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AlternateOneGeneInhibitoryNetworkMinimizableDirector.cpp

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// AlternateOneGeneInhibitoryNetworkMinimizableDirector.cpp: implementation of the CAlternateOneGeneInhibitoryNetworkMinimizableDirector class.
//

#include "AlternateOneGeneInhibitoryNetworkMinimizableDirector.h"

// Construction/Destruction

CAlternateOneGeneInhibitoryNetworkMinimizableDirector::CAlternateOneGeneInhibitoryNetworkMinimizableDirector()
{
        double maxSimTime = 91.0;
        double stepSize = 0.0001;
        double frequency = 1.0;
        int nCells = 1;
        double moveTol = 1.0e-06;

        bool rateFlag = true;
        bool chemFlag = false;
        bool logsFlag = false;
        double timeWeight = 1.0;
        double rateWeight = 0.0;
        double chemWeight = 0.0;

        m_dGammaSquared = 1.0e-08;

        // fake experiment 1 - 1 free promoter, no mRNA or protein
        _networkList.push_back(new CAlternateOneGeneInhibitoryNetwork());
        _experimentList.push_back(new Experiment(_networkList[0],"BigNetwork"));
        _experimentList[0]->AddDataFileToList("bigOneGeneDS.dat");
        // mover and plotter
        _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
        m_vpPlotterList.push_back(new GnuPlotterTimeSeriesObserver());
        // title
        m_vpPlotterList[0]->SetTitle("Big OGN:1 Free Promoter:ODE");
        // minimizable
        _minimizableList.push_back(new SingleNetworkMinimizable());
        // parameters
        _minimizableList[0]->Initialize(_experimentList[0],_moverList[0],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
        _minimizableList[0]->SetRateConstantsWeight(0.0);
        // attach observer
        _minimizableList[0]->Attach(m_vpPlotterList[0]);

        // allocate the master residuals list
        int masterResidualsSize = 0;
        for(int i = 0; i < _minimizableList.size(); i++)
        {
                masterResidualsSize += _minimizableList[i]->GetNResiduals();
        }
        if(m_dGammaSquared > 0.0)
        {
                masterResidualsSize += 1;
        }
        Allocate(masterResidualsSize);

        cout << "Master Residuals size : " << masterResidualsSize << endl;
 
        // define the experiments
        DefineExperiments();
}

CAlternateOneGeneInhibitoryNetworkMinimizableDirector::~CAlternateOneGeneInhibitoryNetworkMinimizableDirector()
{
        for(int i = 0; i < _minimizableList.size(); i++)
        {
                _minimizableList[i]->Detach(m_vpPlotterList[i]);
        }
        for(int i = 0; i < m_vpPlotterList.size(); i++)
        {
                delete m_vpPlotterList[i];
        }
}

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

double CAlternateOneGeneInhibitoryNetworkMinimizableDirector::GetParameter(int parIndex)
{
        // Just return the first set (they are all the same)
        return _minimizableList[0]->GetParameter(parIndex);
}

int CAlternateOneGeneInhibitoryNetworkMinimizableDirector::GetNParameters()
{
        // Return the size of the first set (all have the same size)
        return _minimizableList[0]->GetNParameters();

}

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