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TranscriptionReaction.cpp

Go to the documentation of this file.

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

#ifdef _WINDOWS
#include "stdafx.h"
#endif

#include "TranscriptionReaction.h"

// Construction/Destruction

TranscriptionReaction::TranscriptionReaction(Chemical *freePromoter, Chemical *mRNA, RateConstant *ktm,std::string reactionName)
:Reaction(reactionName)
{

        int numChemicals = 0;


        chemicals.push_back(freePromoter);
        this->freePromoter = numChemicals;      // Number in private array
        numChemicals++;
        numberOfEachChemicalChangedByReaction.push_back(0);

        chemicals.push_back(mRNA);
        this->mRNA = numChemicals;      // Number in private array
        numChemicals ++;
        numberOfEachChemicalChangedByReaction.push_back(+1);

        
        int numRateConstants = 0;

        rateConstants.push_back(ktm);
        this->ktm = numRateConstants;
        numRateConstants++;

        // put enough dummy chemicalJacobian elements on the vector 
        // - they are recomputed every time you ask for the chemicalJacobian
        chemicalJacobian.push_back(new JElement(-1,-1));

        this->SetTeXForm();
}

TranscriptionReaction::~TranscriptionReaction()
{

}

double TranscriptionReaction::GetRate() const
{
        return rateConstants[ktm]->GetValue() * chemicals[freePromoter]->GetAmount();
}

void TranscriptionReaction::SetTeXForm()
{
        std::stringstream stream;
        // TeX form of the reaction
        stream << rateConstants[ktm]->GetTeXName().c_str();
        stream << "\\left [" << chemicals[freePromoter]->GetTeXName().c_str();
        stream << "\\right ]";
        // add a NULL
        stream << ends;
        // set the TeX string equal to what's in the stream
        m_sTeXForm = stream.str();
        // allow memory to be freed
//      stream.rdbuf()->freeze(0);
}

std::vector<Reaction::JElement *> *TranscriptionReaction::GetChemicalJacobian()
{       
        return &chemicalJacobian;
}

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