TwoSubs.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 TWOSUBS_H
#define TWOSUBS_H
#include <Sequence/SeqEnums.hpp>
#include <string>
namespace Sequence
  {
  class RedundancyCom95;
  class WeightingScheme2;
  class TwoSubs
    {
    private:
      double p0, p2S, p2V, p4, q0, q2S, q2V,q4;
      double p0_b1, p2S_b1, p2V_b1, p4_b1, q0_b1, q2S_b1, q2V_b1, q4_b1;
      double p0_b2, p2S_b2, p2V_b2, p4_b2, q0_b2, q2S_b2, q2V_b2, q4_b2;
      double p0_b3, p2S_b3, p2V_b3, p4_b3, q0_b3, q2S_b3, q2V_b3, q4_b3;
      double p0_b4, p2S_b4, p2V_b4, p4_b4, q0_b4, q2S_b4, q2V_b4, q4_b4;
      void Calculate (const RedundancyCom95 * sitesObj, const std::string &codon1,
                      const std::string &int_1, const std::string &int_2,
                      const std::string &codon2, const double w_path1,
                      const double w_path2);
    public:
      explicit TwoSubs(void)
      {}
      void operator() (const RedundancyCom95 * sitesObj,
                       const std::string &cod1, const std::string &cod2,
                       const Sequence::WeightingScheme2 *weights2);
      ~TwoSubs (void);
      double P0 (void) const;
      double P2S (void) const;
      double P2V (void) const;
      double P4 (void) const;
      double Q0 (void) const;
      double Q2S (void) const;
      double Q2V (void) const;
      double Q4 (void) const;
    };
}
#endif

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