Comeron95.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 COMERON95_H
#define COMERON95_H

#include <Sequence/SeqEnums.hpp>
#include <boost/utility.hpp>

namespace Sequence
  {
  class Seq;
  class Sites;
  class RedundancyCom95;
  class WeightingScheme2;
  class WeightingScheme3;
    class Comeron95 : boost::noncopyable
    {
    private:
      bool __2wasNULL,__3wasNULL,__red_was_NULL;
      WeightingScheme2 *weights2;
      WeightingScheme3 *weights3;
      int valid, maxhits, genetic_code, weighting_scheme;
      //see Comeron '95 for a discussion of the method--will document later
      double Qs, Bs, Qa, Ba, A2S, A4, As, A2V, A0, Aa;
      double q0, q2S, q2V, q4, p0, p2S, p2V, p4;
      Sites *sites;
      const RedundancyCom95 *sitesObj;
      void diverge (const Sequence::Seq * seq1, const Sequence::Seq * seq2,
                    WeightingScheme2 *_weights2,
                    WeightingScheme3 *_weights3);
      void omega (const Sequence::Seq * seqobj1, const Sequence::Seq * seqobj2);
      double Ka, Ks;
    public:
      explicit Comeron95 (const Sequence::Seq * seqa,
                          const Sequence::Seq * seqb,
                          int max = 3, 
                          const Sequence::RedundancyCom95 * genetic_code_redundancy = NULL,
                          GeneticCodes code = UNIVERSAL,
                          WeightingScheme2 *weights2 = NULL,
                          WeightingScheme3 *weights3 = NULL)throw (Sequence::SeqException);
      ~Comeron95 (void);
      double ka (void) const;
      double ks (void) const;
      double ratio (void) const;
      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;
      double as (void) const;
      double aa (void) const;
      double bs (void) const;
      double ba (void) const;
      double L0 (void) const;
      double L2S (void) const;
      double L2V (void) const;
      double L4 (void) const;
  };
}

#endif

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