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[MISC] Alphabet: rename sam_dna16 to dna16sam (#2521)
* [DOC] Apply patch: Add `\stableapi` note * [MISC] Rename sam_dna16 into dna16sam Signed-off-by: Lydia Buntrock <[email protected]> * [MISC, TEST] Rename header, test and snippet files Signed-off-by: Lydia Buntrock <[email protected]> * [MISC] add type alias with deprecation for seqan3::sam_dna16 Signed-off-by: Lydia Buntrock <[email protected]> * [DOC] Add changelog entry Signed-off-by: Lydia Buntrock <[email protected]> * Update CHANGELOG.md Co-authored-by: marehr <[email protected]> Co-authored-by: Marcel <[email protected]>
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| Original file line number | Diff line number | Diff line change |
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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 | ||
| // ----------------------------------------------------------------------------------------------------- | ||
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| /*!\file | ||
| * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de> | ||
| * \brief Provides seqan3::dna16sam. | ||
| */ | ||
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| #pragma once | ||
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| #include <seqan3/alphabet/nucleotide/nucleotide_base.hpp> | ||
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| namespace seqan3 | ||
| { | ||
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| /*!\brief A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('='). | ||
| * \ingroup nucleotide | ||
| * \implements seqan3::writable_alphabet | ||
| * \implements seqan3::nucleotide_alphabet | ||
| * \implements seqan3::trivially_copyable | ||
| * \implements seqan3::standard_layout | ||
| * \if DEV \implements seqan3::detail::writable_constexpr_alphabet \endif | ||
| * | ||
| * \details | ||
| * | ||
| * The seqan3::dna16sam alphabet is the nucleotide alphabet used inside the SAM, BAM and CRAM formats. | ||
| * It has all the letters of the seqan3::dna15 alphabet and the extra alphabet character '=' which denotes a | ||
| * nucleotide character identical to the reference. | ||
| * Without the context of this reference sequence, no assumptions can be made about the actual value of '=' letter. | ||
| * | ||
| * Note that you can assign 'U' as a character to dna16sam and it will silently | ||
| * be converted to 'T'. | ||
| * Lower case letters are accepted when assigning from char (just like seqan3::dna15) and unknown characters are | ||
| * silently converted to 'N'. | ||
| * | ||
| * The complement is the same as for seqan3::dna15, with the addition that the complement of '=' is unknown and | ||
| * therefore set to 'N'. | ||
| * | ||
| * \include test/snippet/alphabet/nucleotide/dna16sam.cpp | ||
| * | ||
| * \stableapi{Since version 3.1.} | ||
| */ | ||
| class dna16sam : public nucleotide_base<dna16sam, 16> | ||
| { | ||
| private: | ||
| //!\brief The base class. | ||
| using base_t = nucleotide_base<dna16sam, 16>; | ||
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| //!\brief Befriend seqan3::nucleotide_base. | ||
| friend base_t; | ||
| //!\cond \brief Befriend seqan3::alphabet_base. | ||
| friend base_t::base_t; | ||
| //!\endcond | ||
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| public: | ||
| /*!\name Constructors, destructor and assignment | ||
| * \{ | ||
| */ | ||
| constexpr dna16sam() noexcept = default; //!< Defaulted. | ||
| constexpr dna16sam(dna16sam const &) noexcept = default; //!< Defaulted. | ||
| constexpr dna16sam(dna16sam &&) noexcept = default; //!< Defaulted. | ||
| constexpr dna16sam & operator=(dna16sam const &) noexcept = default; //!< Defaulted. | ||
| constexpr dna16sam & operator=(dna16sam &&) noexcept = default; //!< Defaulted. | ||
| ~dna16sam() noexcept = default; //!< Defaulted. | ||
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| using base_t::base_t; | ||
| //!\} | ||
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| private: | ||
| //!\copydoc seqan3::dna4::rank_to_char_table | ||
| static constexpr char_type rank_to_char_table[alphabet_size] | ||
| { | ||
| '=', | ||
| 'A', | ||
| 'C', | ||
| 'M', | ||
| 'G', | ||
| 'R', | ||
| 'S', | ||
| 'V', | ||
| 'T', | ||
| 'W', | ||
| 'Y', | ||
| 'H', | ||
| 'K', | ||
| 'D', | ||
| 'B', | ||
| 'N' | ||
| }; | ||
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| //!\copydoc seqan3::dna4::char_to_rank_table | ||
| static constexpr std::array<rank_type, 256> char_to_rank_table | ||
| { | ||
| [] () constexpr | ||
| { | ||
| std::array<rank_type, 256> ret{}; | ||
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| // initialize with UNKNOWN (std::array::fill unfortunately not constexpr) | ||
| for (auto & c : ret) | ||
| c = 15; // rank of 'N' | ||
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| // 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; | ||
| } | ||
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| // set U equal to T | ||
| ret['U'] = ret['T']; ret['u'] = ret['t']; | ||
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| return ret; | ||
| }() | ||
| }; | ||
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| //!\copydoc seqan3::dna4::complement_table | ||
| static const std::array<dna16sam, alphabet_size> complement_table; | ||
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| /*!\copydoc seqan3::dna4::rank_to_char | ||
| * | ||
| * The representation is the same as in the SAM specifications (which is NOT in alphabetical order). | ||
| */ | ||
| static constexpr char_type rank_to_char(rank_type const rank) | ||
| { | ||
| return rank_to_char_table[rank]; | ||
| } | ||
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| //!\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)]; | ||
| } | ||
| }; | ||
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| // ------------------------------------------------------------------ | ||
| // containers | ||
| // ------------------------------------------------------------------ | ||
|
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| /*!\brief Alias for an std::vector of seqan3::dna16sam. | ||
| * \relates dna16sam | ||
| * \details | ||
| * \stableapi{Since version 3.1.} | ||
| */ | ||
| using dna16sam_vector = std::vector<dna16sam>; | ||
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| // ------------------------------------------------------------------ | ||
| // literals | ||
| // ------------------------------------------------------------------ | ||
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| /*!\name Literals | ||
| * \{ | ||
| */ | ||
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| /*!\brief The seqan3::dna16sam char literal. | ||
| * \relates seqan3::dna16sam | ||
| * \returns seqan3::dna16sam | ||
| * \param[in] c The character to assign from. | ||
| * \details | ||
| * \stableapi{Since version 3.1.} | ||
| */ | ||
| constexpr dna16sam operator""_dna16sam(char const c) noexcept | ||
| { | ||
| return dna16sam{}.assign_char(c); | ||
| } | ||
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| /*!\brief The seqan3::dna16sam string literal. | ||
| * \relates seqan3::dna16sam | ||
| * \returns seqan3::dna16sam_vector | ||
| * \param[in] s The string literal to assign from. | ||
| * \param[in] n The length of the string literal s. | ||
| * | ||
| * You can use this string literal to easily assign to seqan3::dna16sam_vector: | ||
| * | ||
| * \include test/snippet/alphabet/nucleotide/dna16sam_literal.cpp | ||
| * | ||
| * \stableapi{Since version 3.1.} | ||
| */ | ||
| inline dna16sam_vector operator""_dna16sam(char const * s, size_t n) | ||
| { | ||
| dna16sam_vector r; | ||
| r.resize(n); | ||
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| for (size_t i = 0; i < n; ++i) | ||
| r[i].assign_char(s[i]); | ||
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| return r; | ||
| } | ||
| //!\} | ||
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| // ------------------------------------------------------------------ | ||
| // complement deferred definition | ||
| // ------------------------------------------------------------------ | ||
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| constexpr std::array<dna16sam, dna16sam::alphabet_size> dna16sam::complement_table | ||
| { | ||
| 'N'_dna16sam, // complement of '='_dna16sam | ||
| 'T'_dna16sam, // complement of 'A'_dna16sam | ||
| 'G'_dna16sam, // complement of 'C'_dna16sam | ||
| 'K'_dna16sam, // complement of 'M'_dna16sam | ||
| 'C'_dna16sam, // complement of 'G'_dna16sam | ||
| 'Y'_dna16sam, // complement of 'R'_dna16sam | ||
| 'S'_dna16sam, // complement of 'S'_dna16sam | ||
| 'B'_dna16sam, // complement of 'V'_dna16sam | ||
| 'A'_dna16sam, // complement of 'T'_dna16sam | ||
| 'W'_dna16sam, // complement of 'W'_dna16sam | ||
| 'R'_dna16sam, // complement of 'Y'_dna16sam | ||
| 'D'_dna16sam, // complement of 'H'_dna16sam | ||
| 'M'_dna16sam, // complement of 'K'_dna16sam | ||
| 'H'_dna16sam, // complement of 'D'_dna16sam | ||
| 'V'_dna16sam, // complement of 'B'_dna16sam | ||
| 'N'_dna16sam // complement of 'N'_dna16sam | ||
| }; | ||
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| } // namespace seqan3 |
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