utility::io::izstream Class Reference

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...
virtual	~izstream ()
	Destructor. More...
	operator bool () const
	bool conversion More...
	operator std::istream const & () const
	Stream conversion. More...
	operator std::istream & ()
	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)
	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 ()
	Clear the stream(s) More...
void	close ()
	Close the ifstream and reset the state. More...
void	seek_beg ()
	Seek to the beginning. More...
int	get ()
	Get the next character. More...
izstream &	get (char &c)
	Get the next character. More...
izstream &	get (char *str, std::streamsize const count)
	Get the next specified number of characters. More...
izstream &	get (char *str, std::streamsize const count, char const delim)
	Get the next specified number of characters. More...
izstream &	get (std::string &str, std::streamsize const count)
	Get the next specified number of characters. More...
izstream &	get (std::string &str, std::streamsize const count, char const delim)
	Get the next specified number of characters. More...
izstream &	getline (char *line, std::streamsize const count)
	Get the rest of the line. More...
izstream &	getline (char *line, std::streamsize const count, char const delim)
	Get the rest of the line. More...
izstream &	getline (std::string &line)
	Get the rest of the line. More...
izstream &	getline (std::string &line, char const delim)
	Get the rest of the line. More...
izstream &	read (char *str, std::streamsize const count)
	Read the next specified number of characters. More...
izstream &	read (std::string &str, std::streamsize const count)
	Read the next specified number of characters. More...
std::streamsize	readsome (char *str, std::streamsize const count)
	Read the next available specified number of characters. More...
std::streamsize	readsome (std::string &str, std::streamsize const count)
	Read the next available specified number of characters. More...
izstream &	ignore ()
	Skip over the next character. More...
izstream &	ignore (std::streamsize const count)
	Skip over the next specified number of characters. More...
izstream &	ignore (std::streamsize const count, char const delim)
	Skip over the next specified number of characters. More...
int	peek ()
	Returns the next character without extracting it. More...
izstream &	unget ()
	Put the last character read back into the stream. More...
izstream &	putback (char c)
	Put the last character read back into the stream and check that passed character is correct. More...
std::istream const &	operator() () const
	Stream access. More...
std::istream &	operator() ()
	Stream access. More...
std::istream const &	stream () const
	Stream access. More...
std::istream &	stream ()
	Stream access. More...
std::streambuf *	rdbuf () const
	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
	Good? More...
bool	eof () const
	End of file? More...
bool	fail () const
	Fail? More...
bool	bad () const
	Bad? More...
bool	compressed () const
	Compressed? More...
bool	uncompressed () const
	Uncompressed? More...
bool	gzipped () const
	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 constructor. More...

Detailed Description

izstream: Input file stream wrapper for uncompressed and compressed files

Member Typedef Documentation

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

private

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

private

Member Enumeration Documentation

enum utility::io::izstream::Compression

private

Enumerator
NONE
UNCOMPRESSED
GZIP

Constructor & Destructor Documentation

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

inline

Default constructor.

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

inlineexplicit

Filename constructor.

References open().

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

inlinevirtual

Destructor.

References if_stream_, and zip_stream_p_.

Member Function Documentation

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

inlinevirtual

Bad?

Implements utility::io::irstream.

References stream().

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_.

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

inlinevirtual

Clear the stream(s)

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

Referenced by basic::database::open().

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

inline

Close the ifstream and reset the state.

References compression_, filename_, if_stream_, NONE, and zip_stream_p_.

Referenced by utility::exit(), utility::file_contents(), utility::io::get_lines_from_file_data(), load_loops_from_file(), basic::database::open(), open(), basic::sampling::orientations::QuaternionGridManager::request_by_name(), numeric::interpolation::spline_from_file(), and basic::options::start_files().

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

inlinevirtual

Compressed?

Implements utility::io::irstream.

References compression_, and GZIP.

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

inlinevirtual

End of file?

Implements utility::io::irstream.

References stream().

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

inlinevirtual

Fail?

Implements utility::io::irstream.

References stream().

Referenced by APDBCMover::read_in_insert_loop_info().

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

inline

File name.

References filename_.

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

inline

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

References stream().

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

inlinevirtual

Get the next character.

Implements utility::io::irstream.

References stream().

Referenced by app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView::getCurrentLine().

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

inlinevirtual

Get the next character.

Implements utility::io::irstream.

References stream().

Referenced by app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView::getCurrentLine().

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

inlinevirtual

Get the next specified number of characters.

Implements utility::io::irstream.

References clean_pdb_keep_ligand::count, and stream().

Referenced by app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView::getCurrentLine().

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

inlinevirtual

Get the next specified number of characters.

Implements utility::io::irstream.

References clean_pdb_keep_ligand::count, and stream().

Referenced by app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView::getCurrentLine().

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

inlinevirtual

Get the next specified number of characters.

Implements utility::io::irstream.

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

Referenced by app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView::getCurrentLine().

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

inlinevirtual

Get the next specified number of characters.

Implements utility::io::irstream.

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

Referenced by app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView::getCurrentLine().

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

inlinestatic

References alternative_search_paths_.

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

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

inlineprivate

CRC of the uncompressed data (see zipstream documentation)

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

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_.

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

inlineprivate

Uncompressed data size.

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

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

inlinevirtual

Get the rest of the line.

Implements utility::io::irstream.

References stream().

Referenced by main(), and basic::options::start_files().

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

inlinevirtual

Get the rest of the line.

Implements utility::io::irstream.

References stream().

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

inlinevirtual

Get the rest of the line.

Implements utility::io::irstream.

References utility::io::getline(), and stream().

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

inlinevirtual

Get the rest of the line.

Implements utility::io::irstream.

References utility::io::getline(), and stream().

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

inlinevirtual

Good?

Implements utility::io::irstream.

References stream().

Referenced by basic::database::find_database_path(), utility::io::get_lines_from_file_data(), main(), basic::database::open(), and basic::options::start_files().

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

inlinevirtual

gzipped?

Implements utility::io::irstream.

References compression_, and GZIP.

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

inlinevirtual

Skip over the next character.

Implements utility::io::irstream.

References stream().

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

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

inlinevirtual

Skip over the next specified number of characters.

Implements utility::io::irstream.

References stream().

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

inlinevirtual

Skip over the next specified number of characters.

Implements utility::io::irstream.

References stream().

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_.

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

Open a file.

References utility::io::oc::cerr, close(), compression_, utility::file::file_extension(), utility::SingletonBase< Inline_File_Provider >::get_instance(), utility::Inline_File_Provider::get_istream(), GZIP, if_stream_, basic::options::OptionKeys::in::in, zlib_stream::basic_zip_istream< Elem, Tr, ElemA, ByteT, ByteAT >::is_gzip(), NONE, open_ifstream(), basic::options::OptionKeys::canonical_sampling::out::out, utility::file::trytry_ifstream_open(), UNCOMPRESSED, and zip_stream_p_.

Referenced by izstream(), basic::database::open(), basic::resource_manager::locator::FileStream::open(), and numeric::interpolation::spline_from_file().

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_, if_stream_, basic::options::OptionKeys::in::in, name, platform::file::PATH_SEPARATOR(), and utility::file::trytry_ifstream_open().

Referenced by open().

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

inlinevirtual

bool conversion

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

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

inlinevirtual

Stream conversion.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

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

inlinevirtual

Stream conversion.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

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

inlinevirtual

Stream access.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

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

inlinevirtual

Stream access.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

template<typename T >

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

inline

Stream input.

References stream(), and basic::options::OptionKeys::in::file::t.

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

inline

Stream manipulator input.

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

inlinevirtual

Stream manipulator input.

Implements utility::io::irstream.

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

inlinevirtual

Returns the next character without extracting it.

Implements utility::io::irstream.

References stream().

Referenced by yaml.scanner.Scanner::check_block_entry(), yaml.scanner.Scanner::check_document_end(), yaml.scanner.Scanner::check_document_start(), yaml.scanner.Scanner::check_key(), yaml.scanner.Scanner::check_plain(), yaml.scanner.Scanner::check_value(), yaml.scanner.Scanner::fetch_more_tokens(), yaml.scanner.Scanner::scan_anchor(), yaml.scanner.Scanner::scan_block_scalar(), yaml.scanner.Scanner::scan_block_scalar_breaks(), yaml.scanner.Scanner::scan_block_scalar_ignored_line(), yaml.scanner.Scanner::scan_block_scalar_indentation(), yaml.scanner.Scanner::scan_block_scalar_indicators(), yaml.scanner.Scanner::scan_directive(), yaml.scanner.Scanner::scan_directive_ignored_line(), yaml.scanner.Scanner::scan_directive_name(), yaml.scanner.Scanner::scan_flow_scalar(), yaml.scanner.Scanner::scan_tag(), yaml.scanner.Scanner::scan_tag_directive_handle(), yaml.scanner.Scanner::scan_tag_directive_prefix(), yaml.scanner.Scanner::scan_tag_directive_value(), yaml.scanner.Scanner::scan_yaml_directive_number(), and yaml.scanner.Scanner::scan_yaml_directive_value().

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

inlinevirtual

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

Implements utility::io::irstream.

References stream().

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

inlinevirtual

Pointer to the stream buffer.

Implements utility::io::irstream.

References stream().

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

inlinevirtual

Read the next specified number of characters.

Implements utility::io::irstream.

References stream().

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

inlinevirtual

Read the next specified number of characters.

Implements utility::io::irstream.

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

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

inlinevirtual

Read the next available specified number of characters.

Implements utility::io::irstream.

References stream().

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

inlinevirtual

Read the next available specified number of characters.

Implements utility::io::irstream.

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

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

inlinevirtual

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_.

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

inlinestatic

References alternative_search_paths_.

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

inlinevirtual

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().

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

inlinevirtual

Stream access.

Implements utility::io::irstream.

References if_stream_, and zip_stream_p_.

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

inlinevirtual

Uncompressed?

Implements utility::io::irstream.

References compression_, and UNCOMPRESSED.

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

inlinevirtual

Put the last character read back into the stream.

Implements utility::io::irstream.

References stream().

Friends And Related Function Documentation

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

friend

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

friend

Member Data Documentation

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 utility::io::izstream::compression_

private

Compression state.

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

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

private

File name.

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

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().

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