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37 * Implements functions in parsetree.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
43 * \page page_module_selection_parser Selection parsing
45 * The selection parser is implemented in the following files:
47 * Tokenizer implemented using Flex, splits the input into tokens
48 * (scanner.c and scanner_flex.h are generated from this file).
49 * - scanner.h, scanner_internal.h, scanner_internal.cpp:
50 * Helper functions for scanner.l and for interfacing between
51 * scanner.l and parser.y. Functions in scanner_internal.h are only
52 * used from scanner.l, while scanner.h is used from the parser.
53 * - symrec.h, symrec.cpp:
54 * Functions used by the tokenizer to handle the symbol table, i.e.,
55 * the recognized keywords. Some basic keywords are hardcoded into
56 * scanner.l, but all method and variable references go through the
57 * symbol table, as do position evaluation keywords.
59 * Semantic rules for parsing the grammar
60 * (parser.cpp and parser.h are generated from this file by Bison).
61 * - parsetree.h, parsetree.cpp:
62 * Functions called from actions in parser.y to construct the
63 * evaluation elements corresponding to different grammar elements.
65 * Defines a function that processes the parameters of selection
66 * methods and initializes the children of the method element.
67 * - selectioncollection.h, selectioncollection.cpp:
68 * These files define the high-level public interface to the parser
69 * through SelectionCollection::parseFromStdin(),
70 * SelectionCollection::parseFromFile() and
71 * SelectionCollection::parseFromString().
73 * The basic control flow in the parser is as follows: when a parser function
74 * in SelectionCollection gets called, it performs some
75 * initialization, and then calls the _gmx_sel_yyparse() function generated
76 * by Bison. This function then calls _gmx_sel_yylex() to repeatedly read
77 * tokens from the input (more complex tasks related to token recognition
78 * and bookkeeping are done by functions in scanner_internal.cpp) and uses the
79 * grammar rules to decide what to do with them. Whenever a grammar rule
80 * matches, a corresponding function in parsetree.cpp is called to construct
81 * either a temporary representation for the object or a
82 * gmx::SelectionTreeElement object
83 * (some simple rules are handled internally in parser.y).
84 * When a complete selection has been parsed, the functions in parsetree.cpp
85 * also take care of updating the ::gmx_ana_selcollection_t structure
88 * The rest of this page describes the resulting gmx::SelectionTreeElement
90 * Before the selections can be evaluated, this tree needs to be passed to
91 * the selection compiler, which is described on a separate page:
92 * \ref page_module_selection_compiler
95 * \section selparser_tree Element tree constructed by the parser
97 * The parser initializes the following fields in all selection elements:
98 * gmx::SelectionTreeElement::name, gmx::SelectionTreeElement::type,
99 * gmx::SelectionTreeElement::v\c .type,
100 * gmx::SelectionTreeElement::flags, gmx::SelectionTreeElement::child, and
101 * gmx::SelectionTreeElement::next.
102 * Some other fields are also initialized for particular element types as
104 * Fields that are not initialized are set to zero, NULL, or other similar
108 * \subsection selparser_tree_root Root elements
110 * The parser creates a \ref SEL_ROOT selection element for each variable
111 * assignment and each selection. However, there are two exceptions that do
112 * not result in a \ref SEL_ROOT element (in these cases, only the symbol
113 * table is modified):
114 * - Variable assignments that assign a variable to another variable.
115 * - Variable assignments that assign a non-group constant.
117 * The \ref SEL_ROOT elements are linked together in a chain in the same order
120 * The children of the \ref SEL_ROOT elements can be used to distinguish
121 * the two types of root elements from each other:
122 * - For variable assignments, the first and only child is always
123 * a \ref SEL_SUBEXPR element.
124 * - For selections, the first child is a \ref SEL_EXPRESSION or a
125 * \ref SEL_MODIFIER element that evaluates the final positions (if the
126 * selection defines a constant position, the child is a \ref SEL_CONST).
127 * The rest of the children are \ref SEL_MODIFIER elements with
128 * \ref NO_VALUE, in the order given by the user.
130 * The name of the selection/variable is stored in
131 * gmx::SelectionTreeElement::cgrp\c .name.
132 * It is set to either the name provided by the user or the selection string
133 * for selections not explicitly named by the user.
134 * \ref SEL_ROOT or \ref SEL_SUBEXPR elements do not appear anywhere else.
137 * \subsection selparser_tree_const Constant elements
139 * \ref SEL_CONST elements are created for every constant that is required
140 * for later evaluation.
141 * Currently, \ref SEL_CONST elements can be present for
142 * - selections that consist of a constant position,
143 * - \ref GROUP_VALUE method parameters if provided using external index
146 * For group-valued elements, the value is stored in
147 * gmx::SelectionTreeElement::cgrp; other types of values are stored in
148 * gmx::SelectionTreeElement::v.
149 * Constants that appear as parameters for selection methods are not present
150 * in the selection tree unless they have \ref GROUP_VALUE.
151 * \ref SEL_CONST elements have no children.
154 * \subsection selparser_tree_method Method evaluation elements
156 * \ref SEL_EXPRESSION and \ref SEL_MODIFIER elements are treated very
157 * similarly. The \c gmx_ana_selmethod_t structure corresponding to the
158 * evaluation method is in gmx::SelectionTreeElement::method, and the method
159 * data in gmx::SelectionTreeElement::mdata has been allocated using
161 * If a non-standard reference position type was set,
162 * gmx::SelectionTreeElement::pc has also been created, but only the type has
164 * All children of these elements are of the type \ref SEL_SUBEXPRREF, and
165 * each describes a selection that needs to be evaluated to obtain a value
166 * for one parameter of the method.
167 * No children are present for parameters that were given a constant
168 * non-\ref GROUP_VALUE value.
169 * The children are sorted in the order in which the parameters appear in the
170 * \ref gmx_ana_selmethod_t structure.
172 * In addition to actual selection keywords, \ref SEL_EXPRESSION elements
173 * are used internally to implement numerical comparisons (e.g., "x < 5")
174 * and keyword matching (e.g., "resnr 1 to 3" or "name CA").
177 * \subsection selparser_tree_subexpr Subexpression elements
179 * \ref SEL_SUBEXPR elements only appear for variables, as described above.
180 * gmx::SelectionTreeElement::name points to the name of the variable (from the
181 * \ref SEL_ROOT element).
182 * The element always has exactly one child, which represents the value of
185 * \ref SEL_SUBEXPRREF elements are used for two purposes:
186 * - Variable references that need to be evaluated (i.e., there is a
187 * \ref SEL_SUBEXPR element for the variable) are represented using
188 * \ref SEL_SUBEXPRREF elements.
189 * In this case, gmx::SelectionTreeElement::param is NULL, and the first and
190 * only child of the element is the \ref SEL_SUBEXPR element of the
192 * Such references can appear anywhere where the variable value
193 * (the child of the \ref SEL_SUBEXPR element) would be valid.
194 * - Children of \ref SEL_EXPRESSION and \ref SEL_MODIFIER elements are
195 * always of this type. For these elements, gmx::SelectionTreeElement::param
196 * is initialized to point to the parameter that receives the value from
198 * Each such element has exactly one child, which can be of any type;
199 * the \ref SEL_SUBEXPR element of a variable is used if the value comes
200 * from a variable, otherwise the child type is not \ref SEL_SUBEXPR.
203 * \subsection selparser_tree_bool Boolean elements
205 * One \ref SEL_BOOLEAN element is created for each boolean keyword in the
206 * input, and the tree structure represents the evaluation order.
207 * The gmx::SelectionTreeElement::boolt type gives the type of the operation.
208 * Each element has exactly two children (one for \ref BOOL_NOT elements),
209 * which are in the order given in the input.
210 * The children always have \ref GROUP_VALUE, but different element types
214 * \subsection selparser_tree_arith Arithmetic elements
216 * One \ref SEL_ARITHMETIC element is created for each arithmetic operation in
217 * the input, and the tree structure represents the evaluation order.
218 * The gmx::SelectionTreeElement::optype type gives the name of the operation.
219 * Each element has exactly two children (one for unary negation elements),
220 * which are in the order given in the input.
224 #include "parsetree.h"
229 #include <boost/exception_ptr.hpp>
230 #include <boost/shared_ptr.hpp>
232 #include "gromacs/selection/selection.h"
233 #include "gromacs/utility/cstringutil.h"
234 #include "gromacs/utility/exceptions.h"
235 #include "gromacs/utility/file.h"
236 #include "gromacs/utility/messagestringcollector.h"
237 #include "gromacs/utility/smalloc.h"
238 #include "gromacs/utility/stringutil.h"
240 #include "keywords.h"
243 #include "selectioncollection-impl.h"
245 #include "selmethod.h"
248 using gmx::SelectionLocation;
249 using gmx::SelectionParserValue;
250 using gmx::SelectionParserValueList;
251 using gmx::SelectionParserValueListPointer;
252 using gmx::SelectionParserParameter;
253 using gmx::SelectionParserParameterList;
254 using gmx::SelectionParserParameterListPointer;
255 using gmx::SelectionParserValue;
256 using gmx::SelectionTreeElement;
257 using gmx::SelectionTreeElementPointer;
263 * Formats context string for errors.
265 * The returned string is used as the context for errors reported during
269 formatCurrentErrorContext(yyscan_t scanner)
271 return gmx::formatString(
272 "While parsing '%s'",
273 _gmx_sel_lexer_get_current_text(scanner).c_str());
279 _gmx_selparser_error(yyscan_t scanner, const char *fmt, ...)
281 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
282 // FIXME: Use an arbitrary length buffer.
286 vsnprintf(buf, 1024, fmt, ap);
292 _gmx_selparser_handle_exception(yyscan_t scanner, std::exception *ex)
296 bool canContinue = false;
297 gmx::GromacsException *gromacsException
298 = dynamic_cast<gmx::GromacsException *>(ex);
299 if (gromacsException != NULL)
301 gromacsException->prependContext(formatCurrentErrorContext(scanner));
302 canContinue = (dynamic_cast<gmx::UserInputError *>(ex) != NULL);
304 _gmx_sel_lexer_set_exception(scanner, boost::current_exception());
307 catch (const std::exception &)
309 _gmx_sel_lexer_set_exception(scanner, boost::current_exception());
315 _gmx_selparser_handle_error(yyscan_t scanner)
317 std::string context(gmx::formatString("In selection '%s'",
318 _gmx_sel_lexer_pselstr(scanner)));
319 // The only way to prepend context to the exception is to rethrow it.
322 _gmx_sel_lexer_rethrow_exception_if_occurred(scanner);
324 catch (gmx::UserInputError &ex)
326 ex.prependContext(context);
327 if (_gmx_sel_is_lexer_interactive(scanner))
329 gmx::formatExceptionMessageToFile(stderr, ex);
334 catch (gmx::GromacsException &ex)
336 ex.prependContext(context);
339 // Do legacy processing for non-exception cases.
340 // This is only reached if there was no active exception.
341 _gmx_selparser_error(scanner, "Invalid selection '%s'",
342 _gmx_sel_lexer_pselstr(scanner));
343 return _gmx_sel_is_lexer_interactive(scanner);
349 /********************************************************************
350 * SelectionParserValue
353 SelectionParserValue::SelectionParserValue(
354 e_selvalue_t type, const SelectionLocation &location)
355 : type(type), location_(location)
357 memset(&u, 0, sizeof(u));
360 SelectionParserValue::SelectionParserValue(
361 const SelectionTreeElementPointer &expr)
362 : type(expr->v.type), expr(expr), location_(expr->location())
364 memset(&u, 0, sizeof(u));
367 /********************************************************************
368 * SelectionParserParameter
371 SelectionParserParameter::SelectionParserParameter(
373 SelectionParserValueListPointer values,
374 const SelectionLocation &location)
375 : name_(name != NULL ? name : ""), location_(location),
376 values_(values ? move(values)
377 : SelectionParserValueListPointer(new SelectionParserValueList))
384 * \param[in,out] sel Root of the selection element tree to initialize.
386 * Propagates the \ref SEL_DYNAMIC flag from the children of \p sel to \p sel
387 * (if any child of \p sel is dynamic, \p sel is also marked as such).
388 * The \ref SEL_DYNAMIC flag is also set for \ref SEL_EXPRESSION elements with
390 * Also, sets one of the \ref SEL_SINGLEVAL, \ref SEL_ATOMVAL, or
391 * \ref SEL_VARNUMVAL flags, either based on the children or on the type of
392 * the selection method.
393 * If the types of the children conflict, an error is returned.
395 * The flags of the children of \p sel are also updated if not done earlier.
396 * The flags are initialized only once for any element; if \ref SEL_FLAGSSET
397 * is set for an element, the function returns immediately, and the recursive
398 * operation does not descend beyond such elements.
401 _gmx_selelem_update_flags(const gmx::SelectionTreeElementPointer &sel)
403 bool bUseChildType = false;
404 bool bOnlySingleChildren;
406 /* Return if the flags have already been set */
407 if (sel->flags & SEL_FLAGSSET)
411 /* Set the flags based on the current element type */
416 sel->flags |= SEL_SINGLEVAL;
417 bUseChildType = false;
421 if (sel->u.expr.method->flags & SMETH_DYNAMIC)
423 sel->flags |= SEL_DYNAMIC;
425 if (sel->u.expr.method->flags & SMETH_SINGLEVAL)
427 sel->flags |= SEL_SINGLEVAL;
429 else if (sel->u.expr.method->flags & SMETH_VARNUMVAL)
431 sel->flags |= SEL_VARNUMVAL;
435 sel->flags |= SEL_ATOMVAL;
437 bUseChildType = false;
441 sel->flags |= SEL_ATOMVAL;
442 bUseChildType = false;
446 if (sel->v.type != NO_VALUE)
448 sel->flags |= SEL_VARNUMVAL;
450 bUseChildType = false;
454 bUseChildType = false;
460 bUseChildType = true;
463 /* Loop through children to propagate their flags upwards */
464 bOnlySingleChildren = true;
465 SelectionTreeElementPointer child = sel->child;
468 /* Update the child */
469 _gmx_selelem_update_flags(child);
470 /* Propagate the dynamic and unsorted flags */
471 sel->flags |= (child->flags & (SEL_DYNAMIC | SEL_UNSORTED));
472 /* Propagate the type flag if necessary and check for problems */
475 if ((sel->flags & SEL_VALTYPEMASK)
476 && !(sel->flags & child->flags & SEL_VALTYPEMASK))
478 // TODO: Recollect when this is triggered, and whether the type
480 GMX_THROW(gmx::InvalidInputError("Invalid combination of selection expressions"));
482 sel->flags |= (child->flags & SEL_VALTYPEMASK);
484 if (!(child->flags & SEL_SINGLEVAL))
486 bOnlySingleChildren = false;
491 /* For arithmetic expressions consisting only of single values,
492 * the result is also a single value. */
493 if (sel->type == SEL_ARITHMETIC && bOnlySingleChildren)
495 sel->flags = (sel->flags & ~SEL_VALTYPEMASK) | SEL_SINGLEVAL;
497 /* For root elements, the type should be propagated here, after the
498 * children have been updated. */
499 if (sel->type == SEL_ROOT)
501 GMX_ASSERT(sel->child, "Root elements should always have a child");
502 sel->flags |= (sel->child->flags & SEL_VALTYPEMASK);
504 /* Mark that the flags are set */
505 sel->flags |= SEL_FLAGSSET;
509 * \param[in,out] sel Selection element to initialize.
510 * \param[in] scanner Scanner data structure.
512 * A deep copy of the parameters is made to allow several
513 * expressions with the same method to coexist peacefully.
514 * Calls sel_datafunc() if one is specified for the method.
517 _gmx_selelem_init_method_params(const gmx::SelectionTreeElementPointer &sel,
521 gmx_ana_selparam_t *orgparam;
522 gmx_ana_selparam_t *param;
526 nparams = sel->u.expr.method->nparams;
527 orgparam = sel->u.expr.method->param;
528 snew(param, nparams);
529 memcpy(param, orgparam, nparams*sizeof(gmx_ana_selparam_t));
530 for (i = 0; i < nparams; ++i)
532 param[i].flags &= ~SPAR_SET;
533 _gmx_selvalue_setstore(¶m[i].val, NULL);
534 if (param[i].flags & SPAR_VARNUM)
536 param[i].val.nr = -1;
538 /* Duplicate the enum value array if it is given statically */
539 if ((param[i].flags & SPAR_ENUMVAL) && orgparam[i].val.u.ptr != NULL)
543 /* Count the values */
545 while (orgparam[i].val.u.s[n] != NULL)
549 _gmx_selvalue_reserve(¶m[i].val, n+1);
550 memcpy(param[i].val.u.s, orgparam[i].val.u.s,
551 (n+1)*sizeof(param[i].val.u.s[0]));
555 if (sel->u.expr.method->init_data)
557 mdata = sel->u.expr.method->init_data(nparams, param);
559 if (sel->u.expr.method->set_poscoll)
561 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
563 sel->u.expr.method->set_poscoll(&sc->pcc, mdata);
565 /* Store the values */
566 sel->u.expr.method->param = param;
567 sel->u.expr.mdata = mdata;
571 * \param[in,out] sel Selection element to initialize.
572 * \param[in] method Selection method to set.
573 * \param[in] scanner Scanner data structure.
575 * Makes a copy of \p method and stores it in \p sel->u.expr.method,
576 * and calls _gmx_selelem_init_method_params();
579 _gmx_selelem_set_method(const gmx::SelectionTreeElementPointer &sel,
580 gmx_ana_selmethod_t *method,
583 _gmx_selelem_set_vtype(sel, method->type);
584 sel->setName(method->name);
585 snew(sel->u.expr.method, 1);
586 memcpy(sel->u.expr.method, method, sizeof(gmx_ana_selmethod_t));
587 _gmx_selelem_init_method_params(sel, scanner);
591 * Initializes the reference position calculation for a \ref SEL_EXPRESSION
594 * \param[in,out] pcc Position calculation collection to use.
595 * \param[in,out] sel Selection element to initialize.
596 * \param[in] rpost Reference position type to use (NULL = default).
597 * \param[in] scanner Scanner data structure.
598 * \returns 0 on success, a non-zero error code on error.
601 set_refpos_type(gmx::PositionCalculationCollection *pcc,
602 const SelectionTreeElementPointer &sel,
603 const char *rpost, yyscan_t scanner)
610 if (sel->u.expr.method->pupdate)
612 /* By default, use whole residues/molecules. */
614 = pcc->createCalculationFromEnum(rpost, POS_COMPLWHOLE);
618 // TODO: Should this be treated as a real error?
619 _gmx_selparser_error(scanner, "modifier '%s' is not applicable for '%s'",
620 rpost, sel->u.expr.method->name);
624 gmx::SelectionTreeElementPointer
625 _gmx_sel_init_arithmetic(const gmx::SelectionTreeElementPointer &left,
626 const gmx::SelectionTreeElementPointer &right,
627 char op, yyscan_t scanner)
629 SelectionTreeElementPointer sel(
630 new SelectionTreeElement(
631 SEL_ARITHMETIC, _gmx_sel_lexer_get_current_location(scanner)));
632 sel->v.type = REAL_VALUE;
635 case '+': sel->u.arith.type = ARITH_PLUS; break;
636 case '-': sel->u.arith.type = (right ? ARITH_MINUS : ARITH_NEG); break;
637 case '*': sel->u.arith.type = ARITH_MULT; break;
638 case '/': sel->u.arith.type = ARITH_DIV; break;
639 case '^': sel->u.arith.type = ARITH_EXP; break;
645 sel->u.arith.opstr = gmx_strdup(buf);
647 sel->child->next = right;
652 * \param[in] left Selection element for the left hand side.
653 * \param[in] right Selection element for the right hand side.
654 * \param[in] cmpop String representation of the comparison operator.
655 * \param[in] scanner Scanner data structure.
656 * \returns The created selection element.
658 * This function handles the creation of a gmx::SelectionTreeElement object for
659 * comparison expressions.
661 SelectionTreeElementPointer
662 _gmx_sel_init_comparison(const gmx::SelectionTreeElementPointer &left,
663 const gmx::SelectionTreeElementPointer &right,
664 const char *cmpop, yyscan_t scanner)
666 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
667 gmx::MessageStringContext context(errors, formatCurrentErrorContext(scanner));
669 SelectionTreeElementPointer sel(
670 new SelectionTreeElement(
671 SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
672 _gmx_selelem_set_method(sel, &sm_compare, scanner);
674 SelectionParserParameterList params;
676 // Create the parameter for the left expression.
677 name = left->v.type == INT_VALUE ? "int1" : "real1";
678 params.push_back(SelectionParserParameter::createFromExpression(name, left));
679 // Create the parameter for the right expression.
680 name = right->v.type == INT_VALUE ? "int2" : "real2";
681 params.push_back(SelectionParserParameter::createFromExpression(name, right));
682 // Create the parameter for the operator.
683 // TODO: Consider whether a proper location is needed.
684 SelectionLocation location(SelectionLocation::createEmpty());
686 SelectionParserParameter::create(
687 "op", SelectionParserValue::createString(cmpop, location),
689 if (!_gmx_sel_parse_params(params, sel->u.expr.method->nparams,
690 sel->u.expr.method->param, sel, scanner))
692 return SelectionTreeElementPointer();
699 * Implementation method for keyword expression creation.
701 * \param[in] method Method to use.
702 * \param[in] matchType String matching type (only used if \p method is
703 * a string keyword and \p args is not empty.
704 * \param[in] args Pointer to the first argument.
705 * \param[in] rpost Reference position type to use (NULL = default).
706 * \param[in] scanner Scanner data structure.
707 * \returns The created selection element.
709 * This function handles the creation of a gmx::SelectionTreeElement object for
710 * selection methods that do not take parameters.
712 static SelectionTreeElementPointer
713 init_keyword_internal(gmx_ana_selmethod_t *method,
714 gmx::SelectionStringMatchType matchType,
715 SelectionParserValueListPointer args,
716 const char *rpost, yyscan_t scanner)
718 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
720 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
721 gmx::MessageStringContext context(errors, formatCurrentErrorContext(scanner));
723 if (method->nparams > 0)
725 // TODO: Would assert be better?
726 GMX_THROW(gmx::InternalError(
727 "Keyword initialization called with non-keyword method"));
730 const SelectionLocation &location = _gmx_sel_lexer_get_current_location(scanner);
731 // TODO: If there are arguments, the location would be better as just the
732 // location of the keyword itself.
733 SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION, location));
734 SelectionTreeElementPointer child = root;
735 _gmx_selelem_set_method(child, method, scanner);
737 /* Initialize the evaluation of keyword matching if values are provided */
740 gmx_ana_selmethod_t *kwmethod;
741 switch (method->type)
743 case INT_VALUE: kwmethod = &sm_keyword_int; break;
744 case REAL_VALUE: kwmethod = &sm_keyword_real; break;
745 case STR_VALUE: kwmethod = &sm_keyword_str; break;
747 GMX_THROW(gmx::InternalError(
748 "Unknown type for keyword selection"));
750 /* Initialize the selection element */
751 root.reset(new SelectionTreeElement(SEL_EXPRESSION, location));
752 _gmx_selelem_set_method(root, kwmethod, scanner);
753 if (method->type == STR_VALUE)
755 _gmx_selelem_set_kwstr_match_type(root, matchType);
757 SelectionParserParameterList params;
759 SelectionParserParameter::createFromExpression(NULL, child));
761 SelectionParserParameter::create(NULL, move(args), location));
762 if (!_gmx_sel_parse_params(params, root->u.expr.method->nparams,
763 root->u.expr.method->param, root, scanner))
765 return SelectionTreeElementPointer();
768 set_refpos_type(&sc->pcc, child, rpost, scanner);
774 * \param[in] method Method to use.
775 * \param[in] args Pointer to the first argument.
776 * \param[in] rpost Reference position type to use (NULL = default).
777 * \param[in] scanner Scanner data structure.
778 * \returns The created selection element.
780 * This function handles the creation of a gmx::SelectionTreeElement object for
781 * selection methods that do not take parameters.
783 SelectionTreeElementPointer
784 _gmx_sel_init_keyword(gmx_ana_selmethod_t *method,
785 gmx::SelectionParserValueListPointer args,
786 const char *rpost, yyscan_t scanner)
788 return init_keyword_internal(method, gmx::eStringMatchType_Auto, move(args),
793 * \param[in] method Method to use.
794 * \param[in] matchType String matching type.
795 * \param[in] args Pointer to the first argument.
796 * \param[in] rpost Reference position type to use (NULL = default).
797 * \param[in] scanner Scanner data structure.
798 * \returns The created selection element.
800 * This function handles the creation of a gmx::SelectionTreeElement object for
801 * keyword string matching.
803 SelectionTreeElementPointer
804 _gmx_sel_init_keyword_strmatch(gmx_ana_selmethod_t *method,
805 gmx::SelectionStringMatchType matchType,
806 gmx::SelectionParserValueListPointer args,
807 const char *rpost, yyscan_t scanner)
809 GMX_RELEASE_ASSERT(method->type == STR_VALUE,
810 "String keyword method called for a non-string-valued method");
811 GMX_RELEASE_ASSERT(args && !args->empty(),
812 "String keyword matching method called without any values");
813 return init_keyword_internal(method, matchType, move(args), rpost, scanner);
817 * \param[in] method Method to use for initialization.
818 * \param[in] group Selection in which the keyword should be evaluated.
819 * \param[in] rpost Reference position type to use (NULL = default).
820 * \param[in] scanner Scanner data structure.
821 * \returns The created selection element.
823 * This function handles the creation of a gmx::SelectionTreeElement object for
824 * expressions like "z of ...".
826 SelectionTreeElementPointer
827 _gmx_sel_init_keyword_of(gmx_ana_selmethod_t *method,
828 const gmx::SelectionTreeElementPointer &group,
829 const char *rpost, yyscan_t scanner)
831 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
832 gmx::MessageStringContext context(errors, formatCurrentErrorContext(scanner));
834 GMX_UNUSED_VALUE(rpost);
835 return _gmx_sel_init_keyword_evaluator(method, group, scanner);
839 * \param[in] method Method to use for initialization.
840 * \param[in] params Pointer to the first parameter.
841 * \param[in] rpost Reference position type to use (NULL = default).
842 * \param[in] scanner Scanner data structure.
843 * \returns The created selection element.
845 * This function handles the creation of a gmx::SelectionTreeElement object for
846 * selection methods that take parameters.
848 * Part of the behavior of the \c same selection keyword is hardcoded into
849 * this function (or rather, into _gmx_selelem_custom_init_same()) to allow the
850 * use of any keyword in \c "same KEYWORD as" without requiring special
851 * handling somewhere else (or sacrificing the simple syntax).
853 SelectionTreeElementPointer
854 _gmx_sel_init_method(gmx_ana_selmethod_t *method,
855 gmx::SelectionParserParameterListPointer params,
856 const char *rpost, yyscan_t scanner)
858 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
861 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
862 gmx::MessageStringContext context(errors, formatCurrentErrorContext(scanner));
864 _gmx_sel_finish_method(scanner);
865 /* The "same" keyword needs some custom massaging of the parameters. */
866 rc = _gmx_selelem_custom_init_same(&method, params, scanner);
869 return SelectionTreeElementPointer();
871 SelectionTreeElementPointer root(
872 new SelectionTreeElement(
873 SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
874 _gmx_selelem_set_method(root, method, scanner);
875 /* Process the parameters */
876 if (!_gmx_sel_parse_params(*params, root->u.expr.method->nparams,
877 root->u.expr.method->param, root, scanner))
879 return SelectionTreeElementPointer();
881 set_refpos_type(&sc->pcc, root, rpost, scanner);
887 * \param[in] method Modifier to use for initialization.
888 * \param[in] params Pointer to the first parameter.
889 * \param[in] sel Selection element that the modifier should act on.
890 * \param[in] scanner Scanner data structure.
891 * \returns The created selection element.
893 * This function handles the creation of a gmx::SelectionTreeElement object for
894 * selection modifiers.
896 SelectionTreeElementPointer
897 _gmx_sel_init_modifier(gmx_ana_selmethod_t *method,
898 gmx::SelectionParserParameterListPointer params,
899 const gmx::SelectionTreeElementPointer &sel,
902 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
903 gmx::MessageStringContext context(errors, formatCurrentErrorContext(scanner));
905 _gmx_sel_finish_method(scanner);
906 SelectionTreeElementPointer modifier(
907 new SelectionTreeElement(
908 SEL_MODIFIER, _gmx_sel_lexer_get_current_location(scanner)));
909 _gmx_selelem_set_method(modifier, method, scanner);
910 SelectionTreeElementPointer root;
911 if (method->type == NO_VALUE)
913 SelectionTreeElementPointer child = sel;
918 child->next = modifier;
924 SelectionParserParameter::createFromExpression(NULL, sel));
927 /* Process the parameters */
928 if (!_gmx_sel_parse_params(*params, modifier->u.expr.method->nparams,
929 modifier->u.expr.method->param, modifier, scanner))
931 return SelectionTreeElementPointer();
938 * \param[in] expr Input selection element for the position calculation.
939 * \param[in] type Reference position type or NULL for default.
940 * \param[in] scanner Scanner data structure.
941 * \returns The created selection element.
943 * This function handles the creation of a gmx::SelectionTreeElement object for
944 * evaluation of reference positions.
946 SelectionTreeElementPointer
947 _gmx_sel_init_position(const gmx::SelectionTreeElementPointer &expr,
948 const char *type, yyscan_t scanner)
950 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
951 gmx::MessageStringContext context(errors, formatCurrentErrorContext(scanner));
953 SelectionTreeElementPointer root(
954 new SelectionTreeElement(
955 SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
956 _gmx_selelem_set_method(root, &sm_keyword_pos, scanner);
957 _gmx_selelem_set_kwpos_type(root.get(), type);
958 /* Create the parameters for the parameter parser. */
959 SelectionParserParameterList params;
960 params.push_back(SelectionParserParameter::createFromExpression(NULL, expr));
961 /* Parse the parameters. */
962 if (!_gmx_sel_parse_params(params, root->u.expr.method->nparams,
963 root->u.expr.method->param, root, scanner))
965 return SelectionTreeElementPointer();
972 * \param[in] x,y,z Coordinates for the position.
973 * \param[in] scanner Scanner data structure.
974 * \returns The creates selection element.
976 SelectionTreeElementPointer
977 _gmx_sel_init_const_position(real x, real y, real z, yyscan_t scanner)
981 SelectionTreeElementPointer sel(
982 new SelectionTreeElement(
983 SEL_CONST, _gmx_sel_lexer_get_current_location(scanner)));
984 _gmx_selelem_set_vtype(sel, POS_VALUE);
985 _gmx_selvalue_reserve(&sel->v, 1);
989 gmx_ana_pos_init_const(sel->v.u.p, pos);
994 * \param[in] name Name of an index group to search for.
995 * \param[in] scanner Scanner data structure.
996 * \returns The created selection element.
998 * See gmx_ana_indexgrps_find() for information on how \p name is matched
999 * against the index groups.
1001 SelectionTreeElementPointer
1002 _gmx_sel_init_group_by_name(const char *name, yyscan_t scanner)
1005 SelectionTreeElementPointer sel(
1006 new SelectionTreeElement(
1007 SEL_GROUPREF, _gmx_sel_lexer_get_current_location(scanner)));
1008 _gmx_selelem_set_vtype(sel, GROUP_VALUE);
1009 sel->setName(gmx::formatString("group \"%s\"", name));
1010 sel->u.gref.name = gmx_strdup(name);
1011 sel->u.gref.id = -1;
1013 if (_gmx_sel_lexer_has_groups_set(scanner))
1015 gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
1016 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1017 sel->resolveIndexGroupReference(grps, sc->gall.isize);
1024 * \param[in] id Zero-based index number of the group to extract.
1025 * \param[in] scanner Scanner data structure.
1026 * \returns The created selection element.
1028 SelectionTreeElementPointer
1029 _gmx_sel_init_group_by_id(int id, yyscan_t scanner)
1031 SelectionTreeElementPointer sel(
1032 new SelectionTreeElement(
1033 SEL_GROUPREF, _gmx_sel_lexer_get_current_location(scanner)));
1034 _gmx_selelem_set_vtype(sel, GROUP_VALUE);
1035 sel->setName(gmx::formatString("group %d", id));
1036 sel->u.gref.name = NULL;
1037 sel->u.gref.id = id;
1039 if (_gmx_sel_lexer_has_groups_set(scanner))
1041 gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
1042 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1043 sel->resolveIndexGroupReference(grps, sc->gall.isize);
1050 * \param[in,out] sel Value of the variable.
1051 * \param scanner Scanner data structure.
1052 * \returns The created selection element that references \p sel.
1054 * The reference count of \p sel is updated, but no other modifications are
1057 SelectionTreeElementPointer
1058 _gmx_sel_init_variable_ref(const gmx::SelectionTreeElementPointer &sel,
1061 SelectionTreeElementPointer ref;
1063 if (sel->v.type == POS_VALUE && sel->type == SEL_CONST)
1069 ref.reset(new SelectionTreeElement(
1070 SEL_SUBEXPRREF, _gmx_sel_lexer_get_current_location(scanner)));
1071 _gmx_selelem_set_vtype(ref, sel->v.type);
1072 ref->setName(sel->name());
1079 * \param[in] name Name for the selection
1080 * (if NULL, a default name is constructed).
1081 * \param[in] sel The selection element that evaluates the selection.
1082 * \param scanner Scanner data structure.
1083 * \returns The created root selection element.
1085 * This function handles the creation of root (\ref SEL_ROOT)
1086 * gmx::SelectionTreeElement objects for selections.
1088 SelectionTreeElementPointer
1089 _gmx_sel_init_selection(const char *name,
1090 const gmx::SelectionTreeElementPointer &sel,
1093 if (sel->v.type != POS_VALUE)
1095 /* FIXME: Better handling of this error */
1096 GMX_THROW(gmx::InternalError(
1097 "Each selection must evaluate to a position"));
1100 SelectionTreeElementPointer root(
1101 new SelectionTreeElement(
1102 SEL_ROOT, _gmx_sel_lexer_get_current_location(scanner)));
1106 root->setName(name);
1108 /* Update the flags */
1109 _gmx_selelem_update_flags(root);
1110 gmx::ExceptionInitializer errors("Invalid index group reference(s)");
1111 root->checkUnsortedAtoms(true, &errors);
1112 if (errors.hasNestedExceptions())
1114 GMX_THROW(gmx::InconsistentInputError(errors));
1117 root->fillNameIfMissing(_gmx_sel_lexer_pselstr(scanner));
1119 /* Print out some information if the parser is interactive */
1120 if (_gmx_sel_is_lexer_interactive(scanner))
1122 fprintf(stderr, "Selection '%s' parsed\n",
1123 _gmx_sel_lexer_pselstr(scanner));
1131 * \param[in] name Name of the variable.
1132 * \param[in] expr The selection element that evaluates the variable.
1133 * \param scanner Scanner data structure.
1134 * \returns The created root selection element.
1136 * This function handles the creation of root gmx::SelectionTreeElement objects
1137 * for variable assignments. A \ref SEL_ROOT element and a \ref SEL_SUBEXPR
1138 * element are both created.
1140 SelectionTreeElementPointer
1141 _gmx_sel_assign_variable(const char *name,
1142 const gmx::SelectionTreeElementPointer &expr,
1145 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1146 const char *pselstr = _gmx_sel_lexer_pselstr(scanner);
1147 SelectionTreeElementPointer root;
1149 _gmx_selelem_update_flags(expr);
1150 /* Check if this is a constant non-group value */
1151 if (expr->type == SEL_CONST && expr->v.type != GROUP_VALUE)
1153 /* If so, just assign the constant value to the variable */
1154 sc->symtab->addVariable(name, expr);
1156 /* Check if we are assigning a variable to another variable */
1157 else if (expr->type == SEL_SUBEXPRREF)
1159 /* If so, make a simple alias */
1160 sc->symtab->addVariable(name, expr->child);
1164 SelectionLocation location(_gmx_sel_lexer_get_current_location(scanner));
1165 /* Create the root element */
1166 root.reset(new SelectionTreeElement(SEL_ROOT, location));
1167 root->setName(name);
1168 /* Create the subexpression element */
1169 root->child.reset(new SelectionTreeElement(SEL_SUBEXPR, location));
1170 root->child->setName(name);
1171 _gmx_selelem_set_vtype(root->child, expr->v.type);
1172 root->child->child = expr;
1174 _gmx_selelem_update_flags(root);
1175 gmx::ExceptionInitializer errors("Invalid index group reference(s)");
1176 root->checkUnsortedAtoms(true, &errors);
1177 if (errors.hasNestedExceptions())
1179 GMX_THROW(gmx::InconsistentInputError(errors));
1181 /* Add the variable to the symbol table */
1182 sc->symtab->addVariable(name, root->child);
1184 srenew(sc->varstrs, sc->nvars + 1);
1185 sc->varstrs[sc->nvars] = gmx_strdup(pselstr);
1187 if (_gmx_sel_is_lexer_interactive(scanner))
1189 fprintf(stderr, "Variable '%s' parsed\n", pselstr);
1195 * \param sel Selection to append (can be NULL, in which
1196 * case nothing is done).
1197 * \param last Last selection, or NULL if not present or not known.
1198 * \param scanner Scanner data structure.
1199 * \returns The last selection after the append.
1201 * Appends \p sel after the last root element, and returns either \p sel
1202 * (if it was non-NULL) or the last element (if \p sel was NULL).
1204 SelectionTreeElementPointer
1205 _gmx_sel_append_selection(const gmx::SelectionTreeElementPointer &sel,
1206 gmx::SelectionTreeElementPointer last,
1209 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1211 /* Append sel after last, or the last element of sc if last is NULL */
1232 /* Initialize a selection object if necessary */
1236 /* Add the new selection to the collection if it is not a variable. */
1237 if (sel->child->type != SEL_SUBEXPR)
1239 gmx::SelectionDataPointer selPtr(
1240 new gmx::internal::SelectionData(
1241 sel.get(), _gmx_sel_lexer_pselstr(scanner)));
1242 sc->sel.push_back(gmx::move(selPtr));
1245 /* Clear the selection string now that we've saved it */
1246 _gmx_sel_lexer_clear_pselstr(scanner);
1251 * \param[in] scanner Scanner data structure.
1252 * \returns true if the parser should finish, false if parsing should
1255 * This function is called always after _gmx_sel_append_selection() to
1256 * check whether a sufficient number of selections has already been provided.
1257 * This is used to terminate interactive parsers when the correct number of
1258 * selections has been provided.
1261 _gmx_sel_parser_should_finish(yyscan_t scanner)
1263 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1264 return (int)sc->sel.size() == _gmx_sel_lexer_exp_selcount(scanner);