dnadamage/include/ClassifiedDamage.hh

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0027 //
0028 /// \file ClassifiedDamage.hh
0029 /// \brief Definition of the ClassifiedDamage class
0030
0031 #ifndef CLASSIFIEDDAMAGE_HH
0032 #define CLASSIFIEDDAMAGE_HH
0033
0034 #include "Damage.hh"
0035
0036 #include <vector>
0037
0038 /// \brief defines a classified DNA damage
0039 class ClassifiedDamage
0040 {
0041 public:
0042
0043 // DNA Classified Damage type
0044 //   Defines the type of damage ollowing SDD formalism
0045   enum ClassifiedDamageType{
0046     fNA = -1,
0047     fSSB = 0,
0048     fDSB = 1
0049   };
0050
0051   /// \brief constructor
0052   ClassifiedDamage();
0053   /// \brief destructor
0054   ~ClassifiedDamage() = default;
0055
0056   // Compute the type of classified damage i.e. SSB or DSB
0057   void ComputeType();
0058   ClassifiedDamageType GetClassifiedDamageType() const {return fType;};
0059
0060   const int GetNumDamage() const {return fDamage.size();};
0061   // Add a damage to the lst of damage
0062   void AddDamage(Damage);
0063
0064   // Compute the position in terms of bp of the classified damage
0065   void ComputeBp();
0066   unsigned long int GetBpBegin() const{return fBp_begin;};
0067   unsigned long int GetBpEnd() const{return fBp_end;};
0068   unsigned long int GetBpBarycenter() const{return fBp_barycenter;};
0069
0070   // TODO
0071   // Compute the coordinates of the classified damage
0072   void ComputePosition();
0073   /*
0074   Point GetPosBegin(){return fPos_begin;};
0075   Point GetPosEnd(){return fPos_end;};
0076   Point GetPosBarycenter(){return fPos_barycenter;};
0077   */
0078
0079   // Compute the complexity of the classified damage
0080   void ComputeComplexity();
0081   int GetComplexity() const{return fComplexity;};
0082
0083   // Reset the classified damage
0084   void Reset();
0085
0086   // Tell if base damages have to be taken into account
0087   void SetIncludeBase(bool pVal) {fIncludeBase =  pVal;};
0088   bool GetIncludeBase() const {return fIncludeBase;};
0089
0090   // Le Tuan Anh:
0091   bool GetIsThereDirectComponentContribution() const
0092   {return fIsThereDirectContribution;} // Return true if there is at least 1 direct SB in this cluster
0093   bool GetIsThereIndirectComponentContribution() const
0094   {return fIsThereIndirectContribution;} // Return true if there is at least 1 indirect SB in this cluster
0095
0096 private:
0097
0098   // CLASSIFIED DAMAGE MEMBERS
0099
0100   std::vector<Damage>   fDamage;              // List of damage
0101   ClassifiedDamageType  fType;                // SSB or DSB or other?
0102   unsigned long int     fBp_begin{0};            // Position
0103   unsigned long int     fBp_end{0};
0104   unsigned long int     fBp_barycenter{0};
0105   int                   fComplexity{0};          // Complexity
0106   bool                  fIncludeBase{false};        // Base inclusion in the complexity
0107   bool fIsThereDirectContribution = false; // check if Direct damage appears in cluster a not?
0108   bool fIsThereIndirectContribution = false; // check if Indirect damage appears in cluster a not?
0109
0110   };
0111
0112 #endif // CLASSIFIEDDAMAGE_HH