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/WeightingSchemes.hpp>
#include <Sequence/SeqEnums.hpp>
#include <Sequence/Seq.hpp>
#include <array>
#include <memory>

namespace Sequence
  {
    using Com95_t = std::array<double,19>;
    class Comeron95 
    {
    private:
      struct Com95impl;
      std::unique_ptr<Com95impl> impl;
    public:
      explicit Comeron95( GeneticCodes code = GeneticCodes::UNIVERSAL );
      Comeron95( const Comeron95 & ) = delete;
      Comeron95 & operator=(const Comeron95 & ) = delete;
      ~Comeron95();
      Com95_t operator()(const Sequence::Seq & seqa,
                         const Sequence::Seq & seqb,
                         int maxdiffs = 3);
      Com95_t operator()(const Sequence::Seq & seqa,
                         const Sequence::Seq & seqb,
                         const WeightingScheme2 *weights2,
                         const WeightingScheme3 *weights3,
                         int maxdiffs = 3);
  };
}

#endif