AbstractCellPopulation< DIM > Class Template Reference

#include <AbstractCellPopulation.hpp>

Inherits Identifiable.

Inherited by AbstractOffLatticeCellPopulation< DIM >, and AbstractOnLatticeCellPopulation< DIM >.

Collaboration diagram for AbstractCellPopulation< DIM >:
Collaboration graph
[legend]

List of all members.

Classes

class  Iterator

Public Member Functions

 AbstractCellPopulation (std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
virtual ~AbstractCellPopulation ()
void InitialiseCells ()
std::list< CellPtr > & rGetCells ()
virtual unsigned GetNumNodes ()=0
virtual c_vector< double, DIM > GetLocationOfCellCentre (CellPtr pCell)=0
virtual Node< DIM > * GetNode (unsigned index)=0
virtual void SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)=0
virtual bool IsCellAssociatedWithADeletedLocation (CellPtr pCell)=0
virtual CellPtr AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr())=0
virtual unsigned RemoveDeadCells ()=0
virtual void Update (bool hasHadBirthsOrDeaths=true)=0
std::vector< unsigned > GetCellMutationStateCount ()
const std::vector< unsigned > & rGetCellProliferativeTypeCount () const
const std::vector< unsigned > & rGetCellCyclePhaseCount () const
unsigned GetNumRealCells ()
void SetCellAncestorsToLocationIndices ()
void WriteCellIdDataToFile ()
std::set< unsigned > GetCellAncestors ()
CellPtr GetCellUsingLocationIndex (unsigned index)
unsigned GetLocationIndexUsingCell (CellPtr pCell)
boost::shared_ptr
< CellPropertyRegistry > 		GetCellPropertyRegistry ()
void SetDefaultMutationStateOrdering ()
virtual double GetWidth (const unsigned &rDimension)=0
virtual std::set< unsigned > GetNeighbouringNodeIndices (unsigned index)=0
c_vector< double, DIM > GetCentroidOfCellPopulation ()
virtual void CreateOutputFiles (const std::string &rDirectory, bool cleanOutputDirectory)
virtual void WriteResultsToFiles ()
virtual void WriteTimeAndNodeResultsToFiles ()
virtual void GenerateCellResultsAndWriteToFiles ()=0
virtual void GenerateCellResults (unsigned locationIndex, std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
virtual void WriteCellVolumeResultsToFile ()=0
void WriteCellResultsToFiles (std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter)
virtual void CloseOutputFiles ()
void OutputCellPopulationInfo (out_stream &rParamsFile)
virtual void OutputCellPopulationParameters (out_stream &rParamsFile)=0
bool GetOutputCellIdData ()
bool GetOutputCellMutationStates ()
bool GetOutputCellAncestors ()
bool GetOutputCellProliferativeTypes ()
bool GetOutputCellVariables ()
bool GetOutputCellCyclePhases ()
bool GetOutputCellAges ()
bool GetOutputCellVolumes ()
void SetOutputCellIdData (bool outputCellIdData)
void SetOutputCellMutationStates (bool outputCellMutationStates)
void SetOutputCellAncestors (bool outputCellAncestors)
void SetOutputCellProliferativeTypes (bool outputCellProliferativeTypes)
void SetOutputCellVariables (bool outputCellVariables)
void SetOutputCellCyclePhases (bool outputCellCyclePhases)
void SetOutputCellAges (bool outputCellAges)
void SetOutputCellVolumes (bool outputCellVolumes)
c_vector< double, DIM > GetSizeOfCellPopulation ()
Iterator Begin ()
Iterator End ()

Protected Member Functions

virtual void Validate ()=0
virtual void WriteVtkResultsToFile ()=0
 AbstractCellPopulation ()

Protected Attributes

std::list< CellPtr > mCells
std::map< unsigned, CellPtr > mLocationCellMap
std::map< Cell *, unsigned > mCellLocationMap
std::vector< unsigned > mCellProliferativeTypeCount
std::vector< unsigned > mCellCyclePhaseCount
c_vector< double, DIM > mCentroid
out_stream mpVizNodesFile
out_stream mpVizCellProliferativeTypesFile
out_stream mpVizCellProliferativePhasesFile
out_stream mpCellMutationStatesFile
out_stream mpVizCellAncestorsFile
out_stream mpCellProliferativeTypesFile
out_stream mpCellCyclePhasesFile
out_stream mpCellVariablesFile
out_stream mpCellAgesFile
out_stream mpCellIdFile
out_stream mpCellVolumesFile
out_stream mpVizBoundaryNodesFile
std::string mDirPath
out_stream mpVtkMetaFile
boost::shared_ptr
< CellPropertyRegistry > 		mpCellPropertyRegistry
bool mOutputCellIdData
bool mOutputCellMutationStates
bool mOutputCellAncestors
bool mOutputCellProliferativeTypes
bool mOutputCellVariables
bool mOutputCellCyclePhases
bool mOutputCellAges
bool mOutputCellVolumes

Private Member Functions

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

Friends

class boost::serialization::access

Detailed Description

template<unsigned DIM>
class AbstractCellPopulation< DIM >

An abstract facade class encapsulating a cell population.

Contains a group of cells and associated methods.

Definition at line 66 of file AbstractCellPopulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>
AbstractCellPopulation< DIM >::AbstractCellPopulation (  )  [inline, protected]

Constructor for use by archiving only. Please use the other constructor.

Doesn't take in cells, since these are dealt with by the serialize method.

Definition at line 206 of file AbstractCellPopulation.hpp.

template<unsigned DIM>
AbstractCellPopulation< DIM >::AbstractCellPopulation ( std::vector< CellPtr > &  rCells,
const std::vector< unsigned >  locationIndices = std::vector<unsigned>() 
) [inline]

AbstractCellPopulation Constructor.

Note:
Warning: the passed-in vector of cells will be emptied, even if the constructor throws an exception!
Parameters:
rCells a vector of cells. Copies of the cells will be stored in the cell population, and the passed-in vector cleared.
locationIndices an optional vector of location indices that correspond to real cells

Definition at line 34 of file AbstractCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< DIM >::mCellCyclePhaseCount, AbstractCellPopulation< DIM >::mCellLocationMap, AbstractCellPopulation< DIM >::mCellProliferativeTypeCount, AbstractCellPopulation< DIM >::mCells, AbstractCellPopulation< DIM >::mLocationCellMap, and AbstractCellPopulation< DIM >::mpCellPropertyRegistry.

template<unsigned DIM>
AbstractCellPopulation< DIM >::~AbstractCellPopulation (  )  [inline, virtual]

Base class with virtual methods needs a virtual destructor.

Definition at line 99 of file AbstractCellPopulation.cpp.

Member Function Documentation

template<unsigned DIM>
virtual CellPtr AbstractCellPopulation< DIM >::AddCell ( CellPtr  pNewCell,
const c_vector< double, DIM > &  rCellDivisionVector,
CellPtr  pParentCell = CellPtr() 
) [pure virtual]

Add a new cell to the cell population.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
pNewCell the cell to add
rCellDivisionVector a vector providing information regarding how the cell division should occur (for cell-centre cell populations, this vector is the position of the daughter cell; for vertex cell populations it can be used by any subclass of CellBasedSimulation to as a means of dictating the axis along which the parent cell divides)
pParentCell pointer to a parent cell (if required)
Returns:
address of cell as it appears in the cell list (internal of this method uses a copy constructor along the way).

Implemented in AbstractCentreBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>
AbstractCellPopulation< DIM >::Iterator AbstractCellPopulation< DIM >::Begin (  )  [inline]
Returns:
iterator pointing to the first cell in the cell population

Definition at line 788 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< DIM >::mCells.

Referenced by CryptProjectionForce::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), PottsBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCellPopulation< DIM >::GetCellAncestors(), AbstractCellPopulation< DIM >::GetCentroidOfCellPopulation(), CryptStatistics::GetCryptSection(), CryptProjectionStatistics::GetCryptSection(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), AbstractCellPopulation< DIM >::GetNumRealCells(), AbstractCellPopulation< DIM >::GetSizeOfCellPopulation(), AbstractCellPopulation< DIM >::InitialiseCells(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), AbstractCellPopulation< DIM >::OutputCellPopulationInfo(), AbstractCellPopulation< DIM >::SetCellAncestorsToLocationIndices(), CellwiseDataGradient< DIM >::SetupGradients(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), RadialSloughingCellKiller::TestAndLabelCellsForApoptosisOrDeath(), RandomCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), PlaneBasedCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), OxygenBasedCellKiller< SPACE_DIM >::TestAndLabelCellsForApoptosisOrDeath(), CaBasedCellPopulation< DIM >::UpdateCellLocations(), CryptProjectionForce::UpdateNode3dLocationMap(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations(), VertexBasedCellPopulation< DIM >::Validate(), PottsBasedCellPopulation< DIM >::Validate(), NodeBasedCellPopulation< DIM >::Validate(), MeshBasedCellPopulationWithGhostNodes< DIM >::Validate(), MeshBasedCellPopulation< DIM >::Validate(), CaBasedCellPopulation< DIM >::Validate(), AbstractCellPopulation< DIM >::WriteCellIdDataToFile(), VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), PottsBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), NodeBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), CaBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
void AbstractCellPopulation< DIM >::CloseOutputFiles (  )  [inline, virtual]

Close any output files.

Reimplemented in MeshBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 329 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAges, AbstractCellPopulation< DIM >::mOutputCellAncestors, AbstractCellPopulation< DIM >::mOutputCellCyclePhases, AbstractCellPopulation< DIM >::mOutputCellIdData, AbstractCellPopulation< DIM >::mOutputCellMutationStates, AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes, AbstractCellPopulation< DIM >::mOutputCellVariables, AbstractCellPopulation< DIM >::mOutputCellVolumes, AbstractCellPopulation< DIM >::mpCellAgesFile, AbstractCellPopulation< DIM >::mpCellCyclePhasesFile, AbstractCellPopulation< DIM >::mpCellIdFile, AbstractCellPopulation< DIM >::mpCellMutationStatesFile, AbstractCellPopulation< DIM >::mpCellProliferativeTypesFile, AbstractCellPopulation< DIM >::mpCellVariablesFile, AbstractCellPopulation< DIM >::mpCellVolumesFile, AbstractCellPopulation< DIM >::mpVizBoundaryNodesFile, AbstractCellPopulation< DIM >::mpVizCellAncestorsFile, AbstractCellPopulation< DIM >::mpVizCellProliferativePhasesFile, AbstractCellPopulation< DIM >::mpVizCellProliferativeTypesFile, AbstractCellPopulation< DIM >::mpVizNodesFile, and AbstractCellPopulation< DIM >::mpVtkMetaFile.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::CreateOutputFiles ( const std::string &  rDirectory,
bool  cleanOutputDirectory 
) [inline, virtual]

Use an output file handler to create output files for visualizer and post-processing.

Parameters:
rDirectory pathname of the output directory, relative to where Chaste output is stored
cleanOutputDirectory whether to delete the contents of the output directory prior to output file creation

Reimplemented in MeshBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 260 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mDirPath, AbstractCellPopulation< DIM >::mOutputCellAges, AbstractCellPopulation< DIM >::mOutputCellAncestors, AbstractCellPopulation< DIM >::mOutputCellCyclePhases, AbstractCellPopulation< DIM >::mOutputCellIdData, AbstractCellPopulation< DIM >::mOutputCellMutationStates, AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes, AbstractCellPopulation< DIM >::mOutputCellVariables, AbstractCellPopulation< DIM >::mOutputCellVolumes, AbstractCellPopulation< DIM >::mpCellAgesFile, AbstractCellPopulation< DIM >::mpCellCyclePhasesFile, AbstractCellPopulation< DIM >::mpCellIdFile, AbstractCellPopulation< DIM >::mpCellMutationStatesFile, AbstractCellPopulation< DIM >::mpCellProliferativeTypesFile, AbstractCellPopulation< DIM >::mpCellPropertyRegistry, AbstractCellPopulation< DIM >::mpCellVariablesFile, AbstractCellPopulation< DIM >::mpCellVolumesFile, AbstractCellPopulation< DIM >::mpVizBoundaryNodesFile, AbstractCellPopulation< DIM >::mpVizCellAncestorsFile, AbstractCellPopulation< DIM >::mpVizCellProliferativePhasesFile, AbstractCellPopulation< DIM >::mpVizCellProliferativeTypesFile, AbstractCellPopulation< DIM >::mpVizNodesFile, AbstractCellPopulation< DIM >::mpVtkMetaFile, OutputFileHandler::OpenOutputFile(), and AbstractCellPopulation< DIM >::SetDefaultMutationStateOrdering().

template<unsigned DIM>
AbstractCellPopulation< DIM >::Iterator AbstractCellPopulation< DIM >::End (  )  [inline]
Returns:
iterator pointing to one past the last cell in the cell population

Definition at line 794 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< DIM >::mCells.

Referenced by CryptProjectionForce::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), PottsBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCellPopulation< DIM >::GetCellAncestors(), AbstractCellPopulation< DIM >::GetCentroidOfCellPopulation(), CryptStatistics::GetCryptSection(), CryptProjectionStatistics::GetCryptSection(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), AbstractCellPopulation< DIM >::GetNumRealCells(), AbstractCellPopulation< DIM >::GetSizeOfCellPopulation(), AbstractCellPopulation< DIM >::InitialiseCells(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), AbstractCellPopulation< DIM >::OutputCellPopulationInfo(), AbstractCellPopulation< DIM >::SetCellAncestorsToLocationIndices(), CellwiseDataGradient< DIM >::SetupGradients(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), RadialSloughingCellKiller::TestAndLabelCellsForApoptosisOrDeath(), RandomCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), PlaneBasedCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), OxygenBasedCellKiller< SPACE_DIM >::TestAndLabelCellsForApoptosisOrDeath(), CaBasedCellPopulation< DIM >::UpdateCellLocations(), CryptProjectionForce::UpdateNode3dLocationMap(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations(), VertexBasedCellPopulation< DIM >::Validate(), PottsBasedCellPopulation< DIM >::Validate(), NodeBasedCellPopulation< DIM >::Validate(), MeshBasedCellPopulationWithGhostNodes< DIM >::Validate(), MeshBasedCellPopulation< DIM >::Validate(), CaBasedCellPopulation< DIM >::Validate(), AbstractCellPopulation< DIM >::WriteCellIdDataToFile(), VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), PottsBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), NodeBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), CaBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
void AbstractCellPopulation< DIM >::GenerateCellResults ( unsigned  locationIndex,
std::vector< unsigned > &  rCellProliferativeTypeCounter,
std::vector< unsigned > &  rCellCyclePhaseCounter 
) [inline, virtual]

Generate results for a given cell in the current cell population state to output files.

Parameters:
locationIndex location index of the cell
rCellProliferativeTypeCounter cell type counter
rCellCyclePhaseCounter cell cycle phase counter

Reimplemented in AbstractCentreBasedCellPopulation< DIM >, and CaBasedCellPopulation< DIM >.

Definition at line 377 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetLocationOfCellCentre(), CellPropertyCollection::GetProperty(), AbstractCellPopulation< DIM >::mLocationCellMap, AbstractCellPopulation< DIM >::mOutputCellAges, AbstractCellPopulation< DIM >::mOutputCellAncestors, AbstractCellPopulation< DIM >::mOutputCellCyclePhases, AbstractCellPopulation< DIM >::mOutputCellMutationStates, AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes, AbstractCellPopulation< DIM >::mOutputCellVariables, AbstractCellPopulation< DIM >::mpCellAgesFile, AbstractCellPopulation< DIM >::mpCellVariablesFile, AbstractCellPopulation< DIM >::mpVizCellAncestorsFile, AbstractCellPopulation< DIM >::mpVizCellProliferativePhasesFile, AbstractCellPopulation< DIM >::mpVizCellProliferativeTypesFile, NEVER_REACHED, and UNSIGNED_UNSET.

Referenced by VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), and PottsBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles().

template<unsigned DIM>
virtual void AbstractCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles (  )  [pure virtual]

Calls GenerateCellResults() on each cell then calls WriteCellResultsToFiles().

Implemented in AbstractCentreBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Referenced by AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
std::set< unsigned > AbstractCellPopulation< DIM >::GetCellAncestors (  )  [inline]

Loops over cells and makes a list of the ancestors that are part of the cell population.

Returns:
remaining_ancestors The size of this set tells you how many clonal populations remain.

Definition at line 139 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), and AbstractCellPopulation< DIM >::End().

template<unsigned DIM>
std::vector< unsigned > AbstractCellPopulation< DIM >::GetCellMutationStateCount (  )  [inline]

Find out how many cells of each mutation state there are

Returns:
The number of cells of each mutation state (evaluated at each visualizer output) [0] = healthy count [1] = APC one hit [2] = APC two hit [3] = beta catenin one hit

Definition at line 150 of file AbstractCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< DIM >::mOutputCellMutationStates, AbstractCellPopulation< DIM >::mpCellPropertyRegistry, and AbstractCellPopulation< DIM >::SetDefaultMutationStateOrdering().

Referenced by AbstractCellPopulation< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>
boost::shared_ptr< CellPropertyRegistry > AbstractCellPopulation< DIM >::GetCellPropertyRegistry (  )  [inline]
Returns:
registry of cell properties used in this cell population.

Definition at line 219 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mpCellPropertyRegistry.

Referenced by AbstractCellPopulation< DIM >::SetDefaultMutationStateOrdering().

template<unsigned DIM>
CellPtr AbstractCellPopulation< DIM >::GetCellUsingLocationIndex ( unsigned  index  )  [inline]

Get the cell corresponding to a given location index.

Currently assumes there is one cell for each location index, and they are ordered identically in their vectors. An assertion fails if not.

Parameters:
index the location index
Returns:
the cell.

Definition at line 196 of file AbstractCellPopulation.cpp.

References EXCEPTION, and AbstractCellPopulation< DIM >::mLocationCellMap.

Referenced by NagaiHondaForce< DIM >::AddForceContribution(), CryptProjectionForce::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), MeshBasedCellPopulation< DIM >::CheckCellPointers(), AdhesionPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), VertexBasedCellPopulation< DIM >::GetDampingConstant(), AbstractCentreBasedCellPopulation< DIM >::GetDampingConstant(), CellwiseDataGradient< DIM >::SetupGradients(), TargetedCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), and LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor().

template<unsigned DIM>
c_vector< double, DIM > AbstractCellPopulation< DIM >::GetCentroidOfCellPopulation (  )  [inline]

Returns the centroid of the cell population.

Definition at line 240 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), AbstractCellPopulation< DIM >::GetLocationOfCellCentre(), AbstractCellPopulation< DIM >::GetNumRealCells(), and AbstractCellPopulation< DIM >::mCentroid.

Referenced by AbstractCellPopulation< DIM >::GetSizeOfCellPopulation().

template<unsigned DIM>
unsigned AbstractCellPopulation< DIM >::GetLocationIndexUsingCell ( CellPtr  pCell  )  [inline]

Get the location index corresponding to a given cell.

Currently assumes there is one cell for each location index, and they are ordered identically in their vectors. An assertion fails if not.

Parameters:
pCell the cell
Returns:
the location index.

Definition at line 213 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mCellLocationMap.

Referenced by NodeBasedCellPopulation< DIM >::AddCell(), CryptProjectionForce::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), CryptSimulation1d::CalculateCellDivisionVector(), VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), PottsBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), CaBasedCellPopulation< DIM >::RemoveDeadCells(), CellwiseDataGradient< DIM >::SetupGradients(), CaBasedCellPopulation< DIM >::UpdateCellLocations(), CryptProjectionForce::UpdateNode3dLocationMap(), VertexBasedCellPopulation< DIM >::Validate(), PottsBasedCellPopulation< DIM >::Validate(), MeshBasedCellPopulation< DIM >::Validate(), VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), PottsBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), NodeBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), CaBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), VertexBasedCellPopulation< DIM >::WriteResultsToFiles(), PottsBasedCellPopulation< DIM >::WriteResultsToFiles(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
virtual c_vector<double, DIM> AbstractCellPopulation< DIM >::GetLocationOfCellCentre ( CellPtr  pCell  )  [pure virtual]

Find where a given cell is in space.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
pCell the cell
Returns:
the location of the cell

Implemented in AbstractCentreBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Referenced by AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GetCentroidOfCellPopulation(), AbstractCellPopulation< DIM >::GetSizeOfCellPopulation(), SloughingCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), RadialSloughingCellKiller::TestAndLabelCellsForApoptosisOrDeath(), PlaneBasedCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath(), CryptProjectionForce::UpdateNode3dLocationMap(), and AbstractCellPopulation< DIM >::WriteCellIdDataToFile().

template<unsigned DIM>
virtual std::set<unsigned> AbstractCellPopulation< DIM >::GetNeighbouringNodeIndices ( unsigned  index  )  [pure virtual]

Given a node index, returns the set of neighbouring node indices.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
index the node index
Returns:
the set of neighbouring node indices.

Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>
virtual Node<DIM>* AbstractCellPopulation< DIM >::GetNode ( unsigned  index  )  [pure virtual]

Get a pointer to the node with a given index.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
index global index of the specified node
Returns:
a pointer to the node with a given index.

Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Referenced by RepulsionForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), CryptProjectionForce::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), BuskeElasticForce< DIM >::CalculateForceBetweenNodes(), BuskeAdhesiveForce< DIM >::CalculateForceBetweenNodes(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCentreBasedCellPopulation< DIM >::GetNodeCorrespondingToCell(), AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations(), AbstractCentreBasedCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), and AbstractCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
virtual unsigned AbstractCellPopulation< DIM >::GetNumNodes (  )  [pure virtual]

As this method is pure virtual, it must be overridden in subclasses.

Returns:
the number of nodes in the cell population.

Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Referenced by AbstractCentreBasedCellPopulation< DIM >::AddCell(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCentreBasedCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), and AbstractCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
unsigned AbstractCellPopulation< DIM >::GetNumRealCells (  )  [inline]

Get the number of real cells.

Definition at line 119 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), and AbstractCellPopulation< DIM >::End().

Referenced by AbstractCellPopulation< DIM >::GetCentroidOfCellPopulation(), and TargetedCellKiller< DIM >::TestAndLabelCellsForApoptosisOrDeath().

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::GetOutputCellAges (  )  [inline]
Returns:
mOutputCellAges

Definition at line 767 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAges.

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::GetOutputCellAncestors (  )  [inline]
Returns:
mOutputCellAncestors

Definition at line 743 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAncestors.

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::GetOutputCellCyclePhases (  )  [inline]
Returns:
mOutputCellCyclePhases

Definition at line 761 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellCyclePhases.

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::GetOutputCellIdData (  )  [inline]
Returns:
mOutputCellIdData

Definition at line 731 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellIdData.

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::GetOutputCellMutationStates (  )  [inline]
Returns:
mOutputCellMutationStates

Definition at line 737 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellMutationStates.

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::GetOutputCellProliferativeTypes (  )  [inline]
Returns:
mOutputCellProliferativeTypes

Definition at line 749 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes.

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::GetOutputCellVariables (  )  [inline]
Returns:
mOutputCellVariables

Definition at line 755 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVariables.

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::GetOutputCellVolumes (  )  [inline]
Returns:
mOutputCellVolumes

Definition at line 773 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVolumes.

template<unsigned DIM>
c_vector< double, DIM > AbstractCellPopulation< DIM >::GetSizeOfCellPopulation (  )  [inline]
Returns:
The width (maximum distance to centroid) of the cell population in each dimension

Definition at line 831 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), AbstractCellPopulation< DIM >::GetCentroidOfCellPopulation(), and AbstractCellPopulation< DIM >::GetLocationOfCellCentre().

template<unsigned DIM>
virtual double AbstractCellPopulation< DIM >::GetWidth ( const unsigned &  rDimension  )  [pure virtual]

Calculate the 'width' of any dimension of the cell population.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
rDimension a dimension (0,1 or 2)
Returns:
The maximum distance between any nodes in this dimension.

Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::InitialiseCells (  )  [inline]

Initialise each cell's cell-cycle model.

Definition at line 104 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), and AbstractCellPopulation< DIM >::End().

template<unsigned DIM>
virtual bool AbstractCellPopulation< DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr  pCell  )  [pure virtual]

Helper method for establishing if a cell is real.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
pCell the cell
Returns:
whether a given cell is associated with a deleted node (cell-centre models) or element (vertex models).

Implemented in AbstractCentreBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Referenced by AbstractCellPopulation< DIM >::Iterator::IsRealCell().

template<unsigned DIM>
void AbstractCellPopulation< DIM >::OutputCellPopulationInfo ( out_stream &  rParamsFile  )  [inline]

Outputs CellPopulation used in the simulation to file and then calls OutputCellPopulationParameters to output all relevant parameters.

Parameters:
rParamsFile the file stream to which the parameters are output

Definition at line 673 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), Identifiable::GetIdentifier(), and AbstractCellPopulation< DIM >::OutputCellPopulationParameters().

template<unsigned DIM>
void AbstractCellPopulation< DIM >::OutputCellPopulationParameters ( out_stream &  rParamsFile  )  [inline, pure virtual]

Outputs CellPopulation parameters to file

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
rParamsFile the file stream to which the parameters are output

Implemented in AbstractCentreBasedCellPopulation< DIM >, AbstractOffLatticeCellPopulation< DIM >, AbstractOnLatticeCellPopulation< DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 714 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAges, AbstractCellPopulation< DIM >::mOutputCellAncestors, AbstractCellPopulation< DIM >::mOutputCellCyclePhases, AbstractCellPopulation< DIM >::mOutputCellIdData, AbstractCellPopulation< DIM >::mOutputCellMutationStates, AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes, AbstractCellPopulation< DIM >::mOutputCellVariables, and AbstractCellPopulation< DIM >::mOutputCellVolumes.

Referenced by AbstractCellPopulation< DIM >::OutputCellPopulationInfo().

template<unsigned DIM>
virtual unsigned AbstractCellPopulation< DIM >::RemoveDeadCells (  )  [pure virtual]

Remove all cells labelled as dead.

As this method is pure virtual, it must be overridden in subclasses.

Returns:
number of cells removed

Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>
const std::vector< unsigned > & AbstractCellPopulation< DIM >::rGetCellCyclePhaseCount (  )  const [inline]

Find out how many cells in each cell cycle phase there are

Returns:
The number of cells of each phase (evaluated at each visualizer output) [0] = G_ZERO_PHASE [1] = G_ONE_PHASE [2] = S_PHASE [3] = G_TWO_PHASE [4] = M_PHASE

Definition at line 186 of file AbstractCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< DIM >::mCellCyclePhaseCount, and AbstractCellPopulation< DIM >::mOutputCellCyclePhases.

template<unsigned DIM>
const std::vector< unsigned > & AbstractCellPopulation< DIM >::rGetCellProliferativeTypeCount (  )  const [inline]

Find out how many cells of each type there are

Returns:
The number of cells of each type (evaluated at each visualizer output) [0] = STEM [1] = TRANSIT [2] = DIFFERENTIATED

Definition at line 176 of file AbstractCellPopulation.cpp.

References EXCEPTION, AbstractCellPopulation< DIM >::mCellProliferativeTypeCount, and AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes.

template<unsigned DIM>
std::list< CellPtr > & AbstractCellPopulation< DIM >::rGetCells (  )  [inline]
Returns:
reference to mCells.

Definition at line 113 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mCells.

Referenced by AbstractCellPopulation< DIM >::Iterator::IsAtEnd(), and AbstractCellPopulation< DIM >::Iterator::Iterator().

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

Serialize the object and its member variables.

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

Reimplemented in AbstractCentreBasedCellPopulation< DIM >, AbstractOffLatticeCellPopulation< DIM >, AbstractOnLatticeCellPopulation< DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 78 of file AbstractCellPopulation.hpp.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetCellAncestorsToLocationIndices (  )  [inline]

Sets the Ancestor index of all the cells at this time to be the same as their location index, can be used to trace clonal populations.

Definition at line 130 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), and AbstractCellPopulation< DIM >::mCellLocationMap.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetDefaultMutationStateOrdering (  )  [inline]

Set a default ordering on mutation states, so that existing tests don't need to specify the old ordering explicitly.

Definition at line 225 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetCellPropertyRegistry().

Referenced by AbstractCellPopulation< DIM >::CreateOutputFiles(), and AbstractCellPopulation< DIM >::GetCellMutationStateCount().

template<unsigned DIM>
virtual void AbstractCellPopulation< DIM >::SetNode ( unsigned  nodeIndex,
ChastePoint< DIM > &  rNewLocation 
) [pure virtual]

Move the node with a given index to a new point in space.

As this method is pure virtual, it must be overridden in subclasses.

Parameters:
nodeIndex the index of the node to be moved
rNewLocation the new target location of the node

Implemented in AbstractOffLatticeCellPopulation< DIM >, AbstractOnLatticeCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetOutputCellAges ( bool  outputCellAges  )  [inline]

Set mOutputCellAges.

Parameters:
outputCellAges the new value of mOutputCellAges

Definition at line 819 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAges.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetOutputCellAncestors ( bool  outputCellAncestors  )  [inline]

Set mOutputCellAncestors.

Parameters:
outputCellAncestors the new value of mOutputCellAncestors

Definition at line 795 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAncestors.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetOutputCellCyclePhases ( bool  outputCellCyclePhases  )  [inline]

Set mOutputCellCyclePhases.

Parameters:
outputCellCyclePhases the new value of mOutputCellCyclePhases

Definition at line 813 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellCyclePhases.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetOutputCellIdData ( bool  outputCellIdData  )  [inline]

Set mOutputCellIdData.

Parameters:
outputCellIdData the new value of mOutputCellIdData

Definition at line 783 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellIdData.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetOutputCellMutationStates ( bool  outputCellMutationStates  )  [inline]

Set mOutputCellMutationStates.

Parameters:
outputCellMutationStates the new value of mOutputCellMutationStates

Definition at line 789 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellMutationStates.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetOutputCellProliferativeTypes ( bool  outputCellProliferativeTypes  )  [inline]

Set mOutputCellProliferativeTypes.

Parameters:
outputCellProliferativeTypes the new value of mOutputCellProliferativeTypes

Definition at line 801 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetOutputCellVariables ( bool  outputCellVariables  )  [inline]

Set mOutputCellVariables.

Parameters:
outputCellVariables the new value of mOutputCellVariables

Definition at line 807 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVariables.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetOutputCellVolumes ( bool  outputCellVolumes  )  [inline]

Set mOutputCellVolumes.

Parameters:
outputCellVolumes the new value of mOutputCellVolumes

Definition at line 825 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVolumes.

template<unsigned DIM>
virtual void AbstractCellPopulation< DIM >::Update ( bool  hasHadBirthsOrDeaths = true  )  [pure virtual]

Remove the Nodes (for cell-centre) or VertexElements (for cell-vertex) which have been marked as deleted and update the correspondence with Cells.

Parameters:
hasHadBirthsOrDeaths - a bool saying whether cell population has had Births Or Deaths

Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>
virtual void AbstractCellPopulation< DIM >::Validate (  )  [protected, pure virtual]

Check consistency of our internal data structures.

As this method is pure virtual, it must be overridden in subclasses.

Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::WriteCellIdDataToFile (  )  [inline]

Write cell ID data to mpCellIdFile.

Definition at line 650 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::Begin(), AbstractCellPopulation< DIM >::End(), AbstractCellPopulation< DIM >::GetLocationOfCellCentre(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellPopulation< DIM >::mCellLocationMap, and AbstractCellPopulation< DIM >::mpCellIdFile.

Referenced by AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
void AbstractCellPopulation< DIM >::WriteCellResultsToFiles ( std::vector< unsigned > &  rCellProliferativeTypeCounter,
std::vector< unsigned > &  rCellCyclePhaseCounter 
) [inline]

Write the current state of each cell to output files.

Parameters:
rCellProliferativeTypeCounter cell type counter
rCellCyclePhaseCounter cell cycle phase counter

Definition at line 510 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetCellMutationStateCount(), AbstractCellPopulation< DIM >::mCellCyclePhaseCount, AbstractCellPopulation< DIM >::mCellProliferativeTypeCount, AbstractCellPopulation< DIM >::mOutputCellAges, AbstractCellPopulation< DIM >::mOutputCellAncestors, AbstractCellPopulation< DIM >::mOutputCellCyclePhases, AbstractCellPopulation< DIM >::mOutputCellMutationStates, AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes, AbstractCellPopulation< DIM >::mOutputCellVariables, AbstractCellPopulation< DIM >::mpCellAgesFile, AbstractCellPopulation< DIM >::mpCellCyclePhasesFile, AbstractCellPopulation< DIM >::mpCellMutationStatesFile, AbstractCellPopulation< DIM >::mpCellProliferativeTypesFile, AbstractCellPopulation< DIM >::mpCellVariablesFile, AbstractCellPopulation< DIM >::mpVizCellAncestorsFile, AbstractCellPopulation< DIM >::mpVizCellProliferativePhasesFile, and AbstractCellPopulation< DIM >::mpVizCellProliferativeTypesFile.

Referenced by VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), PottsBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), CaBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), and AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles().

template<unsigned DIM>
virtual void AbstractCellPopulation< DIM >::WriteCellVolumeResultsToFile (  )  [pure virtual]

Write the current volume of each cell to file. As this method is pure virtual, it must be overridden in subclasses.

Implemented in CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Referenced by AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
void AbstractCellPopulation< DIM >::WriteResultsToFiles (  )  [inline, virtual]

Write results from the current cell population state to output files.

Reimplemented in MeshBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 596 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellPopulation< DIM >::mOutputCellAges, AbstractCellPopulation< DIM >::mOutputCellAncestors, AbstractCellPopulation< DIM >::mOutputCellCyclePhases, AbstractCellPopulation< DIM >::mOutputCellIdData, AbstractCellPopulation< DIM >::mOutputCellMutationStates, AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes, AbstractCellPopulation< DIM >::mOutputCellVariables, AbstractCellPopulation< DIM >::mOutputCellVolumes, AbstractCellPopulation< DIM >::mpCellAgesFile, AbstractCellPopulation< DIM >::mpCellCyclePhasesFile, AbstractCellPopulation< DIM >::mpCellMutationStatesFile, AbstractCellPopulation< DIM >::mpCellProliferativeTypesFile, AbstractCellPopulation< DIM >::mpCellVariablesFile, AbstractCellPopulation< DIM >::mpVizCellAncestorsFile, AbstractCellPopulation< DIM >::mpVizCellProliferativePhasesFile, AbstractCellPopulation< DIM >::mpVizCellProliferativeTypesFile, AbstractCellPopulation< DIM >::WriteCellIdDataToFile(), AbstractCellPopulation< DIM >::WriteCellVolumeResultsToFile(), AbstractCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), and AbstractCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
void AbstractCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles (  )  [inline, virtual]

Write the current time and node results to output files.

Reimplemented in AbstractCentreBasedCellPopulation< DIM >.

Definition at line 570 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetNode(), AbstractCellPopulation< DIM >::GetNumNodes(), SimulationTime::GetTime(), SimulationTime::Instance(), AbstractCellPopulation< DIM >::mpVizBoundaryNodesFile, and AbstractCellPopulation< DIM >::mpVizNodesFile.

Referenced by AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
virtual void AbstractCellPopulation< DIM >::WriteVtkResultsToFile (  )  [protected, pure virtual]

Write the current results to mpVtkMetaFile.

As this method is pure virtual, it must be overridden in subclasses.

Implemented in AbstractCentreBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Referenced by AbstractCellPopulation< DIM >::WriteResultsToFiles().

Friends And Related Function Documentation

template<unsigned DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented in AbstractCentreBasedCellPopulation< DIM >, AbstractOffLatticeCellPopulation< DIM >, AbstractOnLatticeCellPopulation< DIM >, CaBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithBuskeUpdate< DIM >, PottsBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 70 of file AbstractCellPopulation.hpp.

Member Data Documentation

template<unsigned DIM>
std::vector<unsigned> AbstractCellPopulation< DIM >::mCellCyclePhaseCount [protected]

Current cell cycle phase counts

Definition at line 111 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::AbstractCellPopulation(), VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), PottsBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), CaBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCellPopulation< DIM >::rGetCellCyclePhaseCount(), AbstractCellPopulation< SPACE_DIM >::serialize(), and AbstractCellPopulation< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>
std::map<Cell*, unsigned> AbstractCellPopulation< DIM >::mCellLocationMap [protected]

Map cells to location (node or VertexElement) indices

Definition at line 105 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::AbstractCellPopulation(), VertexBasedCellPopulation< DIM >::AddCell(), PottsBasedCellPopulation< DIM >::AddCell(), MeshBasedCellPopulationWithGhostNodes< DIM >::AddCell(), CaBasedCellPopulation< DIM >::AddCell(), AbstractCentreBasedCellPopulation< DIM >::AddCell(), MeshBasedCellPopulation< DIM >::CheckCellPointers(), VertexBasedCellPopulation< DIM >::GetElementCorrespondingToCell(), PottsBasedCellPopulation< DIM >::GetElementCorrespondingToCell(), AbstractCellPopulation< DIM >::GetLocationIndexUsingCell(), VertexBasedCellPopulation< DIM >::GetLocationOfCellCentre(), PottsBasedCellPopulation< DIM >::GetLocationOfCellCentre(), CaBasedCellPopulation< DIM >::GetLocationOfCellCentre(), AbstractCentreBasedCellPopulation< DIM >::GetNodeCorrespondingToCell(), CaBasedCellPopulation< DIM >::MoveCell(), VertexBasedCellPopulation< DIM >::RemoveDeadCells(), PottsBasedCellPopulation< DIM >::RemoveDeadCells(), NodeBasedCellPopulation< DIM >::RemoveDeadCells(), MeshBasedCellPopulation< DIM >::RemoveDeadCells(), CaBasedCellPopulation< DIM >::RemoveDeadCells(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetCellAncestorsToLocationIndices(), VertexBasedCellPopulation< DIM >::Update(), NodeBasedCellPopulation< DIM >::Update(), MeshBasedCellPopulation< DIM >::Update(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations(), NodeBasedCellPopulation< DIM >::Validate(), MeshBasedCellPopulationWithGhostNodes< DIM >::Validate(), CaBasedCellPopulation< DIM >::Validate(), and AbstractCellPopulation< DIM >::WriteCellIdDataToFile().

template<unsigned DIM>
std::vector<unsigned> AbstractCellPopulation< DIM >::mCellProliferativeTypeCount [protected]

Current cell type counts

Definition at line 108 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::AbstractCellPopulation(), VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), PottsBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), CaBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCellPopulation< DIM >::rGetCellProliferativeTypeCount(), AbstractCellPopulation< SPACE_DIM >::serialize(), and AbstractCellPopulation< DIM >::WriteCellResultsToFiles().

template<unsigned DIM>
std::list<CellPtr> AbstractCellPopulation< DIM >::mCells [protected]

List of cells

Definition at line 99 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::AbstractCellPopulation(), VertexBasedCellPopulation< DIM >::AddCell(), PottsBasedCellPopulation< DIM >::AddCell(), CaBasedCellPopulation< DIM >::AddCell(), AbstractCentreBasedCellPopulation< DIM >::AddCell(), AbstractCellPopulation< DIM >::Begin(), CaBasedCellPopulation< DIM >::CaBasedCellPopulation(), MeshBasedCellPopulation< DIM >::CheckCellPointers(), AbstractCellPopulation< DIM >::End(), MeshBasedCellPopulation< DIM >::MeshBasedCellPopulation(), VertexBasedCellPopulation< DIM >::RemoveDeadCells(), PottsBasedCellPopulation< DIM >::RemoveDeadCells(), NodeBasedCellPopulation< DIM >::RemoveDeadCells(), MeshBasedCellPopulation< DIM >::RemoveDeadCells(), CaBasedCellPopulation< DIM >::RemoveDeadCells(), AbstractCellPopulation< DIM >::rGetCells(), AbstractCellPopulation< SPACE_DIM >::serialize(), VertexBasedCellPopulation< DIM >::Update(), NodeBasedCellPopulation< DIM >::Update(), MeshBasedCellPopulation< DIM >::Update(), VertexBasedCellPopulation< DIM >::WriteResultsToFiles(), and PottsBasedCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
c_vector<double, DIM> AbstractCellPopulation< DIM >::mCentroid [protected]

Population centroid

Definition at line 114 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::GetCentroidOfCellPopulation().

template<unsigned DIM>
std::string AbstractCellPopulation< DIM >::mDirPath [protected]

A cache of where the results are going (used for VTK writer).

Definition at line 153 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CreateOutputFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
std::map<unsigned, CellPtr> AbstractCellPopulation< DIM >::mLocationCellMap [protected]

Map location (node or VertexElement) indices back to cells

Definition at line 102 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::AbstractCellPopulation(), VertexBasedCellPopulation< DIM >::AddCell(), PottsBasedCellPopulation< DIM >::AddCell(), CaBasedCellPopulation< DIM >::AddCell(), AbstractCentreBasedCellPopulation< DIM >::AddCell(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCellPopulation< DIM >::GetCellUsingLocationIndex(), CaBasedCellPopulation< DIM >::MoveCell(), NodeBasedCellPopulation< DIM >::RemoveDeadCells(), MeshBasedCellPopulation< DIM >::RemoveDeadCells(), CaBasedCellPopulation< DIM >::RemoveDeadCells(), AbstractCellPopulation< SPACE_DIM >::serialize(), VertexBasedCellPopulation< DIM >::Update(), NodeBasedCellPopulation< DIM >::Update(), MeshBasedCellPopulation< DIM >::Update(), MeshBasedCellPopulation< DIM >::WriteCellPopulationVolumeResultsToFile(), VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), PottsBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), MeshBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), VertexBasedCellPopulation< DIM >::WriteResultsToFiles(), PottsBasedCellPopulation< DIM >::WriteResultsToFiles(), MeshBasedCellPopulation< DIM >::WriteResultsToFiles(), AbstractCentreBasedCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::mOutputCellAges [protected]

Whether to write the cell ages to a file.

Definition at line 180 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GetOutputCellAges(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellAges(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), AbstractCellPopulation< DIM >::WriteResultsToFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::mOutputCellAncestors [protected]

Whether to output the ancestor of each cell to a visualizer file.

Definition at line 168 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GetOutputCellAncestors(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellAncestors(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), AbstractCellPopulation< DIM >::WriteResultsToFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::mOutputCellCyclePhases [protected]

Whether to write the cell cycle phases to a file.

Definition at line 177 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GetOutputCellCyclePhases(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< DIM >::rGetCellCyclePhaseCount(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellCyclePhases(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), AbstractCellPopulation< DIM >::WriteResultsToFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::mOutputCellIdData [protected]

Whether to write cell ID data to file.

Definition at line 162 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GetOutputCellIdData(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellIdData(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::mOutputCellMutationStates [protected]

Whether to count the number of each cell mutation state and output to file.

Definition at line 165 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GetCellMutationStateCount(), AbstractCellPopulation< DIM >::GetOutputCellMutationStates(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellMutationStates(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), AbstractCellPopulation< DIM >::WriteResultsToFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes [protected]

Whether to count the number of each cell type and output to file.

Definition at line 171 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GetOutputCellProliferativeTypes(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< DIM >::rGetCellProliferativeTypeCount(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellProliferativeTypes(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), AbstractCellPopulation< DIM >::WriteResultsToFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::mOutputCellVariables [protected]

Whether to write the cell variables to a file.

Definition at line 174 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GetOutputCellVariables(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellVariables(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
bool AbstractCellPopulation< DIM >::mOutputCellVolumes [protected]

Whether to write the cell volumes (in 3D) or areas (in 2D) to a file.

Definition at line 183 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GetOutputCellVolumes(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), AbstractCellPopulation< DIM >::SetOutputCellVolumes(), MeshBasedCellPopulation< DIM >::TessellateIfNeeded(), AbstractCellPopulation< DIM >::WriteResultsToFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpCellAgesFile [protected]

Results file for cell ages

Definition at line 141 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpCellCyclePhasesFile [protected]

Results file for cell cycle phases

Definition at line 135 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpCellIdFile [protected]

Results file for logged cell data.

Definition at line 144 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), and AbstractCellPopulation< DIM >::WriteCellIdDataToFile().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpCellMutationStatesFile [protected]

Results file for cell mutation states

Definition at line 126 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpCellProliferativeTypesFile [protected]

Results file for cell types

Definition at line 132 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
boost::shared_ptr<CellPropertyRegistry> AbstractCellPopulation< DIM >::mpCellPropertyRegistry [protected]

Cell property registry.

Definition at line 159 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::AbstractCellPopulation(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GetCellMutationStateCount(), AbstractCellPopulation< DIM >::GetCellPropertyRegistry(), and AbstractCellPopulation< SPACE_DIM >::serialize().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpCellVariablesFile [protected]

Results file for cell variables

Definition at line 138 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpCellVolumesFile [protected]

Results file for cell volume (in 3D) or area (in 2D) data.

Definition at line 147 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), PottsBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), NodeBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), MeshBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), and CaBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpVizBoundaryNodesFile [protected]

Results file for boundary nodes.

Definition at line 150 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCentreBasedCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), and AbstractCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpVizCellAncestorsFile [protected]

Results file for cell ancestors

Definition at line 129 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpVizCellProliferativePhasesFile [protected]

Results file for cell visualization

Definition at line 123 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpVizCellProliferativeTypesFile [protected]

Results file for cell visualization

Definition at line 120 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), CaBasedCellPopulation< DIM >::GenerateCellResults(), AbstractCentreBasedCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::GenerateCellResults(), AbstractCellPopulation< DIM >::WriteCellResultsToFiles(), and AbstractCellPopulation< DIM >::WriteResultsToFiles().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpVizNodesFile [protected]

Results file for node visualization

Definition at line 117 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), AbstractCentreBasedCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), and AbstractCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles().

template<unsigned DIM>
out_stream AbstractCellPopulation< DIM >::mpVtkMetaFile [protected]

Meta results file for VTK.

Definition at line 156 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::CloseOutputFiles(), AbstractCellPopulation< DIM >::CreateOutputFiles(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

The documentation for this class was generated from the following files:
Generated on Thu Dec 22 13:00:47 2011 for Chaste by  doxygen 1.6.3