Population Class Reference

Population genotypes. More...

#include <population.h>

Inheritance diagram for Population:

Collaboration diagram for Population:

Public Member Functions
	Population ()
	simple constructor.
	Population (const Sample_name &)
	constructor using sample names. More...
	Population (const std::vector< std::string > &)
	constructor needed by map_file. String should be coloumn names.
	Population (const Population &)
	constructor using a Population_Genotype
	~Population ()
	destructor.
size_t	size () const
	Returns the number of samples. More...
void	add (const Genotype &likelihood)
	append a sample to the likelihood.
void	add (const float_t &lMM, const float_t &lMm, const float_t &lmm, const count_t &N)
	append a sample to the likelihood.
void	clear ()
	clear likelihoods.
std::string	header (void) const
	print header.
const bool	get_binary () const
std::vector< std::string >	get_sample_names (void) const
void	set_sample_names (const std::vector< std::string > &sample_names)
	names of the samples sequenced.
Population &	operator= (const Population &)
	names of the samples sequenced. More...
void	write (std::ostream &) const
	The write function must be defined in the child class.
void	read (std::istream &)
	The read function must be defined in the child class.
const std::string	get_file_name () const
const std::string	get_table_name () const
void	write_binary (std::ostream &) const
void	read_binary (std::istream &)
Public Member Functions inherited from Indexed_data
void	write_pos (std::ostream &str) const
void	read_pos (std::istream &str)
	Indexed_data (std::vector< std::string > &)
id1_t	get_abs_pos (void) const
	Indexed data needs to associate each datum with a position in the genome.
void	set_abs_pos (const id1_t &)
	Indexed data needs to associate each datum with a position in the genome.
const bool	indexed () const
Public Member Functions inherited from Data
void	read_binary (std::istream &str)
void	write_binary (std::ostream &str) const
	Data (std::vector< std::string > &)
virtual const std::string	sql_header (void) const
	Return the names of the columns, along with variable type.
virtual const std::string	sql_column_names (void) const
	Return the names of the columns.
virtual const std::string	sql_values (void) const
	Return the values to be placed in columns.
virtual void	sql_read (std::istream &)
	Reads the values...

Data Fields
std::vector< Genotype >	likelihoods
	Genotypic likelihood.
gt_t	major
	identity of the major allele
gt_t	minor
	identity of the minor allele
float_t	m
	minor allele frequency
float_t	f
	departure from HWE

Static Public Attributes
static const std::string	table_name ="GENOTYPES"
	destination table in Db.
static const std::string	file_name =".gcf"
	defualt file extention.
static const bool	binary =true
Static Public Attributes inherited from Data
static const std::string	file_name =".txt"
	The read function must be defined in the child class. More...
static const std::string	table_name ="NONE"
	The read function must be defined in the child class. More...

Static Private Member Functions
static Data *	create (const std::vector< std::string > &Columns)

Private Attributes
std::vector< Genotype >::iterator	igl_
	an iterator to allow us to iterate over the likelihoods.
std::vector< std::string >	sample_names_
	a vector of sample names.

Static Private Attributes
static const Registration	registered =Registration(Population::table_name, Population::create)

Additional Inherited Members
Static Public Member Functions inherited from Data
static Data *	new_from_str (const std::string &, const std::vector< std::string > &)
	Constructs an instance of the class Registered w/ string.
Protected Attributes inherited from Indexed_data
id1_t	abs_pos_

Detailed Description

Population genotypes.

Constructor & Destructor Documentation

Population::Population

(

const Sample_name &

names

)

constructor using sample names.

constuctor w/ initial values.

Member Function Documentation

Population & Population::operator=

(

const Population &

rhs

)

names of the samples sequenced.

< a vector of sample names.

< genotypic likelihood

< an iterator to allow us to iterate over the likelihoods.

< identity of the major allele

< identity of the minor allele

< minor allele frequency

< minor allele frequency

< scaffold number

size_t Population::size ( void  ) const

virtual

Returns the number of samples.

return size of Population if Population is set, 0 otherwise

Reimplemented from Data.

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

• mapgd_0.4/data_types/population.h
• mapgd_0.4/data_types/population.cc