ThreeSubs.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 THREESUBS_H
#define THREESUBS_H

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

namespace Sequence
  {
  class RedundancyCom95;
  class  WeightingScheme3;
  class ThreeSubs
    {
    private:
      double p0, p2S, p2V, p4, q0, q2S, q2V, q4;
      void Calculate (const RedundancyCom95 * sitesObj,
                      const std::string *intermediates,
                      const std::string &codon1, const std::string &codon2,
                      double w_path1,double w_path2, double w_path3,
                      double w_path4,double w_path5,double w_path6);
    public:
      explicit ThreeSubs(void)
      {}
      void operator() (const RedundancyCom95 * sitesObj,
                       const std::string &codon1, const std::string &codon2,
                       const Sequence::WeightingScheme3 *weights3);
      ~ThreeSubs(void);
      double
      P0 (void) const
      {
        return p0;
      }

      double
      P2S (void) const
      {
        return p2S;
      }

      double
      P2V (void) const
      {
        return p2V;
      }

      double
      P4 (void) const
      {
        return p4;
      }

      double
      Q0 (void) const
      {
        return q0;
      }

      double
      Q2S (void) const
      {
        return q2S;
      }

      double
      Q2V (void) const
      {
        return q2V;
      }

      double
      Q4 (void) const
      {
        return q4;
      }
    };
}
#endif

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