/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
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*
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*
- * GROningen MAchine for Chemical Simulations
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+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
*
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
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*
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- * files - if they are missing, get the official version at www.gromacs.org.
+ * If you want to redistribute modifications to GROMACS, please
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*
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/*! \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
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <stdlib.h>
-#include "macros.h"
-#include "smalloc.h"
-#include "string2.h"
-
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/legacyheaders/macros.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,
- t_selexpr_param *params,
- void *scanner)
+_gmx_selelem_custom_init_same(gmx_ana_selmethod_t **method,
+ const gmx::SelectionParserParameterListPointer ¶ms,
+ void *scanner)
{
- gmx_ana_selmethod_t *kwmethod;
- t_selelem *kwelem;
- t_selexpr_param *param;
- char *pname;
- int rc;
/* Do nothing if this is not a same method. */
- if (!*method || (*method)->name != sm_same.name)
+ if (!*method || (*method)->name != sm_same.name || params->empty())
{
return 0;
}
- if (params->nval != 1 || !params->value->bExpr
- || params->value->u.expr->type != SEL_EXPRESSION)
+ const gmx::SelectionParserValueList &kwvalues = params->front().values();
+ if (kwvalues.size() != 1 || !kwvalues.front().hasExpressionValue()
+ || kwvalues.front().expr->type != SEL_EXPRESSION)
{
_gmx_selparser_error(scanner, "'same' should be followed by a single keyword");
return -1;
}
- kwmethod = params->value->u.expr->u.expr.method;
-
+ gmx_ana_selmethod_t *kwmethod = kwvalues.front().expr->u.expr.method;
if (kwmethod->type == STR_VALUE)
{
*method = &sm_same_str;
}
- /* We do custom processing with the second parameter, so remove it from
- * the params list, but save the name for later. */
- param = params->next;
- params->next = NULL;
- pname = param->name;
- param->name = NULL;
- /* Create a second keyword evaluation element for the keyword given as
- * the first parameter, evaluating the keyword in the group given by the
- * second parameter. */
- rc = _gmx_sel_init_keyword_evaluator(&kwelem, kwmethod, param, scanner);
- if (rc != 0)
+ /* We do custom processing for the "as" parameter. */
+ gmx::SelectionParserParameterList::iterator asparam = ++params->begin();
+ if (asparam != params->end() && asparam->name() == sm_same.param[1].name)
{
- sfree(pname);
- return rc;
+ gmx::SelectionParserParameterList kwparams;
+ gmx::SelectionParserValueListPointer values(
+ new gmx::SelectionParserValueList(asparam->values()));
+ kwparams.push_back(
+ gmx::SelectionParserParameter::create(NULL, move(values)));
+
+ /* Create a second keyword evaluation element for the keyword given as
+ * the first parameter, evaluating the keyword in the group given by the
+ * second parameter. */
+ gmx::SelectionTreeElementPointer kwelem
+ = _gmx_sel_init_keyword_evaluator(kwmethod, kwparams, scanner);
+ // FIXME: Use exceptions.
+ if (!kwelem)
+ {
+ return -1;
+ }
+ /* Replace the second parameter with one with a value from \p kwelem. */
+ std::string pname = asparam->name();
+ *asparam = gmx::SelectionParserParameter::createFromExpression(pname, kwelem);
}
- /* Replace the second parameter with one with a value from \p kwelem. */
- param = _gmx_selexpr_create_param(pname);
- param->nval = 1;
- param->value = _gmx_selexpr_create_value_expr(kwelem);
- params->next = param;
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"));
}
}
t_methoddata_same *d = (t_methoddata_same *)data;
sfree(d->as_s_sorted);
+ sfree(d);
}
/*! \brief
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
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff