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OneGeneStochasticNetworkRunDirector.cpp

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// OneGeneStochasticNetworkRunDirector.cpp: implementation of the COneGeneStochasticNetworkRunDirector class.
//

#include "OneGeneStochasticNetworkRunDirector.h"

// Construction/Destruction

COneGeneStochasticNetworkRunDirector::COneGeneStochasticNetworkRunDirector()
{
        double maxSimTime = 120.0;
        int intTime = (int) maxSimTime + 2;
        double stepSize = 0.001;
        double frequency = 1.0;
        double moveTol = 1.0e-06;
        int seed = 298989;

        // unbound promoter, diff eq.
        m_vpRxnNetworks.push_back(new OneGeneInhibitoryNetwork());
//      m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
        m_vpRxnMovers.push_back(new CContinuousTimeMonteCarloMover(seed,frequency));
        int nChemicals = m_vpRxnNetworks[0]->GetNumberOfChemicals();
        m_vpCellObservers.push_back(new CellAverageObserver(nChemicals,intTime,1));
        m_vpRunnables.push_back(new CRunnable());
        m_vpRunnables[0]->SetComponents(m_vpRxnNetworks[0],m_vpRxnMovers[0],m_vpCellObservers[0]);
        // create an observer for the runnable
        m_vpGnuPlotters.push_back(new GnuPlotterRunnableObserver());
        m_vpGnuPlotters[0]->AddChemicalNumberToList(2);
        m_vpGnuPlotters[0]->AddChemicalNumberToList(3);
        // attach the observer
        m_vpRunnables[0]->Attach(m_vpGnuPlotters[0]);

        // define runs
        DefineRuns();

}

COneGeneStochasticNetworkRunDirector::~COneGeneStochasticNetworkRunDirector()
{

}

void COneGeneStochasticNetworkRunDirector::DefineRuns()
{
        // set parameters in the runnables to those read from a previous
        // optimization pass; assumes all runnables have same number of 
        // rate constants

        ParameterReader *pReader = new ParameterReader("onegene_cg.par");
        int nRC = m_vpRunnables[0]->GetReactionNetwork()->GetNumberOfRateConstants();
        for(int j = 0; j < nRC; j++)
        {
                double rate = pReader->ReadParameter();
                for(int i = 0; i < m_vpRunnables.size(); i++)
                {
                        m_vpRunnables[i]->GetReactionNetwork()->GetRateConstant(j)->SetRateConstant(rate);
                }
        }
        delete pReader;

        // specific to this simulation
        // 1 free promoter
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.0);
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(0)->Reset();
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(0.0);
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(1)->Reset();
        m_vpGnuPlotters[0]->SetTitle("Promoter Binding, ODE");

}

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