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OneGeneEnsembleDirector.cpp

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// OneGeneEnsembleDirector.cpp: implementation of the COneGeneEnsembleDirector class.
//

#include "OneGeneEnsembleDirector.h"

// Construction/Destruction

COneGeneEnsembleDirector::COneGeneEnsembleDirector(int ensembleSize)
:CEnsembleCombinationDirector(ensembleSize)
{
        double maxSimTime = 91.0;
        int intTime = (int) maxSimTime + 2;
        double stepSize = 0.0001;
        double frequency = 1.0;
        double moveTol = 1.0e-6;
        bool rateFlag = true;
        bool chemFlag = false;
        bool logsFlag = false;
        double timeWeight = 1.0;
        double rateWeight = 0.0;
        double chemWeight = 0.0;
        int nCells = 1;
        /*
        // runnable
        m_vpRxnNetworks.push_back(new OneGeneInhibitoryNetwork());
        m_vpRxnMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
        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]);
        m_vpEnsembleRunPlotters.push_back(new GnuPlotterEnsembleRunDirectorObserver());
        m_vpEnsembleRunPlotters[0]->SetTitle("OGN : 1 Bound Promoter, No Protein : ODE");
        m_vpEnsembleRunPlotters[0]->FixRunnable(0);
        m_vpEnsembleRunPlotters[0]->AddChemicalToList(2);
        m_vpEnsembleRunPlotters[0]->AddChemicalToList(3);
        this->Attach(m_vpEnsembleRunPlotters[0]);
        */
        // minimizable 1 - 1 free promoter, no mRNA or protein
        m_vpNetworks.push_back(new OneGeneInhibitoryNetwork());
        m_vpExperiments.push_back(new Experiment(m_vpNetworks[0],"Free Promoter"));
        // data files
        m_vpExperiments[0]->AddDataFileToList("smallOneGeneDS.dat");
        // mover 
        m_vpMovers.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
        m_vpMinimizables.push_back(new SingleNetworkMinimizable());
        // parameters
        m_vpMinimizables[0]->Initialize(m_vpExperiments[0],m_vpMovers[0],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
        m_vpMinimizables[0]->SetRateConstantsWeight(0.0);
        m_vpEnsembleDataPlotters.push_back(new GnuPlotterEnsembleDataDirectorObserver());
        m_vpEnsembleDataPlotters[0]->SetTitle("OGN : 1 Free Promoter, No Protein : ODE");
        m_vpEnsembleDataPlotters[0]->FixMinimizable(0);
        this->Attach(m_vpEnsembleDataPlotters[0]);

        // allocate space to accumulate statistics
        SumAllocate();

        // Define runs
        DefineRuns();

        // Define experiments
        DefineExperiments();

        // Load in the ensemble information
        LoadEnsembleInfo("ensemble.par");

}

COneGeneEnsembleDirector::~COneGeneEnsembleDirector()
{
        for(int i = 0; i < m_vpEnsembleRunPlotters.size(); i++)
        {
                this->Detach(m_vpEnsembleRunPlotters[i]);
        }
        for(int i = 0; i < m_vpEnsembleDataPlotters.size(); i++)
        {
                this->Detach(m_vpEnsembleDataPlotters[i]);
        }
}

void COneGeneEnsembleDirector::DefineExperiments()
{
        // 1 free promoter region, no bound, no mRNA, no protein
        m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.0);
        m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->Reset();
        m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(0.0);
        m_vpMinimizables[0]->GetExperiment()->GetReactionNetwork()->GetChemical(1)->Reset();
}

void COneGeneEnsembleDirector::DefineRuns()
{
        /*
        // 1 bound promoter, none free, no mRNA, no protein
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(0.0);
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(0)->Reset();        
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(1.0);
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(1)->Reset();        
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(3)->SetInitialAmount(0.0);
        m_vpRunnables[0]->GetReactionNetwork()->GetChemical(3)->Reset();
        */
}

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