AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractCellBasedWriter.hpp>

Inherits Identifiable.

Inherited by AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM >, AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >, and AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >.

Collaboration diagram for AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >:
Collaboration graph
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List of all members.

Public Member Functions

 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 ()

Protected Attributes

std::string mFileName
out_stream mpOutStream

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)

Friends

class boost::serialization::access

Detailed Description

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

Abstract class for a writer that takes data from an AbstractCellPopulation and writes it to file.

Definition at line 48 of file AbstractCellBasedWriter.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::AbstractCellBasedWriter ( const std::string &  rFileName  )  [inline]

Constructor.

Parameters:
rFileName the name of the file to write to.

Definition at line 39 of file AbstractCellBasedWriter.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::~AbstractCellBasedWriter (  )  [inline, virtual]

Virtual destructor.

Definition at line 45 of file AbstractCellBasedWriter.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::CloseFile (  )  [inline]

Close mpOutStream.

Definition at line 50 of file AbstractCellBasedWriter.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mpOutStream.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::string AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::GetFileName (  )  [inline]
Returns:
the output file name.

Definition at line 86 of file AbstractCellBasedWriter.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mFileName.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFile ( OutputFileHandler &  rOutputFileHandler  )  [inline, virtual]

Open mpOutStream for writing.

Parameters:
rOutputFileHandler handler for the directory in which to open this file.

Definition at line 56 of file AbstractCellBasedWriter.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mFileName, AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mpOutStream, and OutputFileHandler::OpenOutputFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFileForAppend ( OutputFileHandler &  rOutputFileHandler  )  [inline]

Open mpOutStream for appending.

Parameters:
rOutputFileHandler handler for the directory in which to open this file.

Definition at line 62 of file AbstractCellBasedWriter.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mFileName, AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mpOutStream, and OutputFileHandler::OpenOutputFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
template<class Archive >
void AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Serialize the object.

Parameters:
archive the archive
version the current version of this class

Reimplemented in AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >, CellAgesWriter< ELEMENT_DIM, SPACE_DIM >, CellAncestorWriter< ELEMENT_DIM, SPACE_DIM >, CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >, CellIdWriter< ELEMENT_DIM, SPACE_DIM >, CellLabelWriter< ELEMENT_DIM, SPACE_DIM >, CellLocationIndexWriter< ELEMENT_DIM, SPACE_DIM >, CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativePhasesWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativeTypesWriter< ELEMENT_DIM, SPACE_DIM >, CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >, CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >, AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM >, CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >, AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >, BoundaryNodeWriter< ELEMENT_DIM, SPACE_DIM >, CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >, CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >, HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >, NodeLocationWriter< ELEMENT_DIM, SPACE_DIM >, NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >, VertexT1SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >, VertexT2SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >, VertexT3SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >, VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >, and CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 61 of file AbstractCellBasedWriter.hpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mFileName.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::SetFileName ( std::string  fileName  )  [inline]

Set the output file name. This method allows the user to change mFileName from its default value, which is set in each subclass's constructor.

Parameters:
fileName the output file name

Definition at line 80 of file AbstractCellBasedWriter.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mFileName.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::WriteNewline (  )  [inline, virtual]

Add a newline character to mpOutStream.

Definition at line 74 of file AbstractCellBasedWriter.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mpOutStream.

Referenced by CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::WriteHeader().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::WriteTimeStamp (  )  [inline, virtual]

Write the current time stamp to mpOutStream.

Definition at line 68 of file AbstractCellBasedWriter.cpp.

References SimulationTime::GetTime(), SimulationTime::Instance(), and AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mpOutStream.

Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented in AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >, CellAgesWriter< ELEMENT_DIM, SPACE_DIM >, CellAncestorWriter< ELEMENT_DIM, SPACE_DIM >, CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >, CellIdWriter< ELEMENT_DIM, SPACE_DIM >, CellLabelWriter< ELEMENT_DIM, SPACE_DIM >, CellLocationIndexWriter< ELEMENT_DIM, SPACE_DIM >, CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativePhasesWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativeTypesWriter< ELEMENT_DIM, SPACE_DIM >, CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >, CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >, AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM >, CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >, CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >, AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM >, BoundaryNodeWriter< ELEMENT_DIM, SPACE_DIM >, CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >, CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >, HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >, NodeLocationWriter< ELEMENT_DIM, SPACE_DIM >, NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >, VertexT1SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >, VertexT2SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >, VertexT3SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >, VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >, and CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >.

Definition at line 53 of file AbstractCellBasedWriter.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::string AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mFileName [protected]

The name of the output file.

Definition at line 69 of file AbstractCellBasedWriter.hpp.

Referenced by AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::GetFileName(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFile(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFileForAppend(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::serialize(), and AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::SetFileName().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
out_stream AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::mpOutStream [protected]

An output stream for writing data.

Definition at line 72 of file AbstractCellBasedWriter.hpp.

Referenced by AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::CloseFile(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFile(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFileForAppend(), VoronoiDataWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), VertexT3SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), VertexT2SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), VertexT1SwapLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeLocationWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), BoundaryNodeWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeLocationWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), BoundaryNodeWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellProliferativeTypesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellProliferativePhasesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellMutationStatesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellLocationIndexWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellLabelWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellIdWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellAncestorWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellAgesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::WriteHeader(), AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::WriteNewline(), and AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::WriteTimeStamp().

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