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+ * the research papers on the package. Check out http://www.gromacs.org.
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/*! \internal \file
* \brief
* Implements the \p same selection method.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_selection
*/
+#include "gmxpre.h"
+
#include <stdlib.h>
#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/string2.h"
-
-#include "gromacs/selection/selmethod.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
#include "keywords.h"
#include "parsetree.h"
#include "selelem.h"
+#include "selmethod.h"
-/*! \internal \brief
+/*! \internal
+ * \brief
* Data structure for the \p same selection method.
*
* To avoid duplicate initialization code, the same data structure is used
* for matching both integer and string keywords; hence the unions.
+ *
+ * \ingroup module_selection
*/
typedef struct
{
bool bSorted;
} t_methoddata_same;
-/** Allocates data for the \p same selection method. */
+/*! \brief
+ * Allocates data for the \p same selection method.
+ *
+ * \param[in] npar Not used (should be 2).
+ * \param[in,out] param Method parameters (should point to a copy of
+ * ::smparams_same_int or ::smparams_same_str).
+ * \returns Pointer to the allocated data (\ref t_methoddata_same).
+ */
static void *
init_data_same(int npar, gmx_ana_selparam_t *param);
-/** Initializes the \p same selection method. */
+/*! \brief
+ * Initializes the \p same selection method.
+ *
+ * \param top Not used.
+ * \param npar Not used (should be 2).
+ * \param param Initialized method parameters (should point to a copy of
+ * ::smparams_same_int or ::smparams_same_str).
+ * \param data Pointer to \ref t_methoddata_same to initialize.
+ * \returns 0 on success, -1 on failure.
+ */
static void
init_same(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Frees the data allocated for the \p same selection method. */
static void
free_data_same(void *data);
-/** Initializes the evaluation of the \p same selection method for a frame. */
+/*! \brief
+ * Initializes the evaluation of the \p same selection method for a frame.
+ *
+ * \param[in] top Not used.
+ * \param[in] fr Current frame.
+ * \param[in] pbc PBC structure.
+ * \param data Should point to a \ref t_methoddata_same.
+ *
+ * Sorts the \c data->as.i array and removes identical values for faster and
+ * simpler lookup.
+ */
static void
init_frame_same_int(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
/** Evaluates the \p same selection method. */
static void
-evaluate_same_int(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_same_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
-/** Initializes the evaluation of the \p same selection method for a frame. */
+/*! \brief
+ * Initializes the evaluation of the \p same selection method for a frame.
+ *
+ * \param[in] top Not used.
+ * \param[in] fr Current frame.
+ * \param[in] pbc PBC structure.
+ * \param data Should point to a \ref t_methoddata_same.
+ *
+ * Sorts the \c data->as.s array and removes identical values for faster and
+ * simpler lookup.
+ */
static void
init_frame_same_str(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
/** Evaluates the \p same selection method. */
static void
-evaluate_same_str(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
+evaluate_same_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Parameters for the \p same selection method. */
static gmx_ana_selparam_t smparams_same_int[] = {
{"same KEYWORD as ATOM_EXPR", asize(help_same), help_same},
};
-/*!
- * \param[in] npar Not used (should be 2).
- * \param[in,out] param Method parameters (should point to a copy of
- * ::smparams_same_int or ::smparams_same_str).
- * \returns Pointer to the allocated data (\ref t_methoddata_same).
- */
static void *
-init_data_same(int npar, gmx_ana_selparam_t *param)
+init_data_same(int /* npar */, gmx_ana_selparam_t *param)
{
t_methoddata_same *data;
snew(data, 1);
data->as_s_sorted = NULL;
- param[1].nvalptr = &data->nas;
+ param[1].nvalptr = &data->nas;
return data;
}
* immediately.
*/
int
-_gmx_selelem_custom_init_same(gmx_ana_selmethod_t **method,
+_gmx_selelem_custom_init_same(gmx_ana_selmethod_t **method,
const gmx::SelectionParserParameterListPointer ¶ms,
- void *scanner)
+ void *scanner)
{
/* Do nothing if this is not a same method. */
gmx::SelectionParserParameterList::iterator asparam = ++params->begin();
if (asparam != params->end() && asparam->name() == sm_same.param[1].name)
{
- gmx::SelectionParserParameterList kwparams;
+ gmx::SelectionParserParameterList kwparams;
gmx::SelectionParserValueListPointer values(
new gmx::SelectionParserValueList(asparam->values()));
kwparams.push_back(
return 0;
}
-/*!
- * \param top Not used.
- * \param npar Not used (should be 2).
- * \param param Initialized method parameters (should point to a copy of
- * ::smparams_same_int or ::smparams_same_str).
- * \param data Pointer to \ref t_methoddata_same to initialize.
- * \returns 0 on success, -1 on failure.
- */
static void
-init_same(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+init_same(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_same *d = (t_methoddata_same *)data;
if (!(param[0].flags & SPAR_ATOMVAL))
{
GMX_THROW(gmx::InvalidInputError(
- "The 'same' selection keyword combined with a "
- "non-keyword does not make sense"));
+ "The 'same' selection keyword combined with a "
+ "non-keyword does not make sense"));
}
}
return 0;
}
-/*!
- * \param[in] top Not used.
- * \param[in] fr Current frame.
- * \param[in] pbc PBC structure.
- * \param data Should point to a \ref t_methoddata_same.
- *
- * Sorts the \c data->as.i array and removes identical values for faster and
- * simpler lookup.
- */
static void
-init_frame_same_int(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data)
+init_frame_same_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */, void *data)
{
t_methoddata_same *d = (t_methoddata_same *)data;
int i, j;
* \c data->val.
*/
static void
-evaluate_same_int(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_same_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
- t_methoddata_same *d = (t_methoddata_same *)data;
+ t_methoddata_same *d = (t_methoddata_same *)data;
int i, j;
out->u.g->isize = 0;
- i = j = 0;
+ i = j = 0;
while (j < g->isize)
{
if (d->bSorted)
{
/* If we are sorted, we can do a simple linear scan. */
- while (i < d->nas && d->as.i[i] < d->val.i[j]) ++i;
+ while (i < d->nas && d->as.i[i] < d->val.i[j])
+ {
+ ++i;
+ }
}
else
{
/* If not, skip all atoms with the same value. */
int tmpval = d->val.i[j];
++j;
- while (j < g->isize && d->val.i[j] == tmpval) ++j;
+ while (j < g->isize && d->val.i[j] == tmpval)
+ {
+ ++j;
+ }
}
else
{
return strcmp(*(char **)a, *(char **)b);
}
-/*!
- * \param[in] top Not used.
- * \param[in] fr Current frame.
- * \param[in] pbc PBC structure.
- * \param data Should point to a \ref t_methoddata_same.
- *
- * Sorts the \c data->as.s array and removes identical values for faster and
- * simpler lookup.
- */
static void
-init_frame_same_str(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data)
+init_frame_same_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */, void *data)
{
t_methoddata_same *d = (t_methoddata_same *)data;
int i, j;
/* Collapse adjacent values.
* For strings, it's unlikely that the values would be sorted originally,
* so set bSorted always to false. */
- d->bSorted = false;
+ d->bSorted = false;
d->as_s_sorted[0] = d->as.s[0];
for (i = 1, j = 0; i < d->nas; ++i)
{
* \c data->val.
*/
static void
-evaluate_same_str(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_same_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
- t_methoddata_same *d = (t_methoddata_same *)data;
+ t_methoddata_same *d = (t_methoddata_same *)data;
int j;
out->u.g->isize = 0;
- j = 0;
+ j = 0;
while (j < g->isize)
{
/* Do a binary search of the strings. */
/* If not, skip all atoms with the same value. */
const char *tmpval = d->val.s[j];
++j;
- while (j < g->isize && strcmp(d->val.s[j], tmpval) == 0) ++j;
+ while (j < g->isize && strcmp(d->val.s[j], tmpval) == 0)
+ {
+ ++j;
+ }
}
else
{