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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.
225 #include <boost/exception_ptr.hpp>
226 #include <boost/shared_ptr.hpp>
228 #include "gromacs/selection/poscalc.h"
229 #include "gromacs/selection/selection.h"
230 #include "gromacs/selection/selmethod.h"
231 #include "gromacs/utility/exceptions.h"
232 #include "gromacs/utility/file.h"
233 #include "gromacs/utility/messagestringcollector.h"
234 #include "gromacs/utility/smalloc.h"
235 #include "gromacs/utility/stringutil.h"
237 #include "keywords.h"
238 #include "parsetree.h"
239 #include "selectioncollection-impl.h"
245 using gmx::SelectionParserValue;
246 using gmx::SelectionParserValueList;
247 using gmx::SelectionParserValueListPointer;
248 using gmx::SelectionParserParameter;
249 using gmx::SelectionParserParameterList;
250 using gmx::SelectionParserParameterListPointer;
251 using gmx::SelectionParserValue;
252 using gmx::SelectionTreeElement;
253 using gmx::SelectionTreeElementPointer;
256 _gmx_selparser_error(yyscan_t scanner, const char *fmt, ...)
258 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
259 // FIXME: Use an arbitrary length buffer.
263 vsnprintf(buf, 1024, fmt, ap);
269 _gmx_selparser_handle_exception(yyscan_t scanner, const std::exception &ex)
271 if (dynamic_cast<const gmx::UserInputError *>(&ex) != NULL)
273 // TODO: Consider whether also the non-interactive parser should
274 // postpone the exception such that the whole selection can be added as
276 if (_gmx_sel_is_lexer_interactive(scanner))
278 // TODO: Handle exceptions that printing the message may produce.
279 gmx::formatExceptionMessageToFile(stderr, ex);
283 _gmx_sel_lexer_set_exception(scanner, boost::current_exception());
290 /********************************************************************
291 * SelectionParserValue
294 SelectionParserValue::SelectionParserValue(e_selvalue_t type)
297 memset(&u, 0, sizeof(u));
300 SelectionParserValue::SelectionParserValue(
301 const SelectionTreeElementPointer &expr)
302 : type(expr->v.type), expr(expr)
304 memset(&u, 0, sizeof(u));
307 /********************************************************************
308 * SelectionParserParameter
311 SelectionParserParameter::SelectionParserParameter(
313 SelectionParserValueListPointer values)
314 : name_(name != NULL ? name : ""),
315 values_(values ? move(values)
316 : SelectionParserValueListPointer(new SelectionParserValueList))
323 * \param[in,out] sel Root of the selection element tree to initialize.
325 * Propagates the \ref SEL_DYNAMIC flag from the children of \p sel to \p sel
326 * (if any child of \p sel is dynamic, \p sel is also marked as such).
327 * The \ref SEL_DYNAMIC flag is also set for \ref SEL_EXPRESSION elements with
329 * Also, sets one of the \ref SEL_SINGLEVAL, \ref SEL_ATOMVAL, or
330 * \ref SEL_VARNUMVAL flags, either based on the children or on the type of
331 * the selection method.
332 * If the types of the children conflict, an error is returned.
334 * The flags of the children of \p sel are also updated if not done earlier.
335 * The flags are initialized only once for any element; if \ref SEL_FLAGSSET
336 * is set for an element, the function returns immediately, and the recursive
337 * operation does not descend beyond such elements.
340 _gmx_selelem_update_flags(const gmx::SelectionTreeElementPointer &sel)
342 bool bUseChildType = false;
343 bool bOnlySingleChildren;
345 /* Return if the flags have already been set */
346 if (sel->flags & SEL_FLAGSSET)
350 /* Set the flags based on the current element type */
355 sel->flags |= SEL_SINGLEVAL;
356 bUseChildType = false;
360 if (sel->u.expr.method->flags & SMETH_DYNAMIC)
362 sel->flags |= SEL_DYNAMIC;
364 if (sel->u.expr.method->flags & SMETH_SINGLEVAL)
366 sel->flags |= SEL_SINGLEVAL;
368 else if (sel->u.expr.method->flags & SMETH_VARNUMVAL)
370 sel->flags |= SEL_VARNUMVAL;
374 sel->flags |= SEL_ATOMVAL;
376 bUseChildType = false;
380 sel->flags |= SEL_ATOMVAL;
381 bUseChildType = false;
385 if (sel->v.type != NO_VALUE)
387 sel->flags |= SEL_VARNUMVAL;
389 bUseChildType = false;
393 bUseChildType = false;
399 bUseChildType = true;
402 /* Loop through children to propagate their flags upwards */
403 bOnlySingleChildren = true;
404 SelectionTreeElementPointer child = sel->child;
407 /* Update the child */
408 _gmx_selelem_update_flags(child);
409 /* Propagate the dynamic and unsorted flags */
410 sel->flags |= (child->flags & (SEL_DYNAMIC | SEL_UNSORTED));
411 /* Propagate the type flag if necessary and check for problems */
414 if ((sel->flags & SEL_VALTYPEMASK)
415 && !(sel->flags & child->flags & SEL_VALTYPEMASK))
417 // TODO: Recollect when this is triggered, and whether the type
419 GMX_THROW(gmx::InvalidInputError("Invalid combination of selection expressions"));
421 sel->flags |= (child->flags & SEL_VALTYPEMASK);
423 if (!(child->flags & SEL_SINGLEVAL))
425 bOnlySingleChildren = false;
430 /* For arithmetic expressions consisting only of single values,
431 * the result is also a single value. */
432 if (sel->type == SEL_ARITHMETIC && bOnlySingleChildren)
434 sel->flags = (sel->flags & ~SEL_VALTYPEMASK) | SEL_SINGLEVAL;
436 /* For root elements, the type should be propagated here, after the
437 * children have been updated. */
438 if (sel->type == SEL_ROOT)
440 GMX_ASSERT(sel->child, "Root elements should always have a child");
441 sel->flags |= (sel->child->flags & SEL_VALTYPEMASK);
443 /* Mark that the flags are set */
444 sel->flags |= SEL_FLAGSSET;
448 * \param[in,out] sel Selection element to initialize.
449 * \param[in] scanner Scanner data structure.
451 * A deep copy of the parameters is made to allow several
452 * expressions with the same method to coexist peacefully.
453 * Calls sel_datafunc() if one is specified for the method.
456 _gmx_selelem_init_method_params(const gmx::SelectionTreeElementPointer &sel,
460 gmx_ana_selparam_t *orgparam;
461 gmx_ana_selparam_t *param;
465 nparams = sel->u.expr.method->nparams;
466 orgparam = sel->u.expr.method->param;
467 snew(param, nparams);
468 memcpy(param, orgparam, nparams*sizeof(gmx_ana_selparam_t));
469 for (i = 0; i < nparams; ++i)
471 param[i].flags &= ~SPAR_SET;
472 _gmx_selvalue_setstore(¶m[i].val, NULL);
473 if (param[i].flags & SPAR_VARNUM)
475 param[i].val.nr = -1;
477 /* Duplicate the enum value array if it is given statically */
478 if ((param[i].flags & SPAR_ENUMVAL) && orgparam[i].val.u.ptr != NULL)
482 /* Count the values */
484 while (orgparam[i].val.u.s[n] != NULL)
488 _gmx_selvalue_reserve(¶m[i].val, n+1);
489 memcpy(param[i].val.u.s, orgparam[i].val.u.s,
490 (n+1)*sizeof(param[i].val.u.s[0]));
494 if (sel->u.expr.method->init_data)
496 mdata = sel->u.expr.method->init_data(nparams, param);
498 if (sel->u.expr.method->set_poscoll)
500 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
502 sel->u.expr.method->set_poscoll(&sc->pcc, mdata);
504 /* Store the values */
505 sel->u.expr.method->param = param;
506 sel->u.expr.mdata = mdata;
510 * \param[in,out] sel Selection element to initialize.
511 * \param[in] method Selection method to set.
512 * \param[in] scanner Scanner data structure.
514 * Makes a copy of \p method and stores it in \p sel->u.expr.method,
515 * and calls _gmx_selelem_init_method_params();
518 _gmx_selelem_set_method(const gmx::SelectionTreeElementPointer &sel,
519 gmx_ana_selmethod_t *method,
522 _gmx_selelem_set_vtype(sel, method->type);
523 sel->setName(method->name);
524 snew(sel->u.expr.method, 1);
525 memcpy(sel->u.expr.method, method, sizeof(gmx_ana_selmethod_t));
526 _gmx_selelem_init_method_params(sel, scanner);
530 * Initializes the reference position calculation for a \ref SEL_EXPRESSION
533 * \param[in,out] pcc Position calculation collection to use.
534 * \param[in,out] sel Selection element to initialize.
535 * \param[in] rpost Reference position type to use (NULL = default).
536 * \param[in] scanner Scanner data structure.
537 * \returns 0 on success, a non-zero error code on error.
540 set_refpos_type(gmx::PositionCalculationCollection *pcc,
541 const SelectionTreeElementPointer &sel,
542 const char *rpost, yyscan_t scanner)
549 if (sel->u.expr.method->pupdate)
551 /* By default, use whole residues/molecules. */
553 = pcc->createCalculationFromEnum(rpost, POS_COMPLWHOLE);
557 // TODO: Should this be treated as a real error?
558 _gmx_selparser_error(scanner, "modifier '%s' is not applicable for '%s'",
559 rpost, sel->u.expr.method->name);
563 gmx::SelectionTreeElementPointer
564 _gmx_sel_init_arithmetic(const gmx::SelectionTreeElementPointer &left,
565 const gmx::SelectionTreeElementPointer &right,
566 char op, yyscan_t /* scanner */)
568 SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_ARITHMETIC));
569 sel->v.type = REAL_VALUE;
572 case '+': sel->u.arith.type = ARITH_PLUS; break;
573 case '-': sel->u.arith.type = (right ? ARITH_MINUS : ARITH_NEG); break;
574 case '*': sel->u.arith.type = ARITH_MULT; break;
575 case '/': sel->u.arith.type = ARITH_DIV; break;
576 case '^': sel->u.arith.type = ARITH_EXP; break;
582 sel->u.arith.opstr = strdup(buf);
584 sel->child->next = right;
589 * \param[in] left Selection element for the left hand side.
590 * \param[in] right Selection element for the right hand side.
591 * \param[in] cmpop String representation of the comparison operator.
592 * \param[in] scanner Scanner data structure.
593 * \returns The created selection element.
595 * This function handles the creation of a gmx::SelectionTreeElement object for
596 * comparison expressions.
598 SelectionTreeElementPointer
599 _gmx_sel_init_comparison(const gmx::SelectionTreeElementPointer &left,
600 const gmx::SelectionTreeElementPointer &right,
601 const char *cmpop, yyscan_t scanner)
603 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
604 gmx::MessageStringContext context(errors, "In comparison initialization");
606 SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_EXPRESSION));
607 _gmx_selelem_set_method(sel, &sm_compare, scanner);
609 SelectionParserParameterList params;
611 // Create the parameter for the left expression.
612 name = left->v.type == INT_VALUE ? "int1" : "real1";
613 params.push_back(SelectionParserParameter::createFromExpression(name, left));
614 // Create the parameter for the right expression.
615 name = right->v.type == INT_VALUE ? "int2" : "real2";
616 params.push_back(SelectionParserParameter::createFromExpression(name, right));
617 // Create the parameter for the operator.
619 SelectionParserParameter::create(
620 "op", SelectionParserValue::createString(cmpop)));
621 if (!_gmx_sel_parse_params(params, sel->u.expr.method->nparams,
622 sel->u.expr.method->param, sel, scanner))
624 return SelectionTreeElementPointer();
631 * Implementation method for keyword expression creation.
633 * \param[in] method Method to use.
634 * \param[in] matchType String matching type (only used if \p method is
635 * a string keyword and \p args is not empty.
636 * \param[in] args Pointer to the first argument.
637 * \param[in] rpost Reference position type to use (NULL = default).
638 * \param[in] scanner Scanner data structure.
639 * \returns The created selection element.
641 * This function handles the creation of a gmx::SelectionTreeElement object for
642 * selection methods that do not take parameters.
644 static SelectionTreeElementPointer
645 init_keyword_internal(gmx_ana_selmethod_t *method,
646 gmx::SelectionStringMatchType matchType,
647 SelectionParserValueListPointer args,
648 const char *rpost, yyscan_t scanner)
650 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
652 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
654 sprintf(buf, "In keyword '%s'", method->name);
655 gmx::MessageStringContext context(errors, buf);
657 if (method->nparams > 0)
659 // TODO: Would assert be better?
660 GMX_THROW(gmx::InternalError(
661 "Keyword initialization called with non-keyword method"));
664 SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION));
665 SelectionTreeElementPointer child = root;
666 _gmx_selelem_set_method(child, method, scanner);
668 /* Initialize the evaluation of keyword matching if values are provided */
671 gmx_ana_selmethod_t *kwmethod;
672 switch (method->type)
674 case INT_VALUE: kwmethod = &sm_keyword_int; break;
675 case REAL_VALUE: kwmethod = &sm_keyword_real; break;
676 case STR_VALUE: kwmethod = &sm_keyword_str; break;
678 GMX_THROW(gmx::InternalError(
679 "Unknown type for keyword selection"));
681 /* Initialize the selection element */
682 root.reset(new SelectionTreeElement(SEL_EXPRESSION));
683 _gmx_selelem_set_method(root, kwmethod, scanner);
684 if (method->type == STR_VALUE)
686 _gmx_selelem_set_kwstr_match_type(root, matchType);
688 SelectionParserParameterList params;
690 SelectionParserParameter::createFromExpression(NULL, child));
691 params.push_back(SelectionParserParameter::create(NULL, move(args)));
692 if (!_gmx_sel_parse_params(params, root->u.expr.method->nparams,
693 root->u.expr.method->param, root, scanner))
695 return SelectionTreeElementPointer();
698 set_refpos_type(&sc->pcc, child, rpost, scanner);
704 * \param[in] method Method to use.
705 * \param[in] args Pointer to the first argument.
706 * \param[in] rpost Reference position type to use (NULL = default).
707 * \param[in] scanner Scanner data structure.
708 * \returns The created selection element.
710 * This function handles the creation of a gmx::SelectionTreeElement object for
711 * selection methods that do not take parameters.
713 SelectionTreeElementPointer
714 _gmx_sel_init_keyword(gmx_ana_selmethod_t *method,
715 gmx::SelectionParserValueListPointer args,
716 const char *rpost, yyscan_t scanner)
718 return init_keyword_internal(method, gmx::eStringMatchType_Auto, move(args),
723 * \param[in] method Method to use.
724 * \param[in] matchType String matching type.
725 * \param[in] args Pointer to the first argument.
726 * \param[in] rpost Reference position type to use (NULL = default).
727 * \param[in] scanner Scanner data structure.
728 * \returns The created selection element.
730 * This function handles the creation of a gmx::SelectionTreeElement object for
731 * keyword string matching.
733 SelectionTreeElementPointer
734 _gmx_sel_init_keyword_strmatch(gmx_ana_selmethod_t *method,
735 gmx::SelectionStringMatchType matchType,
736 gmx::SelectionParserValueListPointer args,
737 const char *rpost, yyscan_t scanner)
739 GMX_RELEASE_ASSERT(method->type == STR_VALUE,
740 "String keyword method called for a non-string-valued method");
741 GMX_RELEASE_ASSERT(args && !args->empty(),
742 "String keyword matching method called without any values");
743 return init_keyword_internal(method, matchType, move(args), rpost, scanner);
747 * \param[in] method Method to use for initialization.
748 * \param[in] params Pointer to the first parameter.
749 * \param[in] rpost Reference position type to use (NULL = default).
750 * \param[in] scanner Scanner data structure.
751 * \returns The created selection element.
753 * This function handles the creation of a gmx::SelectionTreeElement object for
754 * selection methods that take parameters.
756 * Part of the behavior of the \c same selection keyword is hardcoded into
757 * this function (or rather, into _gmx_selelem_custom_init_same()) to allow the
758 * use of any keyword in \c "same KEYWORD as" without requiring special
759 * handling somewhere else (or sacrificing the simple syntax).
761 SelectionTreeElementPointer
762 _gmx_sel_init_method(gmx_ana_selmethod_t *method,
763 gmx::SelectionParserParameterListPointer params,
764 const char *rpost, yyscan_t scanner)
766 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
769 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
771 sprintf(buf, "In keyword '%s'", method->name);
772 gmx::MessageStringContext context(errors, buf);
774 _gmx_sel_finish_method(scanner);
775 /* The "same" keyword needs some custom massaging of the parameters. */
776 rc = _gmx_selelem_custom_init_same(&method, params, scanner);
779 return SelectionTreeElementPointer();
781 SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION));
782 _gmx_selelem_set_method(root, method, scanner);
783 /* Process the parameters */
784 if (!_gmx_sel_parse_params(*params, root->u.expr.method->nparams,
785 root->u.expr.method->param, root, scanner))
787 return SelectionTreeElementPointer();
789 set_refpos_type(&sc->pcc, root, rpost, scanner);
795 * \param[in] method Modifier to use for initialization.
796 * \param[in] params Pointer to the first parameter.
797 * \param[in] sel Selection element that the modifier should act on.
798 * \param[in] scanner Scanner data structure.
799 * \returns The created selection element.
801 * This function handles the creation of a gmx::SelectionTreeElement object for
802 * selection modifiers.
804 SelectionTreeElementPointer
805 _gmx_sel_init_modifier(gmx_ana_selmethod_t *method,
806 gmx::SelectionParserParameterListPointer params,
807 const gmx::SelectionTreeElementPointer &sel,
810 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
812 sprintf(buf, "In keyword '%s'", method->name);
813 gmx::MessageStringContext context(errors, buf);
815 _gmx_sel_finish_method(scanner);
816 SelectionTreeElementPointer modifier(new SelectionTreeElement(SEL_MODIFIER));
817 _gmx_selelem_set_method(modifier, method, scanner);
818 SelectionTreeElementPointer root;
819 if (method->type == NO_VALUE)
821 SelectionTreeElementPointer child = sel;
826 child->next = modifier;
832 SelectionParserParameter::createFromExpression(NULL, sel));
835 /* Process the parameters */
836 if (!_gmx_sel_parse_params(*params, modifier->u.expr.method->nparams,
837 modifier->u.expr.method->param, modifier, scanner))
839 return SelectionTreeElementPointer();
846 * \param[in] expr Input selection element for the position calculation.
847 * \param[in] type Reference position type or NULL for default.
848 * \param[in] scanner Scanner data structure.
849 * \returns The created selection element.
851 * This function handles the creation of a gmx::SelectionTreeElement object for
852 * evaluation of reference positions.
854 SelectionTreeElementPointer
855 _gmx_sel_init_position(const gmx::SelectionTreeElementPointer &expr,
856 const char *type, yyscan_t scanner)
858 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
860 sprintf(buf, "In position evaluation");
861 gmx::MessageStringContext context(errors, buf);
863 SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION));
864 _gmx_selelem_set_method(root, &sm_keyword_pos, scanner);
865 _gmx_selelem_set_kwpos_type(root.get(), type);
866 /* Create the parameters for the parameter parser. */
867 SelectionParserParameterList params;
868 params.push_back(SelectionParserParameter::createFromExpression(NULL, expr));
869 /* Parse the parameters. */
870 if (!_gmx_sel_parse_params(params, root->u.expr.method->nparams,
871 root->u.expr.method->param, root, scanner))
873 return SelectionTreeElementPointer();
880 * \param[in] x,y,z Coordinates for the position.
881 * \returns The creates selection element.
883 SelectionTreeElementPointer
884 _gmx_sel_init_const_position(real x, real y, real z)
888 SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_CONST));
889 _gmx_selelem_set_vtype(sel, POS_VALUE);
890 _gmx_selvalue_reserve(&sel->v, 1);
894 gmx_ana_pos_init_const(sel->v.u.p, pos);
899 * \param[in] name Name of an index group to search for.
900 * \param[in] scanner Scanner data structure.
901 * \returns The created selection element.
903 * See gmx_ana_indexgrps_find() for information on how \p name is matched
904 * against the index groups.
906 SelectionTreeElementPointer
907 _gmx_sel_init_group_by_name(const char *name, yyscan_t scanner)
910 SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
911 _gmx_selelem_set_vtype(sel, GROUP_VALUE);
912 sel->setName(gmx::formatString("group \"%s\"", name));
913 sel->u.gref.name = strdup(name);
916 if (_gmx_sel_lexer_has_groups_set(scanner))
918 gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
919 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
920 sel->resolveIndexGroupReference(grps, sc->gall.isize);
927 * \param[in] id Zero-based index number of the group to extract.
928 * \param[in] scanner Scanner data structure.
929 * \returns The created selection element.
931 SelectionTreeElementPointer
932 _gmx_sel_init_group_by_id(int id, yyscan_t scanner)
934 SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
935 _gmx_selelem_set_vtype(sel, GROUP_VALUE);
936 sel->setName(gmx::formatString("group %d", id));
937 sel->u.gref.name = NULL;
940 if (_gmx_sel_lexer_has_groups_set(scanner))
942 gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
943 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
944 sel->resolveIndexGroupReference(grps, sc->gall.isize);
951 * \param[in,out] sel Value of the variable.
952 * \returns The created selection element that references \p sel.
954 * The reference count of \p sel is updated, but no other modifications are
957 SelectionTreeElementPointer
958 _gmx_sel_init_variable_ref(const gmx::SelectionTreeElementPointer &sel)
960 SelectionTreeElementPointer ref;
962 if (sel->v.type == POS_VALUE && sel->type == SEL_CONST)
968 ref.reset(new SelectionTreeElement(SEL_SUBEXPRREF));
969 _gmx_selelem_set_vtype(ref, sel->v.type);
970 ref->setName(sel->name());
977 * \param[in] name Name for the selection
978 * (if NULL, a default name is constructed).
979 * \param[in] sel The selection element that evaluates the selection.
980 * \param scanner Scanner data structure.
981 * \returns The created root selection element.
983 * This function handles the creation of root (\ref SEL_ROOT)
984 * gmx::SelectionTreeElement objects for selections.
986 SelectionTreeElementPointer
987 _gmx_sel_init_selection(const char *name,
988 const gmx::SelectionTreeElementPointer &sel,
991 if (sel->v.type != POS_VALUE)
993 /* FIXME: Better handling of this error */
994 GMX_THROW(gmx::InternalError(
995 "Each selection must evaluate to a position"));
998 SelectionTreeElementPointer root(new SelectionTreeElement(SEL_ROOT));
1002 root->setName(name);
1004 /* Update the flags */
1005 _gmx_selelem_update_flags(root);
1006 gmx::ExceptionInitializer errors("Invalid index group reference(s)");
1007 root->checkUnsortedAtoms(true, &errors);
1008 if (errors.hasNestedExceptions())
1010 GMX_THROW(gmx::InconsistentInputError(errors));
1013 root->fillNameIfMissing(_gmx_sel_lexer_pselstr(scanner));
1015 /* Print out some information if the parser is interactive */
1016 if (_gmx_sel_is_lexer_interactive(scanner))
1018 fprintf(stderr, "Selection '%s' parsed\n",
1019 _gmx_sel_lexer_pselstr(scanner));
1027 * \param[in] name Name of the variable.
1028 * \param[in] expr The selection element that evaluates the variable.
1029 * \param scanner Scanner data structure.
1030 * \returns The created root selection element.
1032 * This function handles the creation of root gmx::SelectionTreeElement objects
1033 * for variable assignments. A \ref SEL_ROOT element and a \ref SEL_SUBEXPR
1034 * element are both created.
1036 SelectionTreeElementPointer
1037 _gmx_sel_assign_variable(const char *name,
1038 const gmx::SelectionTreeElementPointer &expr,
1041 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1042 const char *pselstr = _gmx_sel_lexer_pselstr(scanner);
1043 SelectionTreeElementPointer root;
1045 _gmx_selelem_update_flags(expr);
1046 /* Check if this is a constant non-group value */
1047 if (expr->type == SEL_CONST && expr->v.type != GROUP_VALUE)
1049 /* If so, just assign the constant value to the variable */
1050 sc->symtab->addVariable(name, expr);
1052 /* Check if we are assigning a variable to another variable */
1053 else if (expr->type == SEL_SUBEXPRREF)
1055 /* If so, make a simple alias */
1056 sc->symtab->addVariable(name, expr->child);
1060 /* Create the root element */
1061 root.reset(new SelectionTreeElement(SEL_ROOT));
1062 root->setName(name);
1063 /* Create the subexpression element */
1064 root->child.reset(new SelectionTreeElement(SEL_SUBEXPR));
1065 root->child->setName(name);
1066 _gmx_selelem_set_vtype(root->child, expr->v.type);
1067 root->child->child = expr;
1069 _gmx_selelem_update_flags(root);
1070 gmx::ExceptionInitializer errors("Invalid index group reference(s)");
1071 root->checkUnsortedAtoms(true, &errors);
1072 if (errors.hasNestedExceptions())
1074 GMX_THROW(gmx::InconsistentInputError(errors));
1076 /* Add the variable to the symbol table */
1077 sc->symtab->addVariable(name, root->child);
1079 srenew(sc->varstrs, sc->nvars + 1);
1080 sc->varstrs[sc->nvars] = strdup(pselstr);
1082 if (_gmx_sel_is_lexer_interactive(scanner))
1084 fprintf(stderr, "Variable '%s' parsed\n", pselstr);
1090 * \param sel Selection to append (can be NULL, in which
1091 * case nothing is done).
1092 * \param last Last selection, or NULL if not present or not known.
1093 * \param scanner Scanner data structure.
1094 * \returns The last selection after the append.
1096 * Appends \p sel after the last root element, and returns either \p sel
1097 * (if it was non-NULL) or the last element (if \p sel was NULL).
1099 SelectionTreeElementPointer
1100 _gmx_sel_append_selection(const gmx::SelectionTreeElementPointer &sel,
1101 gmx::SelectionTreeElementPointer last,
1104 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1106 /* Append sel after last, or the last element of sc if last is NULL */
1127 /* Initialize a selection object if necessary */
1131 /* Add the new selection to the collection if it is not a variable. */
1132 if (sel->child->type != SEL_SUBEXPR)
1134 gmx::SelectionDataPointer selPtr(
1135 new gmx::internal::SelectionData(
1136 sel.get(), _gmx_sel_lexer_pselstr(scanner)));
1137 sc->sel.push_back(gmx::move(selPtr));
1140 /* Clear the selection string now that we've saved it */
1141 _gmx_sel_lexer_clear_pselstr(scanner);
1146 * \param[in] scanner Scanner data structure.
1147 * \returns true if the parser should finish, false if parsing should
1150 * This function is called always after _gmx_sel_append_selection() to
1151 * check whether a sufficient number of selections has already been provided.
1152 * This is used to terminate interactive parsers when the correct number of
1153 * selections has been provided.
1156 _gmx_sel_parser_should_finish(yyscan_t scanner)
1158 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1159 return (int)sc->sel.size() == _gmx_sel_lexer_exp_selcount(scanner);