AbstractCellCentreBasedTissue.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2010
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 ABSTRACTCELLCENTREBASEDTISSUE_HPP_
00029 #define ABSTRACTCELLCENTREBASEDTISSUE_HPP_
00030 
00031 #include "AbstractTissue.hpp"
00032 
00033 // Needed here to avoid serialization errors (on Boost<1.37)
00034 #include "WildTypeCellMutationState.hpp"
00035 
00040 template<unsigned DIM>
00041 class AbstractCellCentreBasedTissue : public AbstractTissue<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<AbstractTissue<DIM> >(*this);
00058     }
00059 
00060 protected:
00065     AbstractCellCentreBasedTissue();
00066 
00067 public:
00068 
00075     AbstractCellCentreBasedTissue(std::vector<TissueCell>& rCells,
00076                                   const std::vector<unsigned> locationIndices=std::vector<unsigned>());
00077 
00086     c_vector<double, DIM> GetLocationOfCellCentre(TissueCell& rCell);
00087 
00095     Node<DIM>* GetNodeCorrespondingToCell(TissueCell& rCell);
00096 
00106     TissueCell* AddCell(TissueCell& rNewCell, const c_vector<double,DIM>& rCellDivisionVector, TissueCell* pParentCell=NULL);
00107 
00115     bool IsCellAssociatedWithADeletedLocation(TissueCell& rCell);
00116 
00123     virtual void UpdateNodeLocations(const std::vector< c_vector<double, DIM> >& rNodeForces, double dt);
00124 
00141     virtual double GetDampingConstant(unsigned nodeIndex);
00142 
00151     void GenerateCellResults(unsigned locationIndex,
00152                              std::vector<unsigned>& rCellProliferativeTypeCounter,
00153                              std::vector<unsigned>& rCellCyclePhaseCounter);
00154 
00158     virtual void GenerateCellResultsAndWriteToFiles();
00159 
00168     virtual bool IsGhostNode(unsigned index);
00169 };
00170 
00171 #endif /*ABSTRACTCELLCENTREBASEDTISSUE_HPP_*/