Inheritance diagram for State:

Collaboration diagram for State:

Public Member Functions
	State ()
	constructor needed by map_file. String should be column names.

	State (const std::vector< std::string > &)

	State (const State &rhs)

	State (State &&rhs)

State &	operator= (const State &rhs)

	State (const uint32_t &)

	State (const uint32_t &, const uint32_t &, const uint32_t &)

void	set_k (const uint8_t &)

uint8_t	get_k (void) const

void	uncompress (uint32_t a, uint32_t b)

void	uncompress_inplace (uint32_t a, uint32_t b)

void	uncompress (uint32_t a, uint32_t b, const uint32_t &k)

void	uncompress (uint32_t a, uint32_t b, State_stream &) const

void	compress (const uint32_t a, const uint32_t b)

void	compress_inplace (const uint32_t a, const uint32_t b)

void	uncompress (uint32_t a, uint32_t b, uint32_t c, uint32_t d)

void	uncompress_inplace (uint32_t a, uint32_t b, uint32_t c, uint32_t d)

void	uncompress (uint32_t a, uint32_t b, uint32_t c, uint32_t d, const uint32_t &k)

void	uncompress (uint32_t a, uint32_t b, uint32_t c, uint32_t d, State_stream &) const

void	compress (const uint32_t a, const uint32_t b, const uint32_t c, const uint32_t d)

void	compress_inplace (const uint32_t a, const uint32_t b, const uint32_t c, const uint32_t d)

void	transpose (void)

void	cache (void)

void	rewind (void)

void	advance (void)

void	finalize (void)

void	clear (void)

const std::string	get_file_name () const

const std::string	get_table_name () const

const size_t &	sample_size (void) const

const size_t &	genome_size (void) const

void	set_streaming (const bool &b)

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 defined in the child class.

void	read_binary (std::istream &str)

void	write_binary (std::ostream &str) const

std::string	header () const

void	set_stream (State_stream &) const

size_t	get_free (void) const

double	compression_ratio (void) const

size_t	buffer_size (void) const

bool	empty (void) const

bool	cached (void) const

void	swap (State &rhs)

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 bool	indexed () const

virtual const bool	get_binary () const

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...

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

Static Public Attributes
static const std::string	file_name =".bgt"
	The dafualt extention for files.

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

static const bool	binary =true
	Destination table in Db.

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	increase_buffer_ (void)

void	uncompress_ (char &, uint32_t &, uint32_t *&) const

void	compress_ (char &, char &, const uint32_t a, const uint32_t b) const

void	uncompress_ (char *&) const

void	compress_ (char &, char &) const

void	set_private_ (const State &rhs)

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

Private Attributes
size_t	size_

size_t	sites_

size_t	cached_sites_

size_t	block_size_

size_t	lz4_buffer_size_

bool	streaming_

bool	cached_

bool	transposed_

bool	masked_

uint8_t	k_

char *	lz4_ptr_

char *	lz4_start_

char *	lz4_end_

char *	lz4_last_

char *	temp_lz4_ptr_

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

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

mapgd_0.4/data_types/state.h
mapgd_0.4/data_conversion/state.cc

Public Member Functions

Static Public Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members