AbstractWntOdeBasedCellCycleModel.cpp

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 #include "AbstractWntOdeBasedCellCycleModel.hpp"
00029 
00030 
00031 #ifdef CHASTE_CVODE
00032 CvodeAdaptor AbstractWntOdeBasedCellCycleModel::msSolver;
00033 #else
00034 RungeKutta4IvpOdeSolver AbstractWntOdeBasedCellCycleModel::msSolver;
00035 #endif //CHASTE_CVODE
00036 
00037 
00038 AbstractWntOdeBasedCellCycleModel::AbstractWntOdeBasedCellCycleModel()
00039 {
00040 #ifdef CHASTE_CVODE
00041     // Chaste solvers always check for stopping events, CVODE needs to be instructed to do so.
00042     msSolver.CheckForStoppingEvents();
00043     msSolver.SetMaxSteps(10000);
00044     //msSolver.SetTolerances(1e-6, 1e-8);
00045 #endif //CHASTE_CVODE
00046 }
00047 
00048 
00049 double AbstractWntOdeBasedCellCycleModel::GetOdeStopTime()
00050 {
00051     assert(msSolver.StoppingEventOccurred());
00052     return msSolver.GetStoppingTime();
00053 }
00054 
00055 
00056 void AbstractWntOdeBasedCellCycleModel::ResetForDivision()
00057 {
00058     AbstractOdeBasedCellCycleModel::ResetForDivision();
00059 
00060     assert(mpOdeSystem!=NULL);
00061 
00062     // This model needs the protein concentrations and phase resetting to G0/G1.
00063     // Keep the Wnt pathway in the same state but reset the cell cycle part
00064     // Cell cycle is proteins 0 to 4 (first 5 ODEs)
00065     std::vector<double> init_conds = mpOdeSystem->GetInitialConditions();
00066     for (unsigned i=0; i<5; i++)
00067     {
00068        mpOdeSystem->rGetStateVariables()[i] = init_conds[i];
00069     }
00070 }
00071 
00072 
00073 void AbstractWntOdeBasedCellCycleModel::UpdateCellType()
00074 {
00075     assert(mpOdeSystem!=NULL);
00076     assert(mpCell!=NULL);
00077     if (SimulationTime::Instance()->GetTime() > mLastTime)
00078     {
00079         EXCEPTION("WntCellCycleModel::UpdateCellType() should only be called when the cell cycle model has been evaluated to the current time\n");
00080     }
00081     ChangeCellTypeDueToCurrentBetaCateninLevel();
00082 }

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