file_index.h

#ifndef _FILE_INDEX_H_
#define _FILE_INDEX_H_

#include <iostream>
#include <map>
#include <vector>
#include <stdio.h>  
#include <cstring>
#include <string>

#ifndef NOSQL
#include "sqlite3.h"
#endif 

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

/* File_index should always be used to re designate pairs of keys into a single record
 * number. 
 */
class File_index : public virtual Data {

private:
    std::map <std::string, id0_t> id0_str_;         

    std::vector <std::string> id0_; 
            
    std::vector <id1_t> size_;              

    std::vector <id1_t> cumulative_size_;   

    id0_t last_id0_;                        

    std::string last_id0_str_;
    
    bool open_;
    size_t byte_size_;

    static const Registration registered;

    static Data * create(const std::vector <std::string> & Columns){
        return new File_index(Columns);
    }

public:
    File_index();                       
    File_index(std::vector<std::string>);
        bool bianary(void) const {return false;};

    id1_off_t get_offset (const std::string &, const id1_t &) const;    

    id1_t get_abs_pos (const std::string &, const id1_t &) const;   

    id1_t get_abs_pos (const id0_t &, const id1_t &) const; 

    id0_t get_id0 (const std::string &) const;  

    id0_t get_id0 (const id1_t &) const;    

    id1_t get_id1 (const id1_t &) const;    

    std::string get_string (const id0_t &) const;   

    void set_string (const id0_t &, const std::string &);   

    void set_size (const std::string &, const id1_t &); 

    void set_size (const id0_t &, const id1_t &);   

    void set_last_size (const id1_t &);         

    void set_next_size (const id1_t &);         

    const std::vector <std::string> get_names (void) const;     

    size_t get_names_size (void) const;     

    const std::vector <id1_t> get_sizes (void) const;       

    id1_t get_size (const id0_t &) const;

    id1_t get_size (const std::string &) const;

    id1_t get_cumulative_size (const id0_t &) const;

    id1_t get_cumulative_size (const std::string &) const;

    id1_t get_reference_size (void) const;

    id1_t get_last_size (void);             

    id1_t get_next_size (void);             

    int read_index(std::istream &);             

    std::istream & from_sam_header(std::istream &);

    int add_id (const std::string &, const id1_t &);

    int write_index(std::ostream &);            

    File_index & operator=(const File_index&);

    bool is_open(void) const;

    std::string header(void) const;
    static const std::string file_name;
    static const std::string table_name;
    static const bool binary;   
    size_t size(void) const;

    void write (std::ostream&) const;   
    void read (std::istream&);  

    const std::string get_file_name() const {return File_index::file_name;};
        const std::string get_table_name() const {return File_index::table_name;};
        const bool get_binary() const;
    const std::string sql_header(void) const;       
    const std::string sql_column_names(void) const;     
    const std::string sql_values(void) const;
    void sql_read(std::istream &) override;
};

#endif