StarParser Class Reference

parser for the STAR file format More...

#include <star_parser.hh>

Inherited by ChemdictParser, ChemdictParser, MMCifReader, and MMCifReader.

Public Member Functions
	StarParser (std::istream &stream, bool items_as_row=false)
	StarParser (const String &filename, bool items_as_row=false)
virtual	~StarParser ()
virtual bool	OnBeginLoop (const StarLoopDesc &header)
virtual void	OnEndLoop ()
virtual void	OnDataRow (const StarLoopDesc &header, const std::vector< StringRef > &columns)
virtual void	OnDataItem (const StarDataItem &item)
virtual bool	OnBeginData (const StringRef &data_name)
virtual void	OnEndData ()
Real	TryGetReal (const StringRef &data, const String &name) const
float	TryGetFloat (const StringRef &data, const String &name) const
std::pair< bool, float >	TryGetFloat (const StringRef &data, const String &name, bool may_fail) const
int	TryGetInt (const StringRef &data, const String &name) const
std::pair< bool, int >	TryGetInt (const StringRef &data, const String &name, bool may_fail) const
bool	TryGetBool (const StringRef &data, const String &name) const
String	FormatDiagnostic (StarDiagType type, const String &message, int line=-1) const
void	SetFilename (const String &filename)
int	GetCurrentLinenum () const
void	Parse ()
	StarParser (std::istream &stream, bool items_as_row=false)
	StarParser (const String &filename, bool items_as_row=false)
virtual	~StarParser ()
virtual bool	OnBeginLoop (const StarLoopDesc &header)
virtual void	OnEndLoop ()
virtual void	OnDataRow (const StarLoopDesc &header, const std::vector< StringRef > &columns)
virtual void	OnDataItem (const StarDataItem &item)
virtual bool	OnBeginData (const StringRef &data_name)
virtual void	OnEndData ()
Real	TryGetReal (const StringRef &data, const String &name) const
float	TryGetFloat (const StringRef &data, const String &name) const
std::pair< bool, float >	TryGetFloat (const StringRef &data, const String &name, bool may_fail) const
int	TryGetInt (const StringRef &data, const String &name) const
std::pair< bool, int >	TryGetInt (const StringRef &data, const String &name, bool may_fail) const
bool	TryGetBool (const StringRef &data, const String &name) const
String	FormatDiagnostic (StarDiagType type, const String &message, int line=-1) const
void	SetFilename (const String &filename)
int	GetCurrentLinenum () const
void	Parse ()
Static Public Member Functions
static bool	SplitLine (const StringRef &line, std::vector< StringRef > &parts, bool clear=true)
static bool	SplitLine (const StringRef &line, std::vector< StringRef > &parts, bool clear=true)

Detailed Description

parser for the STAR file format

STAR format description

In essence, STAR files are structured text files. A few simple control structures control the interpretation of the content.

Commented lines start with a '#'.
a data section starts with data_<id> and ends, whenever another data block starts or at the end of the file.
data-items consist of a name-value pair. Names start with an underscore and are made up of a category and an identifier. The category and the identifier are separated by a '.'. The name is followed by a simple or quoted value.
lists of data items are specified using the loop_ keyword, followed by a list of column names and values.

Definition at line 112 of file star_parser.hh.

Constructor & Destructor Documentation

StarParser	(	std::istream &	stream,
		bool	items_as_row = `false`
	)			`[explicit]`

create a StarParser

Parameters:

	stream	input stream
	items_as_row	if true, data-items are first gathered (identifier as header, values as row) and then parsed like a loop (OnBeginLoop(), OnDataRow(), OnEndLoop())

StarParser	(	const String &	filename,
		bool	items_as_row = `false`
	)			`[explicit]`

virtual ~StarParser ( ) [inline, virtual]

Definition at line 122 of file star_parser.hh.

StarParser	(	std::istream &	stream,
		bool	items_as_row = `false`
	)			`[explicit]`

create a StarParser

Parameters:

	stream	input stream
	items_as_row	if true, data-items are first gathered (identifier as header, values as row) and then parsed like a loop (OnBeginLoop(), OnDataRow(), OnEndLoop())

StarParser	(	const String &	filename,
		bool	items_as_row = `false`
	)			`[explicit]`

virtual ~StarParser ( ) [inline, virtual]

Definition at line 122 of file star_parser.hh.

Member Function Documentation

String FormatDiagnostic	(	StarDiagType	type,
		const String &	message,
		int	line = `-1`
	)			const

format diagnostic and returns it as a string.

String FormatDiagnostic	(	StarDiagType	type,
		const String &	message,
		int	line = `-1`
	)			const

format diagnostic and returns it as a string.

int GetCurrentLinenum ( ) const [inline]

retrieve the line, the parser is currently working on

Definition at line 217 of file star_parser.hh.

int GetCurrentLinenum ( ) const [inline]

retrieve the line, the parser is currently working on

Definition at line 217 of file star_parser.hh.

virtual bool OnBeginData ( const StringRef & data_name ) [inline, virtual]

invoked when a new data control structure is encountered

Returns:: When true, for each data-item belonging to the data block, OnDataItem() is invoked. For every loop, OnBeginLoop() is called.

Reimplemented in ChemdictParser, MMCifReader, ChemdictParser, and MMCifReader.

Definition at line 147 of file star_parser.hh.

virtual bool OnBeginData ( const StringRef & data_name ) [inline, virtual]

invoked when a new data control structure is encountered

Returns:: When true, for each data-item belonging to the data block, OnDataItem() is invoked. For every loop, OnBeginLoop() is called.

Reimplemented in ChemdictParser, MMCifReader, ChemdictParser, and MMCifReader.

Definition at line 147 of file star_parser.hh.

virtual bool OnBeginLoop ( const StarLoopDesc & header ) [inline, virtual]

called when a loop is encountered

Returns:: When true, for each row in the loop, OnDataRow() is returned. If false, the loop is skipped.

Reimplemented in ChemdictParser, MMCifReader, ChemdictParser, and MMCifReader.

Definition at line 129 of file star_parser.hh.

virtual bool OnBeginLoop ( const StarLoopDesc & header ) [inline, virtual]

called when a loop is encountered

Returns:: When true, for each row in the loop, OnDataRow() is returned. If false, the loop is skipped.

Reimplemented in ChemdictParser, MMCifReader, ChemdictParser, and MMCifReader.

Definition at line 129 of file star_parser.hh.

virtual void OnDataItem ( const StarDataItem & item ) [inline, virtual]

invoked when a data item is encountered

Reimplemented in ChemdictParser, and ChemdictParser.

Definition at line 142 of file star_parser.hh.

virtual void OnDataItem ( const StarDataItem & item ) [inline, virtual]

invoked when a data item is encountered

Reimplemented in ChemdictParser, and ChemdictParser.

Definition at line 142 of file star_parser.hh.

virtual void OnDataRow	(	const StarLoopDesc &	header,
		const std::vector< StringRef > &	columns
	)			`[inline, virtual]`

invoked when a data row in a loop is encountered.

Parameters:

	header	describes the row format
	columns	contains the data columns

Reimplemented in ChemdictParser, MMCifReader, ChemdictParser, and MMCifReader.

Definition at line 137 of file star_parser.hh.

virtual void OnDataRow	(	const StarLoopDesc &	header,
		const std::vector< StringRef > &	columns
	)			`[inline, virtual]`

invoked when a data row in a loop is encountered.

Parameters:

	header	describes the row format
	columns	contains the data columns

Reimplemented in ChemdictParser, MMCifReader, ChemdictParser, and MMCifReader.

Definition at line 137 of file star_parser.hh.

virtual void OnEndData ( ) [inline, virtual]

called when leaving a datasection. Will only be invoked when OnBeginData() returned true.

Reimplemented in ChemdictParser, MMCifReader, ChemdictParser, and MMCifReader.

Definition at line 151 of file star_parser.hh.

virtual void OnEndData ( ) [inline, virtual]

called when leaving a datasection. Will only be invoked when OnBeginData() returned true.

Reimplemented in ChemdictParser, MMCifReader, ChemdictParser, and MMCifReader.

Definition at line 151 of file star_parser.hh.

virtual void OnEndLoop ( ) [inline, virtual]

invoked when leaving a loop

OnEndLoop() is only invoked, when OnBeginLoop() returned true.

Definition at line 133 of file star_parser.hh.

virtual void OnEndLoop ( ) [inline, virtual]

invoked when leaving a loop

OnEndLoop() is only invoked, when OnBeginLoop() returned true.

Definition at line 133 of file star_parser.hh.

void Parse ( )

void SetFilename ( const String & filename ) [inline]

Definition at line 211 of file star_parser.hh.

void SetFilename ( const String & filename ) [inline]

Definition at line 211 of file star_parser.hh.

static bool SplitLine	(	const StringRef &	line,
		std::vector< StringRef > &	parts,
		bool	clear = `true`
	)			`[static]`

static bool SplitLine	(	const StringRef &	line,
		std::vector< StringRef > &	parts,
		bool	clear = `true`
	)			`[static]`

bool TryGetBool	(	const StringRef &	data,
		const String &	name
	)			const

try to convert a value to bool, on failure raise an exception.

Parameters:

	data	value to be converted
	name	to be included in the message

Returns:: converted value

bool TryGetBool	(	const StringRef &	data,
		const String &	name
	)			const

try to convert a value to bool, on failure raise an exception.

Parameters:

	data	value to be converted
	name	to be included in the message

Returns:: converted value

std::pair<bool, float> TryGetFloat	(	const StringRef &	data,
		const String &	name,
		bool	may_fail
	)			const

try to convert a value to float, on failure raise an exception.

Parameters:

	data	value to be converted
	name	to be included in the message
	may_fail	decides if an exception is raised (false) or not (true)

Returns:: converted value

float TryGetFloat	(	const StringRef &	data,
		const String &	name
	)			const

try to convert a value to float, on failure raise an exception.

Parameters:

	data	value to be converted
	name	to be included in the message

Returns:: converted value

std::pair<bool, float> TryGetFloat	(	const StringRef &	data,
		const String &	name,
		bool	may_fail
	)			const

try to convert a value to float, on failure raise an exception.

Parameters:

	data	value to be converted
	name	to be included in the message
	may_fail	decides if an exception is raised (false) or not (true)

Returns:: converted value

float TryGetFloat	(	const StringRef &	data,
		const String &	name
	)			const

try to convert a value to float, on failure raise an exception.

Parameters:

	data	value to be converted
	name	to be included in the message

Returns:: converted value

std::pair<bool, int> TryGetInt	(	const StringRef &	data,
		const String &	name,
		bool	may_fail
	)			const

try to convert a value to integer, exception can be turned off.

Parameters:

	data	value to be converted
	name	to be included in the message
	may_fail	decides if an exception is raised (false) or not (true)

Returns:: pair with value and indicator if conversion worked

int TryGetInt	(	const StringRef &	data,
		const String &	name
	)			const

try to convert a value to integer, on failure raise an exception.

Parameters:

	data	value to be converted
	name	to be included in the message

Returns:: converted value

std::pair<bool, int> TryGetInt	(	const StringRef &	data,
		const String &	name,
		bool	may_fail
	)			const

try to convert a value to integer, exception can be turned off.

Parameters:

	data	value to be converted
	name	to be included in the message
	may_fail	decides if an exception is raised (false) or not (true)

Returns:: pair with value and indicator if conversion worked

int TryGetInt	(	const StringRef &	data,
		const String &	name
	)			const

try to convert a value to integer, on failure raise an exception.

Parameters:

	data	value to be converted
	name	to be included in the message

Returns:: converted value

Real TryGetReal	(	const StringRef &	data,
		const String &	name
	)			const

try to convert a value to Real, on failure raise an exception.

Parameters:

	data	value to be converted
	name	to be included in the message

Returns:: converted value

Real TryGetReal	(	const StringRef &	data,
		const String &	name
	)			const

try to convert a value to Real, on failure raise an exception.

Parameters:

	data	value to be converted
	name	to be included in the message

Returns:: converted value

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

stage/include/ost/io/mol/star_parser.hh
stage/include/ost/io/star_parser.hh

StarParser Class Reference

Public Member Functions

Static Public Member Functions

Detailed Description

STAR format description

Constructor & Destructor Documentation

Member Function Documentation