alphabet.cpp

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/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2018-2028 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/alphabet.hpp"
 
#include <cassert>
#include <stdexcept>
 
namespace genesis {
namespace sequence {
 
// ================================================================================================
//     Nucleotide Alphabet
// ================================================================================================
 
std::array<uint8_t, 256> const NucleotideAlphabet::ascii_to_nt4 = {{
    /*   0 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /*  16 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /*  32 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 8,
    /*                                               -        */
    /*  48 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /*  64 */ 8, 0, 8, 1, 8, 8, 8, 2, 8, 8, 8, 8, 8, 8, 4, 8,
    /*           A     C           G                    N     */
    /*  80 */ 8, 8, 8, 8, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /*                    T  U                                */
    /*  96 */ 8, 0, 8, 1, 8, 8, 8, 2, 8, 8, 8, 8, 8, 8, 4, 8,
    /*           a     c           g                    n     */
    /* 112 */ 8, 8, 8, 8, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /*                    t  u                                */
    /* 128 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /* 144 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /* 160 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /* 176 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /* 192 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /* 208 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /* 224 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
    /* 240 */ 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8,
}};
 
} // namespace sequence
} // namespace genesis