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ChemicalSink.cpp

Go to the documentation of this file.

// ChemicalSink.cpp: implementation of the CChemicalSink class.
//

#include "ChemicalSink.h"

// Construction/Destruction

CChemicalSink::CChemicalSink(Chemical *ChangedChemical, Chemical *SinkChemical, std::string reactionName)
:Reaction(reactionName)
{
        // stoichiometry
        this->ChangedChemical = chemicals.size();
        chemicals.push_back(ChangedChemical);
        numberOfEachChemicalChangedByReaction.push_back(-1);

        this->SinkChemical = chemicals.size();
        chemicals.push_back(SinkChemical);
        numberOfEachChemicalChangedByReaction.push_back(0);

        // 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();


}

CChemicalSink::~CChemicalSink()
{

}

double CChemicalSink::GetRate() const
{
        return chemicals[SinkChemical]->GetAmount();
}

void CChemicalSink::SetTeXForm()
{
        strstream stream;
        // TeX form of the reaction
        stream << chemicals[SinkChemical]->GetTeXName().c_str();
        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 *> *CChemicalSink::GetChemicalJacobian()
{
        chemicalJacobian[0]->SetWithRespectTo(chemicals[SinkChemical]->GetChemicalNumber());
        chemicalJacobian[0]->SetJValue(1.0);
        
        return &chemicalJacobian;
}

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