/home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFreactions/transformations/transformationSet.hh

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#ifndef TRANSFORMATIONSET_HH_
#define TRANSFORMATIONSET_HH_


#include "../NFreactions.hh"

using namespace std;

namespace NFcore
{
        //Forward declarations
        class Transformation;
        class TemplateMolecule;
        class Molecule;
        class SpeciesCreator;



        class TransformationSet
        {
                public:

                        TransformationSet(vector <TemplateMolecule *> reactantTemplates);

                        ~TransformationSet();


                        int getNumOfReactants() const { return n_reactants; };

                        bool addStateChangeTransform(TemplateMolecule *t, string cName, int finalStateValue);

                        bool addStateChangeTransform(TemplateMolecule *t, string cName, string finalStateValue);

                        bool addIncrementStateTransform(TemplateMolecule *t, string cName);

                        bool addDecrementStateTransform(TemplateMolecule *t, string cName);


                        bool addBindingTransform(TemplateMolecule *t1, string bSiteName1, TemplateMolecule *t2, string bSiteName2);

                        bool addBindingSeparateComplexTransform(TemplateMolecule *t1, string bSiteName1, TemplateMolecule *t2, string bSiteName2);



                        bool addUnbindingTransform(TemplateMolecule *t, string bSiteName, TemplateMolecule *t2, string bSiteName2);


                        bool addDeleteMolecule(TemplateMolecule *t, int deletionType);

                        bool addAddMolecule(SpeciesCreator *sc);


                        bool addLocalFunctionReference(TemplateMolecule *t, string PointerName, int scope);


                        bool transform(MappingSet **mappingSets);

                        MappingSet *generateBlankMappingSet(unsigned int reactantIndex, unsigned int mappingSetId);


                        TemplateMolecule * getTemplateMolecule(unsigned int reactantIndex) const { return reactants[reactantIndex]; };

                        unsigned int getNreactants() const {return n_reactants; };

                        void finalize();

                        bool isFinalized() const { return finalized; };

                        bool getListOfProducts(MappingSet **mappingSets, list<Molecule *> &products, int traversalLimit);

                        bool hasSymUnbindingTransform() const { return hasSymUnbinding; };

                        bool hasSymBindingTransform() const { return hasSymBinding; };

                        int getNumOfTransformations(int reactantIndex) const { return transformations[reactantIndex].size();};


                        Transformation *getTransformation(int reactantIndex, int index) const { return transformations[reactantIndex].at(index); };




                protected:

                        int find(TemplateMolecule *t);

                        bool finalized;

                        unsigned int n_reactants;

                        TemplateMolecule ** reactants;

                        vector <Transformation *> *transformations;

                        vector <Transformation *> addMoleculeTransformations;

                        static list <Molecule *> deleteList;


                        static list <Molecule *> updateAfterDeleteList;


                        static list <Molecule *>::iterator it;


                        bool hasSymUnbinding;

                        bool hasSymBinding;
        };

}












#endif /*TRANSFORMATIONSET_HH_*/

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