SitePolymorphism Class Reference

Implements diversity analysis at the site level. More...

#include <SitePolymorphism.hpp>

Public Member Functions
	SitePolymorphism ()
	Builds an object. More...
	SitePolymorphism (unsigned int npop)
	Builds an object. More...
virtual	~SitePolymorphism ()
	Destroys an object. More...
	SitePolymorphism (const SitePolymorphism &source)
	Copy constructor. More...
SitePolymorphism &	operator= (const SitePolymorphism &source)
	Assignment operator. More...
void	numberOfPopulations (unsigned int npop)
	Sets the number of populations. More...
void	load (unsigned int populationIndex, char character)
	Adds a character. More...
void	outgroup (char state)
	Loads outgroup state. More...
unsigned int	numberOfAlleles () const
	Number of different alleles. More...
char	allele (unsigned int index) const
	Gets an allele (unsecure) More...
unsigned int	alleleFrequency (unsigned int alleleIndex) const
	Gets a frequency (unsecure) More...
unsigned int	alleleFrequency (unsigned int popIndex, unsigned int alleleIndex) const
	Gets the frequency of an allele in one pop (unsecure) More...
unsigned int	derivedAlleleFrequency () const
	Sums the frequency of derived allele(s) More...
unsigned int	ns () const
	Number of sequences that were analyzed. More...
unsigned int	ns (unsigned int popIndex) const
	Gets the number of analyzed sequences for a population. More...
bool	isOrientable () const
	Checks if the site can be oriented. More...
bool	isPolymorphic (unsigned int popIndex) const
bool	hasSpecificAllele (unsigned int popIndex, bool restrictToDerived) const
bool	haveFixedDifference (unsigned int pop1, unsigned int pop2) const
bool	haveCommonAllele (unsigned int pop1, unsigned int pop2) const
bool	haveSharedAllele (unsigned int pop1, unsigned int pop2) const

Protected Member Functions
void	init ()
void	clear ()
void	copy (const SitePolymorphism &site)

Protected Attributes
unsigned int	m_numberOfPopulations
unsigned int	m_numberOfStates
char *	m_states
unsigned int **	m_frequencies
unsigned int	m_numberOfOutgroups
char *	m_outgroups
unsigned int	m_ns
unsigned int *	m_pop_ns
bool	m_cache_orientable

Detailed Description

Implements diversity analysis at the site level.

Data are loaded along with a population index. It is necessary to set the number of populations prior to use.

Outgroup sequence must be loaded separetedly. There can be any number of outgroups, but they must be all consistent otherwise the site will be considered as not orientable.

Constructor & Destructor Documentation

SitePolymorphism

(

)

Builds an object.

SitePolymorphism

(

unsigned int

npop

)

Builds an object.

Parameters

npop	number of populations

~SitePolymorphism ( )

virtual

Destroys an object.

SitePolymorphism

(

const SitePolymorphism &

source

)

Copy constructor.

Member Function Documentation

char allele

(

unsigned int

index

)

const

Gets an allele (unsecure)

Assumes that the index provided lies in the valid range

unsigned int alleleFrequency

(

unsigned int

alleleIndex

)

const

Gets a frequency (unsecure)

The sum of of frequencies of the allele over populations is computed. Not out-of-bounds check is performed.

unsigned int alleleFrequency	(	unsigned int	popIndex,
		unsigned int	alleleIndex
	)		const

Gets the frequency of an allele in one pop (unsecure)

The frequency of the allele in the given population is returned. Not out-of-bounds check is performed.

unsigned int derivedAlleleFrequency

(

)

const

Sums the frequency of derived allele(s)

This method assumes that the site is orientable. It will use as outgroup the first outgroup character entered, assuming at least one was entered and that all (if more than one) were identical.

bool isOrientable

(

)

const

Checks if the site can be oriented.

Returns true if at least one outgroup datum has been loaded, if all outgroup data are identical (regardless of their value) and if the outgroup allele is one of the allele in the sample.

void load	(	unsigned int	populationIndex,
		char	character
	)

Adds a character.

Parameters

populationIndex	the index of the population from which is sampled this character (do not use "population label").
character	the character value (it is assumed it represents a valid character.

unsigned int ns

(

)

const

Number of sequences that were analyzed.

unsigned int ns

(

unsigned int

popIndex

)

const

Gets the number of analyzed sequences for a population.

No out-of-bound check is performed

unsigned int numberOfAlleles

(

)

const

Number of different alleles.

void numberOfPopulations

(

unsigned int

npop

)

Sets the number of populations.

NOTE THAT all previous data is lost.

SitePolymorphism & operator=

(

const SitePolymorphism &

source

)

Assignment operator.

void outgroup

(

char

state

)

Loads outgroup state.

There can be any number of outgroup states. Only characters that are considered as valid (whatever the list is) should be loaded.

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

• /home/stephane/Documents/devel/egglib2/egglib-cpp/SitePolymorphism.hpp
• /home/stephane/Documents/devel/egglib2/egglib-cpp/SitePolymorphism.cpp