Sites.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 SITES_H
#define SITES_H

#include <string>
#include <memory>
namespace Sequence
  {
    class Seq;
    class RedundancyCom95;
    class Sites
    {
    private:
      struct SitesImpl;
      std::unique_ptr<SitesImpl> impl;
    public:
      explicit Sites ();
      explicit Sites(const Sequence::Seq & seq1,
                     const Sequence::Seq & seq2,
                     const RedundancyCom95 & sitesObj,
                     int maxdiffs = 3);
      Sites(Sites &&) = default;
      void operator()(const Sequence::Seq & seq1,
                      const Sequence::Seq & seq2,
                      const RedundancyCom95 & sitesObj,
                      int maxdiffs = 3);
      ~Sites (void);
      double L0(void) const;
      double L2S(void) const;
      double L2V(void) const;
      double L4(void) const;
    };
}
#endif