PolySIM.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 _POLYSIM_H_
#define _POLYSIM_H_

#include <Sequence/PolySNP.hpp>

namespace Sequence
  {
  class SimData;
  class __attribute__ ((deprecated)) PolySIM : public PolySNP
    {
    private:
      //functions for Hudson's Partition Test
      int poly (int *subslist,  const int & ss,
                const int & subsize, const int & subss, int *seq) const;
      int nextsample (int *subslist, const int &  subsize, const int & nsam, int seq) const;
    protected:
      void WallStats(void) const;
    public:
      explicit PolySIM (const Sequence::SimData * data);
      virtual ~ PolySIM(void);
      //estimators of 4Nu
      double ThetaPi (void) const;
      double ThetaW (void) const;
      double ThetaH (void) const;
      double ThetaL (void) const;

      //calculate various numbers related to polymorphism
      unsigned NumMutations (void) const;
      unsigned NumSingletons (void) const;
      unsigned NumExternalMutations (void) const;
      //summary statistics of the site frequency spectrum
      double TajimasD (void) const;
      double Hprime (const bool & likeThorntonAndolfatto = false) const;
      double Dnominator (void) const;
      double FuLiD (void) const;
      double FuLiF (void) const;
      double FuLiDStar (void) const;
      double FuLiFStar (void) const;
      double WallsB(void) const;
      unsigned WallsBprime(void) const;
      double WallsQ(void) const;
      //Hudson's Haplotype Partition Test
      int HudsonsHaplotypeTest (const int & subsize,const int & subss) const;

      //recombination
      unsigned Minrec (void) const;
    };
}
#endif