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27 //
28 /// \file LEMIVModel.hh
29 /// \brief Definition of the LEMIVModel class
30
31 #ifndef LEMIVMODEL_HH
32 #define LEMIVMODEL_HH
33
34 #include <string>
35 #include <vector>
36 #include <map>
37
38 class Damage;
39
40 class LEMIVModel
41 {
42 public:
43
44 /// \brief constructor
45 // pTfast and pTslow in h-1
46 LEMIVModel(double pLoopLength = 2E6,double pNi = 0, double pNc = 0,
47 double pNDSB = 0,double pFunrej =0,double pTfast =-1,double pTslow =-1);
48 /// \brief destructor
49 ~LEMIVModel() = default;
50
51 double ComputeUnrej(double pTime);
52
53 double GetLoopLength() {return fLoopLength;};
54 void SetLoopLength(double pVal){fLoopLength=pVal;};
55 double GetNumDSB() {return fNDSB;};
56 void SetNumDSB(double pVal){fNDSB=pVal;};
57 double GetNumDomainIsolated(){return fNi;};
58 void SetNumDomainIsolated(double pVal){fNi=pVal;};
59 double GetNumDomainClustered(){return fNc;};
60 void SetNumDomainClustered(double pVal){fNc=pVal;};
61
62 double GetFunrej(){return fFunrej;};
63 void SetFunrej(double pVal){fFunrej=pVal;};
64
65 // Tfast in h-1
66 double GetTfast(){return fTfast;};
67 void SetTfast(double pVal){fTfast=pVal;};
68
69 // Tslow in h-1
70 double GetTslow(){return fTslow;};
71 void SetTslow(double pVal){fTslow=pVal;};
72
73 // Computes and sets input damage parameters of LEMIV
74 void ComputeAndSetDamageInput(std::vector<Damage>);
75
76 // Write U=f(t) curve
77 // pTMax and pDeltaT in h
78 void CalculateRepair(double pTMax, double pDeltaT);
79
80 // Write output
81 void WriteOutput(std::string pFileName);
82
83 unsigned int GetBpForDSB(){return fBpForDSB;};
84 void SetBpForDSB(unsigned int pVal){fBpForDSB = pVal;};
85 void SetDose(double d) {fDose = d;}
86
87 void SetChromosomeBpSizesMap(std::map<int,unsigned long long int> chroSizes) {fChromosomeBpMap = chroSizes;}
88 private:
89
90 double fLoopLength; // length of the loop in bp, default one is 2 Mbp
91
92 //isolated DSB yield in Gy-1
93 double fNi{0};
94 //clustered DSB yield in Gy-1
95 double fNc{0};
96 // DSB yield in Gy-1
97 double fNDSB{0};
98
99 double fFunrej{0};
100
101 // constant time in h-1
102 double fTfast{0};
103 double fTslow{0};
104
105 // Compute the number of DSB for a given loop startint at bp pStartLop
106 int GetDSBPerLoop(std::vector<Damage> pVecDamage,unsigned int pStartLoop);
107
108 // U=f(t) curve, time in h
109 std::vector<std::pair<double,double>> fUCurve;
110 // num of bp to consider a DSB for the MakeCluster function
111 // default value is 10
112 unsigned int fBpForDSB{0};
113 // store dose deposited in nucleus cell
114 double fDose{0};
115 std::vector<double> fDefaultsChromosomeSizes;// Chomosome defaults sizes
116 std::map<int,unsigned long long int> fChromosomeBpMap; //Store number of Bp in each Chomosomes;
117 };
118
119 #endif