Base_file Class Reference

A templet which stores data associated with specific locations in a genome. More...

#include <map_file.h>

Inheritance diagram for Base_file:

Collaboration diagram for Base_file:

Public Member Functions
const std::fstream::openmode &	openmode ()
	returns the open mode.
const std::string &	filename ()
	returns the filename.
	Base_file ()
	returns the concatenated flag. More...
void	open_no_extention (const char *, const std::ios::openmode &)
	The function that opens a indexed_file (if file).
void	open (const std::ios::openmode &)
	Opens a Base_file to the cin/cout.
void	open (std::iostream *, const std::ios_base::openmode &)
	Opens a Base_file to an istream.
void	open (std::istream *, const std::ios_base::openmode &)
	Opens a Base_file to an istream.
void	open (std::ostream *, const std::ios_base::openmode &)
	Opens a Base_file to an istream.
std::istream *	get_in (void)
	returns the istream.
std::ostream *	get_out (void)
	returns the ostream.
void	close (void)
	Close iostreams, writes tail, etc.
void	close_table (void)
	Ends table w/o closing iostreams.
bool	is_open (void) const
	Returns true iff Base_file is open.
bool	table_is_open (void) const
	Returns true iff a table is open in Base_file.
bool	binary (void) const
	Returns true iff a table is open in binary mode.
Data *	read_header (void)
	Returns a pointer to a new instance of the derived data class.
void	write_header (const Data *)
void	write_header (const File_index &, const Data *)
Base_file &	read (Data *)
	Reads from the istream.
Base_file &	read (File_index &, Indexed_data *)
Base_file &	write (const Data *)
	Writes to the ostream.
Base_file &	write (File_index &, const Indexed_data *)
void	seek (const std::streampos &pos)
	sets in and out (for reading and writing) to position pos.
void	seekg (const std::streampos &pos)
	sets in (for reading) to position pos.
void	seekp (const std::streampos &pos)
	sets out (for writing) to position pos.
void	seek (std::streampos pos, std::ios_base::seekdir way)
	TODO.
void	seekg (std::streampos off, std::ios_base::seekdir way)
	TODO.
void	seekp (std::streampos off, std::ios_base::seekdir way)
	TODO.
std::streampos	tellp (void)
	Tells streampos of out (writing)
std::streampos	tellg (void)
	Tells streampos of in (reading)
void	set_delim (const char &)
	Sets the delimiter that separates columns. Only used in text mode.
const char &	get_delim (void) const
	Gets the delimiter that separates columns. Only used in text mode.
size_t	size (void) const
	Returns the number of rows in the file. More...
bool	eof (void)
bool	indexed (void) const
bool	concatenated (void)
bool	check_concatenated (void)
bool	check_compressed (void)

Protected Attributes
bool	open_
	indicates whether the iostream opened succesfully
bool	table_open_
	indicates whether the header has been read successfully
bool	concatenated_
	indicates whether multiple tables are included in the file
bool	compressed_
	indicates whether the input/output stream is compressed.
char	delim_column_
	The delimiter which separates columns.
bool	read_
	File is open for reading.
bool	write_
	File is open for writing.
bool	binary_
	Binary mode flag.
bool	try_binary_
	Attempt to set binary mode flag.
bool	indexed_
	Indexed mode flag.
std::istream *	in_
	All data is read from in.
std::ostream *	out_
	All data is written is written to out.
Tmp_buffer	buffer_
	a buffer which can be rewound.
std::fstream	file_
	The file to read data from.
igzstream	gzin_
	compressed istream.
ogzstream	gzout_
	compressed ostream.
std::ios::openmode	openmode_
	stores information about the mode in which the file was opened.
std::string	filename_
	The name of the file if opened.

Private Member Functions
void	write_binary (const Data *)
	Write in binary mode.
void	write_binary (const Indexed_data *)
	Write in binary mode.
void	write_text (const Data *)
void	write_text (File_index &, const Indexed_data *)

Detailed Description

A templet which stores data associated with specific locations in a genome.

An indexed file is a table with columns specified by the data types stored in the table, which must store a pair of IDs retrieved by the get_id0() and get_id1() member functions. Additionally, data types must return a name for the table in the database where the data may be stored with member function table_name(), and must name the columns of the table with canonical data types listed in the file ?. This allows data to easily be transfered into and out of a database. Finally...

Constructor & Destructor Documentation

Base_file::Base_file

(

void

)

returns the concatenated flag.

default constructor

Member Function Documentation

size_t Base_file::size

(

void

)

const

Returns the number of rows in the file.

Returns 0 if unknown. Note, the number of rows in the file will in general not be equal to the final position in the file_index, since many position will be skipped. .

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

• mapgd_0.4/io/map_file.h
• mapgd_0.4/io/map_file.cc