/home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFcore/reactionSelector/reactionSelector.hh

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/*
 * reactionSelector.hh
 *
 *  Created on: Jul 23, 2009
 *      Author: msneddon
 */

#ifndef REACTIONSELECTOR_HH_
#define REACTIONSELECTOR_HH_



#include "../NFcore.hh"
//#include <vector>


using namespace std;


namespace NFcore
{
        //Forward Declarations
        class ReactionClass;


        // Abstract Interface Class for the Reaction Selection Algorithm
        class ReactionSelector {

                public:

                        //Initializations and basic functionality
                        ReactionSelector() {};
                        virtual ~ReactionSelector() {};

                        virtual double refactorPropensities() = 0;


                        virtual double update(ReactionClass *r,double oldA, double newA) = 0;
                        virtual double getNextReactionClass(ReactionClass *&rc) = 0;
                        virtual double getAtot() = 0;

        };


        class DirectSelector : public ReactionSelector {

                public:
                        //Initializations and basic functionality
                        DirectSelector(vector <ReactionClass *> &rxns);
                        virtual ~DirectSelector();

                        virtual double refactorPropensities();


                        virtual double update(ReactionClass *r,double oldA, double newA);
                        virtual double getNextReactionClass(ReactionClass *&rc);
                        virtual double getAtot();


                protected:
                        double Atot;
                        int n_reactions;
                        ReactionClass ** reactionClassList;

        };


        class LogClassSelector : public ReactionSelector {

                public:
                        //Initializations and basic functionality
                        LogClassSelector(vector <ReactionClass *> &rxns);
                        virtual ~LogClassSelector();

                        virtual double refactorPropensities();


                        virtual double update(ReactionClass *r,double oldA, double newA);
                        virtual double getNextReactionClass(ReactionClass *&rc);
                        virtual double getAtot();


                protected:

                        int calculateClass(double a);

                        void place(ReactionClass *r,int logClass,double a);

                        void setLogClassToActive(int logClass);
                        void setLogClassToInactive(int logClass);


                        // The absolute maximum log class
                        int maxClassLimit;
                        int minClassLimit;
                        int totalLogClassCount;

                        //the current range of log classes that we have to loop over
                        int currentHighClass;
                        int currentLowClass;


                        // A 2d array of the logClasses
                        ReactionClass *** logClassList;

                        // A 1d array of the logClasses sizes
                        int *logClassSize;
                        int *logClassCapacity;


                        //An array to keep track of the log classes with positive values
                        int *activeLogClasses;
                        bool *isLogClassActive;
                        int n_activeLogClasses;



                        // A 1d array of the propensity sum of the logClass
                        double *logClassPropensity;



                        int *mapRxnIdToLogClass;
                        int *mapRxnIdToLogClassPosition;




                        double Atot;
                        int n_reactions;
                        ReactionClass ** reactionClassList;

        };



}








#endif /* REACTIONSELECTOR_HH_ */

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