#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

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.

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

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

pCell	a cell
pCellPopulation	a 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

Serialize the object and its member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 63 of file CellCycleModelProteinConcentrationsWriter.hpp.

References CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::CellCycleModelProteinConcentrationsWriter(), EXPORT_TEMPLATE_CLASS_ALL_DIMS, CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput(), and CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().

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

pCell	a pointer to a cell
pCellPopulation	a 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:

cell_based/src/writers/cell_writers/CellCycleModelProteinConcentrationsWriter.hpp
cell_based/src/writers/cell_writers/CellCycleModelProteinConcentrationsWriter.cpp

Public Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

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