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39 * \brief Implementation of functions in selmethod.h.
51 #include <selmethod.h>
53 #include "selcollection.h"
57 * These global variables cannot be const because gmx_ana_selmethod_register()
58 * modifies them to set some defaults. This is a small price to pay for the
59 * convenience of not having to remember exactly how the selection compiler
60 * expects the structures to be filled, and even more so if the expectations
61 * change. Also, even if the gmx_ana_selmethod_t structures were made const,
62 * the parameters could not be without typecasts somewhere, because the param
63 * field in gmx_ana_selmethod_t cannot be declared const.
65 * Even though the variables may be modified, this should be thread-safe as
66 * modifications are done only in gmx_ana_selmethod_register(), and it should
67 * work even if called more than once for the same structure, and even if
68 * called concurrently from multiple threads (as long as the selection
69 * collection is not the same).
71 * All of these problems should go away if/when the selection methods are
72 * implemented as C++ classes.
76 extern gmx_ana_selmethod_t sm_cog;
77 extern gmx_ana_selmethod_t sm_com;
78 /* From sm_simple.c */
79 extern gmx_ana_selmethod_t sm_all;
80 extern gmx_ana_selmethod_t sm_none;
81 extern gmx_ana_selmethod_t sm_atomnr;
82 extern gmx_ana_selmethod_t sm_resnr;
83 extern gmx_ana_selmethod_t sm_resindex;
84 extern gmx_ana_selmethod_t sm_molindex;
85 extern gmx_ana_selmethod_t sm_atomname;
86 extern gmx_ana_selmethod_t sm_pdbatomname;
87 extern gmx_ana_selmethod_t sm_atomtype;
88 extern gmx_ana_selmethod_t sm_resname;
89 extern gmx_ana_selmethod_t sm_insertcode;
90 extern gmx_ana_selmethod_t sm_chain;
91 extern gmx_ana_selmethod_t sm_mass;
92 extern gmx_ana_selmethod_t sm_charge;
93 extern gmx_ana_selmethod_t sm_altloc;
94 extern gmx_ana_selmethod_t sm_occupancy;
95 extern gmx_ana_selmethod_t sm_betafactor;
96 extern gmx_ana_selmethod_t sm_x;
97 extern gmx_ana_selmethod_t sm_y;
98 extern gmx_ana_selmethod_t sm_z;
99 /* From sm_distance.c */
100 extern gmx_ana_selmethod_t sm_distance;
101 extern gmx_ana_selmethod_t sm_mindistance;
102 extern gmx_ana_selmethod_t sm_within;
103 /* From sm_insolidangle.c */
104 extern gmx_ana_selmethod_t sm_insolidangle;
106 extern gmx_ana_selmethod_t sm_same;
108 /* From sm_merge.c */
109 extern gmx_ana_selmethod_t sm_merge;
110 extern gmx_ana_selmethod_t sm_plus;
111 /* From sm_permute.c */
112 extern gmx_ana_selmethod_t sm_permute;
115 * Helper structure for defining selection methods.
119 * Name to register the method under.
121 * If NULL, use the actual name of the method.
122 * This field is used for defining synonyms.
125 /** Method data structure to register. */
126 gmx_ana_selmethod_t *method;
129 /** Array of selection methods defined in the library. */
130 static const t_register_method smtable_def[] = {
138 {"resid", &sm_resnr},
139 {NULL, &sm_resindex},
140 {"residue", &sm_resindex},
141 {NULL, &sm_molindex},
142 {"mol", &sm_molindex},
143 {"molecule", &sm_molindex},
144 {NULL, &sm_atomname},
145 {"name", &sm_atomname},
146 {NULL, &sm_pdbatomname},
147 {"pdbname", &sm_pdbatomname},
148 {NULL, &sm_atomtype},
149 {"type", &sm_atomtype},
151 {NULL, &sm_insertcode},
156 {NULL, &sm_occupancy},
157 {NULL, &sm_betafactor},
162 {NULL, &sm_distance},
163 {NULL, &sm_mindistance},
165 {NULL, &sm_insolidangle},
174 * Convenience function for reporting errors found in selection methods.
177 report_error(FILE *fp, const char *name, const char *fmt, ...)
183 fprintf(fp, "selection method '%s': ", name);
184 vfprintf(fp, fmt, ap);
191 * Convenience function for reporting errors found in selection method parameters.
194 report_param_error(FILE *fp, const char *mname, const char *pname,
195 const char *fmt, ...)
201 fprintf(fp, "selection method '%s': parameter '%s': ", mname, pname);
202 vfprintf(fp, fmt, ap);
209 * Checks the validity of parameters.
211 * \param[in] fp File handle to use for diagnostic messages
213 * \param[in] name Name of the method (used for error messages).
214 * \param[in] nparams Number of parameters in \p param.
215 * \param[in,out] param Parameter array
216 * (only the \c flags field of gmx_boolean parameters may be modified).
217 * \param[in] symtab Symbol table (used for checking overlaps).
218 * \returns TRUE if there are no problems with the parameters,
221 * This function performs some checks common to both check_method() and
223 * The purpose of these checks is to ensure that the selection parser does not
224 * need to check for the validity of the parameters at each turn, and to
225 * report programming errors as early as possible.
226 * If you remove a check, make sure that the parameter parser can handle the
227 * resulting parameters.
230 check_params(FILE *fp, const char *name, int nparams, gmx_ana_selparam_t param[],
231 gmx_sel_symtab_t *symtab)
234 gmx_sel_symrec_t *sym;
237 if (nparams > 0 && !param)
239 report_error(fp, name, "error: missing parameter data");
242 if (nparams == 0 && param)
244 report_error(fp, name, "warning: parameter data unused because nparams=0");
246 /* Check each parameter */
247 for (i = 0; i < nparams; ++i)
249 /* Check that there is at most one NULL name, in the beginning */
250 if (param[i].name == NULL && i > 0)
252 report_error(fp, name, "error: NULL parameter should be the first one");
256 /* Check for duplicates */
257 for (j = 0; j < i; ++j)
259 if (param[j].name == NULL)
263 if (!gmx_strcasecmp(param[i].name, param[j].name))
265 report_error(fp, name, "error: duplicate parameter name '%s'", param[i].name);
271 if (param[i].flags & SPAR_SET)
273 report_param_error(fp, name, param[i].name, "warning: flag SPAR_SET is set");
274 param[i].flags &= ~SPAR_SET;
276 if (param[i].flags & SPAR_RANGES)
278 if (param[i].val.type != INT_VALUE && param[i].val.type != REAL_VALUE)
280 report_param_error(fp, name, param[i].name, "error: SPAR_RANGES cannot be set for a non-numeric parameter");
283 if (param[i].flags & SPAR_DYNAMIC)
285 report_param_error(fp, name, param[i].name, "warning: SPAR_DYNAMIC does not have effect with SPAR_RANGES");
286 param[i].flags &= ~SPAR_DYNAMIC;
288 if (!(param[i].flags & SPAR_VARNUM) && param[i].val.nr != 1)
290 report_param_error(fp, name, param[i].name, "error: range should take either one or an arbitrary number of values");
293 if (param[i].flags & SPAR_ATOMVAL)
295 report_param_error(fp, name, param[i].name, "error: SPAR_RANGES and SPAR_ATOMVAL both set");
299 if ((param[i].flags & SPAR_VARNUM) && (param[i].flags & SPAR_ATOMVAL))
301 report_param_error(fp, name, param[i].name, "error: SPAR_VARNUM and SPAR_ATOMVAL both set");
304 if (param[i].flags & SPAR_ENUMVAL)
306 if (param[i].val.type != STR_VALUE)
308 report_param_error(fp, name, param[i].name, "error: SPAR_ENUMVAL can only be set for string parameters");
311 if (param[i].val.nr != 1)
313 report_param_error(fp, name, param[i].name, "error: SPAR_ENUMVAL parameters should take exactly one value");
316 if (param[i].flags & (SPAR_DYNAMIC | SPAR_VARNUM | SPAR_ATOMVAL))
318 report_param_error(fp, name, param[i].name, "error: only SPAR_OPTIONAL supported with SPAR_ENUMVAL");
322 /* Check gmx_boolean parameters */
323 if (param[i].val.type == NO_VALUE)
325 if (param[i].val.nr != 0)
327 report_param_error(fp, name, param[i].name, "error: number of values should be zero for gmx_boolean parameters");
330 /* The gmx_boolean parameters should always be optional, so set the
331 * flag for convenience. */
332 param[i].flags |= SPAR_OPTIONAL;
333 /* Any other flags should not be specified */
334 if (param[i].flags & ~SPAR_OPTIONAL)
336 report_param_error(fp, name, param[i].name, "error: gmx_boolean parameter should not have any flags set");
341 if (param[i].flags & (SPAR_VARNUM | SPAR_ATOMVAL))
343 if (param[i].val.nr != -1)
345 report_param_error(fp, name, param[i].name, "warning: val.nr is not -1 although SPAR_VARNUM/SPAR_ATOMVAL is set");
347 param[i].val.nr = -1;
349 else if (param[i].val.type != NO_VALUE)
351 if (param[i].val.nr <= 0)
353 report_param_error(fp, name, param[i].name, "error: val.nr <= 0");
357 /* Check that the value pointer is NULL */
358 if (param[i].nvalptr != NULL)
360 report_param_error(fp, name, param[i].name, "warning: nvalptr is set");
362 if (param[i].val.u.ptr != NULL && !(param[i].flags & SPAR_ENUMVAL))
364 report_param_error(fp, name, param[i].name, "warning: value pointer is set");
366 /* Check that the name contains only valid characters */
367 if (param[i].name == NULL)
371 if (!isalpha(param[i].name[0]))
373 report_param_error(fp, name, param[i].name, "error: name does not begin with a letter");
377 for (j = 1; param[i].name[j] != 0; ++j)
379 if (param[i].name[j] != '_' && !isalnum(param[i].name[j]))
381 report_param_error(fp, name, param[i].name, "error: name contains non-alphanumeric characters");
386 if (param[i].name[j] != 0)
390 /* Check that the name does not conflict with a method */
391 if (_gmx_sel_find_symbol(symtab, param[i].name, TRUE))
393 report_param_error(fp, name, param[i].name, "error: name conflicts with another method or a keyword");
396 } /* End of parameter loop */
397 /* Check parameters of existing methods */
398 sym = _gmx_sel_first_symbol(symtab, SYMBOL_METHOD);
401 gmx_ana_selmethod_t *method = _gmx_sel_sym_value_method(sym);
402 gmx_ana_selparam_t *param =
403 gmx_ana_selmethod_find_param(name, method);
406 report_param_error(fp, method->name, param->name, "error: name conflicts with another method or a keyword");
409 sym = _gmx_sel_next_symbol(sym, SYMBOL_METHOD);
415 * Checks the validity of selection method callback functions.
417 * \param[in] fp File handle to use for diagnostic messages
419 * \param[in] method The method to check.
420 * \returns TRUE if there are no problems, FALSE otherwise.
422 * This function performs some checks common to both check_method() and
424 * This function checks that all the required callbacks are defined, i.e.,
425 * not NULL, to find programming errors.
428 check_callbacks(FILE *fp, gmx_ana_selmethod_t *method)
434 /* Make some checks on init_data and free */
435 if (method->nparams > 0 && !method->init_data)
437 report_error(fp, method->name, "error: init_data should be provided because the method has parameters");
440 if (method->free && !method->init_data)
442 report_error(fp, method->name, "warning: free is not used because of missing init_data");
444 /* Check presence of outinit for position-valued methods */
445 if (method->type == POS_VALUE && !method->outinit)
447 report_error(fp, method->name, "error: outinit should be provided because the method has POS_VALUE");
450 /* Check presence of outinit for variable output count methods */
451 if ((method->flags & SMETH_VARNUMVAL) && !method->outinit)
453 report_error(fp, method->name, "error: outinit should be provided because the method has SMETH_VARNUMVAL");
456 /* Warn of dynamic callbacks in static methods */
457 if (!(method->flags & SMETH_MODIFIER))
459 if (method->pupdate && !(method->flags & SMETH_DYNAMIC))
461 report_error(fp, method->name, "warning: pupdate not used because the method is static");
462 method->pupdate = NULL;
465 /* Check that there is an evaluation function */
466 if (method->type != NO_VALUE && !method->update && !method->pupdate)
468 report_error(fp, method->name, "error: evaluation function missing");
471 /* Loop through the parameters to determine if initialization callbacks
474 for (i = 0; i < method->nparams; ++i)
476 if (method->param[i].val.type != POS_VALUE
477 && (method->param[i].flags & (SPAR_VARNUM | SPAR_ATOMVAL)))
482 /* Check that the callbacks required by the parameters are present */
483 if (bNeedInit && !method->init)
485 report_error(fp, method->name, "error: init should be provided");
492 * Checks the validity of a selection method.
494 * \param[in] fp File handle to use for diagnostic messages
496 * \param[in,out] method Method to check.
497 * \param[in] symtab Symbol table (used for checking overlaps).
499 * Checks the validity of the given selection method data structure
500 * that does not have \ref SMETH_MODIFIER set.
501 * If you remove a check, please make sure that the selection parser,
502 * compiler, and evaluation functions can deal with the method.
505 check_method(FILE *fp, gmx_ana_selmethod_t *method, gmx_sel_symtab_t *symtab)
510 if (method->type == NO_VALUE)
512 report_error(fp, method->name, "error: no value type specified");
515 if (method->type == STR_VALUE && method->nparams > 0)
517 report_error(fp, method->name, "error: evaluates to a string but is not a keyword");
521 if (method->type == GROUP_VALUE)
523 /* Group methods should always have SMETH_SINGLEVAL,
524 * so set it for convenience. */
525 method->flags |= SMETH_SINGLEVAL;
526 /* Check that conflicting flags are not present. */
527 if (method->flags & SMETH_VARNUMVAL)
529 report_error(fp, method->name, "error: SMETH_VARNUMVAL cannot be set for group-valued methods");
535 if ((method->flags & SMETH_SINGLEVAL)
536 && (method->flags & SMETH_VARNUMVAL))
538 report_error(fp, method->name, "error: SMETH_SINGLEVAL and SMETH_VARNUMVAL both set");
542 if ((method->flags & SMETH_CHARVAL) && method->type != STR_VALUE)
544 report_error(fp, method->name, "error: SMETH_CHARVAL can only be specified for STR_VALUE methods");
547 /* Check the parameters */
548 if (!check_params(fp, method->name, method->nparams, method->param, symtab))
552 /* Check the callback pointers */
553 if (!check_callbacks(fp, method))
562 * Checks the validity of a selection modifier method.
564 * \param[in] fp File handle to use for diagnostic messages
566 * \param[in,out] method Method to check.
567 * \param[in] symtab Symbol table (used for checking overlaps).
569 * Checks the validity of the given selection method data structure
570 * that has \ref SMETH_MODIFIER set.
571 * If you remove a check, please make sure that the selection parser,
572 * compiler, and evaluation functions can deal with the method.
575 check_modifier(FILE *fp, gmx_ana_selmethod_t *method, gmx_sel_symtab_t *symtab)
580 if (method->type != NO_VALUE && method->type != POS_VALUE)
582 report_error(fp, method->name, "error: modifier should have type POS_VALUE or NO_VALUE");
586 if (method->flags & (SMETH_SINGLEVAL | SMETH_VARNUMVAL))
588 report_error(fp, method->name, "error: modifier should not have SMETH_SINGLEVAL or SMETH_VARNUMVAL set");
591 /* Check the parameters */
592 /* The first parameter is skipped */
593 if (!check_params(fp, method->name, method->nparams-1, method->param+1, symtab))
597 /* Check the callback pointers */
598 if (!check_callbacks(fp, method))
604 report_error(fp, method->name, "error: modifier should not have update");
607 if (method->type == POS_VALUE && !method->pupdate)
609 report_error(fp, method->name, "error: evaluation function missing");
617 * \param[in,out] sc Selection collection to registered the method to.
618 * \param[in] name Name under which the method should be registered.
619 * \param[in] method Method to register.
620 * \returns 0 on success, EINVAL if there was something wrong with the
623 * \p name does not need to match the name of the method, and the same
624 * method can be registered multiple times under different names.
625 * If \p name equals some previously registered name,
626 * an error message is printed and the method is not registered.
628 * The function also performs some sanity checking on the input method,
629 * and refuses to register it if there are problems.
630 * Some problems only generate warnings.
631 * All problems are described to \p stderr.
634 gmx_ana_selmethod_register(struct gmx_ana_selcollection_t *sc,
635 const char *name, gmx_ana_selmethod_t *method)
639 /* Check the method */
640 if (method->flags & SMETH_MODIFIER)
642 bOk = check_modifier(stderr, method, sc->symtab);
646 bOk = check_method(stderr, method, sc->symtab);
648 /* Try to register the method if everything is ok */
651 if (!_gmx_sel_add_method_symbol(sc->symtab, name, method))
658 report_error(stderr, name, "warning: not registered");
665 * \param[in,out] sc Selection collection to registered the methods to.
666 * \returns 0 on success, -1 if any of the default methods could not be
670 gmx_ana_selmethod_register_defaults(struct gmx_ana_selcollection_t *sc)
677 for (i = 0; i < asize(smtable_def); ++i)
679 gmx_ana_selmethod_t *method = smtable_def[i].method;
681 if (smtable_def[i].name == NULL)
683 rc = gmx_ana_selmethod_register(sc, method->name, method);
687 rc = gmx_ana_selmethod_register(sc, smtable_def[i].name, method);
698 * \param[in] name Name of the parameter to search.
699 * \param[in] method Method to search for the parameter.
700 * \returns Pointer to the parameter in the
701 * \ref gmx_ana_selmethod_t::param "method->param" array,
702 * or NULL if no parameter with name \p name was found.
704 * This is a simple wrapper for gmx_ana_selparam_find().
707 gmx_ana_selmethod_find_param(const char *name, gmx_ana_selmethod_t *method)
709 return gmx_ana_selparam_find(name, method->nparams, method->param);