Comparisons.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 COMPARISONS_H
#define COMPARISONS_H

#include <string>
#include <algorithm>
#include <type_traits>
#include <Sequence/SeqEnums.hpp>

namespace Sequence
{
  Mutations TsTv(const char & i, const char & j);
  Mutations TsTv(const int & i,const int & j);
  bool Different (const std::string & seq1,
                  const std::string & seq2,
                  const bool & skip_missing = true,
                  const bool & nucleic_acid = true);
  
  int NumDiffs(const std::string & seq1,
               const std::string & seq2,
               const bool & skip_missing = true ,
               const bool & nucleic_acid = true);

  bool Gapped(const std::string &s);

  template<typename Iterator> bool Gapped(Iterator beg,Iterator end,
                                          const char & gapchar = '-')
  {
    Iterator itr = std::find(beg,end,gapchar);
    return (itr!=end);
  }

  bool NotAGap(const char &c);
}
#endif