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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <seqan3/alphabet/nucleotide/nucleotide_base.hpp>
#include <seqan3/core/debug_stream.hpp>
// We inherit from seqan3::nucleotide_base s.t. we do not need to implement the full nucleotide interface
// but it is sufficient to define `rank_to_char`, `char_to_rank`, and `complement_table`.
class my_dna4 : public seqan3::nucleotide_base<my_dna4, 4 /*alphabet size is 4*/>
{
public:
using nucleotide_base<my_dna4, 4>::nucleotide_base; // Use constructors of the base class.
private:
// Returns the character representation of rank. This is where rank conversion for to_char() is handled!
static constexpr char_type rank_to_char(rank_type const rank)
{
return rank_to_char_table[rank];
}
// Returns the rank representation of character. This is where char conversion for assign_char() is handled!
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)];
}
// Returns the complement by rank. This is where complement is handled and with this, my_dna4 models
// seqan3::nucleotide_alphabet.
static constexpr rank_type rank_complement(rank_type const rank)
{
return rank_complement_table[rank];
}
private:
// === lookup-table implementation detail ===
// Value to char conversion table.
static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'C', 'G', 'T'}; // rank 0,1,2,3
// Char-to-value conversion table.
static constexpr std::array<rank_type, 256> char_to_rank_table{
[]() constexpr
{
// By default, everything has rank 0 which equals `A`.
std::array<rank_type, 256> conversion_table{};
conversion_table['C'] = conversion_table['c'] = 1;
conversion_table['G'] = conversion_table['g'] = 2;
conversion_table['T'] = conversion_table['t'] = 3;
conversion_table['U'] = conversion_table['T']; // set U equal to T
conversion_table['u'] = conversion_table['t']; // set u equal to t
return conversion_table;
}()};
// The rank complement table.
static constexpr rank_type rank_complement_table[alphabet_size]{
3, // T is complement of 'A'_dna4
2, // G is complement of 'C'_dna4
1, // C is complement of 'G'_dna4
0 // A is complement of 'T'_dna4
};
friend nucleotide_base<my_dna4, 4>; // Grant seqan3::nucleotide_base access to private/protected members.
friend nucleotide_base<my_dna4, 4>::base_t; // Grant seqan3::alphabet_base access to private/protected members.
};
// Defines the `_my_dna4` *char literal* so you can write `'C'_my_dna4` instead of `my_dna4{}.assign_char('C')`.
constexpr my_dna4 operator""_my_dna4(char const c) noexcept
{
return my_dna4{}.assign_char(c);
}
int main()
{
my_dna4 my_letter{'C'_my_dna4};
my_letter.assign_char('S'); // Characters other than A,C,G,T are implicitly converted to `A`.
seqan3::debug_stream << my_letter << "\n"; // "A";
seqan3::debug_stream << seqan3::complement(my_letter) << "\n"; // "T";
}
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