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 <boost/static_assert.hpp>
#include <boost/type_traits.hpp>
#include <Sequence/SeqExceptions.hpp>
#include <Sequence/SeqEnums.hpp>
namespace Sequence
{
  Mutations TsTv(char i, char j);
  Mutations TsTv(int i, int j);
  bool Different (const std::string & seq1,
                  const std::string & seq2,
                  bool skip_missing =1 ,
                  bool nucleic_acid = 1);
  
  template<typename T> bool notDifferent(const T &l,const T &r,
                                         const bool & skip_missing = 1,
                                         const bool & nucleic_acid = 1)
  {
    BOOST_STATIC_ASSERT( (boost::is_convertible<T,std::string>::value) );
    return !Different(std::string(l),std::string(r),
                      skip_missing,nucleic_acid);
  }

  unsigned NumDiffs(const std::string & seq1,
                    const std::string & seq2,
                    bool skip_missing =1 ,
                    bool nucleic_acid = 1);

  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

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