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NormalizedLinearAmplifier.cpp

Go to the documentation of this file.

// NormalizedLinearAmplifier.cpp: implementation of the CNormalizedLinearAmplifier class.
//

#include "NormalizedLinearAmplifier.h"

// Construction/Destruction

CNormalizedLinearAmplifier::CNormalizedLinearAmplifier(Chemical *InputChemical, Chemical *OutputChemical, RateConstant *k_amp, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->InputChemical = chemicals.size();
        chemicals.push_back(InputChemical);
        numberOfEachChemicalChangedByReaction.push_back(0);

        this->OutputChemical = chemicals.size();
        chemicals.push_back(OutputChemical);
        numberOfEachChemicalChangedByReaction.push_back(+1);

        // rates
        this->k_amp = rateConstants.size();
        rateConstants.push_back(k_amp);

        // 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();
}

CNormalizedLinearAmplifier::~CNormalizedLinearAmplifier()
{

}

double CNormalizedLinearAmplifier::GetRate() const
{
        return ((rateConstants[k_amp]->GetValue())/(chemicals[InputChemical]->GetInitialAmount()))*chemicals[InputChemical]->GetAmount();
}

void CNormalizedLinearAmplifier::SetTeXForm()
{
        strstream stream;
        // TeX form of the reaction
        stream << rateConstants[k_amp]->GetTeXName().c_str();
        stream << "{ " << chemicals[InputChemical]->GetTeXName().c_str() << " \\over ";
        stream << chemicals[InputChemical]->GetTeXName().c_str() << "_0 }";
        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 *> *CNormalizedLinearAmplifier::GetChemicalJacobian()
{
        chemicalJacobian[0]->SetWithRespectTo(chemicals[InputChemical]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue((rateConstants[k_amp]->GetValue())/(chemicals[InputChemical]->GetInitialAmount()));
        
        return &chemicalJacobian;
}

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