An interface that transforms pairs of name and position keys into record numbers. More...

#include <file_index.h>

Inheritance diagram for File_index:

Collaboration diagram for File_index:

Public Member Functions
	File_index (std::vector< std::string >)

bool	bianary (void) const

id1_off_t	get_offset (const std::string &, const id1_t &) const
	returns the number of rows until a row with id0, id1.

id1_t	get_abs_pos (const std::string &, const id1_t &) const
	returns the record number corresponding to id0, id1.

id1_t	get_abs_pos (const id0_t &, const id1_t &) const
	returns the record number corresponding to id0, id1.

id0_t	get_id0 (const std::string &) const
	returns the id0 corresponding to string.

id0_t	get_id0 (const id1_t &) const
	returns the id0 corresponding to rowid.

id1_t	get_id1 (const id1_t &) const
	returns the id1 corresponding rowid.

std::string	get_string (const id0_t &) const
	returns the string corresponding to id0.

void	set_string (const id0_t &, const std::string &)
	sets the string corresponding to id0.

void	set_size (const std::string &, const id1_t &)
	set the number of rows (bp) in the scaffold with string id id0.

void	set_size (const id0_t &, const id1_t &)
	set the number of rows (bp) in the scaffold with numeric id id0.

void	set_last_size (const id1_t &)
	set the number of rows in the most recently read scaffold.

void	set_next_size (const id1_t &)
	set the number of rows in the next scaffold to be read.

const std::vector< std::string >	get_names (void) const
	get a vector containing the name of each scaffold.

size_t	get_names_size (void) const
	get the length of the vector containing the name of each scaffold.

const std::vector< id1_t >	get_sizes (void) const
	get a vector containing the sizes of each scaffold.

id1_t	get_size (const id0_t &) const
	get the size of scaffold blarg.

id1_t	get_size (const std::string &) const
	get the size of scaffold blarg.

id1_t	get_cumulative_size (const id0_t &) const
	get the sum of all size less than or equal to id0.

id1_t	get_cumulative_size (const std::string &) const
	get the sum of all size less than or equal to id0.

id1_t	get_reference_size (void) const
	get the sum of all size.

id1_t	get_last_size (void)
	get the size of the last scaffold which has been read from. returns map_file::noid on error.

id1_t	get_next_size (void)
	get the size of the next scaffold to be read. returns map_file::noid on error.

int	read_index (std::istream &)
	read in a File_index (strictly text mode).

std::istream &	from_sam_header (std::istream &)
	read in a file index from a sam header.

int	add_id (const std::string &, const id1_t &)
	add an new id at the end of the index.

int	write_index (std::ostream &)
	write out a File_index

File_index &	operator= (const File_index &)
	not implemented. Do not use.

bool	is_open (void) const

std::string	header (void) const

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

void	write (std::ostream &) const
	use the << operator to write File_index.

void	read (std::istream &)
	use the >> operator to read File_index.

const std::string	get_file_name () const

const std::string	get_table_name () const

const bool	get_binary () const

const std::string	sql_header (void) const
	returns the string needed to create an SQL table.

const std::string	sql_column_names (void) const
	returns the column names (SQL).

const std::string	sql_values (void) const
	returns the column values (SQL).

void	sql_read (std::istream &) override
	binds data to sqlite3_stmt.

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

Static Public Attributes
static const std::string	file_name =".idx"

static const std::string	table_name ="REGIONS"

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...

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

Private Attributes
std::map< std::string, id0_t >	id0_str_
	a hash table to store pairs of strings and the id representing them.

std::vector< std::string >	id0_
	the keys to the hash table id0_str_.

std::vector< id1_t >	size_
	the number of bp per scaffold.

std::vector< id1_t >	cumulative_size_
	the cumulative number of bp per scaffold.

id0_t	last_id0_
	the last numerical id returned by an decodeid0 quarry. Initialized to 0-1.

std::string	last_id0_str_
	the last string id returned by an decodeid0 quarry. Initialized to "".

bool	open_
	TODO: Is this ever used?

size_t	byte_size_

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

Detailed Description

An interface that transforms pairs of name and position keys into record numbers.

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

mapgd_0.4/data_types/file_index.h
mapgd_0.4/data_types/file_index.cc

Public Member Functions

Static Public Attributes

Static Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description