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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/smalloc.h"
237 #include "gromacs/utility/stringutil.h"
239 #include "keywords.h"
242 #include "selectioncollection-impl.h"
244 #include "selmethod.h"
247 using gmx::SelectionLocation;
248 using gmx::SelectionParserValue;
249 using gmx::SelectionParserValueList;
250 using gmx::SelectionParserValueListPointer;
251 using gmx::SelectionParserParameter;
252 using gmx::SelectionParserParameterList;
253 using gmx::SelectionParserParameterListPointer;
254 using gmx::SelectionParserValue;
255 using gmx::SelectionTreeElement;
256 using gmx::SelectionTreeElementPointer;
262 * Formats context string for errors.
264 * The returned string is used as the context for errors reported during
268 formatCurrentErrorContext(yyscan_t scanner)
270 return gmx::formatString(
271 "While parsing '%s'",
272 _gmx_sel_lexer_get_current_text(scanner).c_str());
278 _gmx_selparser_handle_exception(yyscan_t scanner, std::exception *ex)
282 bool canContinue = false;
283 gmx::GromacsException *gromacsException
284 = dynamic_cast<gmx::GromacsException *>(ex);
285 if (gromacsException != NULL)
287 gromacsException->prependContext(formatCurrentErrorContext(scanner));
288 canContinue = (dynamic_cast<gmx::UserInputError *>(ex) != NULL);
290 _gmx_sel_lexer_set_exception(scanner, boost::current_exception());
293 catch (const std::exception &)
295 _gmx_sel_lexer_set_exception(scanner, boost::current_exception());
301 _gmx_selparser_handle_error(yyscan_t scanner)
303 std::string context(gmx::formatString("Invalid selection '%s'",
304 _gmx_sel_lexer_pselstr(scanner)));
305 // The only way to prepend context to the exception is to rethrow it.
308 _gmx_sel_lexer_rethrow_exception_if_occurred(scanner);
310 catch (gmx::UserInputError &ex)
312 ex.prependContext(context);
313 if (_gmx_sel_is_lexer_interactive(scanner))
315 gmx::formatExceptionMessageToFile(stderr, ex);
320 catch (gmx::GromacsException &ex)
322 ex.prependContext(context);
325 GMX_RELEASE_ASSERT(false, "All parsing errors should result in a captured exception");
326 return false; // Some compilers will not believe that the above never returns.
332 /********************************************************************
333 * SelectionParserValue
336 SelectionParserValue::SelectionParserValue(
337 e_selvalue_t type, const SelectionLocation &location)
338 : type(type), location_(location)
340 memset(&u, 0, sizeof(u));
343 SelectionParserValue::SelectionParserValue(
344 const SelectionTreeElementPointer &expr)
345 : type(expr->v.type), expr(expr), location_(expr->location())
347 memset(&u, 0, sizeof(u));
350 /********************************************************************
351 * SelectionParserParameter
354 SelectionParserParameter::SelectionParserParameter(
356 SelectionParserValueListPointer values,
357 const SelectionLocation &location)
358 : name_(name != NULL ? name : ""), location_(location),
359 values_(values ? move(values)
360 : SelectionParserValueListPointer(new SelectionParserValueList))
367 * \param[in,out] sel Root of the selection element tree to initialize.
369 * Propagates the \ref SEL_DYNAMIC flag from the children of \p sel to \p sel
370 * (if any child of \p sel is dynamic, \p sel is also marked as such).
371 * The \ref SEL_DYNAMIC flag is also set for \ref SEL_EXPRESSION elements with
373 * Also, sets one of the \ref SEL_SINGLEVAL, \ref SEL_ATOMVAL, or
374 * \ref SEL_VARNUMVAL flags, either based on the children or on the type of
375 * the selection method.
376 * If the types of the children conflict, an error is returned.
378 * The flags of the children of \p sel are also updated if not done earlier.
379 * The flags are initialized only once for any element; if \ref SEL_FLAGSSET
380 * is set for an element, the function returns immediately, and the recursive
381 * operation does not descend beyond such elements.
384 _gmx_selelem_update_flags(const gmx::SelectionTreeElementPointer &sel)
386 bool bUseChildType = false;
387 bool bOnlySingleChildren;
389 /* Return if the flags have already been set */
390 if (sel->flags & SEL_FLAGSSET)
394 /* Set the flags based on the current element type */
399 sel->flags |= SEL_SINGLEVAL;
400 bUseChildType = false;
404 if (sel->u.expr.method->flags & SMETH_DYNAMIC)
406 sel->flags |= SEL_DYNAMIC;
408 if (sel->u.expr.method->flags & SMETH_SINGLEVAL)
410 sel->flags |= SEL_SINGLEVAL;
412 else if (sel->u.expr.method->flags & SMETH_VARNUMVAL)
414 sel->flags |= SEL_VARNUMVAL;
418 sel->flags |= SEL_ATOMVAL;
420 bUseChildType = false;
424 sel->flags |= SEL_ATOMVAL;
425 bUseChildType = false;
429 if (sel->v.type != NO_VALUE)
431 sel->flags |= SEL_VARNUMVAL;
433 bUseChildType = false;
437 bUseChildType = false;
443 bUseChildType = true;
446 /* Loop through children to propagate their flags upwards */
447 bOnlySingleChildren = true;
448 SelectionTreeElementPointer child = sel->child;
451 /* Update the child */
452 _gmx_selelem_update_flags(child);
453 /* Propagate the dynamic and unsorted flags */
454 sel->flags |= (child->flags & (SEL_DYNAMIC | SEL_UNSORTED));
455 /* Propagate the type flag if necessary and check for problems */
458 if ((sel->flags & SEL_VALTYPEMASK)
459 && !(sel->flags & child->flags & SEL_VALTYPEMASK))
461 // TODO: Recollect when this is triggered, and whether the type
463 GMX_THROW(gmx::InvalidInputError("Invalid combination of selection expressions"));
465 sel->flags |= (child->flags & SEL_VALTYPEMASK);
467 if (!(child->flags & SEL_SINGLEVAL))
469 bOnlySingleChildren = false;
474 /* For arithmetic expressions consisting only of single values,
475 * the result is also a single value. */
476 if (sel->type == SEL_ARITHMETIC && bOnlySingleChildren)
478 sel->flags = (sel->flags & ~SEL_VALTYPEMASK) | SEL_SINGLEVAL;
480 /* For root elements, the type should be propagated here, after the
481 * children have been updated. */
482 if (sel->type == SEL_ROOT)
484 GMX_ASSERT(sel->child, "Root elements should always have a child");
485 sel->flags |= (sel->child->flags & SEL_VALTYPEMASK);
487 /* Mark that the flags are set */
488 sel->flags |= SEL_FLAGSSET;
492 * \param[in,out] sel Selection element to initialize.
493 * \param[in] scanner Scanner data structure.
495 * A deep copy of the parameters is made to allow several
496 * expressions with the same method to coexist peacefully.
497 * Calls sel_datafunc() if one is specified for the method.
500 _gmx_selelem_init_method_params(const gmx::SelectionTreeElementPointer &sel,
504 gmx_ana_selparam_t *orgparam;
505 gmx_ana_selparam_t *param;
509 nparams = sel->u.expr.method->nparams;
510 orgparam = sel->u.expr.method->param;
511 snew(param, nparams);
512 memcpy(param, orgparam, nparams*sizeof(gmx_ana_selparam_t));
513 for (i = 0; i < nparams; ++i)
515 param[i].flags &= ~SPAR_SET;
516 _gmx_selvalue_setstore(¶m[i].val, NULL);
517 if (param[i].flags & SPAR_VARNUM)
519 param[i].val.nr = -1;
521 /* Duplicate the enum value array if it is given statically */
522 if ((param[i].flags & SPAR_ENUMVAL) && orgparam[i].val.u.ptr != NULL)
526 /* Count the values */
528 while (orgparam[i].val.u.s[n] != NULL)
532 _gmx_selvalue_reserve(¶m[i].val, n+1);
533 memcpy(param[i].val.u.s, orgparam[i].val.u.s,
534 (n+1)*sizeof(param[i].val.u.s[0]));
538 if (sel->u.expr.method->init_data)
540 mdata = sel->u.expr.method->init_data(nparams, param);
542 if (sel->u.expr.method->set_poscoll)
544 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
546 sel->u.expr.method->set_poscoll(&sc->pcc, mdata);
548 /* Store the values */
549 sel->u.expr.method->param = param;
550 sel->u.expr.mdata = mdata;
554 * \param[in,out] sel Selection element to initialize.
555 * \param[in] method Selection method to set.
556 * \param[in] scanner Scanner data structure.
558 * Makes a copy of \p method and stores it in \p sel->u.expr.method,
559 * and calls _gmx_selelem_init_method_params();
562 _gmx_selelem_set_method(const gmx::SelectionTreeElementPointer &sel,
563 gmx_ana_selmethod_t *method,
566 _gmx_selelem_set_vtype(sel, method->type);
567 sel->setName(method->name);
568 snew(sel->u.expr.method, 1);
569 memcpy(sel->u.expr.method, method, sizeof(gmx_ana_selmethod_t));
570 _gmx_selelem_init_method_params(sel, scanner);
574 * Initializes the reference position calculation for a \ref SEL_EXPRESSION
577 * \param[in,out] pcc Position calculation collection to use.
578 * \param[in,out] sel Selection element to initialize.
579 * \param[in] rpost Reference position type to use (NULL = default).
582 set_refpos_type(gmx::PositionCalculationCollection *pcc,
583 const SelectionTreeElementPointer &sel,
591 if (sel->u.expr.method->pupdate)
593 /* By default, use whole residues/molecules. */
595 = pcc->createCalculationFromEnum(rpost, POS_COMPLWHOLE);
600 = gmx::formatString("Position modifiers ('%s') is not applicable for '%s'",
601 rpost, sel->u.expr.method->name);
602 GMX_THROW(gmx::InvalidInputError(message));
606 gmx::SelectionTreeElementPointer
607 _gmx_sel_init_arithmetic(const gmx::SelectionTreeElementPointer &left,
608 const gmx::SelectionTreeElementPointer &right,
609 char op, yyscan_t scanner)
611 SelectionTreeElementPointer sel(
612 new SelectionTreeElement(
613 SEL_ARITHMETIC, _gmx_sel_lexer_get_current_location(scanner)));
614 sel->v.type = REAL_VALUE;
617 case '+': sel->u.arith.type = ARITH_PLUS; break;
618 case '-': sel->u.arith.type = (right ? ARITH_MINUS : ARITH_NEG); break;
619 case '*': sel->u.arith.type = ARITH_MULT; break;
620 case '/': sel->u.arith.type = ARITH_DIV; break;
621 case '^': sel->u.arith.type = ARITH_EXP; break;
627 sel->u.arith.opstr = gmx_strdup(buf);
629 sel->child->next = right;
634 * \param[in] left Selection element for the left hand side.
635 * \param[in] right Selection element for the right hand side.
636 * \param[in] cmpop String representation of the comparison operator.
637 * \param[in] scanner Scanner data structure.
638 * \returns The created selection element.
640 * This function handles the creation of a gmx::SelectionTreeElement object for
641 * comparison expressions.
643 SelectionTreeElementPointer
644 _gmx_sel_init_comparison(const gmx::SelectionTreeElementPointer &left,
645 const gmx::SelectionTreeElementPointer &right,
646 const char *cmpop, yyscan_t scanner)
648 SelectionTreeElementPointer sel(
649 new SelectionTreeElement(
650 SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
651 _gmx_selelem_set_method(sel, &sm_compare, scanner);
653 SelectionParserParameterList params;
655 // Create the parameter for the left expression.
656 name = left->v.type == INT_VALUE ? "int1" : "real1";
657 params.push_back(SelectionParserParameter::createFromExpression(name, left));
658 // Create the parameter for the right expression.
659 name = right->v.type == INT_VALUE ? "int2" : "real2";
660 params.push_back(SelectionParserParameter::createFromExpression(name, right));
661 // Create the parameter for the operator.
662 // TODO: Consider whether a proper location is needed.
663 SelectionLocation location(SelectionLocation::createEmpty());
665 SelectionParserParameter::create(
666 "op", SelectionParserValue::createString(cmpop, location),
668 _gmx_sel_parse_params(params, sel->u.expr.method->nparams,
669 sel->u.expr.method->param, sel, scanner);
675 * Implementation method for keyword expression creation.
677 * \param[in] method Method to use.
678 * \param[in] matchType String matching type (only used if \p method is
679 * a string keyword and \p args is not empty.
680 * \param[in] args Pointer to the first argument.
681 * \param[in] rpost Reference position type to use (NULL = default).
682 * \param[in] scanner Scanner data structure.
683 * \returns The created selection element.
685 * This function handles the creation of a gmx::SelectionTreeElement object for
686 * selection methods that do not take parameters.
688 static SelectionTreeElementPointer
689 init_keyword_internal(gmx_ana_selmethod_t *method,
690 gmx::SelectionStringMatchType matchType,
691 SelectionParserValueListPointer args,
692 const char *rpost, yyscan_t scanner)
694 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
696 if (method->nparams > 0)
698 // TODO: Would assert be better?
699 GMX_THROW(gmx::InternalError(
700 "Keyword initialization called with non-keyword method"));
703 const SelectionLocation &location = _gmx_sel_lexer_get_current_location(scanner);
704 // TODO: If there are arguments, the location would be better as just the
705 // location of the keyword itself.
706 SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION, location));
707 SelectionTreeElementPointer child = root;
708 _gmx_selelem_set_method(child, method, scanner);
710 /* Initialize the evaluation of keyword matching if values are provided */
713 gmx_ana_selmethod_t *kwmethod;
714 switch (method->type)
716 case INT_VALUE: kwmethod = &sm_keyword_int; break;
717 case REAL_VALUE: kwmethod = &sm_keyword_real; break;
718 case STR_VALUE: kwmethod = &sm_keyword_str; break;
720 GMX_THROW(gmx::InternalError(
721 "Unknown type for keyword selection"));
723 /* Initialize the selection element */
724 root.reset(new SelectionTreeElement(SEL_EXPRESSION, location));
725 _gmx_selelem_set_method(root, kwmethod, scanner);
726 if (method->type == STR_VALUE)
728 _gmx_selelem_set_kwstr_match_type(root, matchType);
730 SelectionParserParameterList params;
732 SelectionParserParameter::createFromExpression(NULL, child));
734 SelectionParserParameter::create(NULL, move(args), location));
735 _gmx_sel_parse_params(params, root->u.expr.method->nparams,
736 root->u.expr.method->param, root, scanner);
738 set_refpos_type(&sc->pcc, child, rpost);
744 * \param[in] method Method to use.
745 * \param[in] args Pointer to the first argument.
746 * \param[in] rpost Reference position type to use (NULL = default).
747 * \param[in] scanner Scanner data structure.
748 * \returns The created selection element.
750 * This function handles the creation of a gmx::SelectionTreeElement object for
751 * selection methods that do not take parameters.
753 SelectionTreeElementPointer
754 _gmx_sel_init_keyword(gmx_ana_selmethod_t *method,
755 gmx::SelectionParserValueListPointer args,
756 const char *rpost, yyscan_t scanner)
758 return init_keyword_internal(method, gmx::eStringMatchType_Auto, move(args),
763 * \param[in] method Method to use.
764 * \param[in] matchType String matching type.
765 * \param[in] args Pointer to the first argument.
766 * \param[in] rpost Reference position type to use (NULL = default).
767 * \param[in] scanner Scanner data structure.
768 * \returns The created selection element.
770 * This function handles the creation of a gmx::SelectionTreeElement object for
771 * keyword string matching.
773 SelectionTreeElementPointer
774 _gmx_sel_init_keyword_strmatch(gmx_ana_selmethod_t *method,
775 gmx::SelectionStringMatchType matchType,
776 gmx::SelectionParserValueListPointer args,
777 const char *rpost, yyscan_t scanner)
779 GMX_RELEASE_ASSERT(method->type == STR_VALUE,
780 "String keyword method called for a non-string-valued method");
781 GMX_RELEASE_ASSERT(args && !args->empty(),
782 "String keyword matching method called without any values");
783 return init_keyword_internal(method, matchType, move(args), rpost, scanner);
787 * \param[in] method Method to use for initialization.
788 * \param[in] group Selection in which the keyword should be evaluated.
789 * \param[in] rpost Reference position type to use (NULL = default).
790 * \param[in] scanner Scanner data structure.
791 * \returns The created selection element.
793 * This function handles the creation of a gmx::SelectionTreeElement object for
794 * expressions like "z of ...".
796 SelectionTreeElementPointer
797 _gmx_sel_init_keyword_of(gmx_ana_selmethod_t *method,
798 const gmx::SelectionTreeElementPointer &group,
799 const char *rpost, yyscan_t scanner)
801 // TODO Provide an error if rpost is provided.
802 GMX_UNUSED_VALUE(rpost);
803 return _gmx_sel_init_keyword_evaluator(method, group, scanner);
807 * \param[in] method Method to use for initialization.
808 * \param[in] params Pointer to the first parameter.
809 * \param[in] rpost Reference position type to use (NULL = default).
810 * \param[in] scanner Scanner data structure.
811 * \returns The created selection element.
813 * This function handles the creation of a gmx::SelectionTreeElement object for
814 * selection methods that take parameters.
816 * Part of the behavior of the \c same selection keyword is hardcoded into
817 * this function (or rather, into _gmx_selelem_custom_init_same()) to allow the
818 * use of any keyword in \c "same KEYWORD as" without requiring special
819 * handling somewhere else (or sacrificing the simple syntax).
821 SelectionTreeElementPointer
822 _gmx_sel_init_method(gmx_ana_selmethod_t *method,
823 gmx::SelectionParserParameterListPointer params,
824 const char *rpost, yyscan_t scanner)
826 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
828 _gmx_sel_finish_method(scanner);
829 /* The "same" keyword needs some custom massaging of the parameters. */
830 _gmx_selelem_custom_init_same(&method, params, scanner);
831 SelectionTreeElementPointer root(
832 new SelectionTreeElement(
833 SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
834 _gmx_selelem_set_method(root, method, scanner);
835 /* Process the parameters */
836 _gmx_sel_parse_params(*params, root->u.expr.method->nparams,
837 root->u.expr.method->param, root, scanner);
838 set_refpos_type(&sc->pcc, root, rpost);
844 * \param[in] method Modifier to use for initialization.
845 * \param[in] params Pointer to the first parameter.
846 * \param[in] sel Selection element that the modifier should act on.
847 * \param[in] scanner Scanner data structure.
848 * \returns The created selection element.
850 * This function handles the creation of a gmx::SelectionTreeElement object for
851 * selection modifiers.
853 SelectionTreeElementPointer
854 _gmx_sel_init_modifier(gmx_ana_selmethod_t *method,
855 gmx::SelectionParserParameterListPointer params,
856 const gmx::SelectionTreeElementPointer &sel,
859 _gmx_sel_finish_method(scanner);
860 SelectionTreeElementPointer modifier(
861 new SelectionTreeElement(
862 SEL_MODIFIER, _gmx_sel_lexer_get_current_location(scanner)));
863 _gmx_selelem_set_method(modifier, method, scanner);
864 SelectionTreeElementPointer root;
865 if (method->type == NO_VALUE)
867 SelectionTreeElementPointer child = sel;
872 child->next = modifier;
878 SelectionParserParameter::createFromExpression(NULL, sel));
881 /* Process the parameters */
882 _gmx_sel_parse_params(*params, modifier->u.expr.method->nparams,
883 modifier->u.expr.method->param, modifier, scanner);
889 * \param[in] expr Input selection element for the position calculation.
890 * \param[in] type Reference position type or NULL for default.
891 * \param[in] scanner Scanner data structure.
892 * \returns The created selection element.
894 * This function handles the creation of a gmx::SelectionTreeElement object for
895 * evaluation of reference positions.
897 SelectionTreeElementPointer
898 _gmx_sel_init_position(const gmx::SelectionTreeElementPointer &expr,
899 const char *type, yyscan_t scanner)
901 SelectionTreeElementPointer root(
902 new SelectionTreeElement(
903 SEL_EXPRESSION, _gmx_sel_lexer_get_current_location(scanner)));
904 _gmx_selelem_set_method(root, &sm_keyword_pos, scanner);
905 _gmx_selelem_set_kwpos_type(root.get(), type);
906 /* Create the parameters for the parameter parser. */
907 SelectionParserParameterList params;
908 params.push_back(SelectionParserParameter::createFromExpression(NULL, expr));
909 /* Parse the parameters. */
910 _gmx_sel_parse_params(params, root->u.expr.method->nparams,
911 root->u.expr.method->param, root, scanner);
917 * \param[in] x,y,z Coordinates for the position.
918 * \param[in] scanner Scanner data structure.
919 * \returns The creates selection element.
921 SelectionTreeElementPointer
922 _gmx_sel_init_const_position(real x, real y, real z, yyscan_t scanner)
926 SelectionTreeElementPointer sel(
927 new SelectionTreeElement(
928 SEL_CONST, _gmx_sel_lexer_get_current_location(scanner)));
929 _gmx_selelem_set_vtype(sel, POS_VALUE);
930 _gmx_selvalue_reserve(&sel->v, 1);
934 gmx_ana_pos_init_const(sel->v.u.p, pos);
939 * \param[in] name Name of an index group to search for.
940 * \param[in] scanner Scanner data structure.
941 * \returns The created selection element.
943 * See gmx_ana_indexgrps_find() for information on how \p name is matched
944 * against the index groups.
946 SelectionTreeElementPointer
947 _gmx_sel_init_group_by_name(const char *name, yyscan_t scanner)
950 SelectionTreeElementPointer sel(
951 new SelectionTreeElement(
952 SEL_GROUPREF, _gmx_sel_lexer_get_current_location(scanner)));
953 _gmx_selelem_set_vtype(sel, GROUP_VALUE);
954 sel->setName(gmx::formatString("group \"%s\"", name));
955 sel->u.gref.name = gmx_strdup(name);
958 if (_gmx_sel_lexer_has_groups_set(scanner))
960 gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
961 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
962 sel->resolveIndexGroupReference(grps, sc->gall.isize);
969 * \param[in] id Zero-based index number of the group to extract.
970 * \param[in] scanner Scanner data structure.
971 * \returns The created selection element.
973 SelectionTreeElementPointer
974 _gmx_sel_init_group_by_id(int id, yyscan_t scanner)
976 SelectionTreeElementPointer sel(
977 new SelectionTreeElement(
978 SEL_GROUPREF, _gmx_sel_lexer_get_current_location(scanner)));
979 _gmx_selelem_set_vtype(sel, GROUP_VALUE);
980 sel->setName(gmx::formatString("group %d", id));
981 sel->u.gref.name = NULL;
984 if (_gmx_sel_lexer_has_groups_set(scanner))
986 gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
987 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
988 sel->resolveIndexGroupReference(grps, sc->gall.isize);
995 * \param[in,out] sel Value of the variable.
996 * \param scanner Scanner data structure.
997 * \returns The created selection element that references \p sel.
999 * The reference count of \p sel is updated, but no other modifications are
1002 SelectionTreeElementPointer
1003 _gmx_sel_init_variable_ref(const gmx::SelectionTreeElementPointer &sel,
1006 SelectionTreeElementPointer ref;
1008 if (sel->v.type == POS_VALUE && sel->type == SEL_CONST)
1014 ref.reset(new SelectionTreeElement(
1015 SEL_SUBEXPRREF, _gmx_sel_lexer_get_current_location(scanner)));
1016 _gmx_selelem_set_vtype(ref, sel->v.type);
1017 ref->setName(sel->name());
1024 * \param[in] name Name for the selection
1025 * (if NULL, a default name is constructed).
1026 * \param[in] sel The selection element that evaluates the selection.
1027 * \param scanner Scanner data structure.
1028 * \returns The created root selection element.
1030 * This function handles the creation of root (\ref SEL_ROOT)
1031 * gmx::SelectionTreeElement objects for selections.
1033 SelectionTreeElementPointer
1034 _gmx_sel_init_selection(const char *name,
1035 const gmx::SelectionTreeElementPointer &sel,
1038 if (sel->v.type != POS_VALUE)
1040 /* FIXME: Better handling of this error */
1041 GMX_THROW(gmx::InternalError(
1042 "Each selection must evaluate to a position"));
1045 SelectionTreeElementPointer root(
1046 new SelectionTreeElement(
1047 SEL_ROOT, _gmx_sel_lexer_get_current_location(scanner)));
1051 root->setName(name);
1053 /* Update the flags */
1054 _gmx_selelem_update_flags(root);
1055 gmx::ExceptionInitializer errors("Invalid index group reference(s)");
1056 root->checkUnsortedAtoms(true, &errors);
1057 if (errors.hasNestedExceptions())
1059 GMX_THROW(gmx::InconsistentInputError(errors));
1062 root->fillNameIfMissing(_gmx_sel_lexer_pselstr(scanner));
1064 /* Print out some information if the parser is interactive */
1065 if (_gmx_sel_is_lexer_interactive(scanner))
1067 fprintf(stderr, "Selection '%s' parsed\n",
1068 _gmx_sel_lexer_pselstr(scanner));
1076 * \param[in] name Name of the variable.
1077 * \param[in] expr The selection element that evaluates the variable.
1078 * \param scanner Scanner data structure.
1079 * \returns The created root selection element.
1081 * This function handles the creation of root gmx::SelectionTreeElement objects
1082 * for variable assignments. A \ref SEL_ROOT element and a \ref SEL_SUBEXPR
1083 * element are both created.
1085 SelectionTreeElementPointer
1086 _gmx_sel_assign_variable(const char *name,
1087 const gmx::SelectionTreeElementPointer &expr,
1090 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1091 const char *pselstr = _gmx_sel_lexer_pselstr(scanner);
1092 SelectionTreeElementPointer root;
1094 _gmx_selelem_update_flags(expr);
1095 /* Check if this is a constant non-group value */
1096 if (expr->type == SEL_CONST && expr->v.type != GROUP_VALUE)
1098 /* If so, just assign the constant value to the variable */
1099 sc->symtab->addVariable(name, expr);
1101 /* Check if we are assigning a variable to another variable */
1102 else if (expr->type == SEL_SUBEXPRREF)
1104 /* If so, make a simple alias */
1105 sc->symtab->addVariable(name, expr->child);
1109 SelectionLocation location(_gmx_sel_lexer_get_current_location(scanner));
1110 /* Create the root element */
1111 root.reset(new SelectionTreeElement(SEL_ROOT, location));
1112 root->setName(name);
1113 /* Create the subexpression element */
1114 root->child.reset(new SelectionTreeElement(SEL_SUBEXPR, location));
1115 root->child->setName(name);
1116 _gmx_selelem_set_vtype(root->child, expr->v.type);
1117 root->child->child = expr;
1119 _gmx_selelem_update_flags(root);
1120 gmx::ExceptionInitializer errors("Invalid index group reference(s)");
1121 root->checkUnsortedAtoms(true, &errors);
1122 if (errors.hasNestedExceptions())
1124 GMX_THROW(gmx::InconsistentInputError(errors));
1126 /* Add the variable to the symbol table */
1127 sc->symtab->addVariable(name, root->child);
1129 srenew(sc->varstrs, sc->nvars + 1);
1130 sc->varstrs[sc->nvars] = gmx_strdup(pselstr);
1132 if (_gmx_sel_is_lexer_interactive(scanner))
1134 fprintf(stderr, "Variable '%s' parsed\n", pselstr);
1140 * \param sel Selection to append (can be NULL, in which
1141 * case nothing is done).
1142 * \param last Last selection, or NULL if not present or not known.
1143 * \param scanner Scanner data structure.
1144 * \returns The last selection after the append.
1146 * Appends \p sel after the last root element, and returns either \p sel
1147 * (if it was non-NULL) or the last element (if \p sel was NULL).
1149 SelectionTreeElementPointer
1150 _gmx_sel_append_selection(const gmx::SelectionTreeElementPointer &sel,
1151 gmx::SelectionTreeElementPointer last,
1154 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1156 /* Append sel after last, or the last element of sc if last is NULL */
1177 /* Initialize a selection object if necessary */
1181 /* Add the new selection to the collection if it is not a variable. */
1182 if (sel->child->type != SEL_SUBEXPR)
1184 gmx::SelectionDataPointer selPtr(
1185 new gmx::internal::SelectionData(
1186 sel.get(), _gmx_sel_lexer_pselstr(scanner)));
1187 sc->sel.push_back(gmx::move(selPtr));
1190 /* Clear the selection string now that we've saved it */
1191 _gmx_sel_lexer_clear_pselstr(scanner);
1196 * \param[in] scanner Scanner data structure.
1197 * \returns true if the parser should finish, false if parsing should
1200 * This function is called always after _gmx_sel_append_selection() to
1201 * check whether a sufficient number of selections has already been provided.
1202 * This is used to terminate interactive parsers when the correct number of
1203 * selections has been provided.
1206 _gmx_sel_parser_should_finish(yyscan_t scanner)
1208 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1209 return (int)sc->sel.size() == _gmx_sel_lexer_exp_selcount(scanner);