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ExampleNetworkMinimizableDirector.cpp

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// ExampleNetworkMinimizableDirector.cpp: implementation of the CExampleNetworkMinimizableDirector class.
//

#include "ExampleNetworkMinimizableDirector.h"

// Construction/Destruction

CExampleNetworkMinimizableDirector::CExampleNetworkMinimizableDirector()
{
// create networks,experiments,observers,movers,minimizables
        double maxSimTime = 91.0;
        double stepSize = 0.001;
        double frequency = 1.0;
        int nCells = 1;
        double moveTol = 0.0001;
        
        // 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;

        // expt. 1 - 1000 ligand molecules
        // networks and data
        _networkList.push_back(new CExampleNetwork());
        _experimentList.push_back(new Experiment(_networkList[0],"Ligand Stimulation"));
        // put data files here
        _experimentList[0]->AddDataFileToList("ExampleNetwork.dat");
        // mover and plotter
        _moverList.push_back(new CQualityControlRungeKuttaMover(frequency,stepSize,moveTol));
        _plotterList.push_back(new GnuPlotterTimeSeriesObserver());
        // title
        _plotterList[0]->SetTitle("G Protein Activation by RTK");
        // 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(_plotterList[0]);

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

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

        // define the experiments
        DefineExperiments();
}

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

void CExampleNetworkMinimizableDirector::DefineExperiments()
{
        _minimizableList[0]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->SetInitialAmount(1000.0);
        _minimizableList[0]->GetExperiment()->GetReactionNetwork()->GetChemical(0)->Reset();

}

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

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

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