Program Listing for File FMIndex.h

↰ Return to documentation for file (ADS/compression/FMIndex.h)

/*--------------------------------------------------------------------------*/
/*----------------------------- File FMIndex.h -----------------------------*/
/*--------------------------------------------------------------------------*/
/*--------------------------------------------------------------------------*/
/*----------------------------- DEFINITIONS --------------------------------*/
/*--------------------------------------------------------------------------*/

#ifndef __ADS_FMIndex
 #define __ADS_FMIndex
                      /* self-identification: #endif constant */

/*--------------------------------------------------------------------------*/
/*------------------------------ INCLUDES ----------------------------------*/
/*--------------------------------------------------------------------------*/

#include "ADS/Contract.h"
#include "ADS/compression/BurrowsWheeler.h"
#include "ADS/succinct/RankSelect.h"

#include <algorithm>
#include <array>
#include <bit>
#include <cstddef>
#include <cstdint>
#include <cstring>
#include <string>
#include <string_view>
#include <utility>
#include <vector>

/*--------------------------------------------------------------------------*/
/*--------------------------- NAMESPACE ------------------------------------*/
/*--------------------------------------------------------------------------*/

namespace ADS {

/*--------------------------------------------------------------------------*/
/*----------------------------- CLASS FMIndex ------------------------------*/
/*--------------------------------------------------------------------------*/

class FMIndex {

/*--------------------------------------------------------------------------*/
 public:

 explicit FMIndex( std::string_view s , std::size_t b = 64 ,
                   std::size_t mu = 32 );

 [[nodiscard]] std::size_t size( void ) const { return( f_n ); }

 [[nodiscard]] BWT transform( void ) const;

 [[nodiscard]] std::size_t rank( char c , std::size_t k ) const;

 [[nodiscard]] std::pair< std::size_t , std::size_t > range(
                                                  std::string_view P ) const;

 [[nodiscard]] std::size_t count( std::string_view P ) const;

 [[nodiscard]] std::vector< std::size_t > locate( std::string_view P ) const;

 [[nodiscard]] std::string extract( std::size_t i , std::size_t j ) const;

 [[nodiscard]] std::size_t sizeInBits( void ) const;

/*--------------------------------------------------------------------------*/
 private:

 [[nodiscard]] std::size_t lf( std::size_t r ) const;

 [[nodiscard]] std::size_t place( std::size_t r ) const;

 [[nodiscard]] bool marked( std::size_t r ) const { return( f_mark[ r ] ); }

 std::size_t f_n , f_b , f_mu;
 std::string f_L;
 std::size_t f_dollar;
 std::array< std::size_t , 257 > f_C;
 std::array< int , 256 > f_id;
 std::size_t f_sigma = 0;
 std::vector< std::uint32_t > f_occ;
 RankSelect f_mark;
 std::vector< std::size_t > f_place;
 std::vector< std::size_t > f_row;

 };  // end( class FMIndex )

/*--------------------------------------------------------------------------*/

}  // end( namespace ADS )

/*--------------------------------------------------------------------------*/
/*-------------------------- IMPLEMENTATION --------------------------------*/
/*--------------------------------------------------------------------------*/

#include "ADS/compression/impl/FMIndex.tpp"

/*--------------------------------------------------------------------------*/

#endif  /* FMIndex.h included */

/*--------------------------------------------------------------------------*/
/*--------------------------- End File FMIndex.h ---------------------------*/
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