AbstractOdeBasedCellCycleModel.hpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2009
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 <boost/serialization/access.hpp>
00032 #include <boost/serialization/is_abstract.hpp>
00033 #include <boost/serialization/base_object.hpp>
00034 
00035 #include "AbstractCellCycleModel.hpp"
00036 #include "AbstractOdeSystem.hpp"
00037 
00038 // Needs to be included last
00039 #include <boost/serialization/export.hpp>
00040 
00047 class AbstractOdeBasedCellCycleModel : public AbstractCellCycleModel
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         assert(mpOdeSystem!=NULL);
00064         archive & mpOdeSystem->rGetStateVariables();
00065         archive & mLastTime;
00066         archive & mDivideTime;
00067         archive & mFinishedRunningOdes;
00068         archive & mG2PhaseStartTime;
00069     }
00070 
00071 protected:
00072 
00074     AbstractOdeSystem* mpOdeSystem;
00075 
00077     double mLastTime;
00078 
00080     double mDivideTime;
00081 
00083     bool mFinishedRunningOdes;
00084 
00086     double mG2PhaseStartTime;
00087 
00088 public:
00089 
00097     AbstractOdeBasedCellCycleModel(double lastTime = SimulationTime::Instance()->GetTime());
00098 
00102     virtual ~AbstractOdeBasedCellCycleModel();
00103 
00110     virtual void UpdateCellCyclePhase();
00111 
00119     virtual bool SolveOdeToTime(double currentTime)=0;
00120 
00129     virtual double GetOdeStopTime()=0;
00130 
00137     void SetBirthTime(double birthTime);
00138 
00144     std::vector<double> GetProteinConcentrations() const;
00145 
00153     void SetProteinConcentrationsForTestsOnly(double lastTime, std::vector<double> proteinConcentrations);
00154 
00160     virtual void ResetForDivision();
00161 };
00162 
00163 BOOST_IS_ABSTRACT(AbstractOdeBasedCellCycleModel)
00164 
00165 #endif /*ABSTRACTODEBASEDCELLCYCLEMODEL_HPP_*/

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