Sequence::nmuts< counter > Class Template Reference

Calculate the number of mutations at a polymorphic site. More...

#include <Sequence/PolyFunctional.hpp>

List of all members.

Public Types
typedef unsigned	result_type
Public Member Functions
unsigned	operator() (unsigned &nm, const polymorphicSite &site, const bool &haveOutgroup=false, const unsigned &outgroup=0) const

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Detailed Description

template<typename counter>
class Sequence::nmuts< counter >

Calculate the number of mutations at a polymorphic site.

Function object to keep track of the number of mutations in a range of polymorphic sites. The template argument specifies the counting behavior, i.e. countStates or countDerivedStates. It is designed to be used with std::accumulate, and will need boost::bind for the necessary arguments

    #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 # mutations via algorithm
    unsigned nm = std::accumulate(p.sbegin(),p.send(),0u,
    boost::bind(nmuts<countStates>(),_1,_2,
    false,0));
    std::cout << nm
    << '\n';
    //for comparison, use Sequence::PolySNP
    Sequence::PolySNP a(&p);
    std::cout << a.NumMutations() << '\n';
    }

Definition at line 225 of file PolyFunctional.hpp.

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Member Typedef Documentation

template<typename counter >

typedef unsigned Sequence::nmuts< counter >::result_type

allows boost::bind to be used in a simple way

Definition at line 230 of file PolyFunctional.hpp.

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Member Function Documentation

template<typename counter >

unsigned Sequence::nmuts< counter >::operator()	(	unsigned &	nm,
		const polymorphicSite &	site,
		const bool &	haveOutgroup = false,
		const unsigned &	outgroup = 0
	)			const [inline]

Parameters:

	nm	a value of nmuts 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 231 of file PolyFunctional.hpp.

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

• PolyFunctional.hpp