---

OneGeneReplicaMinimizableDirector.cpp

Go to the documentation of this file.

// OneGeneReplicaMinimizableDirector.cpp: implementation of the COneGeneReplicaMinimizableDirector class.
//

#include "OneGeneReplicaMinimizableDirector.h"

// Construction/Destruction

COneGeneReplicaMinimizableDirector::COneGeneReplicaMinimizableDirector(double epsSqr, double deltaSqr)
:CReplicaMinimizableDirector(epsSqr, deltaSqr)
{
        double maxSimTime = 91.0;
        double stepSize = 0.0001;
        double frequency = 1.0;
        int nCells = 1;

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

        // penalty for long integrations
        m_dGammaSquared = 0.0;

        // fake experiment 1 - large network
        _networkList.push_back(new CAlternateOneGeneInhibitoryNetwork());
        _experimentList.push_back(new Experiment(_networkList[0],"Big Network"));
        // data files
        _experimentList[0]->AddDataFileToList("bigOneGeneDS.dat");
        // mover and plotter
        _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,1.0e-06));
        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);
        // attach observer
        _minimizableList[0]->Attach(m_vpPlotterList[0]);

        // fake experiment 2 - small network
        _networkList.push_back(new OneGeneInhibitoryNetwork());
        _experimentList.push_back(new Experiment(_networkList[1],"Small Network"));
        // data files
        _experimentList[1]->AddDataFileToList("smallOneGeneDS.dat");
        // mover and plotter
        _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,1.0e-06));
        m_vpPlotterList.push_back(new GnuPlotterTimeSeriesObserver());
        // title
        m_vpPlotterList[1]->SetTitle("Small OGN:1 Free Promoter:ODE");
        // minimizable
        _minimizableList.push_back(new SingleNetworkMinimizable());
        // parameters
        _minimizableList[1]->Initialize(_experimentList[1],_moverList[1],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
        // attach observer
        _minimizableList[1]->Attach(m_vpPlotterList[1]);

        // find the parameter intersection lists
        SetIntersectionLists();

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

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

COneGeneReplicaMinimizableDirector::~COneGeneReplicaMinimizableDirector()
{
        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 COneGeneReplicaMinimizableDirector::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();

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

}

---