HKA.hpp

/*

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 __HKA_HPP__
#define __HKA_HPP__

#include <vector>
#include <boost/tuple/tuple.hpp>

namespace Sequence
{
  struct HKAdata
  {
    mutable unsigned SA,SB; //# seg sites
    mutable double D;       // divergence
    mutable unsigned nA,nB; //sample sizes
    HKAdata();
    HKAdata(const HKAdata & d);
    HKAdata(unsigned sa,unsigned sb,double d,
            unsigned na,unsigned nb);
  };

  struct HKAresults
  {
    const std::vector< double > thetas;
    typedef boost::tuple<double,double,double,double> chisq_tuple;
    enum chisq_tuple_elements {POLY,DIV,POLYA,POLYB};
    std::vector< chisq_tuple > chisquareds;
    const double fhat;
    const double That;
    const double xsq;
    const double xsqA;
    const double xsqB;
    explicit HKAresults (const std::vector<double> & _thetas,
                         const std::vector< chisq_tuple > & _chisquareds,
                         const double & _fhat, const double & _That,
                         const double & _xsq,
                         const double & _xsqA, const double & _xsqB);
  };

  HKAresults calcHKA ( const std::vector< HKAdata > & data );
} //namespace Sequence

#endif

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