PolySNP.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 _POLYSNP_H_
#define _POLYSNP_H_

#include <vector>
#include <memory>
#include <limits>
#include <Sequence/Recombination.hpp>

namespace Sequence 
  {
    class __attribute__ ((deprecated)) PolyTable;
    struct _PolySNPImpl;
    class PolySNP 
    {
    private:
    protected:
      std::unique_ptr<_PolySNPImpl> rep;
      void DepaulisVeuilleStatistics (void) const;
      virtual void WallStats(void) const;
      //various things one needs to know to calculate the summary statistics
      double a_sub_n (void) const ;
      double a_sub_n_plus1 (void) const;
      double b_sub_n (void) const;
      double b_sub_n_plus1 (void) const;
      double c_sub_n (void) const;
      double d_sub_n (void) const;
    public:
      explicit PolySNP (const Sequence::PolyTable * data, bool haveOutgroup = false,
                        unsigned outgroup = 0, bool totMuts = true);
      PolySNP( const PolySNP & ) = delete;
      PolySNP & operator=(const PolySNP &) = delete;
      virtual ~ PolySNP (void);
      //estimators of 4Nu
      virtual double ThetaPi (void) const;                           //Nucleotide diversity (Tajima 1983)
      virtual double ThetaW (void) const;                            //Watterson's (1975) Theta
      virtual double ThetaH (void) const;                            //Theta from homozygosity (Fay and Wu 2001)
      virtual double ThetaL (void) const;                            //A variant on Fay and Wu's H
      //variances of estimators of 4Nu
      double VarPi (void) const;
      double StochasticVarPi(void) const;
      double SamplingVarPi (void) const;
      double VarThetaW (void) const;
      //calculate various numbers related to polymorphism
      unsigned NumPoly (void) const;                                 //number of polymorphic sites in data
      virtual unsigned NumMutations (void) const;                    //number of inferred mutations 
      virtual unsigned NumSingletons (void) const;                   //number of mutants at frequency 1
      virtual unsigned NumExternalMutations (void) const;            //number of derived mutations 
      //summary statistics of the site frequency spectrum
      virtual double TajimasD (void) const;                          //Tajima's (1989) D
      virtual double Hprime (const bool & likeThorntonAndolfatto = false) const;  //A normalized statistic 
                                                                    //related to Fay and Wu's H
      virtual double Dnominator (void) const;                        //Denominator of Tajima's D
      virtual double FuLiD (void) const;                             //Fu & Li's (1996) D
      virtual double FuLiF (void) const;                             //Fu & Li's (1996) F
      virtual double FuLiDStar (void) const;                         //Fu & Li's (1996) D*
      virtual double FuLiFStar (void) const;                         //Fu & Li's (1996) F*
      //summary statistics of haplotypes
      double DandVH (void) const;                                    //Depaulis & Veuille (1998) Haplotype diversity
      unsigned DandVK (void) const;                                  //Depaulis & Veuille (1998) number of haplotypes
      virtual double WallsB(void) const;                             //Jeff Wall's (1999) B  statistic
      virtual unsigned WallsBprime(void) const;                      //Jeff Wall's (1999) B' statistic
      virtual double WallsQ(void) const;                             //Jeff Wall's (1999) Q  statistic
      //recombination
      double HudsonsC (void) const;                                  //Dick Hudson's (1987) Chat = 4Nr
      virtual unsigned Minrec (void) const;                          //Hudson & Kaplan's (1985) min # of recombination events
      std::vector <PairwiseLDstats>
      Disequilibrium( const unsigned & mincount = 1,
                      const double & max_marker_distance = std::numeric_limits<double>::max()) const;                 //summary stats of pairwise LD
    };
}
#endif