Sequence::ssh Struct Reference

Calculate nucleotide diversity from a polymorphic site. More...

#include <Sequence/PolyFunctional.hpp>

List of all members.

Public Member Functions
double	operator() (double &_ssh, const polymorphicSite &site, const bool &haveOutgroup=false, const unsigned &outgroup=0) const

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Detailed Description

Calculate nucleotide diversity from a polymorphic site.

A function object to keep track of "ssh", the sum of site heterozygosity, aka pi, aka nucleotide diversity. It can be used with std::accumulate to do calculations accross a range of sites, i.e.:

    #include <numeric>
    #include <algorithm>
    #include <iostream>
    #include <boost/bind.hpp>
    #include <Sequence/FastaExplicit.hpp>
    #include <Sequence/PolySites.hpp>
    #include <Sequence/PolySNP.hpp>
    #include <Sequence/stateCounter.hpp>
    #include <Sequence/PolyFunctional.hpp>
                 
    int main()
    {
    std::vector< Sequence::Fasta > data;
    Sequence::Alignment::GetData(data,std::cin);
    Sequence::PolySites p(data);
    //calculate nucleotide diversity using STL
    double pi = std::accumulate(p.sbegin(),p.send(),0.,ssh());
    std::cout << pi
    << '\n';
    //calculate nucleotide diversity using Sequence::PolySNP
    Sequence::PolySNP a(&p);
    std::cout << a.ThetaPi() 
    << '\n';
    }

Definition at line 153 of file PolyFunctional.hpp.

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Member Function Documentation

double Sequence::ssh::operator()	(	double &	_ssh,
		const polymorphicSite &	site,
		const bool &	haveOutgroup = false,
		const unsigned &	outgroup = 0
	)			const [inline]

Parameters:

	_ssh	a value of ssh to increment
	site	an object representing the value type of PolyTable::const_site_iterator
	haveOutgroup	true of one of the elements of site is an outgroup state, false otherwise
	outgroup	the index of the outgroup sequence in site

Definition at line 156 of file PolyFunctional.hpp.

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The documentation for this struct was generated from the following file:

• PolyFunctional.hpp