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/// \file AnalysisHandler.hh
/// \brief Definition of the AnalysisHandler class

#ifndef AnalysisHandler_h
#define AnalysisHandler_h 1

#include <memory>
#include "ScanDamage.hh"
#include "TLKModel.hh"
#include "LEMIVModel.hh"
#include "BelovModel.hh"

class AnalysisHandler
{
    public:
    AnalysisHandler(/* args */);
    ~AnalysisHandler() = default;
    void SetThresholdEnergy(double e);
    void GetAllDamageAndScanSB();
    void GiveMeSBs();
    void ApplyDNAModel(const std::string dnamodel);
    void SetBpForDSB(unsigned int pVal);
    void SetParametersForTLKModel(double pLambda1 = 3.0,double pLambda2=0.03, 
                                    double pBeta1=0.01, double pBeta2=0.06,double pEta=0.002);
    void SetParametersForLEMIVModel(double pLoopLength=2e6,double pFunrej=0,
                                    double pTfast=0.24,double pTslow=2.81);
    void CreateSDD(std::string filename);
private:
    ///void GetDoseFromEdep();
    std::unique_ptr<ScanDamage> fScanDamage;
    std::unique_ptr<TLKModel> fTLKModel;
    std::unique_ptr<LEMIVModel> fLEMIVModel;
    std::unique_ptr<BelovModel> fBelovModel;
    std::vector<Damage> fAllDamage;
    
    std::pair<float,float> fNsDSBandError = {0,0};
    std::pair<float,float> fNcDSBandError = {0,0};
    std::pair<float,float> fNDSBandError = {0,0};
    std::pair<float,float> fNDSBdirandError = {0,0}; // DSB has contribution from at least one direct  damage
    std::pair<float,float> fNDSBIndandError = {0,0}; // DSB has contribution from at least one indirect  damage
    std::pair<float,float> fNDSBdirIandError = {0,0}; // DSB has contribution from both direct and indirect damage
    std::pair<float,float> fNSSBandError = {0,0};
    std::pair<float,float> fNSBandError = {0,0};
    std::pair<float,float> fNdirSBandError = {0,0};
    std::pair<float,float> fNindirSBandError = {0,0};

    bool fIsSBScanned = false;
    // num of bp to consider a DSB for the MakeCluster function
	// default value is 10
	unsigned int fBpForDSB{10};
    // store dose deposited in nucleus cell
	double fDose{0};
    //TLK: Compute a SF Curve
    double pTLKDoseMax{0}, pTLKDeltaDose{0};
    //LEMIV: compute fraction of unrejoined DSB up to pLEMIVTimeMax (h) and  pLEMIVDeltaTime steps
    double pLEMIVtimeMax{0}, pLEMIVdeltaTime{0};

    double fNBp{0};// number of base pairs
    double fEdepInNucleus{0}; // eV
    double fNucleusVolume{0};

    std::map<int,unsigned long long int> fChromosomeBpMap; //Store number of Bp in each Chomosomes;
};

#endif