Computes diversity statistics using third-party library Bio++. More...

#include <BppDiversity.hpp>

Public Member Functions
	BppDiversity ()
	Builds an object. More...

virtual	~BppDiversity ()
	Destroys an object. More...

void	load (Align &align, unsigned int dataType=1)
	Performs polymorphism analysis using Bio++ tools. More...

bool	hasOutgroup () const
	true if an ougroup was available

unsigned int	S () const
	Number of polymorphic sites.

unsigned int	Sinf () const
	Number of parsimony informative sites.

unsigned int	Ssin () const
	Number of singleton sites.

unsigned int	eta () const
	Minimal number of mutations.

unsigned int	Sext () const
	Mutations on external branches (if an outgroup was used)

double	He () const
	Heterozygosity.

double	He2 () const
	Squared heterozygosity.

double	tW () const
	Watterson theta.

double	T83 () const
	Tajima theta.

unsigned int	K () const
	Number of haplotypes.

double	H () const
	Haplotypic diversity.

unsigned int	Ti () const
	Number of transitions.

unsigned int	Tv () const
	Number of transversions.

double	TiTv () const
	Transition/transversion ratio.

unsigned int	nstop () const
	Number of codon sites with a stop codon (if coding)

unsigned int	ncodon1mut () const
	Number of codon sites with one change (if coding)

unsigned int	nsyn () const
	Number of codon sites with a synonymous change (if coding)

double	tWS () const
	Synonymous Watterson theta (if coding)

double	tWNS () const
	Non-synonymous Watterson theta (if coding)

double	PiS () const
	Synonymous Pi (if coding)

double	PiNS () const
	Non-synonymous Pi (if coding)

double	Ssites () const
	Average number of synonymous sites (if coding)

double	NSsites () const
	Average number of non-synonymous sites (if coding)

unsigned int	SS () const
	Aynonymous polymorphic sites (if coding)

unsigned int	SNS () const
	Non-synonymous polymorphic sites (if coding)

const std::vector< unsigned int > &	MK () const
	McDonald-Kreitman test table, as a vector (if coding + outgroup)

double	NI () const
	Neutrality index (if coding + outgroup)

double	D () const
	Tajima's D.

double	Deta () const
	Tajima's D computed with eta instead of S.

double	Dfl () const
	Fu and Li's D (if an outgroup was used)

double	Dflstar () const
	Fu and Li's D*.

double	F () const
	Fu's F (if an outgroup was used)

double	Fstar () const
	Fu's F*.

double	rhoH () const
	Hudson's estimator of rho (recombination rate)

Protected Member Functions
void	reset ()

void	computeSingle (bpp::AlignedSequenceContainer &align)

void	computeDouble (bpp::AlignedSequenceContainer &ingroup, bpp::AlignedSequenceContainer &outgroup)

Protected Attributes
bpp::DNA	dna

bpp::GeneticCode *	p_code

bpp::StandardGeneticCode *	p_code4

bpp::VertebrateMitochondrialGeneticCode *	p_code5

bpp::InvertebrateMitochondrialGeneticCode *	p_code6

bpp::EchinodermMitochondrialGeneticCode *	p_code7

unsigned int	v_Ss

unsigned int	v_Sinf

unsigned int	v_Ssin

unsigned int	v_eta

unsigned int	v_Sext

double	v_He

double	v_He2

double	v_tW

double	v_T83

unsigned int	v_K

double	v_H

unsigned int	v_Ti

unsigned int	v_Tv

double	v_TiTv

unsigned int	v_nstop

unsigned int	v_ncodon1mut

unsigned int	v_nsyn

double	v_tWS

double	v_tWNS

double	v_PiS

double	v_PiNS

double	v_Ssites

double	v_NSsites

unsigned int	v_SS

unsigned int	v_SNS

std::vector< unsigned int >	v_MK

double	v_NI

double	v_D

double	v_Deta

double	v_Dfl

double	v_Dflstar

double	v_F

double	v_Fstar

double	v_rhoH

bool	b_loaded

bool	b_outgroup

bool	b_coding

Detailed Description

Computes diversity statistics using third-party library Bio++.

Uses the PopGen library of Bio++ and computes statistics of diversity.

Constructor & Destructor Documentation

BppDiversity ( )

Builds an object.

~BppDiversity ( )

virtual

Destroys an object.

Member Function Documentation

void load	(	Align &	align,
		unsigned int	dataType = `1`
	)

Performs polymorphism analysis using Bio++ tools.

Automatically computes statistics. Some statistics require the presence of outgroup sequences (with group labels 999) in the passed object, and some statistics are computed only if the data type is >=4. (Some both.) Calling this method clears all previous data in the instance (including if less statistics can be computed with the new alignment compared with the previous one).

Parameters

align	an alignment object (Align class). The presence of outgroup sequences will be automatically detected based on the group member of the passed object. Only label 999 will be considered and use as outgroup for statistics were it is useful. If several outgroups are used, they will all be passed to C++ tools.
dataType	an integer what kind of data must be analyzed: 1 for DNA 2 for RNA 3 for protein sequences 4 for standard codons 5 for vertebrate mitochondrial codons 6 for invertebrate mitochondrial codons 7 for echinoderm mitochondrial codons Other values will result in an exception.

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

/home/stephane/Documents/devel/egglib2/egglib-cpp/BppDiversity.hpp
/home/stephane/Documents/devel/egglib2/egglib-cpp/BppDiversity.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation