#include <CellCycleModelProteinConcentrationsWriter.hpp>
Inheritance diagram for CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >: Collaboration diagram for CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >:Public Member Functions | |
| CellCycleModelProteinConcentrationsWriter () | |
| double | GetCellDataForVtkOutput (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation) |
| virtual void | VisitCell (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation) |
| Public Member Functions inherited from AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > | |
| AbstractCellWriter (const std::string &rFileName) | |
| virtual c_vector< double, SPACE_DIM > | GetVectorCellDataForVtkOutput (CellPtr pCell, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > *pCellPopulation) |
| bool | GetOutputScalarData () |
| bool | GetOutputVectorData () |
| void | SetVtkCellDataName (std::string vtkCellDataName) |
| void | SetVtkVectorCellDataName (std::string vtkCellDataName) |
| std::string | GetVtkCellDataName () |
| std::string | GetVtkVectorCellDataName () |
| Public Member Functions inherited from AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM > | |
| AbstractCellBasedWriter (const std::string &rFileName) | |
| virtual | ~AbstractCellBasedWriter () |
| void | CloseFile () |
| virtual void | OpenOutputFile (OutputFileHandler &rOutputFileHandler) |
| void | OpenOutputFileForAppend (OutputFileHandler &rOutputFileHandler) |
| virtual void | WriteTimeStamp () |
| virtual void | WriteNewline () |
| void | SetFileName (std::string fileName) |
| std::string | GetFileName () |
| Public Member Functions inherited from Identifiable | |
| virtual | ~Identifiable () |
| std::string | GetIdentifier () const |
Private Member Functions | |
| template<class Archive > | |
| void | serialize (Archive &archive, const unsigned int version) |
Friends | |
| class | boost::serialization::access |
Additional Inherited Members | |
| Protected Attributes inherited from AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > | |
| bool | mOutputScalarData |
| bool | mOutputVectorData |
| std::string | mVtkCellDataName |
| std::string | mVtkVectorCellDataName |
| Protected Attributes inherited from AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM > | |
| std::string | mFileName |
| out_stream | mpOutStream |
Detailed Description
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >
A class written using the visitor pattern for writing cell-cycle model protein concentrations to file.
The output file is called proteinconcentrations.dat by default. If VTK is switched on, then the writer also specifies the VTK output for each cell, which is stored in the VTK cell data "Protein concentrations" by default.
Definition at line 51 of file CellCycleModelProteinConcentrationsWriter.hpp.
Constructor & Destructor Documentation
| CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::CellCycleModelProteinConcentrationsWriter | ( | ) |
Default constructor.
Definition at line 41 of file CellCycleModelProteinConcentrationsWriter.cpp.
References AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >::mVtkCellDataName.
Member Function Documentation
|
virtual |
Overridden GetCellDataForVtkOutput() method.
Get a double associated with a cell. This method reduces duplication of code between the methods VisitCell() and AddVtkData().
- Parameters
-
pCell a cell pCellPopulation a pointer to the cell population owning the cell
- Returns
- data associated with the cell
Reimplemented from AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 48 of file CellCycleModelProteinConcentrationsWriter.cpp.
|
inlineprivate |
Serialize the object and its member variables.
- Parameters
-
archive the archive version the current version of this class
Definition at line 63 of file CellCycleModelProteinConcentrationsWriter.hpp.
|
virtual |
Overridden VisitCell() method.
Visit a cell and write the protein concentrations associated with its cell-cycle model, if its cell-cycle model is a subclass of AbstractOdeBasedPhaseBasedCellCycleModel.
Outputs a line of space-separated values of the form: ...[location index] [protein 1 conc] [protein 2 conc] ... [protein n conc] ...
This is appended to the output written by AbstractCellBasedWriter, which is a single value [present simulation time], followed by a tab.
Note that the "protein concentrations" refer to the solution of the ODE system that is present in the cell-cycle model. If the cell-cycle model does not inherit from AbstractOdeBasedPhaseBasedCellCycleModel, then an exception is thrown.
- Parameters
-
pCell a pointer to a cell pCellPopulation a pointer to the cell population owning the cell
Implements AbstractCellWriter< ELEMENT_DIM, SPACE_DIM >.
Definition at line 60 of file CellCycleModelProteinConcentrationsWriter.cpp.
References EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), and CellCycleModelOdeHandler::GetProteinConcentrations().
Friends And Related Function Documentation
|
friend |
Needed for serialization.
Definition at line 55 of file CellCycleModelProteinConcentrationsWriter.hpp.
The documentation for this class was generated from the following files:
- cell_based/src/writers/cell_writers/CellCycleModelProteinConcentrationsWriter.hpp
- cell_based/src/writers/cell_writers/CellCycleModelProteinConcentrationsWriter.cpp
