CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <CellMutationStatesWriter.hpp>

Inheritance diagram for CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	CellMutationStatesWriter ()
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 CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >

A class written using the visitor pattern for writing cell mutation states to file.

The output file is called results.vizmutationstates 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 "Mutation states" by default.

Definition at line 51 of file CellMutationStatesWriter.hpp.

Constructor & Destructor Documentation

CellMutationStatesWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >::CellMutationStatesWriter

(

)

Default constructor.

Definition at line 42 of file CellMutationStatesWriter.cpp.

References AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mVtkCellDataName.

Member Function Documentation

GetCellDataForVtkOutput()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput ( CellPtr  pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *  pCellPopulation  )

virtual

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

By default this method returns a DOUBLE_UNSET, but it may be overridden in subclasses

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 49 of file CellMutationStatesWriter.cpp.

References CellPropertyCollection::GetProperties(), CellPropertyCollection::GetProperty(), and CellPropertyCollection::GetSize().

serialize()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void CellMutationStatesWriter< 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 CellMutationStatesWriter.hpp.

VisitCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell ( CellPtr  pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *  pCellPopulation  )

virtual

Overridden VisitCell() method.

Visit a cell and write its mutation state, as given by this property's member mColour.

Outputs a line of space-separated values of the form: ...[cell mutation state] ...

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

Parameters

pCell	a cell
pCellPopulation	a pointer to the cell population owning the cell

Todo:

split these all off as cell label not mutation states (see #2534)

Implements AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 66 of file CellMutationStatesWriter.cpp.

References CellPropertyCollection::GetProperties(), CellPropertyCollection::GetProperty(), and CellPropertyCollection::GetSize().

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 55 of file CellMutationStatesWriter.hpp.

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

• cell_based/src/writers/cell_writers/CellMutationStatesWriter.hpp
• cell_based/src/writers/cell_writers/CellMutationStatesWriter.cpp