gmx::anonymous_namespace{selectioncollection.cpp} Namespace Reference

Functions
bool	promptLine (TextInputStream *inputStream, TextWriter *statusWriter, std::string *line)
	Reads a single selection line from stdin. More...
int	runParserLoop (yyscan_t scanner, _gmx_sel_yypstate *parserState, bool bInteractive)
	Helper function for tokenizing the input and pushing them to the parser. More...
void	printCurrentStatus (TextWriter *writer, gmx_ana_selcollection_t *sc, gmx_ana_indexgrps_t *grps, size_t firstSelection, int maxCount, const std::string &context, bool bFirst)
	Print current status in response to empty line in interactive input. More...
void	printHelp (TextWriter *writer, gmx_ana_selcollection_t *sc, const std::string &line)
	Prints selection help in interactive selection input. More...
SelectionList	runParser (yyscan_t scanner, TextInputStream *inputStream, bool bInteractive, int maxnr, const std::string &context)
	Helper function that runs the parser once the tokenizer has been initialized. More...
void	checkExternalGroups (const SelectionTreeElementPointer &root, int natoms, ExceptionInitializer *errors)
	Checks that index groups have valid atom indices. More...
void	checkTopologyProperties (const gmx_mtop_t *top, const SelectionTopologyProperties &props)
	Checks whether the given topology properties are available.
std::unique_ptr< TextWriter >	initStatusWriter (TextOutputStream *statusStream)
	Helper function to initialize status writer for interactive selection parsing.

Function Documentation

void gmx::anonymous_namespace{selectioncollection.cpp}::checkExternalGroups	(	const SelectionTreeElementPointer &	root,
		int	natoms,
		ExceptionInitializer *	errors
	)

Checks that index groups have valid atom indices.

Parameters

[in]	root	Root of selection tree to process.
[in]	natoms	Maximum number of atoms that the selections are set to evaluate.
	errors	Object for reporting any error messages.

Exceptions

std::bad_alloc

if out of memory.

Recursively checks the selection tree for index groups. Each found group is checked that it only contains atom indices that match the topology/maximum number of atoms set for the selection collection. Any issues are reported to errors.

void gmx::anonymous_namespace{selectioncollection.cpp}::printCurrentStatus	(	TextWriter *	writer,
		gmx_ana_selcollection_t *	sc,
		gmx_ana_indexgrps_t *	grps,
		size_t	firstSelection,
		int	maxCount,
		const std::string &	context,
		bool	bFirst
	)

Print current status in response to empty line in interactive input.

Parameters

[in]	writer	Writer to use for the output.
[in]	sc	Selection collection data structure.
[in]	grps	Available index groups.
[in]	firstSelection	Index of first selection from this interactive session.
[in]	maxCount	Maximum number of selections.
[in]	context	Context to print for what the selections are for.
[in]	bFirst	Whether this is the header that is printed before any user input.

Prints the available index groups and currently provided selections.

void gmx::anonymous_namespace{selectioncollection.cpp}::printHelp	(	TextWriter *	writer,
		gmx_ana_selcollection_t *	sc,
		const std::string &	line
	)

Prints selection help in interactive selection input.

Parameters

[in]	writer	Writer to use for the output.
[in]	sc	Selection collection data structure.
[in]	line	Line of user input requesting help (starting with help).

Initializes the selection help if not yet initialized, and finds the help topic based on words on the input line.

bool gmx::anonymous_namespace{selectioncollection.cpp}::promptLine	(	TextInputStream *	inputStream,
		TextWriter *	statusWriter,
		std::string *	line
	)

Reads a single selection line from stdin.

Parameters

[in]	inputStream	Stream to read from (typically the StandardInputStream).
[in]	statusWriter	Stream to print prompts to (if NULL, no output is done).
[out]	line	The read line in stored here.

Returns

true if something was read, false if at end of input.

Handles line continuation, reading also the continuing line(s) in one call.

SelectionList gmx::anonymous_namespace{selectioncollection.cpp}::runParser	(	yyscan_t	scanner,
		TextInputStream *	inputStream,
		bool	bInteractive,
		int	maxnr,
		const std::string &	context
	)

Helper function that runs the parser once the tokenizer has been initialized.

Parameters

[in,out]	scanner	Scanner data structure.
[in]	inputStream	Stream to use for input (currently only with bInteractive==true).
[in]	bInteractive	Whether to use a line-based reading algorithm designed for interactive input.
[in]	maxnr	Maximum number of selections to parse (if -1, parse as many as provided by the user).
[in]	context	Context to print for what the selections are for.

Returns

Vector of parsed selections.

Exceptions

std::bad_alloc	if out of memory.
InvalidInputError	if there is a parsing error.

Used internally to implement parseInteractive(), parseFromFile() and parseFromString().

int gmx::anonymous_namespace{selectioncollection.cpp}::runParserLoop	(	yyscan_t	scanner,
		_gmx_sel_yypstate *	parserState,
		bool	bInteractive
	)

Helper function for tokenizing the input and pushing them to the parser.

Parameters

	scanner	Tokenizer data structure.
	parserState	Parser data structure.
[in]	bInteractive	Whether to operate in interactive mode.

Repeatedly reads tokens using scanner and pushes them to the parser with parserState until there is no more input, or until enough input is given (only in interactive mode).