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37 * Implements the \p same selection method.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_selection
47 #include "gromacs/utility/arraysize.h"
48 #include "gromacs/utility/exceptions.h"
49 #include "gromacs/utility/smalloc.h"
52 #include "parsetree.h"
54 #include "selmethod.h"
55 #include "selmethod_impl.h"
59 * Data structure for the \p same selection method.
61 * To avoid duplicate initialization code, the same data structure is used
62 * for matching both integer and string keywords; hence the unions.
64 * \ingroup module_selection
68 /** Value for each atom to match. */
76 * Number of values in the \p as array.
78 * For string values, this is actually the number of values in the
79 * \p as_s_sorted array.
82 /** Values to match against. */
90 * Separate array for sorted \p as.s array.
92 * The array of strings returned as the output value of a parameter should
93 * not be messed with to avoid memory corruption (the pointers in the array
94 * may be reused for several evaluations), so we keep our own copy for
98 /** Whether simple matching can be used. */
103 * Allocates data for the \p same selection method.
105 * \param[in] npar Not used (should be 2).
106 * \param[in,out] param Method parameters (should point to a copy of
107 * ::smparams_same_int or ::smparams_same_str).
108 * \returns Pointer to the allocated data (\ref t_methoddata_same).
111 init_data_same(int npar
, gmx_ana_selparam_t
*param
);
113 * Initializes the \p same selection method.
115 * \param top Not used.
116 * \param npar Not used (should be 2).
117 * \param param Initialized method parameters (should point to a copy of
118 * ::smparams_same_int or ::smparams_same_str).
119 * \param data Pointer to \ref t_methoddata_same to initialize.
120 * \returns 0 on success, -1 on failure.
123 init_same(const gmx_mtop_t
*top
, int npar
, gmx_ana_selparam_t
*param
, void *data
);
124 /** Frees the data allocated for the \p same selection method. */
126 free_data_same(void *data
);
128 * Initializes the evaluation of the \p same selection method for a frame.
130 * \param[in] context Not used.
131 * \param data Should point to a \ref t_methoddata_same.
133 * Sorts the \c data->as.i array and removes identical values for faster and
137 init_frame_same_int(const gmx::SelMethodEvalContext
&context
, void *data
);
138 /** Evaluates the \p same selection method. */
140 evaluate_same_int(const gmx::SelMethodEvalContext
&context
,
141 gmx_ana_index_t
*g
, gmx_ana_selvalue_t
*out
, void *data
);
143 * Initializes the evaluation of the \p same selection method for a frame.
145 * \param[in] context Not used.
146 * \param data Should point to a \ref t_methoddata_same.
148 * Sorts the \c data->as.s array and removes identical values for faster and
152 init_frame_same_str(const gmx::SelMethodEvalContext
&context
, void *data
);
153 /** Evaluates the \p same selection method. */
155 evaluate_same_str(const gmx::SelMethodEvalContext
&context
,
156 gmx_ana_index_t
*g
, gmx_ana_selvalue_t
*out
, void *data
);
158 /** Parameters for the \p same selection method. */
159 static gmx_ana_selparam_t smparams_same_int
[] = {
160 {nullptr, {INT_VALUE
, -1, {nullptr}}, nullptr, SPAR_DYNAMIC
| SPAR_ATOMVAL
},
161 {"as", {INT_VALUE
, -1, {nullptr}}, nullptr, SPAR_DYNAMIC
| SPAR_VARNUM
},
164 /** Parameters for the \p same selection method. */
165 static gmx_ana_selparam_t smparams_same_str
[] = {
166 {nullptr, {STR_VALUE
, -1, {nullptr}}, nullptr, SPAR_DYNAMIC
| SPAR_ATOMVAL
},
167 {"as", {STR_VALUE
, -1, {nullptr}}, nullptr, SPAR_DYNAMIC
| SPAR_VARNUM
},
170 /** Help text for the \p same selection method. */
171 static const char *const help_same
[] = {
174 " same KEYWORD as ATOM_EXPR",
177 "The keyword [TT]same[tt] can be used to select all atoms for which",
178 "the given [TT]KEYWORD[tt] matches any of the atoms in [TT]ATOM_EXPR[tt].",
179 "Keywords that evaluate to integer or string values are supported.",
182 /*! \internal \brief Selection method data for the \p same method. */
183 gmx_ana_selmethod_t sm_same
= {
184 "same", GROUP_VALUE
, 0,
185 asize(smparams_same_int
), smparams_same_int
,
191 &init_frame_same_int
,
194 {"same KEYWORD as ATOM_EXPR",
195 "Extending selections", asize(help_same
), help_same
},
199 * Selection method data for the \p same method.
201 * This selection method is used for matching string keywords. The parser
202 * never sees this method; _gmx_selelem_custom_init_same() replaces sm_same
203 * with this method in cases where it is required.
205 static gmx_ana_selmethod_t sm_same_str
= {
206 "same", GROUP_VALUE
, SMETH_SINGLEVAL
,
207 asize(smparams_same_str
), smparams_same_str
,
213 &init_frame_same_str
,
216 {nullptr, nullptr, 0, nullptr},
220 init_data_same(int /* npar */, gmx_ana_selparam_t
*param
)
222 t_methoddata_same
*data
;
225 data
->as_s_sorted
= nullptr;
226 param
[1].nvalptr
= &data
->nas
;
231 * \param[in,out] method The method to initialize.
232 * \param[in,out] params Pointer to the first parameter.
233 * \param[in] scanner Scanner data structure.
235 * If \p *method is not a \c same method, this function returns
239 _gmx_selelem_custom_init_same(gmx_ana_selmethod_t
**method
,
240 const gmx::SelectionParserParameterListPointer
¶ms
,
244 /* Do nothing if this is not a same method. */
245 if (!*method
|| (*method
)->name
!= sm_same
.name
|| params
->empty())
250 const gmx::SelectionParserValueList
&kwvalues
= params
->front().values();
251 if (kwvalues
.size() != 1 || !kwvalues
.front().hasExpressionValue()
252 || kwvalues
.front().expr
->type
!= SEL_EXPRESSION
)
254 GMX_THROW(gmx::InvalidInputError("'same' should be followed by a single keyword"));
256 gmx_ana_selmethod_t
*kwmethod
= kwvalues
.front().expr
->u
.expr
.method
;
257 if (kwmethod
->type
== STR_VALUE
)
259 *method
= &sm_same_str
;
262 /* We do custom processing for the "as" parameter. */
263 gmx::SelectionParserParameterList::iterator asparam
= ++params
->begin();
264 if (asparam
!= params
->end() && asparam
->name() == sm_same
.param
[1].name
)
266 const gmx::SelectionParserValueList
&asvalues
= asparam
->values();
267 if (asvalues
.size() != 1 || !asvalues
.front().hasExpressionValue())
269 // TODO: Think about providing more informative context.
270 GMX_THROW(gmx::InvalidInputError("'same ... as' should be followed by a single expression"));
272 const gmx::SelectionTreeElementPointer
&child
= asvalues
.front().expr
;
273 /* Create a second keyword evaluation element for the keyword given as
274 * the first parameter, evaluating the keyword in the group given by the
275 * second parameter. */
276 gmx::SelectionTreeElementPointer kwelem
277 = _gmx_sel_init_keyword_evaluator(kwmethod
, child
, scanner
);
278 /* Replace the second parameter with one with a value from \p kwelem. */
279 std::string pname
= asparam
->name();
280 *asparam
= gmx::SelectionParserParameter::createFromExpression(pname
, kwelem
);
285 init_same(const gmx_mtop_t
* /* top */, int /* npar */, gmx_ana_selparam_t
*param
, void *data
)
287 t_methoddata_same
*d
= static_cast<t_methoddata_same
*>(data
);
289 d
->val
.ptr
= param
[0].val
.u
.ptr
;
290 d
->as
.ptr
= param
[1].val
.u
.ptr
;
291 if (param
[1].val
.type
== STR_VALUE
)
293 snew(d
->as_s_sorted
, d
->nas
);
295 if (!(param
[0].flags
& SPAR_ATOMVAL
))
297 GMX_THROW(gmx::InvalidInputError(
298 "The 'same' selection keyword combined with a "
299 "non-keyword does not make sense"));
304 * \param data Data to free (should point to a \ref t_methoddata_same).
307 free_data_same(void *data
)
309 t_methoddata_same
*d
= static_cast<t_methoddata_same
*>(data
);
311 sfree(d
->as_s_sorted
);
316 * Helper function for comparison of two integers.
319 cmp_int(const void *a
, const void *b
)
321 if (*reinterpret_cast<const int*>(a
) < *reinterpret_cast<const int*>(b
))
325 if (*reinterpret_cast<const int*>(a
) > *reinterpret_cast<const int*>(b
))
333 init_frame_same_int(const gmx::SelMethodEvalContext
& /*context*/, void *data
)
335 t_methoddata_same
*d
= static_cast<t_methoddata_same
*>(data
);
338 /* Collapse adjacent values, and check whether the array is sorted. */
344 for (i
= 1, j
= 0; i
< d
->nas
; ++i
)
346 if (d
->as
.i
[i
] != d
->as
.i
[j
])
348 if (d
->as
.i
[i
] < d
->as
.i
[j
])
353 d
->as
.i
[j
] = d
->as
.i
[i
];
360 qsort(d
->as
.i
, d
->nas
, sizeof(d
->as
.i
[0]), &cmp_int
);
361 /* More identical values may become adjacent after sorting. */
362 for (i
= 1, j
= 0; i
< d
->nas
; ++i
)
364 if (d
->as
.i
[i
] != d
->as
.i
[j
])
367 d
->as
.i
[j
] = d
->as
.i
[i
];
375 * See sel_updatefunc() for description of the parameters.
376 * \p data should point to a \c t_methoddata_same.
378 * Calculates which values in \c data->val.i can be found in \c data->as.i
379 * (assumed sorted), and writes the corresponding atoms to output.
380 * If \c data->val is sorted, uses a linear scan of both arrays, otherwise a
381 * binary search of \c data->as is performed for each block of values in
385 evaluate_same_int(const gmx::SelMethodEvalContext
& /*context*/,
386 gmx_ana_index_t
*g
, gmx_ana_selvalue_t
*out
, void *data
)
388 t_methoddata_same
*d
= static_cast<t_methoddata_same
*>(data
);
397 /* If we are sorted, we can do a simple linear scan. */
398 while (i
< d
->nas
&& d
->as
.i
[i
] < d
->val
.i
[j
])
405 /* If not, we must do a binary search of all the values. */
412 int itry
= (i1
+ i2
) / 2;
413 if (d
->as
.i
[itry
] <= d
->val
.i
[j
])
422 i
= (d
->as
.i
[i1
] == d
->val
.i
[j
] ? i1
: d
->nas
);
424 /* Check whether the value was found in the as list. */
425 if (i
== d
->nas
|| d
->as
.i
[i
] != d
->val
.i
[j
])
427 /* If not, skip all atoms with the same value. */
428 int tmpval
= d
->val
.i
[j
];
430 while (j
< g
->isize
&& d
->val
.i
[j
] == tmpval
)
437 /* Copy all the atoms with this value to the output. */
438 while (j
< g
->isize
&& d
->val
.i
[j
] == d
->as
.i
[i
])
440 out
->u
.g
->index
[out
->u
.g
->isize
++] = g
->index
[j
];
444 if (j
< g
->isize
&& d
->val
.i
[j
] < d
->val
.i
[j
- 1])
452 * Helper function for comparison of two strings.
455 cmp_str(const void *a
, const void *b
)
457 return strcmp(*static_cast<char *const*>(a
), *static_cast<char *const*>(b
));
461 init_frame_same_str(const gmx::SelMethodEvalContext
& /*context*/, void *data
)
463 t_methoddata_same
*d
= static_cast<t_methoddata_same
*>(data
);
466 /* Collapse adjacent values.
467 * For strings, it's unlikely that the values would be sorted originally,
468 * so set bSorted always to false. */
474 d
->as_s_sorted
[0] = d
->as
.s
[0];
475 for (i
= 1, j
= 0; i
< d
->nas
; ++i
)
477 if (strcmp(d
->as
.s
[i
], d
->as_s_sorted
[j
]) != 0)
480 d
->as_s_sorted
[j
] = d
->as
.s
[i
];
485 qsort(d
->as_s_sorted
, d
->nas
, sizeof(d
->as_s_sorted
[0]), &cmp_str
);
486 /* More identical values may become adjacent after sorting. */
487 for (i
= 1, j
= 0; i
< d
->nas
; ++i
)
489 if (strcmp(d
->as_s_sorted
[i
], d
->as_s_sorted
[j
]) != 0)
492 d
->as_s_sorted
[j
] = d
->as_s_sorted
[i
];
499 * See sel_updatefunc() for description of the parameters.
500 * \p data should point to a \c t_methoddata_same.
502 * Calculates which strings in \c data->val.s can be found in \c data->as.s
503 * (assumed sorted), and writes the corresponding atoms to output.
504 * A binary search of \c data->as is performed for each block of values in
508 evaluate_same_str(const gmx::SelMethodEvalContext
& /*context*/,
509 gmx_ana_index_t
*g
, gmx_ana_selvalue_t
*out
, void *data
)
511 t_methoddata_same
*d
= static_cast<t_methoddata_same
*>(data
);
518 /* Do a binary search of the strings. */
520 ptr
= bsearch(&d
->val
.s
[j
], d
->as_s_sorted
, d
->nas
,
521 sizeof(d
->as_s_sorted
[0]), &cmp_str
);
522 /* Check whether the value was found in the as list. */
525 /* If not, skip all atoms with the same value. */
526 const char *tmpval
= d
->val
.s
[j
];
528 while (j
< g
->isize
&& strcmp(d
->val
.s
[j
], tmpval
) == 0)
535 const char *tmpval
= d
->val
.s
[j
];
536 /* Copy all the atoms with this value to the output. */
537 while (j
< g
->isize
&& strcmp(d
->val
.s
[j
], tmpval
) == 0)
539 out
->u
.g
->index
[out
->u
.g
->isize
++] = g
->index
[j
];