analysis/include/AnalysisHandler.hh

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0027 //
0028 /// \file AnalysisHandler.hh
0029 /// \brief Definition of the AnalysisHandler class
0030
0031 #ifndef AnalysisHandler_h
0032 #define AnalysisHandler_h 1
0033
0034 #include <memory>
0035 #include "ScanDamage.hh"
0036 #include "TLKModel.hh"
0037 #include "LEMIVModel.hh"
0038 #include "BelovModel.hh"
0039
0040 class AnalysisHandler
0041 {
0042     public:
0043     AnalysisHandler(/* args */);
0044     ~AnalysisHandler() = default;
0045     void SetThresholdEnergy(double e);
0046     void GetAllDamageAndScanSB();
0047     void GiveMeSBs();
0048     void ApplyDNAModel(const std::string dnamodel);
0049     void SetBpForDSB(unsigned int pVal);
0050     void SetParametersForTLKModel(double pLambda1 = 3.0,double pLambda2=0.03,
0051                                     double pBeta1=0.01, double pBeta2=0.06,double pEta=0.002);
0052     void SetParametersForLEMIVModel(double pLoopLength=2e6,double pFunrej=0,
0053                                     double pTfast=0.24,double pTslow=2.81);
0054     void CreateSDD(std::string filename);
0055 private:
0056     ///void GetDoseFromEdep();
0057     std::unique_ptr<ScanDamage> fScanDamage;
0058     std::unique_ptr<TLKModel> fTLKModel;
0059     std::unique_ptr<LEMIVModel> fLEMIVModel;
0060     std::unique_ptr<BelovModel> fBelovModel;
0061     std::vector<Damage> fAllDamage;
0062
0063     std::pair<float,float> fNsDSBandError = {0,0};
0064     std::pair<float,float> fNcDSBandError = {0,0};
0065     std::pair<float,float> fNDSBandError = {0,0};
0066     std::pair<float,float> fNDSBdirandError = {0,0}; // DSB has contribution from at least one direct  damage
0067     std::pair<float,float> fNDSBIndandError = {0,0}; // DSB has contribution from at least one indirect  damage
0068     std::pair<float,float> fNDSBdirIandError = {0,0}; // DSB has contribution from both direct and indirect damage
0069     std::pair<float,float> fNSSBandError = {0,0};
0070     std::pair<float,float> fNSBandError = {0,0};
0071     std::pair<float,float> fNdirSBandError = {0,0};
0072     std::pair<float,float> fNindirSBandError = {0,0};
0073
0074     bool fIsSBScanned = false;
0075     // num of bp to consider a DSB for the MakeCluster function
0076     // default value is 10
0077     unsigned int fBpForDSB{10};
0078     // store dose deposited in nucleus cell
0079     double fDose{0};
0080     //TLK: Compute a SF Curve
0081     double pTLKDoseMax{0}, pTLKDeltaDose{0};
0082     //LEMIV: compute fraction of unrejoined DSB up to pLEMIVTimeMax (h) and  pLEMIVDeltaTime steps
0083     double pLEMIVtimeMax{0}, pLEMIVdeltaTime{0};
0084
0085     double fNBp{0};// number of base pairs
0086     double fEdepInNucleus{0}; // eV
0087     double fNucleusVolume{0};
0088
0089     std::map<int,unsigned long long int> fChromosomeBpMap; //Store number of Bp in each Chomosomes;
0090 };
0091
0092 #endif