Kimura80.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 KIMURA80_H
#define KIMURA80_H

namespace Sequence
  {
  class Seq;
  class Kimura80
    {
    private:
      unsigned num_Ts, num_Tv;
      size_t seqlen;            //total sequence length
      size_t sites_compared;    //number of ungapped sites in the data
      void Compute (const Sequence::Seq *seq1, const Sequence::Seq *seq2);
      double divergence, P, Q;
    public:
      explicit Kimura80 (const Sequence::Seq * seqa,const  Sequence::Seq * seqb);
      double K() const;
      size_t sites (void) const;
    };
}
#endif