A class to store linkage information. More...

#include <linkage_data.h>

Inheritance diagram for Linkage:

Collaboration diagram for Linkage:

Public Member Functions
	Linkage (const std::vector< std::string > &)

std::string	header (void) const

size_t	size (void) const
	The size of the class in bytes.

const std::string	get_file_name (void) const
	The default extension for files.

const std::string	get_table_name (void) const
	The default extension for files.

const bool	get_binary (void) const
	The default extension for files.

const std::string	sql_header (void) const
	Destination table in Db.

const std::string	sql_column_names (void) const
	Destination table in Db.

const std::string	sql_values (void) const
	Destination table in Db.

void	set_D (const float_t &)

void	set_fit (const float_t &)

void	set_null (const float_t &)

void	set_Ni (const float_t &)

void	set_p (const float_t &)

void	set_q (const float_t &)

float_t	ll (void) const

float_t	dist (void) const

float_t	D (void) const

float_t	Dmax (void) const

float_t	Dmin (void) const

float_t	Dsq (void) const

float_t	Dprime (void) const

float_t	r (void) const

float_t	rsq (void) const

float_t	adj_D (void) const

float_t	adj_Dsq (void) const

float_t	adj_Dprime (void) const

float_t	adj_r (void) const

float_t	adj_rsq (void) const

float_t	adj_Dmax (void) const

float_t	adj_Dmin (void) const

Linkage &	operator= (const Linkage &lhs)

Public Member Functions inherited from Double_indexed_data
void	write_pos (std::ostream &str) const

void	read_pos (std::istream &str)

	Double_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.

id1_t	get_abs_pos2 (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.

void	set_abs_pos2 (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 void	sql_read (std::istream &)
	Reads the values...

Data Fields
char	delim
	< Set the absolute position of the Locus. More...

Static Public Attributes
static const std::string	file_name =".lds"
	delegating the constructor ftw. More...

static const std::string	table_name ="LINKAGE"
	Destination table in Db.

static const bool	binary =false
	Returns the destination table name.

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...

Private Member Functions
void	read (std::istream &str)
	The read function must be defined in the child class.

void	write (std::ostream &str) const
	! the write function must be ? by the child class.

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

Private Attributes
id0_t	id0
	The scaffold of site X.

id1_t	id1
	The pos of site X.

float_t	p_
	freq_major site numero uno

float_t	q_
	freq_major site numero dos

float_t	D_
	the magnitude of the ld, j0

float_t	Ni_
	The number of individuals used in the calculation.

float_t	fit_
	fit statistic (thar be ld here!)

float_t	null_
	null statistic (i.e. no ld)

Static Private Attributes
static const Registration	registered =Registration(Linkage::table_name, Linkage::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 Double_indexed_data
id1_t	abs_pos1_

id1_t	abs_pos2_

Detailed Description

A class to store linkage information.

Many of these data classes need to have things moved over to static functions. The problem popped up because I just copied over all the output people wanted into values in the class, but really a lot of this is just simple transformation of other representions of the data. If you are reading this may god have mercy on your soul, because I really have no idea why you would choose to read the comments on what is doubtlessly a dead project. please enjoy this link to a Kraftwork video to see if Doxygen automatically incorporates HTML tags right (IT DOES!). Listening to Kraftwerk improves your coding skillz. It's totally a fact. I'll start fixing allele stat now.

Member Function Documentation

Linkage& Linkage::operator= ( const Linkage & lhs )

inline

< The scaffold of site X

< The pos of site X

< freq_major site numero uno

< freq_major site numero dos

< the magnitude of the ld, j0

< The number of individuals used in the calculation

< fit statistic (thar be ld here!)

< null statistic (i.e. no ld)

Field Documentation

char Linkage::delim

< Set the absolute position of the Locus.

the delimiter used when reading/writing the class in text mode.

const std::string Linkage::file_name =".lds"

static

delegating the constructor ftw.

The default extension for files.

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

mapgd_0.4/data_types/linkage_data.h
mapgd_0.4/data_types/linkage_data.cc

Public Member Functions

Data Fields

Static Public Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

Field Documentation