// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

/*!\file
 * \author Sara Hetzel <sara.hetzel AT fu-berlin.de>
 * \brief Provides seqan3::dna15, container aliases and string literals.
 */

#pragma once

#include <vector>

#include <seqan3/alphabet/nucleotide/nucleotide_base.hpp>
#include <seqan3/utility/char_operations/transform.hpp>

// ------------------------------------------------------------------
// dna15
// ------------------------------------------------------------------

namespace seqan3
{

class rna15;

/*!\brief The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap.
 * \ingroup alphabet_nucleotide
 * \implements seqan3::nucleotide_alphabet
 * \implements seqan3::writable_alphabet
 * \implements seqan3::detail::writable_constexpr_alphabet
 * \implements seqan3::trivially_copyable
 * \implements seqan3::standard_layout
 * \implements std::regular
 *
 * \details
 * Note that you can assign 'U' as a character to dna15 and it will silently
 * be converted to 'T'.
 *
 * Like most alphabets, this alphabet cannot be initialised directly from its character representation.
 * Instead initialise/assign from the character literal \ref seqan3_dna15_char_literal "'A'_dna15" or use the
 * function seqan3::dna15::assign_char().
 *
 * \include test/snippet/alphabet/nucleotide/dna15.cpp
 *
 * \stableapi{Since version 3.1.}
 */
class dna15 : public nucleotide_base<dna15, 15>
{
private:
    //!\brief The base class.
    using base_t = nucleotide_base<dna15, 15>;

    //!\brief Befriend seqan3::nucleotide_base.
    friend base_t;
    //!\cond
    //!\brief Befriend seqan3::alphabet_base.
    friend base_t::base_t;
    //!\endcond
    //!\brief Befriend seqan3::rna15 so it can copy #char_to_rank.
    friend rna15;

public:
    /*!\name Constructors, destructor and assignment
     * \{
     */
    constexpr dna15() noexcept = default;                          //!< Defaulted.
    constexpr dna15(dna15 const &) noexcept = default;             //!< Defaulted.
    constexpr dna15(dna15 &&) noexcept = default;                  //!< Defaulted.
    constexpr dna15 & operator=(dna15 const &) noexcept = default; //!< Defaulted.
    constexpr dna15 & operator=(dna15 &&) noexcept = default;      //!< Defaulted.
    ~dna15() noexcept = default;                                   //!< Defaulted.

    using base_t::base_t;

    /*!\brief Allow implicit construction from seqan3::rna15 of the same size.
     * \details
     *
     * \include{doc} doc/fragments/dna15_implicit_conversion_from_rna15.md
     *
     * \stableapi{Since version 3.1.}
     */
    template <std::same_as<rna15> t> // Accept incomplete type
    constexpr dna15(t const & r) noexcept
    {
        assign_rank(r.to_rank());
    }
    //!\}

private:
    //!\copydoc seqan3::dna4::rank_to_char_table
    static constexpr char_type
        rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'D', 'G', 'H', 'K', 'M', 'N', 'R', 'S', 'T', 'V', 'W', 'Y'};

    //!\copydoc seqan3::dna4::rank_complement_table
    static constexpr rank_type rank_complement_table[alphabet_size]{
        11, // T is complement of 'A'_dna15
        12, // V is complement of 'B'_dna15
        4,  // G is complement of 'C'_dna15
        5,  // H is complement of 'D'_dna15
        2,  // C is complement of 'G'_dna15
        3,  // D is complement of 'H'_dna15
        7,  // M is complement of 'K'_dna15
        6,  // K is complement of 'M'_dna15
        8,  // N is complement of 'N'_dna15
        14, // Y is complement of 'R'_dna15
        10, // S is complement of 'S'_dna15
        0,  // A is complement of 'T'_dna15
        1,  // B is complement of 'V'_dna15
        13, // W is complement of 'W'_dna15
        9   // R is complement of 'Y'_dna15
    };

    //!\copydoc seqan3::dna4::rank_complement
    static constexpr rank_type rank_complement(rank_type const rank)
    {
        return rank_complement_table[rank];
    }

    //!\copydoc seqan3::dna4::rank_to_char
    static constexpr char_type rank_to_char(rank_type const rank)
    {
        return rank_to_char_table[rank];
    }

    //!\copydoc seqan3::dna4::char_to_rank
    static constexpr rank_type char_to_rank(char_type const chr)
    {
        using index_t = std::make_unsigned_t<char_type>;
        return char_to_rank_table[static_cast<index_t>(chr)];
    }

    //!\copydoc seqan3::dna4::char_to_rank
    static constexpr std::array<rank_type, 256> char_to_rank_table{[]() constexpr
                                                                   {
                                                                       std::array<rank_type, 256> ret{};

                                                                       ret.fill(8u); // initialize with UNKNOWN ('N')

                                                                       // reverse mapping for characters and their lowercase
                                                                       for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
                                                                       {
                                                                           ret[rank_to_char_table[rnk]] = rnk;
                                                                           ret[to_lower(rank_to_char_table[rnk])] = rnk;
                                                                       }

                                                                       // set U equal to T
                                                                       ret['U'] = ret['T'];
                                                                       ret['u'] = ret['t'];

                                                                       return ret;
                                                                   }()};
};

// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------

/*!\brief Alias for a std::vector of seqan3::dna15.
 * \relates dna15
 * \details
 * \stableapi{Since version 3.1.}
 */
using dna15_vector = std::vector<dna15>;

// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
inline namespace literals
{

/*!\name Nucleotide literals
 * \{
 */
/*!\brief The seqan3::dna15 char literal.
 * \relatesalso seqan3::dna15
 * \returns seqan3::dna15
 * \details
 * \anchor seqan3_dna15_char_literal
 *
 * You can use this char literal to assign a seqan3::dna15 character:
 * \snippet test/snippet/alphabet/nucleotide/dna15_char_literal.cpp main
 *
 * \stableapi{Since version 3.1.}
 */
constexpr dna15 operator""_dna15(char const c) noexcept
{
    return dna15{}.assign_char(c);
}

/*!\brief The seqan3::dna15 string literal.
 * \relatesalso seqan3::dna15
 * \returns seqan3::dna15_vector
 *
 * You can use this string literal to easily assign to dna15_vector:
 * \include test/snippet/alphabet/nucleotide/dna15_literal.cpp
 *
 * \stableapi{Since version 3.1.}
 */
SEQAN3_WORKAROUND_LITERAL dna15_vector operator""_dna15(char const * s, std::size_t n)
{
    dna15_vector r;
    r.resize(n);

    for (size_t i = 0; i < n; ++i)
        r[i].assign_char(s[i]);

    return r;
}
//!\}

} // namespace literals

} // namespace seqan3
