/*
+ * 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
+ * top-level source directory and at http://www.gromacs.org.
*
- * G R O M A C S
+ * GROMACS is free software; you can redistribute it and/or
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+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
*
- * GROningen MAchine for Chemical Simulations
+ * GROMACS is distributed in the hope that it will be useful,
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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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
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+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
- * If you want to redistribute modifications, please consider that
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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
+ * consider that scientific software is very special. Version
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+ * consider code for inclusion in the official distribution, but
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+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
* 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 internal selection methods for numeric and string keyword
* evaluation.
*
- * \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 <ctype.h>
-#ifdef HAVE_SYS_TYPES_H
-#include <sys/types.h> /*old Mac needs types before regex.h*/
-#endif
-#ifdef HAVE_REGEX_H
-#include <regex.h>
-#define USE_REGEX
-#endif
-
-#include "macros.h"
-#include "smalloc.h"
-#include "string2.h"
-
-#include "gromacs/selection/selmethod.h"
-#include "gromacs/utility/errorcodes.h"
+#include "gmxpre.h"
+
+#include <cctype>
+#include <cstring>
+
+#include <string>
+
+#include <boost/shared_ptr.hpp>
+
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxregex.h"
#include "gromacs/utility/messagestringcollector.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
#include "keywords.h"
#include "parsetree.h"
#include "scanner.h"
#include "selelem.h"
+#include "selmethod.h"
-/** Allocates data for integer keyword evaluation. */
+/*! \brief
+ * Allocates data for integer keyword evaluation.
+ *
+ * \param[in] npar Not used.
+ * \param param Not used.
+ * \returns Pointer to the allocated data (\ref t_methoddata_kwint).
+ *
+ * Allocates memory for a \ref t_methoddata_kwint structure.
+ */
static void *
-init_data_kwint(int npar, gmx_ana_selparam_t *param);
-/** Allocates data for real keyword evaluation. */
+init_data_kwint(int npar, gmx_ana_selparam_t * param);
+/*! \brief
+ * Allocates data for real keyword evaluation.
+ *
+ * \param[in] npar Not used.
+ * \param param Not used.
+ * \returns Pointer to the allocated data (\ref t_methoddata_kwreal).
+ *
+ * Allocates memory for a \ref t_methoddata_kwreal structure.
+ */
static void *
-init_data_kwreal(int npar, gmx_ana_selparam_t *param);
-/** Allocates data for string keyword evaluation. */
+init_data_kwreal(int npar, gmx_ana_selparam_t * param);
+/*! \brief
+ * Allocates data for string keyword evaluation.
+ *
+ * \param[in] npar Not used.
+ * \param param Not used.
+ * \returns Pointer to the allocated data (t_methoddata_kwstr).
+ *
+ * Allocates memory for a t_methoddata_kwstr structure.
+ */
static void *
-init_data_kwstr(int npar, gmx_ana_selparam_t *param);
-/** Initializes data for integer keyword evaluation. */
+init_data_kwstr(int npar, gmx_ana_selparam_t * param);
+/** /brief Initializes data for integer keyword evaluation.
+ *
+ * \param[in] top Not used.
+ * \param[in] npar Not used (should be 2).
+ * \param[in] param Method parameters (should point to \ref smparams_keyword_int).
+ * \param[in] data Should point to \ref t_methoddata_kwint.
+ */
static void
init_kwint(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
-/** Initializes data for real keyword evaluation. */
+/*! \brief
+ * Initializes data for real keyword evaluation.
+ *
+ * \param[in] top Not used.
+ * \param[in] npar Not used (should be 2).
+ * \param[in] param Method parameters (should point to \ref smparams_keyword_real).
+ * \param[in] data Should point to \ref t_methoddata_kwreal.
+ * \returns 0 (the initialization always succeeds).
+ */
static void
init_kwreal(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
-/** Initializes data for string keyword evaluation. */
+/*! \brief
+ * Initializes data for string keyword evaluation.
+ *
+ * \param[in] top Not used.
+ * \param[in] npar Not used (should be 2).
+ * \param[in] param Method parameters (should point to \ref smparams_keyword_str).
+ * \param[in] data Should point to t_methoddata_kwstr.
+ */
static void
init_kwstr(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Frees the memory allocated for string keyword evaluation. */
free_data_kwstr(void *data);
/** Evaluates integer selection keywords. */
static void
-evaluate_keyword_int(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_keyword_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates real selection keywords. */
static void
-evaluate_keyword_real(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_keyword_real(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates string selection keywords. */
static void
-evaluate_keyword_str(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_keyword_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/*! \internal \brief
real *r;
} t_methoddata_kwreal;
+namespace
+{
+
+/*! \internal \brief
+ * Single item in the list of strings/regular expressions to match.
+ *
+ * \ingroup module_selection
+ */
+class StringKeywordMatchItem
+{
+ public:
+ /*! \brief
+ * Constructs a matcher from a string.
+ *
+ * \param[in] matchType String matching type.
+ * \param[in] str String to use for matching.
+ */
+ StringKeywordMatchItem(gmx::SelectionStringMatchType matchType,
+ const char *str)
+ : str_(str)
+ {
+ bool bRegExp = (matchType == gmx::eStringMatchType_RegularExpression);
+ if (matchType == gmx::eStringMatchType_Auto)
+ {
+ for (size_t j = 0; j < std::strlen(str); ++j)
+ {
+ if (std::ispunct(str[j]) && str[j] != '?' && str[j] != '*')
+ {
+ bRegExp = true;
+ break;
+ }
+ }
+ }
+ if (bRegExp)
+ {
+ if (!gmx::Regex::isSupported())
+ {
+ GMX_THROW(gmx::InvalidInputError(gmx::formatString(
+ "No regular expression support, "
+ "cannot match \"%s\"", str)));
+ }
+ regex_.reset(new gmx::Regex(str));
+ }
+ }
+
+ /*! \brief
+ * Checks whether this item matches a string.
+ *
+ * \param[in] matchType String matching type.
+ * \param[in] value String to match.
+ * \returns true if this item matches \p value.
+ */
+ bool match(gmx::SelectionStringMatchType matchType,
+ const char *value) const
+ {
+ if (matchType == gmx::eStringMatchType_Exact)
+ {
+ return str_ == value;
+ }
+ else if (regex_)
+ {
+ return gmx::regexMatch(value, *regex_);
+ }
+ else
+ {
+ return gmx_wcmatch(str_.c_str(), value) == 0;
+ }
+ }
+
+ private:
+ //! The raw string passed for the matcher.
+ std::string str_;
+ //! Regular expression compiled from \p str_, if applicable.
+ boost::shared_ptr<gmx::Regex> regex_;
+};
+
/*! \internal \brief
* Data structure for string keyword expression evaluation.
*/
-typedef struct t_methoddata_kwstr
+struct t_methoddata_kwstr
{
+ /** Matching type for the strings. */
+ gmx::SelectionStringMatchType matchType;
/** Array of values for the keyword. */
- char **v;
- /** Number of elements in the \p val array. */
- int n;
- /*! \internal \brief
- * Array of strings/regular expressions to match against.
- */
- struct t_methoddata_kwstr_match {
- /** true if the expression is a regular expression, false otherwise. */
- bool bRegExp;
- /** The value to match against. */
- union {
-#ifdef USE_REGEX
- /** Compiled regular expression if \p bRegExp is true. */
- regex_t r;
-#endif
- /** The string if \p bRegExp is false; */
- char *s;
- } u;
- } *m;
- /**< Array of strings/regular expressions to match against.*/
-} t_methoddata_kwstr;
+ char **v;
+ /** Array of strings/regular expressions to match against.*/
+ std::vector<StringKeywordMatchItem> matches;
+};
+
+} // namespace
/** Parameters for integer keyword evaluation. */
static gmx_ana_selparam_t smparams_keyword_int[] = {
{NULL, {STR_VALUE, -1, {NULL}}, NULL, SPAR_VARNUM},
};
-/** \internal Selection method data for integer keyword evaluation. */
+/** Selection method data for integer keyword evaluation. */
gmx_ana_selmethod_t sm_keyword_int = {
"kw_int", GROUP_VALUE, SMETH_SINGLEVAL,
asize(smparams_keyword_int), smparams_keyword_int,
&init_data_kwint,
- NULL,
+ NULL,
&init_kwint,
- NULL,
- NULL,
- NULL,
+ NULL,
+ NULL,
+ NULL,
&evaluate_keyword_int,
- NULL,
+ NULL,
{NULL, 0, NULL},
};
-/** \internal Selection method data for real keyword evaluation. */
+/** Selection method data for real keyword evaluation. */
gmx_ana_selmethod_t sm_keyword_real = {
"kw_real", GROUP_VALUE, SMETH_SINGLEVAL,
asize(smparams_keyword_real), smparams_keyword_real,
&init_data_kwreal,
- NULL,
+ NULL,
&init_kwreal,
- NULL,
- NULL,
- NULL,
+ NULL,
+ NULL,
+ NULL,
&evaluate_keyword_real,
- NULL,
+ NULL,
{NULL, 0, NULL},
};
-/** \internal Selection method data for string keyword evaluation. */
+/** Selection method data for string keyword evaluation. */
gmx_ana_selmethod_t sm_keyword_str = {
"kw_str", GROUP_VALUE, SMETH_SINGLEVAL,
asize(smparams_keyword_str), smparams_keyword_str,
&init_data_kwstr,
- NULL,
+ NULL,
&init_kwstr,
- NULL,
+ NULL,
&free_data_kwstr,
- NULL,
+ NULL,
&evaluate_keyword_str,
- NULL,
+ NULL,
{NULL, 0, NULL},
};
-/** Initializes keyword evaluation for an arbitrary group. */
+/*! \brief
+ * Initializes keyword evaluation for an arbitrary group.
+ *
+ * \param[in] top Not used.
+ * \param[in] npar Not used.
+ * \param[in] param Not used.
+ * \param[in] data Should point to \ref t_methoddata_kweval.
+ * \returns 0 on success, a non-zero error code on return.
+ *
+ * Calls the initialization method of the wrapped keyword.
+ */
static void
-init_kweval(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
-/** Initializes output for keyword evaluation in an arbitrary group. */
+init_kweval(t_topology *top, int npar, gmx_ana_selparam_t * param, void *data);
+/*! \brief
+ * Initializes output for keyword evaluation in an arbitrary group.
+ *
+ * \param[in] top Not used.
+ * \param[in,out] out Pointer to output data structure.
+ * \param[in,out] data Should point to \c t_methoddata_kweval.
+ * \returns 0 for success.
+ */
static void
init_output_kweval(t_topology *top, gmx_ana_selvalue_t *out, void *data);
/** Frees the data allocated for keyword evaluation in an arbitrary group. */
init_frame_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
/** Evaluates keywords in an arbitrary group. */
static void
-evaluate_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
+evaluate_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data);
/*! \internal \brief
* Data structure for keyword evaluation in arbitrary groups.
* INTEGER KEYWORD EVALUATION
********************************************************************/
-/*!
- * \param[in] npar Not used.
- * \param param Not used.
- * \returns Pointer to the allocated data (\ref t_methoddata_kwint).
- *
- * Allocates memory for a \ref t_methoddata_kwint structure.
- */
static void *
-init_data_kwint(int npar, gmx_ana_selparam_t *param)
+init_data_kwint(int /* npar */, gmx_ana_selparam_t * /* param */)
{
t_methoddata_kwint *data;
return data;
}
-/*!
- * \param[in] top Not used.
- * \param[in] npar Not used (should be 2).
- * \param[in] param Method parameters (should point to \ref smparams_keyword_int).
- * \param[in] data Should point to \ref t_methoddata_kwint.
- */
static void
-init_kwint(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+init_kwint(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_kwint *d = (t_methoddata_kwint *)data;
* Matching atoms are stored in \p out->u.g.
*/
static void
-evaluate_keyword_int(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_keyword_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_kwint *d = (t_methoddata_kwint *)data;
int val;
out->u.g->isize = 0;
- n = d->n;
+ n = d->n;
for (i = 0; i < g->isize; ++i)
{
val = d->v[i];
* REAL KEYWORD EVALUATION
********************************************************************/
-/*!
- * \param[in] npar Not used.
- * \param param Not used.
- * \returns Pointer to the allocated data (\ref t_methoddata_kwreal).
- *
- * Allocates memory for a \ref t_methoddata_kwreal structure.
- */
static void *
-init_data_kwreal(int npar, gmx_ana_selparam_t *param)
+init_data_kwreal(int /* npar */, gmx_ana_selparam_t * /* param */)
{
t_methoddata_kwreal *data;
return data;
}
-/*!
- * \param[in] top Not used.
- * \param[in] npar Not used (should be 2).
- * \param[in] param Method parameters (should point to \ref smparams_keyword_real).
- * \param[in] data Should point to \ref t_methoddata_kwreal.
- * \returns 0 (the initialization always succeeds).
- */
static void
-init_kwreal(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+init_kwreal(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_kwreal *d = (t_methoddata_kwreal *)data;
* Matching atoms are stored in \p out->u.g.
*/
static void
-evaluate_keyword_real(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_keyword_real(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+ gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_kwreal *d = (t_methoddata_kwreal *)data;
int n, i, j, jmin, jmax;
real val;
out->u.g->isize = 0;
- n = d->n;
+ n = d->n;
for (i = 0; i < g->isize; ++i)
{
val = d->v[i];
* STRING KEYWORD EVALUATION
********************************************************************/
-/*!
- * \param[in] npar Not used.
- * \param param Not used.
- * \returns Pointer to the allocated data (\ref t_methoddata_kwstr).
- *
- * Allocates memory for a \ref t_methoddata_kwstr structure.
- */
static void *
-init_data_kwstr(int npar, gmx_ana_selparam_t *param)
+init_data_kwstr(int /* npar */, gmx_ana_selparam_t * /* param */)
{
- t_methoddata_kwstr *data;
-
- snew(data, 1);
+ t_methoddata_kwstr *data = new t_methoddata_kwstr();
+ data->matchType = gmx::eStringMatchType_Auto;
return data;
}
/*!
- * \param[in] top Not used.
- * \param[in] npar Not used (should be 2).
- * \param[in] param Method parameters (should point to \ref smparams_keyword_str).
- * \param[in] data Should point to \ref t_methoddata_kwstr.
+ * \param[in,out] sel Selection element to initialize.
+ * \param[in] matchType Method to use to match string values.
+ *
+ * Sets the string matching method for string keyword matching.
*/
+void
+_gmx_selelem_set_kwstr_match_type(const gmx::SelectionTreeElementPointer &sel,
+ gmx::SelectionStringMatchType matchType)
+{
+ t_methoddata_kwstr *d = static_cast<t_methoddata_kwstr *>(sel->u.expr.mdata);
+
+ if (sel->type != SEL_EXPRESSION || !sel->u.expr.method
+ || sel->u.expr.method->name != sm_keyword_str.name)
+ {
+ return;
+ }
+ d->matchType = matchType;
+}
+
static void
-init_kwstr(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+init_kwstr(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
- t_methoddata_kwstr *d = (t_methoddata_kwstr *)data;
- char *s;
- int i;
- size_t j;
- bool bRegExp;
+ t_methoddata_kwstr *d = static_cast<t_methoddata_kwstr *>(data);
d->v = param[0].val.u.s;
- d->n = param[1].val.nr;
/* Return if this is not the first time */
- if (d->m)
+ if (!d->matches.empty())
{
return;
}
- snew(d->m, d->n);
- for (i = 0; i < d->n; ++i)
+ int n = param[1].val.nr;
+ d->matches.reserve(n);
+ for (int i = 0; i < n; ++i)
{
- s = param[1].val.u.s[i];
- bRegExp = false;
- for (j = 0; j < strlen(s); ++j)
- {
- if (ispunct(s[j]) && s[j] != '?' && s[j] != '*')
- {
- bRegExp = true;
- break;
- }
- }
- if (bRegExp)
- {
- // TODO: Get rid of these prints to stderr
-#ifdef USE_REGEX
- char *buf;
- snew(buf, strlen(s) + 3);
- sprintf(buf, "^%s$", s);
- if (regcomp(&d->m[i].u.r, buf, REG_EXTENDED | REG_NOSUB))
- {
- bRegExp = false;
- fprintf(stderr, "WARNING: error in regular expression,\n"
- " will match '%s' as a simple string\n", s);
- }
- sfree(buf);
-#else
- bRegExp = false;
- fprintf(stderr, "WARNING: no regular expressions support,\n"
- " will match '%s' as a simple string\n", s);
-#endif
- }
- if (!bRegExp)
- {
- d->m[i].u.s = s;
- }
- d->m[i].bRegExp = bRegExp;
+ const char *s = param[1].val.u.s[i];
+ d->matches.push_back(StringKeywordMatchItem(d->matchType, s));
}
}
/*!
- * \param data Data to free (should point to a \ref t_methoddata_kwstr).
- *
- * Frees the memory allocated for t_methoddata_kwstr::val.
+ * \param data Data to free (should point to a t_methoddata_kwstr).
*/
static void
free_data_kwstr(void *data)
{
- t_methoddata_kwstr *d = (t_methoddata_kwstr *)data;
- int i;
-
- for (i = 0; i < d->n; ++i)
- {
- if (d->m[i].bRegExp)
- {
-#ifdef USE_REGEX
- /* This branch should only be taken if regular expressions
- * are available, but the ifdef is still needed. */
- regfree(&d->m[i].u.r);
-#endif
- }
- }
- sfree(d->m);
+ t_methoddata_kwstr *d = static_cast<t_methoddata_kwstr *>(data);
+ delete d;
}
/*!
* Matching atoms are stored in \p out->u.g.
*/
static void
-evaluate_keyword_str(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_keyword_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
- t_methoddata_kwstr *d = (t_methoddata_kwstr *)data;
- int i, j;
- bool bFound;
+ t_methoddata_kwstr *d = static_cast<t_methoddata_kwstr *>(data);
out->u.g->isize = 0;
- for (i = 0; i < g->isize; ++i)
+ for (int i = 0; i < g->isize; ++i)
{
- bFound = false;
- for (j = 0; j < d->n && !bFound; ++j)
+ for (size_t j = 0; j < d->matches.size(); ++j)
{
- if (d->m[j].bRegExp)
- {
-#ifdef USE_REGEX
- /* This branch should only be taken if regular expressions
- * are available, but the ifdef is still needed. */
- if (!regexec(&d->m[j].u.r, d->v[i], 0, NULL, 0))
- {
- bFound = true;
- }
-#endif
- }
- else
+ if (d->matches[j].match(d->matchType, d->v[i]))
{
- if (gmx_wcmatch(d->m[j].u.s, d->v[i]) == 0)
- {
- bFound = true;
- }
+ out->u.g->index[out->u.g->isize++] = g->index[i];
+ break;
}
}
- if (bFound)
- {
- out->u.g->index[out->u.g->isize++] = g->index[i];
- }
}
}
* KEYWORD EVALUATION FOR ARBITRARY GROUPS
********************************************************************/
-/*!
- * \param[in] top Not used.
- * \param[in] npar Not used.
- * \param[in] param Not used.
- * \param[in] data Should point to \ref t_methoddata_kweval.
- * \returns 0 on success, a non-zero error code on return.
- *
- * Calls the initialization method of the wrapped keyword.
- */
static void
-init_kweval(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data)
+init_kweval(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void *data)
{
t_methoddata_kweval *d = (t_methoddata_kweval *)data;
d->kwmethod->init(top, 0, NULL, d->kwmdata);
}
-/*!
- * \param[in] top Not used.
- * \param[in,out] out Pointer to output data structure.
- * \param[in,out] data Should point to \c t_methoddata_kweval.
- * \returns 0 for success.
- */
static void
-init_output_kweval(t_topology *top, gmx_ana_selvalue_t *out, void *data)
+init_output_kweval(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_kweval *d = (t_methoddata_kweval *)data;
out->nr = d->g.isize;
+ _gmx_selvalue_reserve(out, out->nr);
}
/*!
t_methoddata_kweval *d = (t_methoddata_kweval *)data;
_gmx_selelem_free_method(d->kwmethod, d->kwmdata);
+ sfree(d);
}
/*!
*/
static void
evaluate_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+ gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_kweval *d = (t_methoddata_kweval *)data;
}
/*!
- * \param[out] selp Pointer to receive a pointer to the created selection
- * element (set to NULL on error).
* \param[in] method Keyword selection method to evaluate.
- * \param[in] param Parameter that gives the group to evaluate \p method in.
+ * \param[in] params Parameter that gives the group to evaluate \p method in.
* \param[in] scanner Scanner data structure.
- * \returns 0 on success, non-zero error code on error.
+ * \returns Pointer to the created selection element (NULL on error).
+ *
+ * Creates a \ref SEL_EXPRESSION selection element that evaluates the keyword
+ * method given by \p method in the group given by \p param.
*
- * Creates a \ref SEL_EXPRESSION selection element (pointer put in \c *selp)
- * that evaluates the keyword method given by \p method in the group given by
- * \p param.
+ * The name of \p param should be empty.
*/
-int
-_gmx_sel_init_keyword_evaluator(t_selelem **selp, gmx_ana_selmethod_t *method,
- t_selexpr_param *param, void *scanner)
+gmx::SelectionTreeElementPointer
+_gmx_sel_init_keyword_evaluator(gmx_ana_selmethod_t *method,
+ const gmx::SelectionParserParameterList ¶ms,
+ void *scanner)
{
- t_selelem *sel;
- t_methoddata_kweval *data;
-
gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
char buf[1024];
sprintf(buf, "In evaluation of '%s'", method->name);
if ((method->flags & (SMETH_SINGLEVAL | SMETH_VARNUMVAL))
|| method->outinit || method->pupdate)
{
- _gmx_selexpr_free_params(param);
- GMX_ERROR(gmx::eeInternalError,
- "Unsupported keyword method for arbitrary group evaluation");
+ GMX_THROW(gmx::InternalError(
+ "Unsupported keyword method for arbitrary group evaluation"));
}
- *selp = NULL;
- sel = _gmx_selelem_create(SEL_EXPRESSION);
+ gmx::SelectionTreeElementPointer sel(
+ new gmx::SelectionTreeElement(SEL_EXPRESSION));
_gmx_selelem_set_method(sel, method, scanner);
+ t_methoddata_kweval *data;
snew(data, 1);
data->kwmethod = sel->u.expr.method;
data->kwmdata = sel->u.expr.mdata;
sel->u.expr.method->param[0].val.u.g = &data->g;
- sfree(param->name);
- param->name = NULL;
- if (!_gmx_sel_parse_params(param, sel->u.expr.method->nparams,
+ if (!_gmx_sel_parse_params(params, sel->u.expr.method->nparams,
sel->u.expr.method->param, sel, scanner))
{
- _gmx_selelem_free(sel);
- return -1;
+ return gmx::SelectionTreeElementPointer();
}
- *selp = sel;
- return 0;
+ return sel;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff