SeqAlphabets.cc

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#include <Sequence/SeqAlphabets.hpp>
#include <algorithm>
#include <cctype>
#include <array>

namespace Sequence {
  const alphabet_t dna_alphabet{ {'A','C','G','T',
        'R','Y','S','W',
        'K','M','B','D',
        'H','V','N','-'} };

  const alphabet_t dna_poly_alphabet{ {'A','C','G','T', //0-3
        '0','1','-','N', //4-7
        '\0', //8
        } };

  const alphabet_t::size_type NOTPOLYCHAR = dna_poly_alphabet.size();
  
  const alphabet_t::size_type POLYEOS = alphabet_t::size_type( std::distance(dna_poly_alphabet.begin(),
                                                                             std::find(dna_poly_alphabet.begin(),
                                                                                       dna_poly_alphabet.end(),
                                                                                       '\0')
                                                                             ) );
  bool isDNA( const char & ch) 
  {
    return std::find( dna_alphabet.begin(),
                      dna_alphabet.end(),
                      std::toupper(ch) ) != dna_alphabet.end();
  }

  bool ambiguousNucleotide::operator()(const char & c) const
  {
    return std::distance( dna_alphabet.begin(),
                          std::find(dna_alphabet.begin(),
                                    dna_alphabet.end(),
                                    std::toupper(c)) ) > 3;
    /*
    const char ch = char(std::toupper(c));
    return (ch != 'A' &&
            ch != 'G' &&
            ch != 'T' &&
            ch != 'C' );
    */
  }
  
  bool invalidPolyChar::operator()(const char & nucleotide) const
    {
      auto itr = std::find(dna_poly_alphabet.begin(),
                           dna_poly_alphabet.end(),
                           std::toupper(nucleotide));
      if(itr == dna_poly_alphabet.end()) return 1;
      auto d = std::distance( dna_alphabet.begin(),
                              itr );
      return ( d > 3 && d < 14 ); 
    }
}