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27 //
28 /// \file ClassifiedDamage.hh
29 /// \brief Definition of the ClassifiedDamage class
30
31 #ifndef CLASSIFIEDDAMAGE_HH
32 #define CLASSIFIEDDAMAGE_HH
33
34 #include "Damage.hh"
35
36 #include <vector>
37
38 /// \brief defines a classified DNA damage
39 class ClassifiedDamage
40 {
41 public:
42
43 // DNA Classified Damage type
44 // Defines the type of damage ollowing SDD formalism
45 enum ClassifiedDamageType{
46 fNA = -1,
47 fSSB = 0,
48 fDSB = 1
49 };
50
51 /// \brief constructor
52 ClassifiedDamage();
53 /// \brief destructor
54 ~ClassifiedDamage() = default;
55
56 // Compute the type of classified damage i.e. SSB or DSB
57 void ComputeType();
58 ClassifiedDamageType GetClassifiedDamageType() const {return fType;};
59
60 const int GetNumDamage() const {return fDamage.size();};
61 // Add a damage to the lst of damage
62 void AddDamage(Damage);
63
64 // Compute the position in terms of bp of the classified damage
65 void ComputeBp();
66 unsigned long int GetBpBegin() const{return fBp_begin;};
67 unsigned long int GetBpEnd() const{return fBp_end;};
68 unsigned long int GetBpBarycenter() const{return fBp_barycenter;};
69
70 // TODO
71 // Compute the coordinates of the classified damage
72 void ComputePosition();
73 /*
74 Point GetPosBegin(){return fPos_begin;};
75 Point GetPosEnd(){return fPos_end;};
76 Point GetPosBarycenter(){return fPos_barycenter;};
77 */
78
79 // Compute the complexity of the classified damage
80 void ComputeComplexity();
81 int GetComplexity() const{return fComplexity;};
82
83 // Reset the classified damage
84 void Reset();
85
86 // Tell if base damages have to be taken into account
87 void SetIncludeBase(bool pVal) {fIncludeBase = pVal;};
88 bool GetIncludeBase() const {return fIncludeBase;};
89
90 // Le Tuan Anh:
91 bool GetIsThereDirectComponentContribution() const
92 {return fIsThereDirectContribution;} // Return true if there is at least 1 direct SB in this cluster
93 bool GetIsThereIndirectComponentContribution() const
94 {return fIsThereIndirectContribution;} // Return true if there is at least 1 indirect SB in this cluster
95
96 private:
97
98 // CLASSIFIED DAMAGE MEMBERS
99
100 std::vector<Damage> fDamage; // List of damage
101 ClassifiedDamageType fType; // SSB or DSB or other?
102 unsigned long int fBp_begin{0}; // Position
103 unsigned long int fBp_end{0};
104 unsigned long int fBp_barycenter{0};
105 int fComplexity{0}; // Complexity
106 bool fIncludeBase{false}; // Base inclusion in the complexity
107 bool fIsThereDirectContribution = false; // check if Direct damage appears in cluster a not?
108 bool fIsThereIndirectContribution = false; // check if Indirect damage appears in cluster a not?
109
110 };
111
112 #endif // CLASSIFIEDDAMAGE_HH