/*
    Copyright (c) 2012-2014
    Artur Meski <meski@ipipan.waw.pl>

    Reuse of the code or its part for any purpose
    without the author's permission is strictly prohibited.
*/

#ifndef RS_RS_HH
#define RS_RS_HH

#include <iostream>
#include <set>
#include <map>
#include <vector>
#include <string>
#include <cstdlib>
#include "macro.hh"
#include "options.hh"
#include "memtime.hh"

using std::cout;
using std::endl;

class RctSys
{
	    friend class SymRS;
	    friend class SymRSstate;
	public:
	    typedef unsigned int Entity;
	    typedef std::set<Entity> Entities;
	    struct Reaction {
	        Entities rctt;
	        Entities inhib;
	        Entities prod;
	    };
	    typedef std::vector<Reaction> Reactions;
	    typedef std::vector<std::string> EntitiesByIds;
	    typedef std::map<std::string, Entity> EntitiesByName;
	    typedef std::set<Entities> EntitiesSets;
	private:
	    Reactions reactions;
	    EntitiesSets initStates;

	    Entities actionEntities;

	    EntitiesByIds entities_ids;
	    EntitiesByName entities_names;

	    Entities tmpReactants;
	    Entities tmpInhibitors;
	    Entities tmpProducts;

	    Entities tmpState;

	    Entity getEntityID(std::string entityName);

	    Options *opts;

	public:
	    void setOptions(Options *opts)
	    {
	        this->opts = opts;
	    }
	    bool hasEntity(std::string entityName);
	    void addEntity(std::string entityName);
	    std::string getEntityName(Entity entityID);
	    void pushReactant(std::string entityName);
	    void pushInhibitor(std::string entityName);
	    void pushProduct(std::string entityName);
	    void commitReaction(void);
	    std::string entityToStr(const Entity entity) {
	        return entities_ids[entity];
	    }
	    std::string entitiesToStr(const Entities &entities);
	    void showReactions(void);
	    void pushStateEntity(std::string entityName);
	    void commitInitState(void);
	    void addActionEntity(std::string entityName);
	    bool isActionEntity(Entity entity);
	    void resetInitStates(void) {
	        initStates.clear();
	    }
	    unsigned int getEntitiesSize(void) {
	        return entities_ids.size();
	    }
	    unsigned int getReactionsSize(void) {
	        return reactions.size();
	    }
	    unsigned int getActionsSize(void) {
	        return actionEntities.size();
	    }
	    void showInitialStates(void);
	    void showActionEntities(void);
	    void printSystem(void);
};

class RctSysWithCtxAut : private RctSys
{
	friend class CtxAut;
	
};

// Context Automaton
class CtxAut
{
	public:
	    typedef unsigned int State;
	    typedef std::vector<std::string> StatesById;
	    typedef std::map<std::string, State> StatesByName;
		struct Transition {
			State src_state;
			RctSys::Entities ctx;
			State dst_state;
		};
		bool hasState(std::string name);
		void addState(std::string stateName);
		void addTransition(std::string srcStateName, std::string dstStateName);
		void pushContextEntity(std::string entityName);	
	    void setOptions(Options *opts)
	    {
	        this->opts = opts;
	    }
		
	private:
	    Options *opts;
		StatesById states_ids;
		StatesByName states_names;
		RctSys::Entities tmpEntities;	
};

#endif