#include "gmxpre.h"
#include "parsetree.h"
#include <cstdarg>
#include <cstdio>
#include <exception>
#include <memory>
#include "gromacs/selection/selection.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textwriter.h"
#include "keywords.h"
#include "poscalc.h"
#include "scanner.h"
#include "selectioncollection_impl.h"
#include "selelem.h"
#include "selmethod.h"
#include "symrec.h"

Include dependency graph for parsetree.cpp:

Description

Implements functions in parsetree.h.

Author: Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com

Functions
std::string	anonymous_namespace{parsetree.cpp}::formatCurrentErrorContext (yyscan_t scanner)
	Formats context string for errors. More...

bool	_gmx_selparser_handle_exception (yyscan_t scanner, std::exception *ex)
	Handles exceptions caught within the Bison code. More...

bool	_gmx_selparser_handle_error (yyscan_t scanner)
	Handles errors in the selection parser. More...

void	_gmx_selelem_update_flags (const gmx::SelectionTreeElementPointer &sel)
	Propagates the flags for selection elements. More...

void	_gmx_selelem_init_method_params (const gmx::SelectionTreeElementPointer &sel, yyscan_t scanner)
	Initializes the method parameter data of SEL_EXPRESSION and SEL_MODIFIER elements. More...

void	_gmx_selelem_set_method (const gmx::SelectionTreeElementPointer &sel, gmx_ana_selmethod_t *method, yyscan_t scanner)
	Initializes the method for a SEL_EXPRESSION selection element. More...

static void	set_refpos_type (gmx::PositionCalculationCollection pcc, const SelectionTreeElementPointer &sel, const char rpost)
	Initializes the reference position calculation for a SEL_EXPRESSION element. More...

gmx::SelectionTreeElementPointer	_gmx_sel_init_arithmetic (const gmx::SelectionTreeElementPointer &left, const gmx::SelectionTreeElementPointer &right, char op, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for arithmetic expression evaluation. More...

SelectionTreeElementPointer	_gmx_sel_init_comparison (const gmx::SelectionTreeElementPointer &left, const gmx::SelectionTreeElementPointer &right, const char *cmpop, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for comparsion expression evaluation. More...

static SelectionTreeElementPointer	init_keyword_internal (gmx_ana_selmethod_t method, gmx::SelectionStringMatchType matchType, SelectionParserValueListPointer args, const char rpost, yyscan_t scanner)
	Implementation method for keyword expression creation. More...

SelectionTreeElementPointer	_gmx_sel_init_keyword (gmx_ana_selmethod_t method, gmx::SelectionParserValueListPointer args, const char rpost, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for a keyword expression from the parsed data. More...

SelectionTreeElementPointer	_gmx_sel_init_keyword_strmatch (gmx_ana_selmethod_t method, gmx::SelectionStringMatchType matchType, gmx::SelectionParserValueListPointer args, const char rpost, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for string-matching keyword expression. More...

SelectionTreeElementPointer	_gmx_sel_init_keyword_of (gmx_ana_selmethod_t method, const gmx::SelectionTreeElementPointer &group, const char rpost, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for "keyword of" expression. More...

SelectionTreeElementPointer	_gmx_sel_init_method (gmx_ana_selmethod_t method, gmx::SelectionParserParameterListPointer params, const char rpost, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for a method expression from the parsed data. More...

SelectionTreeElementPointer	_gmx_sel_init_modifier (gmx_ana_selmethod_t *method, gmx::SelectionParserParameterListPointer params, const gmx::SelectionTreeElementPointer &sel, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for a modifier expression from the parsed data. More...

SelectionTreeElementPointer	_gmx_sel_init_position (const gmx::SelectionTreeElementPointer &expr, const char *type, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for evaluation of reference positions. More...

SelectionTreeElementPointer	_gmx_sel_init_const_position (real x, real y, real z, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for a constant position. More...

SelectionTreeElementPointer	_gmx_sel_init_group_by_name (const char *name, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for a index group expression using group name. More...

SelectionTreeElementPointer	_gmx_sel_init_group_by_id (int id, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for a index group expression using group index. More...

SelectionTreeElementPointer	_gmx_sel_init_variable_ref (const gmx::SelectionTreeElementPointer &sel, yyscan_t scanner)
	Creates a gmx::SelectionTreeElement for a variable reference. More...

SelectionTreeElementPointer	_gmx_sel_init_selection (const char *name, const gmx::SelectionTreeElementPointer &sel, yyscan_t scanner)
	Creates a root gmx::SelectionTreeElement for a selection. More...

SelectionTreeElementPointer	_gmx_sel_assign_variable (const char *name, const gmx::SelectionTreeElementPointer &expr, yyscan_t scanner)
	Creates a root gmx::SelectionTreeElement elements for a variable assignment. More...

SelectionTreeElementPointer	_gmx_sel_append_selection (const gmx::SelectionTreeElementPointer &sel, gmx::SelectionTreeElementPointer last, yyscan_t scanner)
	Appends a root gmx::SelectionTreeElement to a selection collection. More...

bool	_gmx_sel_parser_should_finish (yyscan_t scanner)
	Check whether the parser should finish. More...

Function Documentation

SelectionTreeElementPointer _gmx_sel_append_selection	(	const gmx::SelectionTreeElementPointer &	sel,
		gmx::SelectionTreeElementPointer	last,
		yyscan_t	scanner
	)

Appends a root gmx::SelectionTreeElement to a selection collection.

Parameters

sel	Selection to append (can be NULL, in which case nothing is done).
last	Last selection, or NULL if not present or not known.
scanner	Scanner data structure.

Returns: The last selection after the append.

Appends sel after the last root element, and returns either sel (if it was non-NULL) or the last element (if sel was NULL).

SelectionTreeElementPointer _gmx_sel_assign_variable	(	const char *	name,
		const gmx::SelectionTreeElementPointer &	expr,
		yyscan_t	scanner
	)

Creates a root gmx::SelectionTreeElement elements for a variable assignment.

Parameters

[in]	name	Name of the variable.
[in]	expr	The selection element that evaluates the variable.
	scanner	Scanner data structure.

Returns: The created root selection element.

This function handles the creation of root gmx::SelectionTreeElement objects for variable assignments. A SEL_ROOT element and a SEL_SUBEXPR element are both created.

gmx::SelectionTreeElementPointer _gmx_sel_init_arithmetic	(	const gmx::SelectionTreeElementPointer &	left,
		const gmx::SelectionTreeElementPointer &	right,
		char	op,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for arithmetic expression evaluation.

Parameters

[in]	left	Selection element for the left hand side.
[in]	right	Selection element for the right hand side.
[in]	op	String representation of the operator.
[in]	scanner	Scanner data structure.

Returns: The created selection element.

This function handles the creation of a gmx::SelectionTreeElement object for arithmetic expressions.

SelectionTreeElementPointer _gmx_sel_init_comparison	(	const gmx::SelectionTreeElementPointer &	left,
		const gmx::SelectionTreeElementPointer &	right,
		const char *	cmpop,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for comparsion expression evaluation.

Parameters

[in]	left	Selection element for the left hand side.
[in]	right	Selection element for the right hand side.
[in]	cmpop	String representation of the comparison operator.
[in]	scanner	Scanner data structure.

Returns: The created selection element.

This function handles the creation of a gmx::SelectionTreeElement object for comparison expressions.

SelectionTreeElementPointer _gmx_sel_init_const_position	(	real	x,
		real	y,
		real	z,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for a constant position.

Parameters

[in]	x,y,z	Coordinates for the position.
[in]	scanner	Scanner data structure.

Returns: The creates selection element.

SelectionTreeElementPointer _gmx_sel_init_group_by_id	(	int	id,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for a index group expression using group index.

Parameters

[in]	id	Zero-based index number of the group to extract.
[in]	scanner	Scanner data structure.

Returns: The created selection element.

SelectionTreeElementPointer _gmx_sel_init_group_by_name	(	const char *	name,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for a index group expression using group name.

Parameters

[in]	name	Name of an index group to search for.
[in]	scanner	Scanner data structure.

Returns: The created selection element.

See gmx_ana_indexgrps_find() for information on how name is matched against the index groups.

SelectionTreeElementPointer _gmx_sel_init_keyword	(	gmx_ana_selmethod_t *	method,
		gmx::SelectionParserValueListPointer	args,
		const char *	rpost,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for a keyword expression from the parsed data.

Parameters

[in]	method	Method to use.
[in]	args	Pointer to the first argument.
[in]	rpost	Reference position type to use (NULL = default).
[in]	scanner	Scanner data structure.

Returns: The created selection element.

This function handles the creation of a gmx::SelectionTreeElement object for selection methods that do not take parameters.

SelectionTreeElementPointer _gmx_sel_init_keyword_of	(	gmx_ana_selmethod_t *	method,
		const gmx::SelectionTreeElementPointer &	group,
		const char *	rpost,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for "keyword of" expression.

Parameters

[in]	method	Method to use for initialization.
[in]	group	Selection in which the keyword should be evaluated.
[in]	rpost	Reference position type to use (NULL = default).
[in]	scanner	Scanner data structure.

Returns: The created selection element.

This function handles the creation of a gmx::SelectionTreeElement object for expressions like "z of ...".

SelectionTreeElementPointer _gmx_sel_init_keyword_strmatch	(	gmx_ana_selmethod_t *	method,
		gmx::SelectionStringMatchType	matchType,
		gmx::SelectionParserValueListPointer	args,
		const char *	rpost,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for string-matching keyword expression.

Parameters

[in]	method	Method to use.
[in]	matchType	String matching type.
[in]	args	Pointer to the first argument.
[in]	rpost	Reference position type to use (NULL = default).
[in]	scanner	Scanner data structure.

Returns: The created selection element.

This function handles the creation of a gmx::SelectionTreeElement object for keyword string matching.

SelectionTreeElementPointer _gmx_sel_init_method	(	gmx_ana_selmethod_t *	method,
		gmx::SelectionParserParameterListPointer	params,
		const char *	rpost,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for a method expression from the parsed data.

Parameters

[in]	method	Method to use for initialization.
[in]	params	Pointer to the first parameter.
[in]	rpost	Reference position type to use (NULL = default).
[in]	scanner	Scanner data structure.

Returns: The created selection element.

This function handles the creation of a gmx::SelectionTreeElement object for selection methods that take parameters.

Part of the behavior of the same selection keyword is hardcoded into this function (or rather, into _gmx_selelem_custom_init_same()) to allow the use of any keyword in "same KEYWORD as" without requiring special handling somewhere else (or sacrificing the simple syntax).

SelectionTreeElementPointer _gmx_sel_init_modifier	(	gmx_ana_selmethod_t *	method,
		gmx::SelectionParserParameterListPointer	params,
		const gmx::SelectionTreeElementPointer &	sel,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for a modifier expression from the parsed data.

Parameters

[in]	method	Modifier to use for initialization.
[in]	params	Pointer to the first parameter.
[in]	sel	Selection element that the modifier should act on.
[in]	scanner	Scanner data structure.

Returns: The created selection element.

This function handles the creation of a gmx::SelectionTreeElement object for selection modifiers.

SelectionTreeElementPointer _gmx_sel_init_position	(	const gmx::SelectionTreeElementPointer &	expr,
		const char *	type,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for evaluation of reference positions.

Parameters

[in]	expr	Input selection element for the position calculation.
[in]	type	Reference position type or NULL for default.
[in]	scanner	Scanner data structure.

Returns: The created selection element.

This function handles the creation of a gmx::SelectionTreeElement object for evaluation of reference positions.

SelectionTreeElementPointer _gmx_sel_init_selection	(	const char *	name,
		const gmx::SelectionTreeElementPointer &	sel,
		yyscan_t	scanner
	)

Creates a root gmx::SelectionTreeElement for a selection.

Parameters

[in]	name	Name for the selection (if NULL, a default name is constructed).
[in]	sel	The selection element that evaluates the selection.
	scanner	Scanner data structure.

Returns: The created root selection element.

This function handles the creation of root (SEL_ROOT) gmx::SelectionTreeElement objects for selections.

SelectionTreeElementPointer _gmx_sel_init_variable_ref	(	const gmx::SelectionTreeElementPointer &	sel,
		yyscan_t	scanner
	)

Creates a gmx::SelectionTreeElement for a variable reference.

Parameters

[in,out]	sel	Value of the variable.
	scanner	Scanner data structure.

Returns: The created selection element that references sel.

The reference count of sel is updated, but no other modifications are made.

bool _gmx_sel_parser_should_finish ( yyscan_t scanner )

Check whether the parser should finish.

Parameters

[in] scanner Scanner data structure.

Returns: true if the parser should finish, false if parsing should continue.

This function is called always after _gmx_sel_append_selection() to check whether a sufficient number of selections has already been provided. This is used to terminate interactive parsers when the correct number of selections has been provided.

void _gmx_selelem_init_method_params	(	const gmx::SelectionTreeElementPointer &	sel,
		yyscan_t	scanner
	)

Initializes the method parameter data of SEL_EXPRESSION and SEL_MODIFIER elements.

Parameters

[in,out]	sel	Selection element to initialize.
[in]	scanner	Scanner data structure.

A deep copy of the parameters is made to allow several expressions with the same method to coexist peacefully. Calls sel_datafunc() if one is specified for the method.

void _gmx_selelem_set_method	(	const gmx::SelectionTreeElementPointer &	sel,
		gmx_ana_selmethod_t *	method,
		yyscan_t	scanner
	)

Initializes the method for a SEL_EXPRESSION selection element.

Parameters

[in,out]	sel	Selection element to initialize.
[in]	method	Selection method to set.
[in]	scanner	Scanner data structure.

Makes a copy of method and stores it in sel->u.expr.method, and calls _gmx_selelem_init_method_params();

void _gmx_selelem_update_flags ( const gmx::SelectionTreeElementPointer & sel )

Propagates the flags for selection elements.

Parameters

[in,out] sel Root of the selection element tree to initialize.

Propagates the SEL_DYNAMIC flag from the children of sel to sel (if any child of sel is dynamic, sel is also marked as such). The SEL_DYNAMIC flag is also set for SEL_EXPRESSION elements with a dynamic method. Also, sets one of the SEL_SINGLEVAL, SEL_ATOMVAL, or SEL_VARNUMVAL flags, either based on the children or on the type of the selection method. If the types of the children conflict, an error is returned.

The flags of the children of sel are also updated if not done earlier. The flags are initialized only once for any element; if SEL_FLAGSSET is set for an element, the function returns immediately, and the recursive operation does not descend beyond such elements.

bool _gmx_selparser_handle_error ( void * scanner )

Handles errors in the selection parser.

Returns: true if parsing can continue with the next selection.

Exceptions

std::bad_alloc	if out of memory during the error processing.
unspecified	Can throw the stored exception if recovery from that exception is not possible.

This function is called during error recovery, after Bison has discarded all the symbols for the erroneous selection. At this point, the full selection that caused the error is known, and can be added to the error context.

For an interactive parser, this function returns true to let the parsing continue with the next selection, or to let the user enter the next selection, if it was possible to recover from the exception. For other cases, this will either rethrow the original exception with added context, or return false after adding the context to the error reporter. Any exceptions thrown from this method are again caught by Bison and result in termination of the parsing; the caller can then rethrow them.

bool _gmx_selparser_handle_exception	(	void *	scanner,
		std::exception *	ex
	)

Handles exceptions caught within the Bison code.

Return values

<tt>true</tt>	if the parser should attempt error recovery.
<tt>false</tt>	if the parser should immediately abort.

This function is called whenever an exception is caught within Bison actions. Since exceptions cannot propagate through Bison code, the exception is saved (potentially with some extra context information) so that the caller of the parser can rethrow the exception.

If it is possible to recover from the exception, then the function returns true, and Bison enters error recovery state. At the end of the recovery, _gmx_selparser_handle_error() is called. If this function returns false, then Bison immediately aborts the parsing so that the caller can rethrow the exception.

static SelectionTreeElementPointer init_keyword_internal	(	gmx_ana_selmethod_t *	method,
		gmx::SelectionStringMatchType	matchType,
		SelectionParserValueListPointer	args,
		const char *	rpost,
		yyscan_t	scanner
	)

static

Implementation method for keyword expression creation.

Parameters

[in]	method	Method to use.
[in]	matchType	String matching type (only used if `method` is a string keyword and `args` is not empty.
[in]	args	Pointer to the first argument.
[in]	rpost	Reference position type to use (NULL = default).
[in]	scanner	Scanner data structure.

Returns: The created selection element.

This function handles the creation of a gmx::SelectionTreeElement object for selection methods that do not take parameters.

static void set_refpos_type	(	gmx::PositionCalculationCollection *	pcc,
		const SelectionTreeElementPointer &	sel,
		const char *	rpost
	)

static

Initializes the reference position calculation for a SEL_EXPRESSION element.

Parameters

[in,out]	pcc	Position calculation collection to use.
[in,out]	sel	Selection element to initialize.
[in]	rpost	Reference position type to use (NULL = default).

Description

Functions

Function Documentation