Chaste  Release::2017.1
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)
 
virtual c_vector< double, SPACE_DIM > GetVectorCellDataForVtkOutput (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation)
 
bool GetOutputScalarData ()
 
bool GetOutputVectorData ()
 
void SetVtkCellDataName (std::string vtkCellDataName)
 
void SetVtkVectorCellDataName (std::string vtkCellDataName)
 
std::string GetVtkCellDataName ()
 
std::string GetVtkVectorCellDataName ()
 
- 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 >
bool mOutputScalarData
 
bool mOutputVectorData
 
std::string mVtkCellDataName
 
std::string mVtkVectorCellDataName
 
- 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

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

Reimplemented from AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 48 of file CellCycleModelProteinConcentrationsWriter.cpp.

Referenced by CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::serialize().

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

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 AbstractOdeBasedPhaseBasedCellCycleModel, 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, EXPORT_TEMPLATE_CLASS_ALL_DIMS, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), CellCycleModelOdeHandler::GetProteinConcentrations(), and AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mpOutStream.

Referenced by CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::serialize().

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: