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it holds for a file after the first time it loads it, so if the contents change on disk, the FileContentsMap will be out of date.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	GeneralFileContentsVector
class	GeneralFileManagerVector
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
typedef utility::pointer::shared_ptr< GeneralFileManagerVector >	GeneralFileManagerVectorOP
typedef utility::pointer::shared_ptr< GeneralFileManagerVector const >	GeneralFileManagerVectorCOP
typedef utility::pointer::shared_ptr< GeneralFileContentsVector >	GeneralFileContentsVectorOP
typedef utility::pointer::shared_ptr< GeneralFileContentsVector const >	GeneralFileContentsVectorCOP

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

FileContentsMapCOP

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

FileContentsMapOP

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

GeneralFileContentsCOP

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

GeneralFileContentsOP

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

GeneralFileContentsVectorCOP

typedef utility::pointer::shared_ptr< GeneralFileContentsVector const > utility::io::GeneralFileContentsVectorCOP

GeneralFileContentsVectorOP

typedef utility::pointer::shared_ptr< GeneralFileContentsVector > utility::io::GeneralFileContentsVectorOP

GeneralFileManagerCOP

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

GeneralFileManagerOP

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

GeneralFileManagerVectorCOP

typedef utility::pointer::shared_ptr< GeneralFileManagerVector const > utility::io::GeneralFileManagerVectorCOP

GeneralFileManagerVectorOP

typedef utility::pointer::shared_ptr< GeneralFileManagerVector > utility::io::GeneralFileManagerVectorOP

Function Documentation

base64_decode()

std::string utility::io::base64_decode

(

std::string const &

encoded_string

)

References base64_chars, create_a3b_hbs::i, is_base64(), and create_a3b_hbs::j.

base64_encode()

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

References base64_chars, create_a3b_hbs::i, and create_a3b_hbs::j.

get_lines_from_file_data()

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 data, file_exists(), utility::filename(), getline(), line, solution_counts::lines, utility::trim(), and utility_exit_with_message.

Referenced by main().

getline() [1/2]

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

inline

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

References getline(), and line.

Referenced by get_lines_from_file_data(), and main().

getline() [2/2]

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

inline

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

References getline(), and line.

is_base64()

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

inlinestatic

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c.

Referenced by base64_decode().

read_vector()

template<class T >

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

References vec().

Referenced by protocols::abinitio::JumpSpecificAbrelax::setup_fold().

remove_inline_comments()

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

References line.

skip() [1/2]

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

inline

Skip rest of line and line terminator (manipulator)

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

Referenced by load_checkpoint().

skip() [2/2]

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

inline

Skip rest of line and line terminator (manipulator)

References max().

write_vector() [1/2]

template<class T >

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

References vec().

Referenced by write_vector().

write_vector() [2/2]

template<class T >

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

References utility::filename(), erraser_single_res_analysis::out, vec(), and write_vector().

Variable Documentation

base64_chars

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

static

Initial value:

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

Referenced by base64_decode(), and base64_encode().

OZSTREAM_DEFAULT_BUFFER_SIZE

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