bitvector.hpp

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#ifndef GENESIS_UTILS_MATH_BITVECTOR_H_
#define GENESIS_UTILS_MATH_BITVECTOR_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2024 Lucas Czech
 
    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 <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include <array>
#include <cassert>
#include <cstdint>
#include <iterator>
#include <limits>
#include <stdexcept>
#include <string>
#include <vector>
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     Bitvector
// =================================================================================================
 
class Bitvector
{
public:
 
    // ---------------------------------------------------------
    //     Typedefs, Enums, Constants
    // ---------------------------------------------------------
 
    using IntType = uint64_t;
    static const size_t IntSize = sizeof(IntType) * 8;
 
    static const size_t npos = std::numeric_limits<size_t>::max();
 
    // ---------------------------------------------------------
    //     Constructor and Rule of Five
    // ---------------------------------------------------------
 
    Bitvector() = default;
 
    Bitvector( size_t size, bool initial_value = false)
        : size_(size)
    {
        // Edge case.
        if( size == 0 ) {
            return;
        }
 
        // reserve enough bits, and init them.
        data_.resize( (size / IntSize) + (size % IntSize == 0 ? 0 : 1) );
        set_all(initial_value);
    }
 
    Bitvector( size_t size, std::initializer_list<size_t> list )
        : Bitvector(size, false)
    {
        for( size_t e : list ) {
            set(e);
        }
    }
 
    template<class It>
    Bitvector( It first, It last )
        : Bitvector( std::distance( first,last ), false )
    {
        size_t i = 0;
        for( auto it = first; it != last; ++it ) {
            set( i, *it );
            ++i;
        }
    }
 
    Bitvector( size_t size, Bitvector const& other );
 
    Bitvector( std::string const& values );
 
    // /* *
    //  * @brief Create a Bitvector by copying the first @p max_size of another Bitvector.
    //  *
    //  * If `max_size > other.size()`, all max_size are used.
    //  */
    // Bitvector( Bitvector const& other, size_t max_size );
 
    ~Bitvector() = default;
 
    Bitvector(Bitvector const&) = default;
    Bitvector(Bitvector&&)      = default;
 
    Bitvector& operator= (Bitvector const&) = default;
    Bitvector& operator= (Bitvector&&)      = default;
 
    // ---------------------------------------------------------
    //     Single Bit Functions
    // ---------------------------------------------------------
 
    inline bool operator [] ( size_t index ) const {
        assert( index / IntSize < data_.size() );
        assert( index % IntSize < bit_mask_.size() );
        return static_cast<bool> (data_[index / IntSize] & bit_mask_[index % IntSize]);
    }
 
    inline bool get( size_t index ) const
    {
        if( index >= size_ ) {
            throw std::out_of_range(
                "Cannot access element " + std::to_string(index) + " in Bitvector of size " +
                std::to_string(size())
            );
        }
 
        assert( index / IntSize < data_.size() );
        assert( index % IntSize < bit_mask_.size() );
        return static_cast<bool> (data_[index / IntSize] & bit_mask_[index % IntSize]);
    }
 
    inline void set( size_t index )
    {
        if (index >= size_) {
            throw std::out_of_range(
                "Cannot access element " + std::to_string(index) + " in Bitvector of size " +
                std::to_string(size())
            );
        }
 
        assert( index / IntSize < data_.size() );
        assert( index % IntSize < bit_mask_.size() );
        data_[index / IntSize] |= bit_mask_[index % IntSize];
    }
 
    inline void unset( size_t index )
    {
        if( index >= size_ ) {
            throw std::out_of_range(
                "Cannot access element " + std::to_string(index) + " in Bitvector of size " +
                std::to_string(size())
            );
        }
 
        assert( index / IntSize < data_.size() );
        assert( index % IntSize < bit_mask_.size() );
        data_[index / IntSize] &= ~(bit_mask_[index % IntSize]);
    }
 
    inline void set( size_t index, bool value )
    {
        if( value ) {
            set( index );
        } else {
            unset( index );
        }
    }
 
    void set( size_t first, size_t last, bool value = true );
 
    inline void flip( size_t index )
    {
        if( index >= size_ ) {
            throw std::out_of_range(
                "Cannot access element " + std::to_string(index) + " in Bitvector of size " +
                std::to_string(size())
            );
        }
 
        assert( index / IntSize < data_.size() );
        assert( index % IntSize < bit_mask_.size() );
        data_[index / IntSize] ^= bit_mask_[index % IntSize];
    }
 
    inline void toggle( size_t index )
    {
        return flip( index );
    }
 
    // ---------------------------------------------------------
    //     Operators
    // ---------------------------------------------------------
 
    Bitvector& operator &= (Bitvector const& rhs);
    Bitvector& operator |= (Bitvector const& rhs);
    Bitvector& operator ^= (Bitvector const& rhs);
    Bitvector  operator ~  () const;
 
    friend Bitvector operator & (Bitvector const& lhs, Bitvector const& rhs);
    friend Bitvector operator | (Bitvector const& lhs, Bitvector const& rhs);
    friend Bitvector operator ^ (Bitvector const& lhs, Bitvector const& rhs);
 
    bool operator == (const Bitvector &other) const;
    bool operator != (const Bitvector &other) const;
 
    // ---------------------------------------------------------
    //     Other Functions
    // ---------------------------------------------------------
 
    inline bool empty() const
    {
        return size_ == 0;
    }
 
    inline size_t size() const
    {
        return size_;
    }
 
    size_t count() const;
 
    size_t count( size_t first, size_t last ) const;
 
    bool any_set() const;
 
    size_t find_next_set( size_t start ) const;
 
    size_t hash()  const;
 
    IntType x_hash() const;
 
    void negate();
 
    void normalize();
 
    void set_all(const bool value = false);
 
    std::string dump() const;
    std::string dump_int(IntType x) const;
 
    std::vector<IntType> const& data() const
    {
        return data_;
    }
 
    // ---------------------------------------------------------
    //     Internal Members
    // ---------------------------------------------------------
 
private:
 
    void unset_padding_();
 
    static size_t count_( IntType x );
 
    static const IntType all_0_;
    static const IntType all_1_;
 
    static const std::array<IntType, IntSize> bit_mask_;
 
    static const std::array<IntType, IntSize> ones_mask_;
 
    static const std::array<IntType, 4> count_mask_;
 
    // ---------------------------------------------------------
    //     Data Members
    // ---------------------------------------------------------
 
    size_t               size_ = 0;
    std::vector<IntType> data_;
};
 
// =============================================================================
//     Hashing
// =============================================================================
 
struct BitvectorHash
{
    std::size_t operator() ( genesis::utils::Bitvector const& value ) const
    {
        return value.hash();
    }
};
 
struct BitvectorXhash
{
    std::size_t operator() ( genesis::utils::Bitvector const& value ) const
    {
        return static_cast<std::size_t>( value.x_hash() );
    }
};
 
} // namespace utils
} // namespace genesis
 
// =============================================================================
//     Namespace std extension
// =============================================================================
 
namespace std {
 
template<>
struct hash<genesis::utils::Bitvector>
{
    std::size_t operator() ( genesis::utils::Bitvector const& value ) const
    {
        return value.hash();
    }
};
 
} // namespace std
 
#endif // include guard