linkage_data.h

#ifndef _LINKAGE_H_
#define _LINKAGE_H_

#include <iostream>
#include <cfloat>
#include <iomanip>
#include <vector>

#include "typedef.h"
#include "data.h"
#include "stream_tools.h"


class Linkage : public virtual Double_indexed_data { 
private:
    void read(std::istream& str);
    void write(std::ostream& str) const;
    static const Registration registered;
    static Data * create(const std::vector <std::string> &columns){
        return new Linkage(columns);
    };
    //We are comparing site X to site Y, so we need a total of four ids.
    id0_t id0;  
    id1_t id1;  

    float_t p_;     
    float_t q_;     

    float_t D_;     
    float_t Ni_;        
    float_t fit_;       
    float_t null_;      
public:
    using Double_indexed_data::get_abs_pos1;        
    using Double_indexed_data::get_abs_pos2;        

    using Double_indexed_data::set_abs_pos1;        
    using Double_indexed_data::set_abs_pos2;        

    char delim;     

    Linkage();  
    Linkage(const std::vector <std::string> &) : Linkage(){};   

    static const std::string file_name;             
    static const std::string table_name;                
    static const bool binary;   

    std::string header(void) const;
    size_t size(void) const;

    const std::string get_file_name(void) const;                
    const std::string get_table_name(void) const;               
    const bool get_binary(void) const;              

    const std::string sql_header(void) const;               
    const std::string sql_column_names(void) const;             
    const std::string sql_values(void) const;               

    void set_D(const float_t &);
    void set_fit(const float_t &);
    void set_null(const float_t &);
    void set_Ni(const float_t &);
    void set_p(const float_t &);
    void set_q(const float_t &);

    float_t ll (void) const;
    float_t dist (void) const;
    float_t D (void) const;
    float_t Dmax (void) const;
    float_t Dmin (void) const;
    float_t Dsq (void) const;
    float_t Dprime (void) const;
    float_t r (void) const;
    float_t rsq (void) const;
    float_t adj_D (void) const;
    float_t adj_Dsq (void) const;
    float_t adj_Dprime (void) const;
    float_t adj_r (void) const;
    float_t adj_rsq (void) const;
    float_t adj_Dmax (void) const;
    float_t adj_Dmin (void) const;

/*
        id0_t id0;      //!< The scaffold of site X
        id1_t id1;      //!< The pos of site X

        id1_t id1_y_;   //!< the pos of site Y

        float_t p_;             //!< freq_major site numero uno
        float_t q_;             //!< freq_major site numero dos

        float_t D_;             //!< the magnitude of the ld, j0 
        float_t Ni_;            //!< The number of individuals used in the calculation
        float_t fit_;           //!< fit statistic (thar be ld here!)
        float_t null_;          //!< null statistic (i.e. no ld)
*/


    //TODO SHIT!
    Linkage & operator=(const Linkage &lhs){
//      (Indexed_data)(this)->abs_pos_=(Indexed_data)(&lhs)->abs_pos_;
        this->abs_pos1_=lhs.abs_pos1_;
        this->abs_pos2_=lhs.abs_pos2_;
       
        this->id0=lhs.id0;      
            this->id1=lhs.id1;      

            this->p_=lhs.p_;             
            this->q_=lhs.q_;             

            this->D_=lhs.D_;             
            this->Ni_=lhs.Ni_;            
            this->fit_=lhs.fit_;           
            this->null_=lhs.null_;          
        return *this;
    }

};

#endif