DataMatrix Class Reference

Data table. More...

#include <DataMatrix.hpp>

Inheritance diagram for DataMatrix:

Public Member Functions
	DataMatrix ()
	Default constructor. More...
	DataMatrix (unsigned int numberOfSequences, unsigned int numberOfSites)
	Standard constructor. More...
	DataMatrix (const DataMatrix &)
	Copy constructor. More...
	DataMatrix (const CharMatrix &)
	Copy constructor. More...
virtual DataMatrix &	operator= (const DataMatrix &)
	Assignment operator. More...
virtual DataMatrix &	operator= (const CharMatrix &)
	Assignment operator. More...
virtual	~DataMatrix ()
	Destructor. More...
unsigned int	numberOfSites () const
	Gets number of sites. More...
unsigned int	numberOfSequences () const
	Gets number of sequences. More...
void	set (unsigned int sequence, unsigned int site, int value)
	Sets a value of the data table. More...
int	get (unsigned int sequence, unsigned int site) const
	Gets a value from the data table. More...
int	fget (unsigned int sequence, unsigned int site) const
	Faster and unsecure version of get. More...
void	sitePosition (unsigned int site, double value)
	Sets the position of a site. More...
double	sitePosition (unsigned int site) const
	Gets the position of a site. More...
void	populationLabel (unsigned int sequence, unsigned int value)
	Sets the group label of a sequence. More...
unsigned int	populationLabel (unsigned int sequence) const
	Gets the group label of a sequence. More...
void	clear ()
	Removes all information from the object. More...
void	resize (unsigned int newNumberOfSequences, unsigned int newNumberOfSites)
	Resizes the data matrix. More...
void	shift (int minimum)
	Shifts allele value. More...
char	character (unsigned int sequence, unsigned int site) const
	Gets the character at a given position. More...

Detailed Description

Data table.

Holds a data matrix representing genotype data from simulations. Data are stored as integers, to each site is associated a position, and to each sequence is associated a group index (any integer labelling, for example, a subpopulation). Supports the CharMatrix interface with the condition that allele genotype datum is >=0 and <=9.

Constructor & Destructor Documentation

DataMatrix

(

)

Default constructor.

The data table default dimensions are {0,0}

DataMatrix	(	unsigned int	numberOfSequences,
		unsigned int	numberOfSites
	)

Standard constructor.

The data table dimensions must be given. Each cell default default is 0, and each site position is 0..

Parameters

numberOfSequences	number of lines of the data table.
numberOfSites	number of columns of the data table.

DataMatrix

(

const DataMatrix &

source

)

Copy constructor.

DataMatrix

(

const CharMatrix &

source

)

Copy constructor.

~DataMatrix ( )

virtual

Destructor.

Member Function Documentation

char character ( unsigned int  sequence, unsigned int  site  ) const

virtual

Gets the character at a given position.

An exception is generated if the allele value at this position is not >=0 and <=9. Not out-of-bound check is performed.

Implements CharMatrix.

void clear

(

)

Removes all information from the object.

int fget ( unsigned int  sequence, unsigned int  site  ) const

inline

Faster and unsecure version of get.

int get	(	unsigned int	sequence,
		unsigned int	site
	)		const

Gets a value from the data table.

unsigned int numberOfSequences ( ) const

virtual

Gets number of sequences.

Implements CharMatrix.

unsigned int numberOfSites ( ) const

virtual

Gets number of sites.

Implements CharMatrix.

DataMatrix & operator= ( const DataMatrix &  source )

virtual

Assignment operator.

DataMatrix & operator= ( const CharMatrix &  source )

virtual

Assignment operator.

void populationLabel	(	unsigned int	sequence,
		unsigned int	value
	)

Sets the group label of a sequence.

unsigned int populationLabel ( unsigned int  sequence ) const

virtual

Gets the group label of a sequence.

Implements CharMatrix.

void resize	(	unsigned int	newNumberOfSequences,
		unsigned int	newNumberOfSites
	)

Resizes the data matrix.

Parameters

newNumberOfSequences	number of sequences (rows)
newNumberOfSites	number of sites (columns)

If new values are larger, data already set is left unchanged. New data are set to zero.

void set	(	unsigned int	sequence,
		unsigned int	site,
		int	value
	)

Sets a value of the data table.

void shift

(

int

minimum

)

Shifts allele value.

Parameters

minimum

the minimum allele value.

Shifts all alleles at all sites to ensure that alleles alleles are equal to or larger than minimum. The shifting is specific to each site.

void sitePosition	(	unsigned int	site,
		double	value
	)

Sets the position of a site.

double sitePosition ( unsigned int  site ) const

virtual

Gets the position of a site.

Implements CharMatrix.

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

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