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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/legacyheaders/futil.h"
229 #include "gromacs/legacyheaders/smalloc.h"
230 #include "gromacs/legacyheaders/string2.h"
232 #include "gromacs/onlinehelp/helpmanager.h"
233 #include "gromacs/onlinehelp/helpwritercontext.h"
234 #include "gromacs/selection/poscalc.h"
235 #include "gromacs/selection/selection.h"
236 #include "gromacs/selection/selmethod.h"
237 #include "gromacs/utility/exceptions.h"
238 #include "gromacs/utility/file.h"
239 #include "gromacs/utility/messagestringcollector.h"
240 #include "gromacs/utility/stringutil.h"
242 #include "keywords.h"
243 #include "parsetree.h"
244 #include "selectioncollection-impl.h"
251 using gmx::SelectionParserValue;
252 using gmx::SelectionParserValueList;
253 using gmx::SelectionParserValueListPointer;
254 using gmx::SelectionParserParameter;
255 using gmx::SelectionParserParameterList;
256 using gmx::SelectionParserParameterListPointer;
257 using gmx::SelectionParserValue;
258 using gmx::SelectionTreeElement;
259 using gmx::SelectionTreeElementPointer;
262 _gmx_selparser_error(yyscan_t scanner, const char *fmt, ...)
264 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
265 // FIXME: Use an arbitrary length buffer.
269 vsprintf(buf, fmt, ap);
275 _gmx_selparser_handle_exception(yyscan_t scanner, const std::exception &ex)
277 if (dynamic_cast<const gmx::UserInputError *>(&ex) != NULL)
279 // TODO: Consider whether also the non-interactive parser should
280 // postpone the exception such that the whole selection can be added as
282 if (_gmx_sel_is_lexer_interactive(scanner))
284 // TODO: Handle exceptions that printing the message may produce.
285 gmx::formatExceptionMessageToFile(stderr, ex);
289 _gmx_sel_lexer_set_exception(scanner, boost::current_exception());
296 /********************************************************************
297 * SelectionParserValue
300 SelectionParserValue::SelectionParserValue(e_selvalue_t type)
303 memset(&u, 0, sizeof(u));
306 SelectionParserValue::SelectionParserValue(
307 const SelectionTreeElementPointer &expr)
308 : type(expr->v.type), expr(expr)
310 memset(&u, 0, sizeof(u));
313 /********************************************************************
314 * SelectionParserParameter
317 SelectionParserParameter::SelectionParserParameter(
319 SelectionParserValueListPointer values)
320 : name_(name != NULL ? name : ""),
321 values_(values ? move(values)
322 : SelectionParserValueListPointer(new SelectionParserValueList))
329 * \param[in,out] sel Root of the selection element tree to initialize.
330 * \param[in] scanner Scanner data structure.
331 * \returns 0 on success, an error code on error.
333 * Propagates the \ref SEL_DYNAMIC flag from the children of \p sel to \p sel
334 * (if any child of \p sel is dynamic, \p sel is also marked as such).
335 * The \ref SEL_DYNAMIC flag is also set for \ref SEL_EXPRESSION elements with
337 * Also, sets one of the \ref SEL_SINGLEVAL, \ref SEL_ATOMVAL, or
338 * \ref SEL_VARNUMVAL flags, either based on the children or on the type of
339 * the selection method.
340 * If the types of the children conflict, an error is returned.
342 * The flags of the children of \p sel are also updated if not done earlier.
343 * The flags are initialized only once for any element; if \ref SEL_FLAGSSET
344 * is set for an element, the function returns immediately, and the recursive
345 * operation does not descend beyond such elements.
348 _gmx_selelem_update_flags(const SelectionTreeElementPointer &sel,
351 bool bUseChildType = false;
352 bool bOnlySingleChildren;
354 /* Return if the flags have already been set */
355 if (sel->flags & SEL_FLAGSSET)
359 /* Set the flags based on the current element type */
364 sel->flags |= SEL_SINGLEVAL;
365 bUseChildType = false;
369 if (sel->u.expr.method->flags & SMETH_DYNAMIC)
371 sel->flags |= SEL_DYNAMIC;
373 if (sel->u.expr.method->flags & SMETH_SINGLEVAL)
375 sel->flags |= SEL_SINGLEVAL;
377 else if (sel->u.expr.method->flags & SMETH_VARNUMVAL)
379 sel->flags |= SEL_VARNUMVAL;
383 sel->flags |= SEL_ATOMVAL;
385 bUseChildType = false;
389 sel->flags |= SEL_ATOMVAL;
390 bUseChildType = false;
394 if (sel->v.type != NO_VALUE)
396 sel->flags |= SEL_VARNUMVAL;
398 bUseChildType = false;
402 bUseChildType = false;
408 bUseChildType = true;
411 /* Loop through children to propagate their flags upwards */
412 bOnlySingleChildren = true;
413 SelectionTreeElementPointer child = sel->child;
416 /* Update the child */
417 _gmx_selelem_update_flags(child, scanner);
418 /* Propagate the dynamic flag */
419 sel->flags |= (child->flags & SEL_DYNAMIC);
420 /* Propagate the type flag if necessary and check for problems */
423 if ((sel->flags & SEL_VALTYPEMASK)
424 && !(sel->flags & child->flags & SEL_VALTYPEMASK))
426 _gmx_selparser_error(scanner, "invalid combination of selection expressions");
427 // FIXME: Use an exception.
430 sel->flags |= (child->flags & SEL_VALTYPEMASK);
432 if (!(child->flags & SEL_SINGLEVAL))
434 bOnlySingleChildren = false;
439 /* For arithmetic expressions consisting only of single values,
440 * the result is also a single value. */
441 if (sel->type == SEL_ARITHMETIC && bOnlySingleChildren)
443 sel->flags = (sel->flags & ~SEL_VALTYPEMASK) | SEL_SINGLEVAL;
445 /* For root elements, the type should be propagated here, after the
446 * children have been updated. */
447 if (sel->type == SEL_ROOT)
449 GMX_ASSERT(sel->child, "Root elements should always have a child");
450 sel->flags |= (sel->child->flags & SEL_VALTYPEMASK);
452 /* Mark that the flags are set */
453 sel->flags |= SEL_FLAGSSET;
457 * \param[in,out] sel Selection element to initialize.
458 * \param[in] scanner Scanner data structure.
460 * A deep copy of the parameters is made to allow several
461 * expressions with the same method to coexist peacefully.
462 * Calls sel_datafunc() if one is specified for the method.
465 _gmx_selelem_init_method_params(const SelectionTreeElementPointer &sel,
469 gmx_ana_selparam_t *orgparam;
470 gmx_ana_selparam_t *param;
474 nparams = sel->u.expr.method->nparams;
475 orgparam = sel->u.expr.method->param;
476 snew(param, nparams);
477 memcpy(param, orgparam, nparams*sizeof(gmx_ana_selparam_t));
478 for (i = 0; i < nparams; ++i)
480 param[i].flags &= ~SPAR_SET;
481 _gmx_selvalue_setstore(¶m[i].val, NULL);
482 if (param[i].flags & SPAR_VARNUM)
484 param[i].val.nr = -1;
486 /* Duplicate the enum value array if it is given statically */
487 if ((param[i].flags & SPAR_ENUMVAL) && orgparam[i].val.u.ptr != NULL)
491 /* Count the values */
493 while (orgparam[i].val.u.s[n] != NULL)
497 _gmx_selvalue_reserve(¶m[i].val, n+1);
498 memcpy(param[i].val.u.s, orgparam[i].val.u.s,
499 (n+1)*sizeof(param[i].val.u.s[0]));
503 if (sel->u.expr.method->init_data)
505 mdata = sel->u.expr.method->init_data(nparams, param);
507 if (sel->u.expr.method->set_poscoll)
509 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
511 sel->u.expr.method->set_poscoll(&sc->pcc, mdata);
513 /* Store the values */
514 sel->u.expr.method->param = param;
515 sel->u.expr.mdata = mdata;
519 * \param[in,out] sel Selection element to initialize.
520 * \param[in] method Selection method to set.
521 * \param[in] scanner Scanner data structure.
523 * Makes a copy of \p method and stores it in \p sel->u.expr.method,
524 * and calls _gmx_selelem_init_method_params();
527 _gmx_selelem_set_method(const SelectionTreeElementPointer &sel,
528 gmx_ana_selmethod_t *method,
531 _gmx_selelem_set_vtype(sel, method->type);
532 sel->setName(method->name);
533 snew(sel->u.expr.method, 1);
534 memcpy(sel->u.expr.method, method, sizeof(gmx_ana_selmethod_t));
535 _gmx_selelem_init_method_params(sel, scanner);
539 * Initializes the reference position calculation for a \ref SEL_EXPRESSION
542 * \param[in,out] pcc Position calculation collection to use.
543 * \param[in,out] sel Selection element to initialize.
544 * \param[in] rpost Reference position type to use (NULL = default).
545 * \param[in] scanner Scanner data structure.
546 * \returns 0 on success, a non-zero error code on error.
549 set_refpos_type(gmx::PositionCalculationCollection *pcc,
550 const SelectionTreeElementPointer &sel,
551 const char *rpost, yyscan_t scanner)
558 if (sel->u.expr.method->pupdate)
560 /* By default, use whole residues/molecules. */
562 = pcc->createCalculationFromEnum(rpost, POS_COMPLWHOLE);
566 // TODO: Should this be treated as a real error?
567 _gmx_selparser_error(scanner, "modifier '%s' is not applicable for '%s'",
568 rpost, sel->u.expr.method->name);
573 * \param[in] left Selection element for the left hand side.
574 * \param[in] right Selection element for the right hand side.
575 * \param[in] op String representation of the operator.
576 * \param[in] scanner Scanner data structure.
577 * \returns The created selection element.
579 * This function handles the creation of a gmx::SelectionTreeElement object for
580 * arithmetic expressions.
582 SelectionTreeElementPointer
583 _gmx_sel_init_arithmetic(const SelectionTreeElementPointer &left,
584 const SelectionTreeElementPointer &right,
585 char op, yyscan_t scanner)
587 SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_ARITHMETIC));
588 sel->v.type = REAL_VALUE;
591 case '+': sel->u.arith.type = ARITH_PLUS; break;
592 case '-': sel->u.arith.type = (right ? ARITH_MINUS : ARITH_NEG); break;
593 case '*': sel->u.arith.type = ARITH_MULT; break;
594 case '/': sel->u.arith.type = ARITH_DIV; break;
595 case '^': sel->u.arith.type = ARITH_EXP; break;
601 sel->u.arith.opstr = strdup(buf);
603 sel->child->next = right;
608 * \param[in] left Selection element for the left hand side.
609 * \param[in] right Selection element for the right hand side.
610 * \param[in] cmpop String representation of the comparison operator.
611 * \param[in] scanner Scanner data structure.
612 * \returns The created selection element.
614 * This function handles the creation of a gmx::SelectionTreeElement object for
615 * comparison expressions.
617 SelectionTreeElementPointer
618 _gmx_sel_init_comparison(const SelectionTreeElementPointer &left,
619 const SelectionTreeElementPointer &right,
620 const char *cmpop, yyscan_t scanner)
622 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
623 gmx::MessageStringContext context(errors, "In comparison initialization");
625 SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_EXPRESSION));
626 _gmx_selelem_set_method(sel, &sm_compare, scanner);
628 SelectionParserParameterList params;
630 // Create the parameter for the left expression.
631 name = left->v.type == INT_VALUE ? "int1" : "real1";
632 params.push_back(SelectionParserParameter::createFromExpression(name, left));
633 // Create the parameter for the right expression.
634 name = right->v.type == INT_VALUE ? "int2" : "real2";
635 params.push_back(SelectionParserParameter::createFromExpression(name, right));
636 // Create the parameter for the operator.
638 SelectionParserParameter::create(
639 "op", SelectionParserValue::createString(cmpop)));
640 if (!_gmx_sel_parse_params(params, sel->u.expr.method->nparams,
641 sel->u.expr.method->param, sel, scanner))
643 return SelectionTreeElementPointer();
650 * Implementation method for keyword expression creation.
652 * \param[in] method Method to use.
653 * \param[in] matchType String matching type (only used if \p method is
654 * a string keyword and \p args is not empty.
655 * \param[in] args Pointer to the first argument.
656 * \param[in] rpost Reference position type to use (NULL = default).
657 * \param[in] scanner Scanner data structure.
658 * \returns The created selection element.
660 * This function handles the creation of a gmx::SelectionTreeElement object for
661 * selection methods that do not take parameters.
663 static SelectionTreeElementPointer
664 init_keyword_internal(gmx_ana_selmethod_t *method,
665 gmx::SelectionStringMatchType matchType,
666 SelectionParserValueListPointer args,
667 const char *rpost, yyscan_t scanner)
669 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
671 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
673 sprintf(buf, "In keyword '%s'", method->name);
674 gmx::MessageStringContext context(errors, buf);
676 if (method->nparams > 0)
678 // TODO: Would assert be better?
679 GMX_THROW(gmx::InternalError(
680 "Keyword initialization called with non-keyword method"));
683 SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION));
684 SelectionTreeElementPointer child = root;
685 _gmx_selelem_set_method(child, method, scanner);
687 /* Initialize the evaluation of keyword matching if values are provided */
690 gmx_ana_selmethod_t *kwmethod;
691 switch (method->type)
693 case INT_VALUE: kwmethod = &sm_keyword_int; break;
694 case REAL_VALUE: kwmethod = &sm_keyword_real; break;
695 case STR_VALUE: kwmethod = &sm_keyword_str; break;
697 GMX_THROW(gmx::InternalError(
698 "Unknown type for keyword selection"));
700 /* Initialize the selection element */
701 root.reset(new SelectionTreeElement(SEL_EXPRESSION));
702 _gmx_selelem_set_method(root, kwmethod, scanner);
703 if (method->type == STR_VALUE)
705 _gmx_selelem_set_kwstr_match_type(root, matchType);
707 SelectionParserParameterList params;
709 SelectionParserParameter::createFromExpression(NULL, child));
710 params.push_back(SelectionParserParameter::create(NULL, move(args)));
711 if (!_gmx_sel_parse_params(params, root->u.expr.method->nparams,
712 root->u.expr.method->param, root, scanner))
714 return SelectionTreeElementPointer();
717 set_refpos_type(&sc->pcc, child, rpost, scanner);
723 * \param[in] method Method to use.
724 * \param[in] args Pointer to the first argument.
725 * \param[in] rpost Reference position type to use (NULL = default).
726 * \param[in] scanner Scanner data structure.
727 * \returns The created selection element.
729 * This function handles the creation of a gmx::SelectionTreeElement object for
730 * selection methods that do not take parameters.
732 SelectionTreeElementPointer
733 _gmx_sel_init_keyword(gmx_ana_selmethod_t *method,
734 SelectionParserValueListPointer args,
735 const char *rpost, yyscan_t scanner)
737 return init_keyword_internal(method, gmx::eStringMatchType_Auto, move(args),
742 * \param[in] method Method to use.
743 * \param[in] matchType String matching type.
744 * \param[in] args Pointer to the first argument.
745 * \param[in] rpost Reference position type to use (NULL = default).
746 * \param[in] scanner Scanner data structure.
747 * \returns The created selection element.
749 * This function handles the creation of a gmx::SelectionTreeElement object for
750 * keyword string matching.
752 SelectionTreeElementPointer
753 _gmx_sel_init_keyword_strmatch(gmx_ana_selmethod_t *method,
754 gmx::SelectionStringMatchType matchType,
755 SelectionParserValueListPointer args,
756 const char *rpost, yyscan_t scanner)
758 GMX_RELEASE_ASSERT(method->type == STR_VALUE,
759 "String keyword method called for a non-string-valued method");
760 GMX_RELEASE_ASSERT(args && !args->empty(),
761 "String keyword matching method called without any values");
762 return init_keyword_internal(method, matchType, move(args), rpost, scanner);
766 * \param[in] method Method to use for initialization.
767 * \param[in] params Pointer to the first parameter.
768 * \param[in] rpost Reference position type to use (NULL = default).
769 * \param[in] scanner Scanner data structure.
770 * \returns The created selection element.
772 * This function handles the creation of a gmx::SelectionTreeElement object for
773 * selection methods that take parameters.
775 * Part of the behavior of the \c same selection keyword is hardcoded into
776 * this function (or rather, into _gmx_selelem_custom_init_same()) to allow the
777 * use of any keyword in \c "same KEYWORD as" without requiring special
778 * handling somewhere else (or sacrificing the simple syntax).
780 SelectionTreeElementPointer
781 _gmx_sel_init_method(gmx_ana_selmethod_t *method,
782 SelectionParserParameterListPointer params,
783 const char *rpost, yyscan_t scanner)
785 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
788 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
790 sprintf(buf, "In keyword '%s'", method->name);
791 gmx::MessageStringContext context(errors, buf);
793 _gmx_sel_finish_method(scanner);
794 /* The "same" keyword needs some custom massaging of the parameters. */
795 rc = _gmx_selelem_custom_init_same(&method, params, scanner);
798 return SelectionTreeElementPointer();
800 SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION));
801 _gmx_selelem_set_method(root, method, scanner);
802 /* Process the parameters */
803 if (!_gmx_sel_parse_params(*params, root->u.expr.method->nparams,
804 root->u.expr.method->param, root, scanner))
806 return SelectionTreeElementPointer();
808 set_refpos_type(&sc->pcc, root, rpost, scanner);
814 * \param[in] method Modifier to use for initialization.
815 * \param[in] params Pointer to the first parameter.
816 * \param[in] sel Selection element that the modifier should act on.
817 * \param[in] scanner Scanner data structure.
818 * \returns The created selection element.
820 * This function handles the creation of a gmx::SelectionTreeElement object for
821 * selection modifiers.
823 SelectionTreeElementPointer
824 _gmx_sel_init_modifier(gmx_ana_selmethod_t *method,
825 SelectionParserParameterListPointer params,
826 const SelectionTreeElementPointer &sel, yyscan_t scanner)
828 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
830 sprintf(buf, "In keyword '%s'", method->name);
831 gmx::MessageStringContext context(errors, buf);
833 _gmx_sel_finish_method(scanner);
834 SelectionTreeElementPointer modifier(new SelectionTreeElement(SEL_MODIFIER));
835 _gmx_selelem_set_method(modifier, method, scanner);
836 SelectionTreeElementPointer root;
837 if (method->type == NO_VALUE)
839 SelectionTreeElementPointer child = sel;
844 child->next = modifier;
850 SelectionParserParameter::createFromExpression(NULL, sel));
853 /* Process the parameters */
854 if (!_gmx_sel_parse_params(*params, modifier->u.expr.method->nparams,
855 modifier->u.expr.method->param, modifier, scanner))
857 return SelectionTreeElementPointer();
864 * \param[in] expr Input selection element for the position calculation.
865 * \param[in] type Reference position type or NULL for default.
866 * \param[in] scanner Scanner data structure.
867 * \returns The created selection element.
869 * This function handles the creation of a gmx::SelectionTreeElement object for
870 * evaluation of reference positions.
872 SelectionTreeElementPointer
873 _gmx_sel_init_position(const SelectionTreeElementPointer &expr,
874 const char *type, yyscan_t scanner)
876 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
878 sprintf(buf, "In position evaluation");
879 gmx::MessageStringContext context(errors, buf);
881 SelectionTreeElementPointer root(new SelectionTreeElement(SEL_EXPRESSION));
882 _gmx_selelem_set_method(root, &sm_keyword_pos, scanner);
883 _gmx_selelem_set_kwpos_type(root.get(), type);
884 /* Create the parameters for the parameter parser. */
885 SelectionParserParameterList params;
886 params.push_back(SelectionParserParameter::createFromExpression(NULL, expr));
887 /* Parse the parameters. */
888 if (!_gmx_sel_parse_params(params, root->u.expr.method->nparams,
889 root->u.expr.method->param, root, scanner))
891 return SelectionTreeElementPointer();
898 * \param[in] x,y,z Coordinates for the position.
899 * \returns The creates selection element.
901 SelectionTreeElementPointer
902 _gmx_sel_init_const_position(real x, real y, real z)
906 SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_CONST));
907 _gmx_selelem_set_vtype(sel, POS_VALUE);
908 _gmx_selvalue_reserve(&sel->v, 1);
912 gmx_ana_pos_init_const(sel->v.u.p, pos);
917 * \param[in] name Name of an index group to search for.
918 * \param[in] scanner Scanner data structure.
919 * \returns The created selection element.
921 * See gmx_ana_indexgrps_find() for information on how \p name is matched
922 * against the index groups.
924 SelectionTreeElementPointer
925 _gmx_sel_init_group_by_name(const char *name, yyscan_t scanner)
928 SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
929 _gmx_selelem_set_vtype(sel, GROUP_VALUE);
930 sel->setName(gmx::formatString("group \"%s\"", name));
931 sel->u.gref.name = strdup(name);
934 if (_gmx_sel_lexer_has_groups_set(scanner))
936 gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
937 sel->resolveIndexGroupReference(grps);
944 * \param[in] id Zero-based index number of the group to extract.
945 * \param[in] scanner Scanner data structure.
946 * \returns The created selection element.
948 SelectionTreeElementPointer
949 _gmx_sel_init_group_by_id(int id, yyscan_t scanner)
951 SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
952 _gmx_selelem_set_vtype(sel, GROUP_VALUE);
953 sel->setName(gmx::formatString("group %d", id));
954 sel->u.gref.name = NULL;
957 if (_gmx_sel_lexer_has_groups_set(scanner))
959 gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
960 sel->resolveIndexGroupReference(grps);
967 * \param[in,out] sel Value of the variable.
968 * \returns The created selection element that references \p sel.
970 * The reference count of \p sel is updated, but no other modifications are
973 SelectionTreeElementPointer
974 _gmx_sel_init_variable_ref(const SelectionTreeElementPointer &sel)
976 SelectionTreeElementPointer ref;
978 if (sel->v.type == POS_VALUE && sel->type == SEL_CONST)
984 ref.reset(new SelectionTreeElement(SEL_SUBEXPRREF));
985 _gmx_selelem_set_vtype(ref, sel->v.type);
986 ref->setName(sel->name());
993 * \param[in] name Name for the selection
994 * (if NULL, a default name is constructed).
995 * \param[in] sel The selection element that evaluates the selection.
996 * \param scanner Scanner data structure.
997 * \returns The created root selection element.
999 * This function handles the creation of root (\ref SEL_ROOT)
1000 * gmx::SelectionTreeElement objects for selections.
1002 SelectionTreeElementPointer
1003 _gmx_sel_init_selection(const char *name,
1004 const SelectionTreeElementPointer &sel,
1007 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
1009 sprintf(buf, "In selection '%s'", _gmx_sel_lexer_pselstr(scanner));
1010 gmx::MessageStringContext context(errors, buf);
1012 if (sel->v.type != POS_VALUE)
1014 /* FIXME: Better handling of this error */
1015 GMX_THROW(gmx::InternalError(
1016 "Each selection must evaluate to a position"));
1019 SelectionTreeElementPointer root(new SelectionTreeElement(SEL_ROOT));
1023 root->setName(name);
1025 /* Update the flags */
1026 _gmx_selelem_update_flags(root, scanner);
1028 root->fillNameIfMissing(_gmx_sel_lexer_pselstr(scanner));
1030 /* Print out some information if the parser is interactive */
1031 if (_gmx_sel_is_lexer_interactive(scanner))
1033 fprintf(stderr, "Selection '%s' parsed\n",
1034 _gmx_sel_lexer_pselstr(scanner));
1042 * \param[in] name Name of the variable.
1043 * \param[in] expr The selection element that evaluates the variable.
1044 * \param scanner Scanner data structure.
1045 * \returns The created root selection element.
1047 * This function handles the creation of root gmx::SelectionTreeElement objects
1048 * for variable assignments. A \ref SEL_ROOT element and a \ref SEL_SUBEXPR
1049 * element are both created.
1051 SelectionTreeElementPointer
1052 _gmx_sel_assign_variable(const char *name,
1053 const SelectionTreeElementPointer &expr,
1056 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1057 const char *pselstr = _gmx_sel_lexer_pselstr(scanner);
1058 SelectionTreeElementPointer root;
1060 gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
1062 sprintf(buf, "In selection '%s'", pselstr);
1063 gmx::MessageStringContext context(errors, buf);
1065 _gmx_selelem_update_flags(expr, scanner);
1066 /* Check if this is a constant non-group value */
1067 if (expr->type == SEL_CONST && expr->v.type != GROUP_VALUE)
1069 /* If so, just assign the constant value to the variable */
1070 sc->symtab->addVariable(name, expr);
1073 /* Check if we are assigning a variable to another variable */
1074 if (expr->type == SEL_SUBEXPRREF)
1076 /* If so, make a simple alias */
1077 sc->symtab->addVariable(name, expr->child);
1080 /* Create the root element */
1081 root.reset(new SelectionTreeElement(SEL_ROOT));
1082 root->setName(name);
1083 /* Create the subexpression element */
1084 root->child.reset(new SelectionTreeElement(SEL_SUBEXPR));
1085 root->child->setName(name);
1086 _gmx_selelem_set_vtype(root->child, expr->v.type);
1087 root->child->child = expr;
1089 _gmx_selelem_update_flags(root, scanner);
1090 /* Add the variable to the symbol table */
1091 sc->symtab->addVariable(name, root->child);
1093 srenew(sc->varstrs, sc->nvars + 1);
1094 sc->varstrs[sc->nvars] = strdup(pselstr);
1096 if (_gmx_sel_is_lexer_interactive(scanner))
1098 fprintf(stderr, "Variable '%s' parsed\n", pselstr);
1104 * \param sel Selection to append (can be NULL, in which
1105 * case nothing is done).
1106 * \param last Last selection, or NULL if not present or not known.
1107 * \param scanner Scanner data structure.
1108 * \returns The last selection after the append.
1110 * Appends \p sel after the last root element, and returns either \p sel
1111 * (if it was non-NULL) or the last element (if \p sel was NULL).
1113 SelectionTreeElementPointer
1114 _gmx_sel_append_selection(const SelectionTreeElementPointer &sel,
1115 SelectionTreeElementPointer last,
1118 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1120 /* Append sel after last, or the last element of sc if last is NULL */
1141 /* Initialize a selection object if necessary */
1145 /* Add the new selection to the collection if it is not a variable. */
1146 if (sel->child->type != SEL_SUBEXPR)
1148 gmx::SelectionDataPointer selPtr(
1149 new gmx::internal::SelectionData(
1150 sel.get(), _gmx_sel_lexer_pselstr(scanner)));
1151 sc->sel.push_back(gmx::move(selPtr));
1154 /* Clear the selection string now that we've saved it */
1155 _gmx_sel_lexer_clear_pselstr(scanner);
1160 * \param[in] scanner Scanner data structure.
1161 * \returns true if the parser should finish, false if parsing should
1164 * This function is called always after _gmx_sel_append_selection() to
1165 * check whether a sufficient number of selections has already been provided.
1166 * This is used to terminate interactive parsers when the correct number of
1167 * selections has been provided.
1170 _gmx_sel_parser_should_finish(yyscan_t scanner)
1172 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1173 return (int)sc->sel.size() == _gmx_sel_lexer_exp_selcount(scanner);
1177 * \param[in] scanner Scanner data structure.
1180 _gmx_sel_handle_empty_cmd(yyscan_t scanner)
1182 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1183 gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
1186 if (!_gmx_sel_is_lexer_interactive(scanner))
1193 fprintf(stderr, "Available index groups:\n");
1194 gmx_ana_indexgrps_print(stderr, _gmx_sel_lexer_indexgrps(scanner), 0);
1196 if (sc->nvars > 0 || !sc->sel.empty())
1198 fprintf(stderr, "Currently provided selections:\n");
1199 for (i = 0; i < sc->nvars; ++i)
1201 fprintf(stderr, " %s\n", sc->varstrs[i]);
1203 for (i = 0; i < (int)sc->sel.size(); ++i)
1205 fprintf(stderr, " %2d. %s\n", i+1, sc->sel[i]->selectionText());
1211 * \param[in] topic Topic for which help was requested, or NULL for general
1213 * \param[in] scanner Scanner data structure.
1215 * \p topic is freed by this function.
1218 _gmx_sel_handle_help_cmd(const SelectionParserValueListPointer &topic,
1221 gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
1223 if (sc->rootHelp.get() == NULL)
1225 sc->rootHelp = gmx::createSelectionHelpTopic();
1227 gmx::HelpWriterContext context(&gmx::File::standardError(),
1228 gmx::eHelpOutputFormat_Console);
1229 gmx::HelpManager manager(*sc->rootHelp, context);
1232 SelectionParserValueList::const_iterator value;
1233 for (value = topic->begin(); value != topic->end(); ++value)
1235 manager.enterTopic(value->stringValue());
1238 catch (const gmx::InvalidInputError &ex)
1240 fprintf(stderr, "%s\n", ex.what());
1243 manager.writeCurrentTopic();