Chaste  Release::2018.1
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

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

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
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 49 of file CellMutationStatesWriter.cpp.

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

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
archivethe archive
versionthe current version of this class

Definition at line 63 of file CellMutationStatesWriter.hpp.

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
pCella cell
pCellPopulationa 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 Function Documentation

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

Needed for serialization.

Definition at line 55 of file CellMutationStatesWriter.hpp.


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