AbstractOdeBasedCellCycleModel.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 ABSTRACTODEBASEDCELLCYCLEMODEL_HPP_
00029 #define ABSTRACTODEBASEDCELLCYCLEMODEL_HPP_
00030 
00031 #include <vector>
00032 
00033 #include "ChasteSerialization.hpp"
00034 #include "ClassIsAbstract.hpp"
00035 #include <boost/serialization/base_object.hpp>
00036 
00037 #include "AbstractCellCycleModel.hpp"
00038 #include "CellCycleModelOdeHandler.hpp"
00039 #include "SimulationTime.hpp"
00040 
00047 class AbstractOdeBasedCellCycleModel : public AbstractCellCycleModel, public CellCycleModelOdeHandler
00048 {
00049 private:
00050 
00052     friend class boost::serialization::access;
00059     template<class Archive>
00060     void serialize(Archive & archive, const unsigned int version)
00061     {
00062         archive & boost::serialization::base_object<AbstractCellCycleModel>(*this);
00063         archive & boost::serialization::base_object<CellCycleModelOdeHandler>(*this);
00064         archive & mDivideTime;
00065         archive & mFinishedRunningOdes;
00066         archive & mG2PhaseStartTime;
00067     }
00068 
00069 protected:
00070 
00072     double mDivideTime;
00073 
00075     bool mFinishedRunningOdes;
00076 
00078     double mG2PhaseStartTime;
00079 
00080 public:
00081 
00090     AbstractOdeBasedCellCycleModel(double lastTime = SimulationTime::Instance()->GetTime(),
00091                                    boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>());
00092 
00096     virtual ~AbstractOdeBasedCellCycleModel();
00097 
00104     virtual void UpdateCellCyclePhase();
00105 
00113     double GetOdeStopTime();
00114 
00121     void SetBirthTime(double birthTime);
00122 
00128     std::vector<double> GetProteinConcentrations() const;
00129 
00137     void SetProteinConcentrationsForTestsOnly(double lastTime, std::vector<double> proteinConcentrations);
00138 
00144     virtual void ResetForDivision();
00145 
00151     void SetFinishedRunningOdes(bool finishedRunningOdes);
00152 
00158     void SetDivideTime(double divideTime);
00159 
00165     void SetG2PhaseStartTime(double g2PhaseStartTime);
00166 
00172     virtual void OutputCellCycleModelParameters(out_stream& rParamsFile);
00173 };
00174 
00175 CLASS_IS_ABSTRACT(AbstractOdeBasedCellCycleModel)
00176 
00177 #endif /*ABSTRACTODEBASEDCELLCYCLEMODEL_HPP_*/

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