repairmodels/include/LEMIVModel.hh

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0027 //
0028 /// \file LEMIVModel.hh
0029 /// \brief Definition of the LEMIVModel class
0030
0031 #ifndef LEMIVMODEL_HH
0032 #define LEMIVMODEL_HH
0033
0034 #include <string>
0035 #include <vector>
0036 #include <map>
0037
0038 class Damage;
0039
0040 class LEMIVModel
0041 {
0042 public:
0043
0044   /// \brief constructor
0045     // pTfast and pTslow in h-1
0046     LEMIVModel(double pLoopLength = 2E6,double pNi = 0, double pNc = 0,
0047         double pNDSB = 0,double pFunrej =0,double pTfast =-1,double pTslow =-1);
0048   /// \brief destructor
0049     ~LEMIVModel() = default;
0050
0051     double ComputeUnrej(double pTime);
0052
0053     double GetLoopLength() {return fLoopLength;};
0054     void SetLoopLength(double pVal){fLoopLength=pVal;};
0055     double GetNumDSB() {return fNDSB;};
0056     void SetNumDSB(double pVal){fNDSB=pVal;};
0057     double GetNumDomainIsolated(){return fNi;};
0058     void SetNumDomainIsolated(double pVal){fNi=pVal;};
0059     double GetNumDomainClustered(){return fNc;};
0060     void SetNumDomainClustered(double pVal){fNc=pVal;};
0061
0062     double GetFunrej(){return fFunrej;};
0063     void SetFunrej(double pVal){fFunrej=pVal;};
0064
0065     // Tfast in h-1
0066     double GetTfast(){return fTfast;};
0067     void SetTfast(double pVal){fTfast=pVal;};
0068
0069     // Tslow in h-1
0070     double GetTslow(){return fTslow;};
0071     void SetTslow(double pVal){fTslow=pVal;};
0072
0073     // Computes and sets input damage parameters of LEMIV
0074     void ComputeAndSetDamageInput(std::vector<Damage>);
0075
0076     // Write U=f(t) curve
0077     // pTMax and pDeltaT in h
0078     void CalculateRepair(double pTMax, double pDeltaT);
0079
0080     // Write output
0081     void WriteOutput(std::string pFileName);
0082
0083     unsigned int GetBpForDSB(){return fBpForDSB;};
0084     void SetBpForDSB(unsigned int pVal){fBpForDSB = pVal;};
0085     void SetDose(double d) {fDose = d;}
0086
0087     void SetChromosomeBpSizesMap(std::map<int,unsigned long long int> chroSizes) {fChromosomeBpMap = chroSizes;}
0088 private:
0089
0090     double fLoopLength; // length of the loop in bp, default one is 2 Mbp
0091
0092     //isolated DSB yield in Gy-1
0093     double fNi{0};
0094     //clustered DSB yield in Gy-1
0095     double fNc{0};
0096     // DSB yield in Gy-1
0097     double fNDSB{0};
0098
0099     double fFunrej{0};
0100
0101     // constant time in h-1
0102     double fTfast{0};
0103     double fTslow{0};
0104
0105     // Compute the number of DSB for a given loop startint at bp pStartLop
0106     int GetDSBPerLoop(std::vector<Damage> pVecDamage,unsigned int pStartLoop);
0107
0108     // U=f(t) curve, time in h
0109     std::vector<std::pair<double,double>> fUCurve;
0110     // num of bp to consider a DSB for the MakeCluster function
0111     // default value is 10
0112     unsigned int fBpForDSB{0};
0113     // store dose deposited in nucleus cell
0114     double fDose{0};
0115     std::vector<double> fDefaultsChromosomeSizes;// Chomosome defaults sizes
0116     std::map<int,unsigned long long int> fChromosomeBpMap; //Store number of Bp in each Chomosomes;
0117 };
0118
0119 #endif