RedundancyCom95.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 REDCOM95_H
#define REDCOM95_H

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

using Sequence::GeneticCodes;

namespace Sequence
{
  struct RedundancyCom95impl;
  class RedundancyCom95
  {
  private:
    std::unique_ptr<RedundancyCom95impl> impl;
  public:
    explicit RedundancyCom95 (Sequence::GeneticCodes genetic_code = GeneticCodes::UNIVERSAL);
    RedundancyCom95(RedundancyCom95 &&)=default;
    ~RedundancyCom95(void);
    //counting routines, return values from private matrices of same name
    double FirstNon (const std::string &codon) const;
    double First2S (const std::string &codon) const;
    double First2V (const std::string &codon) const;
    double ThirdNon (const std::string &codon) const;
    double ThirdFour (const std::string &codon) const;
    double Third2S (const std::string &codon) const;
    double Third2V (const std::string &codon) const;
    double L0_vals (const std::string &codon) const;
    double L2S_vals (const std::string &codon) const;
    double L2V_vals (const std::string &codon) const;
    double L4_vals (const std::string &codon) const;
    GeneticCodes gencode()const;
  };
}

#endif