BaseDiversity Class Reference

Base class of diversity classes. More...

#include <BaseDiversity.hpp>

Inheritance diagram for BaseDiversity:

Public Member Functions
	BaseDiversity ()
	Constructor. More...
virtual	~BaseDiversity ()
	Destructor. More...
virtual void	reserve (unsigned int numberOfSites)
	Reserve sufficient memory for a given number of polymorphic sites. More...
const SitePolymorphism *	get_site (unsigned int index) const
	Gets a site.
unsigned int	get_position (unsigned int index) const
	Gets a site position.
virtual void	reset ()
	Clears and re-initializes object.

Static Public Attributes
static const std::string	dnaMapping = "ACGT MRWSYKBDHVN?-"
	Predefined mapping string for DNA data. More...
static const std::string	rnaMapping = "ACGU MRWSYKBDHVN?-"
	Predefined mapping string for RNA data. More...
static const std::string	aaMapping = "GALMFWKQESPVICYHRNDT X-"
	Predefined mapping string for amino acid data. More...

Protected Member Functions
virtual void	init ()
virtual void	clear ()
void	importSites (CharMatrix &data, bool allowMultipleMutations, double minimumExploitableData, unsigned int ignoreFrequency, std::string characterMapping, bool useZeroAsAncestral, bool ignoreOutgroup)
void	analyzeSite (CharMatrix &data, unsigned int index, double maxMissingData, bool ignoreOutgroup)
unsigned int	getPopIndex (unsigned int label) const

Protected Attributes
SitePolymorphism **	v_sites
bool *	v_orientables
unsigned int *	v_sitePositions
unsigned int	v_reserved
unsigned int	v_ns
unsigned int	v_S
unsigned int	v_So
unsigned int	v_eta
double	v_nseff
unsigned int	v_lseff
double	v_nseffo
unsigned int	v_lseffo
unsigned int	v_npop
unsigned int *	v_popLabel
bool	p_allowMultipleMutations
double	p_minimumExploitableData
std::string	p_characterMapping
unsigned int	p_pos_sep_mapping
bool	p_useZeroAsAncestral
unsigned int	p_ignoreFrequency

Detailed Description

Base class of diversity classes.

Mutualizes the analysis of polymorphic sites through the method importSites() and related accessors.

Constructor & Destructor Documentation

BaseDiversity

(

)

Constructor.

~BaseDiversity ( )

virtual

Destructor.

Member Function Documentation

void reserve ( unsigned int  numberOfSites )

virtual

Reserve sufficient memory for a given number of polymorphic sites.

This method makes importSite function faster when you already know how many polymorphic sites to expect, since the necessary memory will be allocated prior the screening of data. It is possible to use reserve() even if with a number of sites that is not matching what importSites() will find.

Parameters

numberOfSites

a strictly positive integer.

Member Data Documentation

const std::string aaMapping = "GALMFWKQESPVICYHRNDT X-"

static

Predefined mapping string for amino acid data.

const std::string dnaMapping = "ACGT MRWSYKBDHVN?-"

static

Predefined mapping string for DNA data.

const std::string rnaMapping = "ACGU MRWSYKBDHVN?-"

static

Predefined mapping string for RNA data.

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

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