---

OneGeneInhibitoryNetworkMinimizableDirector.cpp

Go to the documentation of this file.

// OneGeneInhibitoryNetworkMinimizableDirector.cpp: implementation of the OneGeneInhibitoryNetworkMinimizableDirector class.
//

#include "OneGeneInhibitoryNetworkMinimizableDirector.h"
#include "SharedBFactorNetworkMinimizable.h"
#include "GnuPlotterTimeSeriesSharedBFactorObserver.h"

// Construction/Destruction

COneGeneInhibitoryNetworkMinimizableDirector::COneGeneInhibitoryNetworkMinimizableDirector()
{
        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-07;

        const char* foundFileName;

        // fake experiment 1 - 1 free promoter, no mRNA or protein
        _networkList.push_back(new OneGeneInhibitoryNetwork());
        _experimentList.push_back(new Experiment(_networkList[0],"SmallNetwork"));
        // data files
        LocateInputFileDirectory locate1("smallOneGeneDS1.dat");
        foundFileName = locate1.Get("smallOneGeneDS1.dat");
        _experimentList[0]->AddDataFileToList(foundFileName);
        // mover and plotter
        _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));

        // fake experiment 2 - 1 free promoter, no mRNA or protein
        _networkList.push_back(new OneGeneInhibitoryNetwork());
        _experimentList.push_back(new Experiment(_networkList[1],"SmallNetwork"));
        // data files
        LocateInputFileDirectory locate2("smallOneGeneDS2.dat");
        foundFileName = locate2.Get("smallOneGeneDS2.dat");
        _experimentList[1]->AddDataFileToList(foundFileName);
        // mover and plotter
        _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));

        // minimizable
        _minimizableList.push_back(new SharedBFactorNetworkMinimizable());
        // parameters
        _minimizableList[0]->Initialize(_experimentList,_moverList,nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
        _minimizableList[0]->SetRateConstantsWeight(0.0);

/*      // attach observer
        m_vpPlotterList.push_back(new GnuPlotterTimeSeriesSharedBFactorObserver());
        // title
        m_vpPlotterList[0]->SetTitle("Small OGN:1 Free Promoter:ODE");
        _minimizableList[0]->Attach(m_vpPlotterList[0]);
*/


        // parameters which need a prior
        m_iPriorList.push_back(0);
        m_iPriorList.push_back(1);
        m_iPriorList.push_back(2);
        m_iPriorList.push_back(3);
        m_iPriorList.push_back(4);
        m_iPriorList.push_back(5);


/*
        // fake experiment 2 - 1 free promoter, no mRNA or protein
        _networkList.push_back(new OneGeneInhibitoryNetwork());
        _experimentList.push_back(new Experiment(_networkList[1],"SmallNetwork"));
        // data files
        _experimentList[1]->AddDataFileToList("smallOneGeneDS2.dat");
        // mover and plotter
        _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
        // minimizable
        _minimizableList.push_back(new SharedBFactorNetworkMinimizable());
        // parameters
        _minimizableList[1]->Initialize(_experimentList[1],_moverList[1],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
        _minimizableList[1]->SetRateConstantsWeight(0.0);
        // attach observer
//      m_vpPlotterList.push_back(new GnuPlotterTimeSeriesObserver());
        // title
//      m_vpPlotterList[1]->SetTitle("Small OGN2:1 Free Promoter:ODE");
//      _minimizableList[1]->Attach(m_vpPlotterList[1]);

        // parameters which need a prior
//      m_iPriorList.push_back(0);
//      m_iPriorList.push_back(1);
//      m_iPriorList.push_back(2);
//      m_iPriorList.push_back(3);
//      m_iPriorList.push_back(4);
//      m_iPriorList.push_back(5);

*/

        // allocate the master residuals list
        int masterResidualsSize = 0;
        for(int i = 0; i < _minimizableList.size(); i++)
        {
                int subRes = _minimizableList[i]->GetNResiduals();
                masterResidualsSize += subRes;
                cout << subRes << " residuals in minimizable " << i << endl;
        }
        // add residuals for prior parameter costs, if applicable
        masterResidualsSize += m_iPriorList.size();
        cout << m_iPriorList.size() << " parameters are constrained by a prior " << endl;
        if(m_dGammaSquared > 0.0)
        {
                masterResidualsSize += 1;
        }
        Allocate(masterResidualsSize);

        cout << "Master Residuals size : " << masterResidualsSize << endl;

        // define the experiments
        DefineExperiments();

        // dump info about residuals
        //DumpResidualInfo();
}

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

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

        // 1 free promoter region, no bound, no mRNA, no protein
        _minimizableList[0]->GetExperiment(1)->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1.0);
        _minimizableList[0]->GetExperiment(1)->GetReactionNetwork()->GetChemical(0)->Reset();
        _minimizableList[0]->GetExperiment(1)->GetReactionNetwork()->GetChemical(1)->SetInitialAmount(0.0);
        _minimizableList[0]->GetExperiment(1)->GetReactionNetwork()->GetChemical(1)->Reset();
//      _minimizableList[0]->GetExperiment(1)->GetReactionNetwork()->RemoveReaction(2);

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

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

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

---