/home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFreactions/reactantLists/reactantTree.hh

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#ifndef REACTANTTREE_HH_
#define REACTANTTREE_HH_


#include "../NFreactions.hh"

namespace NFcore
{
        //Forward Declarations
        class TransformationSet;
        class MappingSet;
        class ReactantContainer;



        class ReactantTree : public ReactantContainer {


                public:

                        ReactantTree(unsigned int reactantIndex, TransformationSet *ts, unsigned int init_capacity);


                        virtual ~ReactantTree();

                        virtual int size() const { return n_mappingSets; };

                        virtual MappingSet * pushNextAvailableMappingSet();


                        void confirmPush(int mappingSetId, double rateFactor);



                        virtual void popLastMappingSet();

                        virtual void removeMappingSet(unsigned int mappingSetId);


                        void pickReactantFromValue(MappingSet *&ms, double value, double baseRate);

                        void updateValue(unsigned int mappingSetId, double newRateFactor);

                        virtual MappingSet * getMappingSet(unsigned int mappingSetId) const;



                        virtual void printDetails() const;




                        double getRateFactorSum() const { return leftRateFactorSum[0]; };


                        int getDepthOfTree() const { return treeDepth; };


                protected:

                        void removeFromTreeOnly(int msTreeArrayPosition, unsigned int mappingSetId);

                        void expandTree(int newCapacity);


                        TransformationSet *ts;       //Keeps track of the set of transformations
                        unsigned int reactantIndex;  //the index of the tree

                        //Basic tree parameters and constants
                        int maxElementCount;
                        int treeDepth;
                        int numOfNodes;

                        //The tree stored as 3 arrays indexed as:
                        // Children are at 2i and 2i+1
                        // Parent is at i/2 (using integer division)
                        // root is at index 1
                        // index 0 is empty and always zero
                        double * leftRateFactorSum;
                        int * leftElementCount;
                        int * rightElementCount;

                        //The actual list of mappingSets, stored as a list
                        MappingSet ** mappingSets;




                        //Given a mappingSet Id, this tells us what position it is in
                        //in the mappingSets array
                        int * msPositionMap;

                        //Given a mappingSet Id, this tells us what position it is in
                        //in the actual tree
                        int * msTreePositionMap;

                        //Given a tree position index, this tells us the mappingSet Id
                        //which we can use to get our mappingSet out of the mappingSets array
                        int * reverseMsTreePositionMap;


                        //The number of mappingSets currently set
                        int n_mappingSets;

                        //The index of the first molecule in the tree
                        unsigned int firstMappingTreeIndex;
        };
}







#endif /* REACTANTTREE_HH_ */

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