridden VisitCell() method.

Visit a cell and write the protein concentrations associated with its cell-cycle model, if its cell-cycle model is a subclass of AbstractOdeBasedCellCycleModel.

Outputs a line of space-separated values of the form: ...[location index] [protein 1 conc] [protein 2 conc] ... [protein n conc] ...

This is appended to the output written by AbstractCellBasedWriter, which is a single value [present simulation time], followed by a tab.

Note that the "protein concentrations" refer to the solution of the ODE system that is present in the cell-cycle model. If the cell-cycle model does not inherit from AbstractOdeBasedCellCycleModel, then an exception is thrown.

Parameters
pCella pointer to a cell
pCellPopulationa pointer to the cell population owning the cell

Implements AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 60 of file CellCycleModelProteinConcentrationsWriter.cpp.

References EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), and AbstractOdeBasedCellCycleModel::GetProteinConcentrations().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 55 of file CellCycleModelProteinConcentrationsWriter.hpp.

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