SeqRegexes.hpp

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/*

Copyright (C) 2003-2009 Kevin Thornton, krthornt[]@[]uci.edu

Remove the brackets to email me.

This file is part of libsequence.

libsequence 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.

libsequence 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
long with libsequence.  If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef __SEQ_REGEXES_H__
#define __SEQ_REGEXES_H__

#include <regex>
#include <type_traits>
namespace Sequence
{
  const char *basic_dna_alphabet = "[^AGTCN\\-]";

  const char *full_dna_alphabet =  "[^AGCTNXMRWSKVHDB\\-]";

  const char *pep_alphabet = "[^ARNDBCQEZGHILKMFPSTWYV\\-]";


  template<typename Iter>
  bool validSeq(Iter beg, Iter end, const char *_pattern = Sequence::basic_dna_alphabet, const bool icase = true)
  {
    for( ; beg != end ; ++beg )
      {
        char ch = std::toupper(*beg);
        if( ch != 'A' && ch != 'C' && ch != 'G' && ch != 'T' && ch != 'N' && ch != '-' )
          {
            return false;
          }
      }
    return true;
  }
}

#endif