utility::io Namespace Reference

Namespaces
	ic
	mpi_stream
	oc

Classes
class	FileContentsMap
	The FileContentsMap is a class that will minimize the number of times files are accessed from disk. The first time the contents of a file are requested, it will cache the contents the file in memory as a strings. All subsequent requests for the contents of that file will then be delivered without having to go to disk. WARNING: The FileContentsMap will not update the contents that it holds for a file after the first time it loads it, so if the contents change on disk, the FileContentsMap will be out of date. More...
class	GeneralFileContents
class	GeneralFileManager
class	icstream
	icstream: Input channel stream wrapper class More...
class	irstream
	orstream: Input stream wrapper abstract base class More...
class	izstream
	izstream: Input file stream wrapper for uncompressed and compressed files More...
class	ocstream
	ocstream: Output channel stream wrapper class More...
class	orstream
	orstream: Output stream wrapper base class More...
class	ozstream
	ozstream: Output file stream wrapper for uncompressed and compressed files More...

Typedefs
typedef utility::pointer::shared_ptr < FileContentsMap >	FileContentsMapOP
typedef utility::pointer::shared_ptr < FileContentsMap const >	FileContentsMapCOP
typedef utility::pointer::shared_ptr < GeneralFileManager >	GeneralFileManagerOP
typedef utility::pointer::shared_ptr < GeneralFileManager const >	GeneralFileManagerCOP
typedef utility::pointer::shared_ptr < GeneralFileContents >	GeneralFileContentsOP
typedef utility::pointer::shared_ptr < GeneralFileContents const >	GeneralFileContentsCOP

Functions
static bool	is_base64 (unsigned char c)
std::string	base64_encode (unsigned char const *bytes_to_encode, unsigned int in_len)
std::string	base64_decode (std::string const &encoded_string)
izstream &	getline (izstream &stream, std::string &line)
	std::getline( std::istream, std::string ) wrapper More...
izstream &	getline (izstream &stream, std::string &line, char const delim)
	std::getline( std::istream, std::string, char ) wrapper More...
std::istream &	skip (izstream &stream)
	Skip rest of line and line terminator (manipulator) More...
std::istream &	skip (std::istream &stream)
	Skip rest of line and line terminator (manipulator) More...
utility::vector1< std::string >	get_lines_from_file_data (std::string const &filename)
	General method that opens a file and returns its data as a list of lines after checking for errors. More...
void	remove_inline_comments (std::string &line)
	General method for removing comments from a line read from a database file. More...
template<class T >
void	read_vector (std::istream &is, vector1< T > &vec)
template<class T >
void	write_vector (std::ostream &out, vector1< T > const &vec)
template<class T >
void	write_vector (std::string filename, vector1< T > const &vec)

Variables
static const std::string	base64_chars
std::streamsize const	OZSTREAM_DEFAULT_BUFFER_SIZE = 921600
	default buffer size for ozstreams (900KB) More...

Typedef Documentation

typedef utility::pointer::shared_ptr< FileContentsMap const > utility::io::FileContentsMapCOP

typedef utility::pointer::shared_ptr< FileContentsMap > utility::io::FileContentsMapOP

typedef utility::pointer::shared_ptr< GeneralFileContents const > utility::io::GeneralFileContentsCOP

typedef utility::pointer::shared_ptr< GeneralFileContents > utility::io::GeneralFileContentsOP

typedef utility::pointer::shared_ptr< GeneralFileManager const > utility::io::GeneralFileManagerCOP

typedef utility::pointer::shared_ptr< GeneralFileManager > utility::io::GeneralFileManagerOP

Function Documentation

std::string utility::io::base64_decode

(

std::string const &

encoded_string

)

References base64_chars, is_base64(), and basic::options::OptionKeys::frags::j.

std::string utility::io::base64_encode	(	unsigned char const *	bytes_to_encode,
		unsigned int	in_len
	)

References base64_chars, and basic::options::OptionKeys::frags::j.

utility::vector1< std::string > utility::io::get_lines_from_file_data

(

std::string const &

filename

)

General method that opens a file and returns its data as a list of lines after checking for errors.

Blank and commented lines are not returned and the file is closed before returning the lines.

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References utility::io::izstream::close(), erraser_single_res_analysis::data, basic::options::OptionKeys::in::file::file, utility::file::file_exists(), getline(), utility::io::izstream::good(), line, erraser_analysis::lines, utility::trim(), and utility_exit_with_message.

Referenced by main().

izstream& utility::io::getline ( izstream &  stream, std::string &  line  )

inline

std::getline( std::istream, std::string ) wrapper

References getline().

Referenced by get_lines_from_file_data(), and main().

izstream& utility::io::getline ( izstream &  stream, std::string &  line, char const  delim  )

inline

std::getline( std::istream, std::string, char ) wrapper

Referenced by utility::io::izstream::getline(), and getline().

static bool utility::io::is_base64 ( unsigned char  c )

inlinestatic

Referenced by base64_decode().

template<class T >

void utility::io::read_vector	(	std::istream &	is,
		vector1< T > &	vec
	)

void utility::io::remove_inline_comments

(

std::string &

line

)

General method for removing comments from a line read from a database file.

Inline comments (indicated with #) are trimmed from the end of a passed string.

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

std::istream& utility::io::skip ( izstream &  stream )

inline

Skip rest of line and line terminator (manipulator)

References utility::io::izstream::ignore(), and max().

std::istream& utility::io::skip ( std::istream &  stream )

inline

Skip rest of line and line terminator (manipulator)

References max().

template<class T >

void utility::io::write_vector	(	std::ostream &	out,
		vector1< T > const &	vec
	)

Referenced by write_vector().

template<class T >

void utility::io::write_vector	(	std::string	filename,
		vector1< T > const &	vec
	)

References erraser_single_res_analysis::out, and write_vector().

Variable Documentation

const std::string utility::io::base64_chars

static

Initial value:

=
  "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
  "abcdefghijklmnopqrstuvwxyz"
  "0123456789+/"

Referenced by base64_decode(), and base64_encode().

std::streamsize const utility::io::OZSTREAM_DEFAULT_BUFFER_SIZE = 921600

default buffer size for ozstreams (900KB)

Note

this must be at least 4KB, otherwise zipstream will break