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LaubLoomisDictyNetworkMinimizableDirector.cpp

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// LaubLoomisDictyNetworkMinimizableDirector.cpp: implementation of the CLaubLoomisDictyNetworkMinimizableDirector class.
//

#include "LaubLoomisDictyNetworkMinimizableDirector.h"

// Construction/Destruction

CLaubLoomisDictyNetworkMinimizableDirector::CLaubLoomisDictyNetworkMinimizableDirector()
{
        // create networks,experiments,observers,movers,minimizables
        double maxSimTime = 91.0;
        double stepSize = 0.0001;
        double frequency = 1.0;
        int nCells = 1;
        double moveTol = 1.0e-06;

        m_dGammaSquared = 1.0e-07;
        
        // flags for all minimizables
        bool rateFlag = true;
        bool chemFlag = false;
        bool logsFlag = false;
        double timeWeight = 1.0;
        double rateWeight = 0.0;
        double chemWeight = 0.0;

        int cnt = 0;

        // expt. 1 - Roos 1977
        // networks and data
        _networkList.push_back(new CLaubLoomisDictyNetwork());
        _experimentList.push_back(new Experiment(_networkList[cnt],"Roos et. al. 1977"));
        // put data files here
        _experimentList[cnt]->AddDataFileToList("../DataFiles/TimeSeries/cAMPiRoos.dat");
        // mover and plotter
        _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
        _plotterList.push_back(new GnuPlotterTimeSeriesObserver());
        // title
        _plotterList[cnt]->SetTitle("D. discoideum cAMP Production:Roos et. al. 1977:ODE");
        // minimizable
        _minimizableList.push_back(new SingleNetworkMinimizable());
        // parameters
        _minimizableList[cnt]->Initialize(_experimentList[cnt],_moverList[cnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
        _minimizableList[cnt]->SetRateConstantsWeight(0.0);
        // attach observer
        _minimizableList[cnt]->Attach(_plotterList[cnt]);
        cnt++;
        
        // expt. 2 - Aubry 1997
        // networks and data
        _networkList.push_back(new CLaubLoomisDictyNetwork);
        _experimentList.push_back(new Experiment(_networkList[cnt],"Aubry et. al. 1997"));
        // put data files here
        _experimentList[cnt]->AddDataFileToList("../DataFiles/TimeSeries/dictyERK2Aubry.dat");
        // mover and plotter
        _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
        _plotterList.push_back(new GnuPlotterTimeSeriesObserver());
        // title
        _plotterList[cnt]->SetTitle("WT D. discoideum ERK2 Activation:Aubry et. al. 1997:ODE");
        // minimizable
        _minimizableList.push_back(new SingleNetworkMinimizable());
        // parameters
        _minimizableList[cnt]->Initialize(_experimentList[cnt],_moverList[cnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
        _minimizableList[cnt]->SetRateConstantsWeight(0.0);
        // attach observer
        _minimizableList[cnt]->Attach(_plotterList[cnt]);
        cnt++;

        // expt. 3 - Aubry 1997
        // networks and data
        _networkList.push_back(new CLaubLoomisDictyNetwork);
        _experimentList.push_back(new Experiment(_networkList[cnt],"Aubry et. al. 1997"));
        // put data files here
        _experimentList[cnt]->AddDataFileToList("../DataFiles/TimeSeries/dictyERK2PKANullAubry.dat");
        // mover and plotter
        _moverList.push_back(new CQualityControlCashKarpMover(frequency,stepSize,moveTol));
        _plotterList.push_back(new GnuPlotterTimeSeriesObserver());
        // title
        _plotterList[cnt]->SetTitle("PKA- D. discoideum ERK2 Activation:Aubry et. al. 1997:ODE");
        // minimizable
        _minimizableList.push_back(new SingleNetworkMinimizable());
        // parameters
        _minimizableList[cnt]->Initialize(_experimentList[cnt],_moverList[cnt],nCells,rateFlag,chemFlag,logsFlag,timeWeight,rateWeight,chemWeight);
        _minimizableList[cnt]->SetRateConstantsWeight(0.0);
        // attach observer
        _minimizableList[cnt]->Attach(_plotterList[cnt]);
        cnt++;
        
        // 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;
        }
        if(m_dGammaSquared > 0.0)
        {
                masterResidualsSize += 1;
        }
        Allocate(masterResidualsSize);

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

        // define the experiments
        DefineExperiments();

}

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

}

void CLaubLoomisDictyNetworkMinimizableDirector::DefineExperiments()
{
        
        // treatment with 30 uM cAMP
        _minimizableList[1]->GetExperiment()->GetReactionNetwork()->GetChemical(5)->SetInitialAmount(300000*30);
        _minimizableList[1]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
        
        // treatment with 30 uM cAMP, PKA Null
        _minimizableList[2]->GetExperiment()->GetReactionNetwork()->GetChemical(5)->SetInitialAmount(300000*30);
        _minimizableList[2]->GetExperiment()->GetReactionNetwork()->ChemicalReset();
        _minimizableList[2]->GetExperiment()->GetReactionNetwork()->RemoveReaction(5);
        _minimizableList[2]->GetExperiment()->GetReactionNetwork()->RemoveReaction(3);
        _minimizableList[2]->GetExperiment()->GetReactionNetwork()->RemoveReaction(2);
        _minimizableList[2]->GetExperiment()->GetReactionNetwork()->RemoveReaction(1);
        
}

double CLaubLoomisDictyNetworkMinimizableDirector::GetParameter(int parIndex)
{
        // for this director, everyone has the same parameters so any set 
        // can be returned
        return _minimizableList[0]->GetParameter(parIndex);
}

int CLaubLoomisDictyNetworkMinimizableDirector::GetNParameters()
{
        // ditto as for GetParameters()
        return _minimizableList[0]->GetNParameters();
}

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