AbstractCellPopulation< DIM > Class Template Reference

#include <AbstractCellPopulation.hpp>

Inheritance diagram for AbstractCellPopulation< DIM >:

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List of all members.

Public Member Functions

 AbstractCellPopulation (std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
virtual ~AbstractCellPopulation ()
void InitialiseCells ()
std::list< CellPtr > & rGetCells ()
bool IsMeshBasedCellPopulation ()
virtual unsigned GetNumNodes ()=0
virtual c_vector< double, DIM > GetLocationOfCellCentre (CellPtr pCell)=0
virtual Node< DIM > * GetNode (unsigned index)=0
virtual unsigned AddNode (Node< DIM > *pNewNode)=0
virtual void SetNode (unsigned nodeIndex, ChastePoint< DIM > &rNewLocation)=0
virtual bool IsCellAssociatedWithADeletedLocation (CellPtr pCell)=0
virtual void UpdateNodeLocations (const std::vector< c_vector< double, DIM > > &rNodeForces, double dt)=0
virtual double GetDampingConstant (unsigned nodeIndex)=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 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)
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
double GetDampingConstantNormal ()
double GetDampingConstantMutant ()
bool GetOutputCellIdData ()
bool GetOutputCellMutationStates ()
bool GetOutputCellAncestors ()
bool GetOutputCellProliferativeTypes ()
bool GetOutputCellVariables ()
bool GetOutputCellCyclePhases ()
bool GetOutputCellAges ()
bool GetOutputCellVolumes ()
void SetDampingConstantNormal (double dampingConstantNormal)
void SetDampingConstantMutant (double dampingConstantMutant)
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)
virtual void SetOutputCellVolumes (bool outputCellVolumes)
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
out_stream mpVizNodesFile
out_stream mpVizCellProliferativeTypesFile
out_stream mpCellMutationStatesFile
out_stream mpVizCellAncestorsFile
out_stream mpCellProliferativeTypesFile
out_stream mpCellCyclePhasesFile
out_stream mpCellVariablesFile
out_stream mpCellAgesFile
out_stream mpCellIdFile
out_stream mpVizBoundaryNodesFile
std::string mDirPath
out_stream mpVtkMetaFile
bool mCellPopulationContainsMesh
boost::shared_ptr
< CellPropertyRegistry
mpCellPropertyRegistry
double mDampingConstantNormal
double mDampingConstantMutant
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

Classes

class  Iterator


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 65 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 215 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 101 of file AbstractCellPopulation.cpp.


Member Function Documentation

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

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

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

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

Initialise each cell's cell-cycle model.

Definition at line 106 of file AbstractCellPopulation.cpp.

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

template<unsigned DIM>
std::list< CellPtr > & AbstractCellPopulation< DIM >::rGetCells (  )  [inline]

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

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

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

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

template<unsigned DIM>
virtual unsigned AbstractCellPopulation< DIM >::AddNode ( Node< DIM > *  pNewNode  )  [pure virtual]

Add a new node to the cell population.

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

Parameters:
pNewNode pointer to the new node
Returns:
global index of new node in cell population.

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

Referenced by AbstractCentreBasedCellPopulation< DIM >::AddCell().

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 MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Referenced by AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations().

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 >, and VertexBasedCellPopulation< DIM >.

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

template<unsigned DIM>
virtual void AbstractCellPopulation< DIM >::UpdateNodeLocations ( const std::vector< c_vector< double, DIM > > &  rNodeForces,
double  dt 
) [pure virtual]

Update the location of each node in the cell population given a vector of forces on nodes and a time step over which to integrate the equations of motion.

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

Parameters:
rNodeForces forces on nodes
dt time step

Implemented in AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, VertexBasedCellPopulation< DIM >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

template<unsigned DIM>
virtual double AbstractCellPopulation< DIM >::GetDampingConstant ( unsigned  nodeIndex  )  [pure virtual]

Get the damping constant for this node - ie d in drdt = F/d.

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

Parameters:
nodeIndex the global index of this node
Returns:
the damping constant at the node.

Implemented in AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

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 >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulationWithGhostNodes< 2 >.

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 MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

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 MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

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 158 of file AbstractCellPopulation.cpp.

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

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

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 184 of file AbstractCellPopulation.cpp.

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

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 194 of file AbstractCellPopulation.cpp.

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

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

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 138 of file AbstractCellPopulation.cpp.

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

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

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 147 of file AbstractCellPopulation.cpp.

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

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

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

template<unsigned DIM>
boost::shared_ptr< CellPropertyRegistry > AbstractCellPopulation< DIM >::GetCellPropertyRegistry (  )  [inline]

Returns:
registry of cell properties used in this cell population.

Definition at line 227 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mpCellPropertyRegistry.

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

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 233 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::GetCellPropertyRegistry().

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

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

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

This method is overridden in some daughter classes.

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

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

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 >, VertexBasedCellPopulation< DIM >, MeshBasedCellPopulation< 1 >, and MeshBasedCellPopulation< 2 >.

Definition at line 253 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 >::mpCellAgesFile, AbstractCellPopulation< DIM >::mpCellCyclePhasesFile, AbstractCellPopulation< DIM >::mpCellIdFile, AbstractCellPopulation< DIM >::mpCellMutationStatesFile, AbstractCellPopulation< DIM >::mpCellProliferativeTypesFile, AbstractCellPopulation< DIM >::mpCellPropertyRegistry, AbstractCellPopulation< DIM >::mpCellVariablesFile, AbstractCellPopulation< DIM >::mpVizBoundaryNodesFile, AbstractCellPopulation< DIM >::mpVizCellAncestorsFile, AbstractCellPopulation< DIM >::mpVizCellProliferativeTypesFile, AbstractCellPopulation< DIM >::mpVizNodesFile, AbstractCellPopulation< DIM >::mpVtkMetaFile, OutputFileHandler::OpenOutputFile(), and AbstractCellPopulation< DIM >::SetDefaultMutationStateOrdering().

Referenced by VertexBasedCellPopulation< DIM >::CreateOutputFiles(), and MeshBasedCellPopulation< DIM >::CreateOutputFiles().

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

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

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

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

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

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

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 641 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]

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

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

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

Returns:
mOutputCellIdData

Definition at line 713 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellIdData.

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

Returns:
mOutputCellMutationStates

Definition at line 719 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellMutationStates.

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

Returns:
mOutputCellAncestors

Definition at line 725 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAncestors.

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

Returns:
mOutputCellProliferativeTypes

Definition at line 731 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellProliferativeTypes.

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

Returns:
mOutputCellVariables

Definition at line 737 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVariables.

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

Returns:
mOutputCellCyclePhases

Definition at line 743 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellCyclePhases.

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

Returns:
mOutputCellAges

Definition at line 749 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAges.

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

Returns:
mOutputCellVolumes

Definition at line 755 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVolumes.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetDampingConstantNormal ( double  dampingConstantNormal  )  [inline]

Set mDampingConstantNormal.

Parameters:
dampingConstantNormal the new value of mDampingConstantNormal

Definition at line 765 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mDampingConstantNormal.

template<unsigned DIM>
void AbstractCellPopulation< DIM >::SetDampingConstantMutant ( double  dampingConstantMutant  )  [inline]

Set mDampingConstantMutant.

Parameters:
dampingConstantMutant the new value of mDampingConstantMutant

Definition at line 772 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mDampingConstantMutant.

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

Set mOutputCellIdData.

Parameters:
outputCellIdData the new value of mOutputCellIdData

Definition at line 779 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 785 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellMutationStates.

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

Set mOutputCellAncestors.

Parameters:
outputCellAncestors the new value of mOutputCellAncestors

Definition at line 791 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAncestors.

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

Set mOutputCellProliferativeTypes.

Parameters:
outputCellProliferativeTypes the new value of mOutputCellProliferativeTypes

Definition at line 797 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 803 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVariables.

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

Set mOutputCellCyclePhases.

Parameters:
outputCellCyclePhases the new value of mOutputCellCyclePhases

Definition at line 809 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellCyclePhases.

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

Set mOutputCellAges.

Parameters:
outputCellAges the new value of mOutputCellAges

Definition at line 815 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellAges.

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

Set mOutputCellVolumes.

Parameters:
outputCellVolumes the new value of mOutputCellVolumes

Reimplemented in NodeBasedCellPopulation< DIM >.

Definition at line 821 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< DIM >::mOutputCellVolumes.

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

Returns:
iterator pointing to the first cell in the cell population

Definition at line 830 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< DIM >::mCells.

Referenced by CryptProjectionForce::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCellPopulation< DIM >::GetCellAncestors(), CryptStatistics::GetCryptSection(), CryptProjectionStatistics::GetCryptSection(), AbstractCellPopulation< DIM >::GetNumRealCells(), 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(), CryptProjectionForce::UpdateNode3dLocationMap(), AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations(), VertexBasedCellPopulation< DIM >::Validate(), NodeBasedCellPopulation< DIM >::Validate(), MeshBasedCellPopulationWithGhostNodes< DIM >::Validate(), MeshBasedCellPopulation< DIM >::Validate(), AbstractCellPopulation< DIM >::WriteCellIdDataToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

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 836 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< DIM >::mCells.

Referenced by CryptProjectionForce::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), VertexBasedCellPopulation< DIM >::GenerateCellResultsAndWriteToFiles(), AbstractCellPopulation< DIM >::GetCellAncestors(), CryptStatistics::GetCryptSection(), CryptProjectionStatistics::GetCryptSection(), AbstractCellPopulation< DIM >::GetNumRealCells(), 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(), CryptProjectionForce::UpdateNode3dLocationMap(), AbstractCentreBasedCellPopulation< DIM >::UpdateNodeLocations(), VertexBasedCellPopulation< DIM >::Validate(), NodeBasedCellPopulation< DIM >::Validate(), MeshBasedCellPopulationWithGhostNodes< DIM >::Validate(), MeshBasedCellPopulation< DIM >::Validate(), AbstractCellPopulation< DIM >::WriteCellIdDataToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().


Friends And Related Function Documentation

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


Member Data Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

template<unsigned DIM>
double AbstractCellPopulation< DIM >::mDampingConstantNormal [protected]

Damping constant for normal cells has units of kg s^-1 Represented by the parameter eta in the model by Meineke et al (2001) in their off-lattice model of the intestinal crypt (doi:10.1046/j.0960-7722.2001.00216.x).

Definition at line 163 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< DIM >::GetDampingConstantNormal(), AbstractCellPopulation< DIM >::OutputCellPopulationParameters(), AbstractCellPopulation< SPACE_DIM >::serialize(), and AbstractCellPopulation< DIM >::SetDampingConstantNormal().

template<unsigned DIM>
double AbstractCellPopulation< DIM >::mDampingConstantMutant [protected]

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

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

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

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

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

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

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

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


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

Generated on Tue May 31 14:32:06 2011 for Chaste by  doxygen 1.5.5