dnadamage/include/SDDData.hh

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0026 //
0027 //
0028 /// \file SDDData.hh
0029 /// \brief Definition of the SDDData class
0030
0031 #ifndef SDDDATA_HH
0032 #define SDDDATA_HH
0033
0034 #include <string>
0035 #include <vector>
0036 #include <sstream>
0037 #include <map>
0038 #include "Damage.hh"
0039
0040 class SDDData
0041 {
0042 public:
0043
0044 /** SDD header structure
0045  *
0046  *  Define the content of SSD file header
0047  */
0048     struct SDDHeader
0049     {
0050         std::string        sdd_version{""};
0051
0052         std::string         software{""};
0053
0054         std::string         author{""};
0055
0056         std::string         sim_details{""};
0057
0058         std::string         src_details{""};
0059         int                 src_type{0};
0060         std::vector<int>    src_pdg;
0061         std::vector<double> src_energy;
0062         std::string         energy_dist{""};
0063         std::vector<double> part_fraction;
0064         std::vector<double> dose;
0065         double              dose_rate{0};
0066
0067         std::string         target{""};
0068         std::vector<double> volumes;
0069         std::vector<double> chromo_size;
0070         double              dna_density{0};
0071
0072         std::vector<double> cell_cycle;
0073         std::vector<int>    dna_struct;
0074         int                 vitro_vivo{0};
0075         std::string         proliferation{""};
0076         std::vector<double> microenv;
0077
0078         std::vector<double> damage_def;
0079         double              time{0};
0080         std::vector<int>    damage_prim_count;
0081
0082         std::vector<bool>   entries;
0083
0084         std::string         info{""};
0085     };
0086
0087 /** SDD damage structure
0088  *
0089  *  Define the content of a damage as stored in SDD file
0090  */
0091     struct SDDDamage
0092     {
0093         std::vector<int>        classification;
0094         std::vector<double>     coordinates;
0095         std::vector<int>        chromo_ID;
0096         std::vector<double>     chromo_position;
0097         std::vector<int>        cause;
0098         std::vector<int>        types;
0099
0100         std::vector<int>        break_spec;
0101         std::vector<int>        dna_seq;
0102         std::vector<double>     lesion_time;
0103
0104         std::vector<int>        particles;
0105         std::vector<double>     energy;
0106         std::vector<double>     translation;
0107         std::vector<double>     direction;
0108         std::vector<double>     particle_time;
0109     };
0110
0111     /** Constructor */
0112     SDDData(std::string /*p_name*/);
0113     /** Destructor */
0114     ~SDDData() = default;
0115
0116     /** Read header
0117     *   Reads and returns the header of a SDD file
0118     */
0119     SDDHeader ReadHeader();
0120
0121     /** Chromosome sizes
0122     * Returns the list of sizes of each chromosome in the cell geometry
0123     */
0124     std::map<int,unsigned long long int> GetChromosomeBpSizesMap(double &sum);
0125
0126     /** Dose
0127     * Returns the absorbed dose
0128     */
0129     double GetDose();
0130
0131     /** Parse data
0132     *   Parse data of SDD files and stores the data
0133     *   as SDDDamage in data_
0134     */
0135     void ParseData();
0136     /** Get SDD damage
0137     *   Returns all the SDD damage (i.e. data_)
0138     */
0139     std::vector<SDDDamage>& GetSDDDamage(){return data_;};
0140
0141     /** Get Damage
0142     *   Returns all the damage that have been converted into lighter object
0143     *   see Damage class
0144     */
0145     std::map<unsigned int,std::map<unsigned int,std::vector<Damage> > > GetAllDamage();
0146
0147 private:
0148
0149     std::string filename_;
0150     SDDHeader header_;
0151     std::vector<SDDDamage> data_;
0152
0153     void ParseLineData(std::string&);
0154
0155     void ReadString(std::ifstream&,std::string&);
0156     void ReadInt(std::ifstream&,int&);
0157     void ReadInts(std::ifstream&,std::vector<int>&);
0158     void ReadDouble(std::ifstream&,double&);
0159     void ReadDoubles(std::ifstream&,std::vector<double>&);
0160     void ReadBools(std::ifstream&,std::vector<bool>&);
0161
0162     void ExtractInts(std::string&,int,std::vector<int>&);
0163     void ExtractDoubles(std::string&,int,std::vector<double>&);
0164
0165 };
0166
0167 #endif // SDDDATA_HH