izstream: Input file stream wrapper for uncompressed and compressed files More...

#include <izstream.hh>

Inheritance diagram for utility::io::izstream:

Public Member Functions
	izstream ()
	Default constructor. More...

	izstream (std::string const &filename_a, std::ios_base::openmode open_mode=std::ios_base::in)
	Filename constructor. More...

	~izstream () override
	Destructor. More...

	operator bool () const override
	bool conversion More...

	operator std::istream const & () const override
	Stream conversion. More...

	operator std::istream & () override
	Stream conversion. More...

template<typename T >
std::istream &	operator>> (T &t)
	Stream input. More...

std::istream &	operator>> (manipulator m)
	Stream manipulator input. More...

std::istream &	operator>> (std_manipulator m) override
	Stream manipulator input. More...

void	open (std::string const &filename_a, std::ios_base::openmode open_mode=std::ios_base::in)
	Open a file. More...

void	clear () override
	Clear the stream(s) More...

void	close ()
	Close the ifstream and reset the state. More...

void	seek_beg () override
	Seek to the beginning. More...

int	get () override
	Get the next character. More...

izstream &	get (char &c) override
	Get the next character. More...

izstream &	get (char *str, std::streamsize const count) override
	Get the next specified number of characters. More...

izstream &	get (char *str, std::streamsize const count, char const delim) override
	Get the next specified number of characters. More...

izstream &	get (std::string &str, std::streamsize const count) override
	Get the next specified number of characters. More...

izstream &	get (std::string &str, std::streamsize const count, char const delim) override
	Get the next specified number of characters. More...

izstream &	getline (char *line, std::streamsize const count) override
	Get the rest of the line. More...

izstream &	getline (char *line, std::streamsize const count, char const delim) override
	Get the rest of the line. More...

izstream &	getline (std::string &line) override
	Get the rest of the line. More...

izstream &	getline (std::string &line, char const delim) override
	Get the rest of the line. More...

izstream &	read (char *str, std::streamsize const count) override
	Read the next specified number of characters. More...

izstream &	read (std::string &str, std::streamsize const count) override
	Read the next specified number of characters. More...

std::streamsize	readsome (char *str, std::streamsize const count) override
	Read the next available specified number of characters. More...

std::streamsize	readsome (std::string &str, std::streamsize const count) override
	Read the next available specified number of characters. More...

izstream &	ignore () override
	Skip over the next character. More...

izstream &	ignore (std::streamsize const count) override
	Skip over the next specified number of characters. More...

izstream &	ignore (std::streamsize const count, char const delim) override
	Skip over the next specified number of characters. More...

int	peek () override
	Returns the next character without extracting it. More...

izstream &	unget () override
	Put the last character read back into the stream. More...

izstream &	putback (char c) override
	Put the last character read back into the stream and check that passed character is correct. More...

std::istream const &	operator() () const override
	Stream access. More...

std::istream &	operator() () override
	Stream access. More...

std::istream const &	stream () const override
	Stream access. More...

std::istream &	stream () override
	Stream access. More...

std::streambuf *	rdbuf () const override
	Pointer to the stream buffer. More...

std::string const &	filename () const
	File name. More...

std::streamsize	gcount () const
	Get the number of characters read by the last unformatted read. More...

bool	good () const override
	Good? More...

bool	eof () const override
	End of file? More...

bool	fail () const override
	Fail? More...

bool	bad () const override
	Bad? More...

bool	compressed () const override
	Compressed? More...

bool	uncompressed () const override
	Uncompressed? More...

bool	gzipped () const override
	gzipped? More...

Public Member Functions inherited from utility::io::irstream
virtual	~irstream ()
	Destructor. More...

template<typename T >
irstream &	operator>> (T &t)
	Stream input. More...

Static Public Member Functions
static void	set_alternative_search_paths (vector1< std::string > alternative_search_paths)

static vector1< std::string >	get_alternative_search_paths ()

Private Types
enum	Compression { NONE , UNCOMPRESSED , GZIP }

typedef std::istream &(*	manipulator) (izstream &)

typedef std::istream &(*	std_manipulator) (std::istream &)

Private Member Functions
bool	is_gzip () const
	Is stream attached to a gzip file? More...

bool	check_crc () const
	CRC of gzip file valid? More...

long	get_crc () const
	CRC of the uncompressed data (see zipstream documentation) More...

long	get_in_size () const
	Compressed data size. More...

long	get_out_size () const
	Uncompressed data size. More...

void	open_ifstream (std::string const &name, std::ios_base::openmode open_mode)
	Helper function for opening files with alternative search paths. More...

Private Attributes
Compression	compression_
	Compression state. More...

std::ifstream	if_stream_
	File stream. More...

std::string	filename_
	File name. More...

zlib_stream::zip_istream *	zip_stream_p_
	Zip file stream pointer (owning) More...

Static Private Attributes
static vector1< std::string >	alternative_search_paths_
	Alternative search paths This initialized by the option system -in:path:path Notice that izstream cannot access the option system (because the utility library comes before the basic library), so setting the alternate search paths is it the responsibility of core::init::init() More...

Friends
long	utility::file::gzip (std::string const &uncompressedfile, bool overwrite)

long	utility::file::gunzip (std::string const &compressedfile, bool overwrite)

Additional Inherited Members
Protected Types inherited from utility::io::irstream
typedef std::istream &(*	std_manipulator) (std::istream &)

Protected Member Functions inherited from utility::io::irstream
	irstream ()=default
	Default constructor. More...

Detailed Description

izstream: Input file stream wrapper for uncompressed and compressed files

Member Typedef Documentation

◆ manipulator

typedef std::istream&(* utility::io::izstream::manipulator) (izstream &)

private

◆ std_manipulator

typedef std::istream&(* utility::io::izstream::std_manipulator) (std::istream &)

private

Member Enumeration Documentation

◆ Compression

enum utility::io::izstream::Compression

private

Enumerator
NONE
UNCOMPRESSED
GZIP

Constructor & Destructor Documentation

◆ izstream() [1/2]

utility::io::izstream::izstream ( )

inline

Default constructor.

◆ izstream() [2/2]

utility::io::izstream::izstream	(	std::string const &	filename_a,
		std::ios_base::openmode	open_mode = `std::ios_base::in`
	)

inlineexplicit

Filename constructor.

References open().

◆ ~izstream()

utility::io::izstream::~izstream ( )

inlineoverride

Destructor.

References if_stream_, and zip_stream_p_.

Member Function Documentation

◆ bad()

bool utility::io::izstream::bad ( ) const

inlineoverridevirtual

Bad?

Implements utility::io::irstream.

References stream().

◆ check_crc()

bool utility::io::izstream::check_crc ( ) const

inlineprivate

CRC of gzip file valid?

References zlib_stream::basic_zip_istream< Elem, Tr, ElemA, ByteT, ByteAT >::check_crc(), and zip_stream_p_.

◆ clear()

void utility::io::izstream::clear ( )

inlineoverridevirtual

Clear the stream(s)

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

Referenced by pyrosetta.bindings.pose.ResidueLabelAccessor::discard(), and basic::database::open().

◆ close()

void utility::io::izstream::close ( )

inline

◆ compressed()

bool utility::io::izstream::compressed ( ) const

inlineoverridevirtual

Compressed?

Implements utility::io::irstream.

References compression_, and GZIP.

Referenced by pyrosetta.distributed.cluster.io.IO::_save_results().

◆ eof()

bool utility::io::izstream::eof ( ) const

inlineoverridevirtual

End of file?

Implements utility::io::irstream.

References stream().

Referenced by calculate_total_hASA_within_distance_avg_values(), calculate_total_hASA_within_distance_avgresiduevalues_allnbs_conditionalonnumnbs(), main(), read_rama_map_file(), setup_activity_table(), and symmetrize_map().

◆ fail()

bool utility::io::izstream::fail ( ) const

inlineoverridevirtual

Fail?

Implements utility::io::irstream.

References stream().

Referenced by read_alignment_fasta_file(), read_embeddings(), read_in_extension(), read_membrane(), read_parameters(), and read_penalties().

◆ filename()

std::string const& utility::io::izstream::filename ( ) const

inline

File name.

References filename_.

Referenced by pyrosetta.io.silent_file_map.SilentFileMap::write_file().

◆ gcount()

std::streamsize utility::io::izstream::gcount ( ) const

inline

Get the number of characters read by the last unformatted read.

References stream().

◆ get() [1/6]

int utility::io::izstream::get ( )

inlineoverridevirtual

Get the next character.

Implements utility::io::irstream.

References stream().

◆ get() [2/6]

izstream& utility::io::izstream::get ( char & c )

inlineoverridevirtual

Get the next character.

Implements utility::io::irstream.

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and stream().

◆ get() [3/6]

izstream& utility::io::izstream::get	(	char *	str,
		std::streamsize const	count
	)

inlineoverridevirtual

Get the next specified number of characters.

Implements utility::io::irstream.

References count, str(), and stream().

◆ get() [4/6]

izstream& utility::io::izstream::get	(	char *	str,
		std::streamsize const	count,
		char const	delim
	)

inlineoverridevirtual

Get the next specified number of characters.

Implements utility::io::irstream.

References count, str(), and stream().

◆ get() [5/6]

izstream& utility::io::izstream::get	(	std::string &	str,
		std::streamsize const	count
	)

inlineoverridevirtual

Get the next specified number of characters.

Implements utility::io::irstream.

References count, basic::options::OptionKeys::cp::cp, str(), and stream().

◆ get() [6/6]

izstream& utility::io::izstream::get	(	std::string &	str,
		std::streamsize const	count,
		char const	delim
	)

inlineoverridevirtual

Get the next specified number of characters.

Implements utility::io::irstream.

References count, basic::options::OptionKeys::cp::cp, str(), and stream().

◆ get_alternative_search_paths()

static vector1< std::string > utility::io::izstream::get_alternative_search_paths ( )

inlinestatic

References alternative_search_paths_.

Referenced by basic::resource_manager::locator::FileStream::FileStream().

◆ get_crc()

long utility::io::izstream::get_crc ( ) const

inlineprivate

CRC of the uncompressed data (see zipstream documentation)

References zlib_stream::basic_zip_istream< Elem, Tr, ElemA, ByteT, ByteAT >::get_crc(), and zip_stream_p_.

◆ get_in_size()

long utility::io::izstream::get_in_size ( ) const

inlineprivate

Compressed data size.

References zlib_stream::basic_zip_istreambase< Elem, Tr, ElemA, ByteT, ByteAT >::get_in_size(), and zip_stream_p_.

◆ get_out_size()

long utility::io::izstream::get_out_size ( ) const

inlineprivate

Uncompressed data size.

References zlib_stream::basic_zip_istream< Elem, Tr, ElemA, ByteT, ByteAT >::get_out_size(), and zip_stream_p_.

◆ getline() [1/4]

izstream& utility::io::izstream::getline	(	char *	line,
		std::streamsize const	count
	)

inlineoverridevirtual

Get the rest of the line.

Implements utility::io::irstream.

References count, line, and stream().

Referenced by InterfaceStrandFinderMover::apply(), InterfaceDDGBindJobInputter::fill_jobs(), main(), read_rama_map_file(), basic::options::start_files(), and symmetrize_map().

◆ getline() [2/4]

izstream& utility::io::izstream::getline	(	char *	line,
		std::streamsize const	count,
		char const	delim
	)

inlineoverridevirtual

Get the rest of the line.

Implements utility::io::irstream.

References count, line, and stream().

◆ getline() [3/4]

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

inlineoverridevirtual

Get the rest of the line.

Implements utility::io::irstream.

References getline(), line, and stream().

◆ getline() [4/4]

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

inlineoverridevirtual

Get the rest of the line.

Implements utility::io::irstream.

References getline(), line, and stream().

◆ good()

bool utility::io::izstream::good ( ) const

inlineoverridevirtual

Good?

Implements utility::io::irstream.

References stream().

Referenced by protocols::abinitio::JumpSpecificAbrelax::add_constraints(), InterfaceStrandFinderMover::apply(), compute_intrinsic_deviation(), InterfaceDDGBindJobInputter::fill_jobs(), basic::database::find_database_path(), main(), basic::database::open(), read_rama_map_file(), recover_clustered_frags(), CloudArchiveManagerWrapper::restore_batchlist(), protocols::abinitio::JumpSpecificAbrelax::setup_jumps(), SphereSampler::SphereSampler(), basic::options::start_files(), symmetrize_map(), and write_cluster_frags().

◆ gzipped()

bool utility::io::izstream::gzipped ( ) const

inlineoverridevirtual

gzipped?

Implements utility::io::irstream.

References compression_, and GZIP.

◆ ignore() [1/3]

izstream& utility::io::izstream::ignore ( )

inlineoverridevirtual

Skip over the next character.

Implements utility::io::irstream.

References stream().

Referenced by utility::io::skip().

◆ ignore() [2/3]

izstream& utility::io::izstream::ignore ( std::streamsize const count )

inlineoverridevirtual

Skip over the next specified number of characters.

Implements utility::io::irstream.

References count, and stream().

◆ ignore() [3/3]

izstream& utility::io::izstream::ignore	(	std::streamsize const	count,
		char const	delim
	)

inlineoverridevirtual

Skip over the next specified number of characters.

Implements utility::io::irstream.

References count, and stream().

◆ is_gzip()

bool utility::io::izstream::is_gzip ( ) const

inlineprivate

Is stream attached to a gzip file?

References zlib_stream::basic_zip_istream< Elem, Tr, ElemA, ByteT, ByteAT >::is_gzip(), and zip_stream_p_.

◆ open()

void utility::io::izstream::open	(	std::string const &	filename_a,
		std::ios_base::openmode	open_mode = `std::ios_base::in`
	)

◆ open_ifstream()

void utility::io::izstream::open_ifstream	(	std::string const &	name,
		std::ios_base::openmode	open_mode
	)

private

Helper function for opening files with alternative search paths.

References alternative_search_paths_, filename_, create_a3b_hbs::i, if_stream_, basic::options::OptionKeys::in::in, platform::file::PATH_SEPARATOR(), and utility::file::trytry_ifstream_open().

Referenced by open().

◆ operator bool()

utility::io::izstream::operator bool ( ) const

inlineoverridevirtual

bool conversion

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

◆ operator std::istream &()

utility::io::izstream::operator std::istream & ( )

inlineoverridevirtual

Stream conversion.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

◆ operator std::istream const &()

utility::io::izstream::operator std::istream const & ( ) const

inlineoverridevirtual

Stream conversion.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

◆ operator()() [1/2]

std::istream const& utility::io::izstream::operator() ( ) const

inlineoverridevirtual

Stream access.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

◆ operator()() [2/2]

std::istream& utility::io::izstream::operator() ( )

inlineoverridevirtual

Stream access.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

◆ operator>>() [1/3]

std::istream& utility::io::izstream::operator>> ( manipulator m )

inline

Stream manipulator input.

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::m.

◆ operator>>() [2/3]

std::istream& utility::io::izstream::operator>> ( std_manipulator m )

inlineoverridevirtual

Stream manipulator input.

Implements utility::io::irstream.

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::m.

◆ operator>>() [3/3]

template<typename T >

std::istream& utility::io::izstream::operator>> ( T & t )

inline

Stream input.

References stream(), and predPRE::t.

◆ peek()

int utility::io::izstream::peek ( )

inlineoverridevirtual

Returns the next character without extracting it.

Implements utility::io::irstream.

References stream().

◆ putback()

izstream& utility::io::izstream::putback ( char c )

inlineoverridevirtual

Put the last character read back into the stream and check that passed character is correct.

Implements utility::io::irstream.

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and stream().

◆ rdbuf()

std::streambuf* utility::io::izstream::rdbuf ( ) const

inlineoverridevirtual

Pointer to the stream buffer.

Implements utility::io::irstream.

References stream().

◆ read() [1/2]

izstream& utility::io::izstream::read	(	char *	str,
		std::streamsize const	count
	)

inlineoverridevirtual

Read the next specified number of characters.

Implements utility::io::irstream.

References count, str(), and stream().

Referenced by numeric::read_tensor_from_file().

◆ read() [2/2]

izstream& utility::io::izstream::read	(	std::string &	str,
		std::streamsize const	count
	)

inlineoverridevirtual

Read the next specified number of characters.

Implements utility::io::irstream.

References count, basic::options::OptionKeys::cp::cp, str(), and stream().

◆ readsome() [1/2]

std::streamsize utility::io::izstream::readsome	(	char *	str,
		std::streamsize const	count
	)

inlineoverridevirtual

Read the next available specified number of characters.

Implements utility::io::irstream.

References count, str(), and stream().

◆ readsome() [2/2]

std::streamsize utility::io::izstream::readsome	(	std::string &	str,
		std::streamsize const	count
	)

inlineoverridevirtual

Read the next available specified number of characters.

Implements utility::io::irstream.

References count, basic::options::OptionKeys::cp::cp, str(), and stream().

◆ seek_beg()

void utility::io::izstream::seek_beg ( )

inlineoverridevirtual

Seek to the beginning.

Implements utility::io::irstream.

References if_stream_, zlib_stream::basic_zip_istream< Elem, Tr, ElemA, ByteT, ByteAT >::is_gzip(), and zip_stream_p_.

◆ set_alternative_search_paths()

static void utility::io::izstream::set_alternative_search_paths ( vector1< std::string > alternative_search_paths )

inlinestatic

References alternative_search_paths_.

◆ stream() [1/2]

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

inlineoverridevirtual

Stream access.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

Referenced by bad(), eof(), fail(), gcount(), get(), getline(), good(), ignore(), operator>>(), peek(), putback(), rdbuf(), read(), readsome(), and unget().

◆ stream() [2/2]

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

inlineoverridevirtual

Stream access.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

◆ uncompressed()

bool utility::io::izstream::uncompressed ( ) const

inlineoverridevirtual

Uncompressed?

Implements utility::io::irstream.

References compression_, and UNCOMPRESSED.

◆ unget()

izstream& utility::io::izstream::unget ( )

inlineoverridevirtual

Put the last character read back into the stream.

Implements utility::io::irstream.

References stream().

Friends And Related Function Documentation

◆ utility::file::gunzip

long utility::file::gunzip	(	std::string const &	compressedfile,
		bool	overwrite
	)

friend

◆ utility::file::gzip

long utility::file::gzip	(	std::string const &	uncompressedfile,
		bool	overwrite
	)

friend

Member Data Documentation

◆ alternative_search_paths_

vector1< std::string > utility::io::izstream::alternative_search_paths_

staticprivate

Alternative search paths This initialized by the option system -in:path:path Notice that izstream cannot access the option system (because the utility library comes before the basic library), so setting the alternate search paths is it the responsibility of core::init::init()

Referenced by get_alternative_search_paths(), open_ifstream(), and set_alternative_search_paths().

◆ compression_

Compression utility::io::izstream::compression_

private

Compression state.

Referenced by close(), compressed(), gzipped(), open(), and uncompressed().

◆ filename_

std::string utility::io::izstream::filename_

private

File name.

Referenced by close(), filename(), and open_ifstream().

◆ if_stream_

std::ifstream utility::io::izstream::if_stream_

private

File stream.

Referenced by clear(), close(), open(), open_ifstream(), operator bool(), operator std::istream &(), operator std::istream const &(), operator()(), seek_beg(), stream(), and ~izstream().

◆ zip_stream_p_

zlib_stream::zip_istream* utility::io::izstream::zip_stream_p_

private

Zip file stream pointer (owning)

Referenced by check_crc(), clear(), close(), get_crc(), get_in_size(), get_out_size(), is_gzip(), open(), operator bool(), operator std::istream &(), operator std::istream const &(), operator()(), seek_beg(), stream(), and ~izstream().

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

src/utility/io/izstream.hh
src/utility/io/izstream.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ manipulator

◆ std_manipulator

Member Enumeration Documentation

◆ Compression

Constructor & Destructor Documentation

◆ izstream() [1/2]

◆ izstream() [2/2]

◆ ~izstream()

Member Function Documentation

◆ bad()

◆ check_crc()

◆ clear()

◆ close()

◆ compressed()

◆ eof()

◆ fail()

◆ filename()

◆ gcount()

◆ get() [1/6]

◆ get() [2/6]

◆ get() [3/6]

◆ get() [4/6]

◆ get() [5/6]

◆ get() [6/6]

◆ get_alternative_search_paths()

◆ get_crc()

◆ get_in_size()

◆ get_out_size()

◆ getline() [1/4]

◆ getline() [2/4]

◆ getline() [3/4]

◆ getline() [4/4]

◆ good()

◆ gzipped()

◆ ignore() [1/3]

◆ ignore() [2/3]

◆ ignore() [3/3]

◆ is_gzip()

◆ open()

◆ open_ifstream()

◆ operator bool()

◆ operator std::istream &()

◆ operator std::istream const &()

◆ operator()() [1/2]

◆ operator()() [2/2]

◆ operator>>() [1/3]

◆ operator>>() [2/3]

◆ operator>>() [3/3]

◆ peek()

◆ putback()

◆ rdbuf()

◆ read() [1/2]

◆ read() [2/2]

◆ readsome() [1/2]

◆ readsome() [2/2]

◆ seek_beg()

◆ set_alternative_search_paths()

◆ stream() [1/2]

◆ stream() [2/2]

◆ uncompressed()

◆ unget()

Friends And Related Function Documentation

◆ utility::file::gunzip

◆ utility::file::gzip

Member Data Documentation

◆ alternative_search_paths_

◆ compression_

◆ filename_

◆ if_stream_

◆ zip_stream_p_