Pooled_data Class Reference

Information genereated from pooled data. More...

#include <pooled_data.h>

Inheritance diagram for Pooled_data:

Collaboration diagram for Pooled_data:

Public Member Functions
	Pooled_data (const std::vector< std::string > &)
Allele	to_allele (const size_t &)
void	set_sample_names (const std::vector< std::string > &)
Pooled_data &	operator= (const Pooled_data &)
	use the = operator to assign Pooled_data.
std::string	header (void) const
size_t	size (void) const
	The size of the class in bytes.
const std::string	get_file_name () const
const std::string	get_table_name () const
void	write (std::ostream &) const
	used to write Allele. Inherits << from Data
void	read (std::istream &)
	used to read Allele. Inherits >> from Data
const bool	get_binary () const
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
char	delim
	the delimiter used when reading/writing the class in text mode.
Base	major
Base	minor
Base	ref
count_t	coverage
float_t	error
std::vector< std::string >	names_
	the sample names.
std::vector< float_t >	p
	a vector of allele frequencies
std::vector< float_t >	cov
	a vector of coverage
std::vector< float_t >	polyll
	a vector of polymorphic log likelihoods
std::vector< float_t >	fixedll
	a vector of fixed log likelihoods

Static Public Attributes
static const std::string	file_name =".pol"
	The dafualt extention for files.
static const std::string	table_name ="POOL"
	Destination table in Db.
static const bool	binary =false
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)

Static Private Attributes
static const Registration	registered =Registration(Pooled_data::table_name, Pooled_data::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

Information genereated from pooled data.

This is information generated from pooled population data (i.e. mash everybody up together and sequence the slurry).

Member Function Documentation

Allele Pooled_data::to_allele

(

const size_t &

x

)

< the scaffold identifer of the allele.

< frequency of major allele.

< idenity of ref allele.

< idenity of minor allele.

< idenity major allele.

< idenity of error1

< idenity of error2.

< ml error rate.

< population coverage.

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

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