WntCellCycleOdeSystem.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 WNTCELLCYCLEODESYSTEM_HPP_
00029 #define WNTCELLCYCLEODESYSTEM_HPP_
00030 
00031 #include <cmath>
00032 #include <iostream>
00033 
00034 #include "AbstractOdeSystem.hpp"
00035 #include "AbstractCellMutationState.hpp"
00036 
00037 // Needed here to avoid serialization errors
00038 #include "ApcOneHitCellMutationState.hpp"
00039 #include "ApcTwoHitCellMutationState.hpp"
00040 #include "BetaCateninOneHitCellMutationState.hpp"
00041 
00059 class WntCellCycleOdeSystem : public AbstractOdeSystem
00060 {
00061 private:
00062 
00068     double mk2d;
00070     double mk3d;
00072     double mk34d;
00074     double mk43d;
00076     double mk23d;
00078     double mad;
00080     double mJ11d;
00082     double mJ12d;
00084     double mJ13d;
00086     double mJ61d;
00088     double mJ62d;
00090     double mJ63d;
00092     double mKm1d;
00094     double mkpd;
00096     double mphi_r;
00098     double mphi_i;
00100     double mphi_j;
00102     double mphi_p;
00104     double ma2d;
00106     double ma3d;
00108     double ma4d;
00110     double ma5d;
00112     double mk16d;
00114     double mk61d;
00116     double mPhiE2F1;
00117 
00119     boost::shared_ptr<AbstractCellMutationState> mpMutationState;
00120 
00121 public:
00122 
00129     WntCellCycleOdeSystem(double WntStimulus=0.0,
00130                           boost::shared_ptr<AbstractCellMutationState> pMutationState=boost::shared_ptr<AbstractCellMutationState>());
00131 
00135     ~WntCellCycleOdeSystem();
00136 
00140     void Init();
00141 
00150     void SetMutationState(boost::shared_ptr<AbstractCellMutationState> pMutationState);
00151 
00157     boost::shared_ptr<AbstractCellMutationState> GetMutationState();
00158 
00169     void EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY);
00170 
00180     bool CalculateStoppingEvent(double time, const std::vector<double>& rY);
00181 
00191     double CalculateRootFunction(double time, const std::vector<double>& rY);
00192 
00193 };
00194 
00195 #endif /*WNTCELLCYCLEODESYSTEM_HPP_*/