AbstractCentreBasedCellPopulation.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2011
00004 
00005 University of Oxford means the Chancellor, Masters and Scholars of the
00006 University of Oxford, having an administrative office at Wellington
00007 Square, Oxford OX1 2JD, UK.
00008 
00009 This file is part of Chaste.
00010 
00011 Chaste is free software: you can redistribute it and/or modify it
00012 under the terms of the GNU Lesser General Public License as published
00013 by the Free Software Foundation, either version 2.1 of the License, or
00014 (at your option) any later version.
00015 
00016 Chaste is distributed in the hope that it will be useful, but WITHOUT
00017 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
00018 FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
00019 License for more details. The offer of Chaste under the terms of the
00020 License is subject to the License being interpreted in accordance with
00021 English Law and subject to any action against the University of Oxford
00022 being under the jurisdiction of the English Courts.
00023 
00024 You should have received a copy of the GNU Lesser General Public License
00025 along with Chaste. If not, see <http://www.gnu.org/licenses/>.
00026 
00027 */
00028 #ifndef ABSTRACTCENTREBASEDCELLPOPULATION_HPP_
00029 #define ABSTRACTCENTREBASEDCELLPOPULATION_HPP_
00030 
00031 #include "AbstractCellPopulation.hpp"
00032 
00033 // Needed here to avoid serialization errors (on Boost<1.37)
00034 #include "WildTypeCellMutationState.hpp"
00035 
00040 template<unsigned DIM>
00041 class AbstractCentreBasedCellPopulation : public AbstractCellPopulation<DIM>
00042 {
00043 private:
00045     friend class boost::serialization::access;
00052     template<class Archive>
00053     void serialize(Archive & archive, const unsigned int version)
00054     {
00055         // If Archive is an output archive, then '&' resolves to '<<'
00056         // If Archive is an input archive, then '&' resolves to '>>'
00057         archive & boost::serialization::base_object<AbstractCellPopulation<DIM> >(*this);
00058         archive & mMeinekeDivisionSeparation;
00059     }
00060 
00061 protected:
00062 
00067     double mMeinekeDivisionSeparation;
00068 
00072     AbstractCentreBasedCellPopulation();
00073 
00080     virtual void WriteVtkResultsToFile()=0;
00081 
00082 public:
00083 
00090     AbstractCentreBasedCellPopulation(std::vector<CellPtr>& rCells,
00091                                   const std::vector<unsigned> locationIndices=std::vector<unsigned>());
00092 
00101     c_vector<double, DIM> GetLocationOfCellCentre(CellPtr pCell);
00102 
00110     Node<DIM>* GetNodeCorrespondingToCell(CellPtr pCell);
00111 
00121     CellPtr AddCell(CellPtr pNewCell, const c_vector<double,DIM>& rCellDivisionVector, CellPtr pParentCell=CellPtr());
00122 
00130     bool IsCellAssociatedWithADeletedLocation(CellPtr pCell);
00131 
00138     virtual void UpdateNodeLocations(const std::vector< c_vector<double, DIM> >& rNodeForces, double dt);
00139 
00156     virtual double GetDampingConstant(unsigned nodeIndex);
00157 
00166     void GenerateCellResults(unsigned locationIndex,
00167                              std::vector<unsigned>& rCellProliferativeTypeCounter,
00168                              std::vector<unsigned>& rCellCyclePhaseCounter);
00169 
00173     virtual void GenerateCellResultsAndWriteToFiles();
00174 
00178     virtual void WriteTimeAndNodeResultsToFiles();
00179 
00188     virtual bool IsGhostNode(unsigned index);
00189 
00193     double GetMeinekeDivisionSeparation();
00194 
00200     void SetMeinekeDivisionSeparation(double divisionSeparation);
00201 
00207     virtual void OutputCellPopulationParameters(out_stream& rParamsFile);
00208 };
00209 
00210 #endif /*ABSTRACTCENTREBASEDCELLPOPULATION_HPP_*/

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