range_minimum_query.hpp

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#ifndef GENESIS_UTILS_MATH_RANGE_MINIMUM_QUERY_H_
#define GENESIS_UTILS_MATH_RANGE_MINIMUM_QUERY_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2019 Lucas Czech and HITS gGmbH
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/
 
#include "genesis/utils/containers/matrix.hpp"
 
#include <cmath>
#include <cstddef>
#include <cstdint>
#include <vector>
 
namespace genesis {
namespace utils {
 
class RangeMinimumQuery
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs and Enums
    // -------------------------------------------------------------------------
 
    using IntType       = int32_t;
 
    using SuccinctType  = unsigned char;
    using BlockTypeType = unsigned short;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    RangeMinimumQuery() = default;
    explicit RangeMinimumQuery( std::vector<IntType> const& array );
    explicit RangeMinimumQuery( std::vector<IntType>&&      array );
 
    ~RangeMinimumQuery() = default;
 
    RangeMinimumQuery( RangeMinimumQuery const& ) = default;
    RangeMinimumQuery( RangeMinimumQuery&& )      = default;
 
    RangeMinimumQuery& operator= ( RangeMinimumQuery const& ) = default;
    RangeMinimumQuery& operator= ( RangeMinimumQuery&& )      = default;
 
    // -------------------------------------------------------------------------
    //     Member Functions
    // -------------------------------------------------------------------------
 
    size_t query( size_t i, size_t j ) const;
 
    // -------------------------------------------------------------------------
    //     Internal Inline Functions
    // -------------------------------------------------------------------------
 
private:
 
    inline size_t microblock_( size_t i ) const
    {
        return i / micro_size_;
    }
 
    inline size_t block_( size_t i ) const
    {
        return i / block_size_;
    }
 
    inline size_t superblock_( size_t i ) const
    {
        return i / super_size_;
    }
 
    inline size_t lsb_( SuccinctType v ) const
    {
        return lsb_table_256_[v];
    }
 
    inline size_t m_(size_t k, size_t block) const
    {
        return m_matrix_(k, block)+(block*block_size_);
    }
 
    // -------------------------------------------------------------------------
    //     Internal Functions
    // -------------------------------------------------------------------------
 
    void init_();
 
    size_t log2fast_( size_t v ) const;
    SuccinctType clearbits_( SuccinctType n, size_t x ) const;
 
    // -------------------------------------------------------------------------
    //     Lookup Tables
    // -------------------------------------------------------------------------
 
private:
 
    static const size_t        catalan_numbers_[17][17];
    static const unsigned char log_table_256_[256];
    static const unsigned char lsb_table_256_[256];
    static const SuccinctType  highest_bits_set_[8];
 
    // -------------------------------------------------------------------------
    //     Internal Members
    // -------------------------------------------------------------------------
 
private:
 
    // data
    std::vector<IntType> array_;
 
    // table M for the out-of-block queries (contains indices of block-minima)
    Matrix<SuccinctType> m_matrix_;
 
    // table M' for superblock-queries (contains indices of block-minima)
    Matrix<size_t> m_prime_;
 
    // type of blocks
    std::vector<BlockTypeType> block_types_;
 
    // precomputed in-block queries
    Matrix<SuccinctType> precomputed_queries_;
 
    // microblock size
    size_t micro_size_;
 
    // block size
    size_t block_size_;
 
    // superblock size
    size_t super_size_;
 
    // If the data array is too small, we use the naive approach instead.
    bool naive_ = false;
 
};
 
} // namespace utils
} // namespace genesis
 
#endif // include guard