cigar.hpp

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// -----------------------------------------------------------------------------------------------------
// 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 <seqan3/alphabet/adaptation/uint.hpp>
#include <seqan3/alphabet/cigar/cigar_op.hpp>
#include <seqan3/alphabet/composite/alphabet_tuple_base.hpp>
#include <seqan3/core/detail/debug_stream_type.hpp>
#include <seqan3/range/container/small_string.hpp>
#include <seqan3/std/charconv>
 
// ------------------------------------------------------------------
// cigar
// ------------------------------------------------------------------
 
namespace seqan3
{
 
class cigar : public alphabet_tuple_base<cigar, uint32_t, cigar_op>
{
private:
    using base_t = alphabet_tuple_base<cigar, uint32_t, cigar_op>;
 
    friend base_t;
 
public:
    constexpr cigar()                          noexcept = default; 
    constexpr cigar(cigar const &)             noexcept = default; 
    constexpr cigar(cigar &&)                  noexcept = default; 
    constexpr cigar & operator=(cigar const &) noexcept = default; 
    constexpr cigar & operator=(cigar &&)      noexcept = default; 
    ~cigar()                                   noexcept = default; 
 
    // Inherit constructors from base
    using base_t::base_t;
 
    SEQAN3_DOXYGEN_ONLY(( constexpr cigar(component_type const alph) noexcept {} ))
 
    SEQAN3_DOXYGEN_ONLY(( constexpr cigar & operator=(component_type const alph) noexcept {} ))
 
    // Inherit operators from base
    using base_t::operator=;
 
    small_string<11> to_string() const noexcept
    {
        small_string<11> ret{}; // maximum number of digits for uint32_t + 1 char for the cigar_op
        ret.resize(11);
 
        auto [ ptr, errc ] = std::to_chars(ret.data(), ret.data() + 10, get<0>(*this));
 
        *ptr = seqan3::to_char(get<1>(*this));
        (void)errc;
 
        ret.resize(ptr - ret.data() + 1);
        return ret;
    }
 
    cigar & assign_string(small_string<11> const s) noexcept
    {
        uint32_t num{};
        auto [ ptr, errc ] = std::from_chars(s.data(), s.data() + 10, num);
 
        if ((errc != std::errc{}) || (!char_is_valid_for<cigar_op>(*ptr)) || (*(ptr + 1) != 0))
        {
            get<0>(*this) = 0;
            assign_char_to('P', get<1>(*this));
        }
        else
        {
            get<0>(*this) = num;
            assign_char_to(*ptr, get<1>(*this));
        }
 
        return *this;
    }
 
    SEQAN3_DOXYGEN_ONLY(( template <size_t index> constexpr auto get(cigar & l) noexcept {} ))
 
    
    SEQAN3_DOXYGEN_ONLY(( template <typename type> constexpr auto get(cigar & l) noexcept {} ))
};
 
template <typename char_t>
inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, cigar const c)
{
    s << c.to_string();
    return s;
}
 
} // namespace seqan3