csa_alphabet_strategy.hpp

Go to the documentation of this file.

// Copyright (c) 2018, the SDSL Project Authors. All rights reserved.
// Please see the AUTHORS file for details. Use of this source code is governed
// by a BSD license that can be found in the LICENSE file.
 
// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <string>
 
#include <sdsl/config.hpp>
#include <sdsl/int_vector.hpp>
#include <sdsl/rank_support.hpp>
#include <sdsl/sdsl_concepts.hpp>
#include <sdsl/select_support.hpp>
 
#include <seqan3/core/platform.hpp>
 
namespace sdsl
{
 
    //        This is recommended when the underlying text uses the entire alphabet and not just a small subset.
    class plain_byte_alphabet
    {
    public:
        class mapping_wrapper;
 
        typedef int_vector<>::size_type size_type;
        typedef mapping_wrapper char2comp_type;
        typedef mapping_wrapper comp2char_type;
        typedef int_vector<64> C_type;
        typedef uint16_t sigma_type;
        typedef uint8_t char_type;
        typedef uint8_t comp_char_type;
        typedef std::string string_type;
        typedef byte_alphabet_tag alphabet_category;
        enum { int_width = 8 };
 
        class mapping_wrapper
        {
        public:
            mapping_wrapper() {}
 
            constexpr char_type operator[](char_type const c) const noexcept
            {
                return c;
            }
        };
 
        const char2comp_type char2comp;
        const comp2char_type comp2char;
        const C_type & C;
        const sigma_type & sigma;
 
    private:
        C_type m_C;         // Cumulative counts for the compact alphabet [0..sigma].
        sigma_type m_sigma; // Effective size of the alphabet.
 
    public:
        plain_byte_alphabet() : C(m_C), sigma(m_sigma), m_sigma(0)
        {}
 
        plain_byte_alphabet(int_vector_buffer<8> & text_buf, int_vector_size_type len) : C(m_C), sigma(m_sigma)
        {
            m_sigma = 0;
            if (0 == len || 0 == text_buf.size())
                return;
 
            assert(len <= text_buf.size());
 
            // initialize vectors
            m_C = int_vector<64>(257, 0);
            // count occurrences of each symbol
            for (size_type i = 0; i < len; ++i)
                ++m_C[text_buf[i]];
 
            assert(1 == m_C[0]); // null-byte should occur exactly once
 
            m_sigma = 255;
            for (int i = 0; i < 256; ++i)
            {
                if (m_C[i])
                {
                    m_sigma = i + 1;
                    // m_C[m_sigma] = m_C[i];
                    // ++m_sigma;
                }
            }
            // m_C.resize(m_sigma + 1);
            for (int i = (int) 256; i > 0; --i)
                m_C[i] = m_C[i - 1];
            m_C[0] = 0;
            for (int i = 1; i <= (int) 256; ++i)
                m_C[i] += m_C[i - 1];
 
            assert(C[sigma] == len);
        }
 
        plain_byte_alphabet(plain_byte_alphabet const & strat) : C(m_C),
                                                                 sigma(m_sigma),
                                                                 m_C(strat.m_C),
                                                                 m_sigma(strat.m_sigma)
        {}
 
        plain_byte_alphabet(plain_byte_alphabet && strat) : C(m_C),
                                                            sigma(m_sigma),
                                                            m_C(std::move(strat.m_C)),
                                                            m_sigma(strat.m_sigma)
        {}
 
        plain_byte_alphabet & operator=(plain_byte_alphabet const & strat)
        {
            if (this != &strat)
            {
                plain_byte_alphabet tmp(strat);
                *this = std::move(tmp);
            }
            return *this;
        }
 
        plain_byte_alphabet & operator=(plain_byte_alphabet && strat)
        {
            if (this != &strat)
            {
                m_C = std::move(strat.m_C);
                m_sigma = std::move(strat.m_sigma);
            }
            return *this;
        }
 
        size_type serialize(std::ostream & out, structure_tree_node * v, std::string name = "") const
        {
            structure_tree_node * child = structure_tree::add_child(v, name, util::class_name(*this));
            size_type written_bytes = 0;
            written_bytes += m_C.serialize(out, child, "m_C");
            written_bytes += write_member(m_sigma, out, child, "m_sigma");
            structure_tree::add_size(child, written_bytes);
            return written_bytes;
        }
 
        void load(std::istream & in)
        {
            m_C.load(in);
            read_member(m_sigma, in);
        }
 
        template <typename archive_t>
        void CEREAL_SAVE_FUNCTION_NAME(archive_t & ar) const
        {
            ar(CEREAL_NVP(m_C));
            ar(CEREAL_NVP(m_sigma));
        }
 
        template <typename archive_t>
        void CEREAL_LOAD_FUNCTION_NAME(archive_t & ar)
        {
            ar(CEREAL_NVP(m_C));
            ar(CEREAL_NVP(m_sigma));
        }
 
        bool operator==(plain_byte_alphabet const & other) const noexcept
        {
            return (m_C == other.m_C) && (m_sigma == other.m_sigma);
        }
 
        bool operator!=(plain_byte_alphabet const & other) const noexcept
        {
            return !(*this == other);
        }
    };
 
}