AbstractOdeBasedCellCycleModel.cpp

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 
00029 #include "AbstractOdeBasedCellCycleModel.hpp"
00030 
00031 #include <iostream>
00032 #include <cassert>
00033 
00034 #include "Exception.hpp"
00035 
00036 AbstractOdeBasedCellCycleModel::AbstractOdeBasedCellCycleModel(double lastTime,
00037                                                                boost::shared_ptr<AbstractCellCycleModelOdeSolver> pOdeSolver)
00038     : CellCycleModelOdeHandler(lastTime, pOdeSolver),
00039       mDivideTime(lastTime),
00040       mFinishedRunningOdes(false),
00041       mG2PhaseStartTime(DBL_MAX)
00042 {
00043     AbstractCellCycleModel::SetBirthTime(lastTime);
00044 }
00045 
00046 AbstractOdeBasedCellCycleModel::~AbstractOdeBasedCellCycleModel()
00047 {
00048 }
00049 
00050 void AbstractOdeBasedCellCycleModel::SetBirthTime(double birthTime)
00051 {
00052     AbstractCellCycleModel::SetBirthTime(birthTime);
00053     mLastTime = birthTime;
00054     mDivideTime = birthTime;
00055 }
00056 
00057 std::vector<double> AbstractOdeBasedCellCycleModel::GetProteinConcentrations() const
00058 {
00059     assert(mpOdeSystem != NULL);
00060     return mpOdeSystem->rGetStateVariables();
00061 }
00062 
00063 void AbstractOdeBasedCellCycleModel::SetProteinConcentrationsForTestsOnly(double lastTime, std::vector<double> proteinConcentrations)
00064 {
00065     assert(mpOdeSystem != NULL);
00066     assert(proteinConcentrations.size()==mpOdeSystem->rGetStateVariables().size());
00067     mLastTime = lastTime;
00068     mpOdeSystem->SetStateVariables(proteinConcentrations);
00069 }
00070 
00071 void AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase()
00072 {
00073     assert(mpOdeSystem != NULL);
00074 
00075     double current_time = SimulationTime::Instance()->GetTime();
00076 
00077     // Update the phase from M to G1 when necessary
00078     if (mCurrentCellCyclePhase == M_PHASE)
00079     {
00080         double m_duration = GetMDuration();
00081         if (GetAge() >= m_duration)
00082         {
00083             mCurrentCellCyclePhase = G_ONE_PHASE;
00084             mLastTime = m_duration + mBirthTime;
00085         }
00086         else
00087         {
00088             // Still dividing; don't run ODEs
00089             return;
00090         }
00091     }
00092 
00093     if (current_time > mLastTime)
00094     {
00095         if (!mFinishedRunningOdes)
00096         {
00097             // Update whether a stopping event has occurred
00098             mFinishedRunningOdes = SolveOdeToTime(current_time);
00099 
00100             // Check no concentrations have gone negative
00101             for (unsigned i=0; i<mpOdeSystem->GetNumberOfStateVariables(); i++)
00102             {
00103                 if (mpOdeSystem->rGetStateVariables()[i] < -DBL_EPSILON)
00104                 {
00105                     #define COVERAGE_IGNORE
00106                     std::cout << "Protein[" << i << "] = " << mpOdeSystem->rGetStateVariables()[i] << "\n";
00107                     EXCEPTION("A protein concentration has gone negative\nChaste predicts that the CellCycleModel numerical method is probably unstable.");
00108                     #undef COVERAGE_IGNORE
00109                 }
00110             }
00111 
00112             if (mFinishedRunningOdes)
00113             {
00114                 // Update durations of each phase
00115                 mG1Duration = GetOdeStopTime() - mBirthTime - GetMDuration();
00116                 mG2PhaseStartTime = GetOdeStopTime() + GetSDuration();
00117                 mDivideTime = mG2PhaseStartTime + GetG2Duration();
00118 
00119                 // Update phase
00120                 if (current_time >= mG2PhaseStartTime)
00121                 {
00122                     mCurrentCellCyclePhase = G_TWO_PHASE;
00123                 }
00124                 else
00125                 {
00126                     mCurrentCellCyclePhase = S_PHASE;
00127                 }
00128             }
00129         }
00130         else
00131         {
00132             // ODE model finished, just increasing time until division...
00133             if (current_time >= mG2PhaseStartTime)
00134             {
00135                 mCurrentCellCyclePhase = G_TWO_PHASE;
00136             }
00137         }
00138     }
00139 }
00140 
00141 void AbstractOdeBasedCellCycleModel::ResetForDivision()
00142 {
00143     assert(mFinishedRunningOdes);
00144     AbstractCellCycleModel::ResetForDivision();
00145     mBirthTime = mDivideTime;
00146     mLastTime = mDivideTime;
00147     mFinishedRunningOdes = false;
00148     mG1Duration = DBL_MAX;
00149     mDivideTime = DBL_MAX;
00150 }
00151 
00152 double AbstractOdeBasedCellCycleModel::GetOdeStopTime()
00153 {
00154     double stop_time = DOUBLE_UNSET;
00155     if (mpOdeSolver->StoppingEventOccurred())
00156     {
00157         stop_time = mpOdeSolver->GetStoppingTime();
00158     }
00159     return stop_time;
00160 }
00161 
00162 void AbstractOdeBasedCellCycleModel::SetFinishedRunningOdes(bool finishedRunningOdes)
00163 {
00164     mFinishedRunningOdes = finishedRunningOdes;
00165 }
00166 
00167 void AbstractOdeBasedCellCycleModel::SetDivideTime(double divideTime)
00168 {
00169     mDivideTime = divideTime;
00170 }
00171 
00172 void AbstractOdeBasedCellCycleModel::SetG2PhaseStartTime(double g2PhaseStartTime)
00173 {
00174     mG2PhaseStartTime = g2PhaseStartTime;
00175 }
00176 
00177 void AbstractOdeBasedCellCycleModel::OutputCellCycleModelParameters(out_stream& rParamsFile)
00178 {
00179     // No new parameters to output
00180 
00181     // Call method on direct parent class
00182     AbstractCellCycleModel::OutputCellCycleModelParameters(rParamsFile);
00183 }

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