---

ReactionNetwork.h

Go to the documentation of this file.

// ReactionNetwork.h: interface for the ReactionNetwork class.
//

#if !defined(AFX_REACTIONNETWORK_H__17E9EE61_DB43_11D3_8099_00A0C9B3BB18__INCLUDED_)
#define AFX_REACTIONNETWORK_H__17E9EE61_DB43_11D3_8099_00A0C9B3BB18__INCLUDED_

#if _MSC_VER > 1000
#pragma once
#endif // _MSC_VER > 1000

#ifdef _WIN32
#include <strstream>
#endif

#include <vector>
#include <fstream>
#include <iostream>
//#include <strstrea.h>
#include <algorithm>
#include "Reaction.h"
#include "Chemical.h"
#include "RateConstant.h"
#include "SubjectObserver.h"

class Reaction;         // Avoid recursion
class Chemical;
class RateConstant;

class ReactionNetwork
{
public:
        ReactionNetwork();
        virtual ~ReactionNetwork();
        virtual Chemical *GetChemical(int chemicalNumber);
        virtual RateConstant *GetRateConstant(int rateConstantNumber);
        virtual Reaction *GetReaction(int reactionNumber);
        virtual int GetNumberOfRateConstants() const;
        virtual int GetNumberOfReactions() const;
        virtual int GetNumberOfChemicals() const;
        virtual int GetNumberOfAlgebraicChemicals() const;
        virtual void SetAmount(int chemicalNumber, double amount);
        virtual void AddAlgebraicIndex(Chemical *chemical);
        virtual void ChemicalReset();
        virtual void RateConstantReset();
        virtual std::vector<int> *GetAlgebraicIndices();
        virtual std::vector<Reaction*> *GetReactions();
        virtual std::vector<Chemical*> *GetChemicals();
        virtual std::vector<RateConstant*> *GetRateConstants();
        virtual std::vector<double> *GetReactionRates();
        // this could be a dangerous function, but used properly it allows one to 
        // model simple Loss-of-Function mutations without changing the number of
        // parameters (very useful for ensembles where a couple of the networks 
        // are only different in a subtle way)
        virtual void RemoveReaction(int rxnNumber);
        virtual void DumpTeXForm(std::string fileName);
        virtual void DumpPetriNetDotFile(std::string fileName);
        virtual int GetNTermsPerLine() {return 1;}
        virtual bool GetLRGraph() {return false;}
protected:      // Probably should be private!  protected should be fine.
        std::vector<Chemical*> chemicals;
        std::vector<Reaction*> reactions;
        std::vector<RateConstant*> rateConstants;       
        std::vector<double> reactionRates;
        std::vector<int> algebraicIndices;
};

#endif // !defined(AFX_REACTIONNETWORK_H__17E9EE61_DB43_11D3_8099_00A0C9B3BB18__INCLUDED_)

---