alphabet.hpp

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#ifndef GENESIS_SEQUENCE_KMER_ALPHABET_H_
#define GENESIS_SEQUENCE_KMER_ALPHABET_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2024 Lucas Czech
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@sund.ku.dk>
    University of Copenhagen, Globe Institute, Section for GeoGenetics
    Oster Voldgade 5-7, 1350 Copenhagen K, Denmark
*/
 
#include "genesis/sequence/kmer/kmer.hpp"
#include "genesis/utils/text/char.hpp"
 
#include <array>
#include <cassert>
#include <cstdint>
#include <iostream>
#include <stdexcept>
#include <string>
#include <type_traits>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Nucleotide Alphabet
// =================================================================================================
 
class NucleotideAlphabet
{
    static const std::array<uint8_t, 256> ascii_to_nt4;
 
    inline uint8_t char_to_rank( char c )
    {
        c = utils::to_upper( c );
        if(( c != 'A' ) && ( c != 'C' ) && ( c != 'G' ) && ( c != 'T' ) && ( c != 'N' )) {
            throw std::invalid_argument(
                "Cannot use char " + utils::char_to_hex( c ) + " to construct ACGT k-mer"
            );
        }
        return 0 * ( c == 'A' ) + 1 * ( c == 'C' ) + 2 * ( c == 'G' ) + 3 * ( c == 'T' );
 
        // auto const r = ascii_to_nt4[c];
        // if( r > 3 ) {
        //     // ...
        // }
        // return ;
    }
};
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard