/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * 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.
*
* GROMACS is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* Each element has exactly two children (one for unary negation elements),
* which are in the order given in the input.
*/
-#include <stdio.h>
+#include "gmxpre.h"
+
+#include "parsetree.h"
+
#include <stdarg.h>
+#include <stdio.h>
#include <boost/exception_ptr.hpp>
#include <boost/shared_ptr.hpp>
-#include "gromacs/legacyheaders/futil.h"
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/string2.h"
-
-#include "gromacs/onlinehelp/helpmanager.h"
-#include "gromacs/onlinehelp/helpwritercontext.h"
-#include "gromacs/selection/poscalc.h"
#include "gromacs/selection/selection.h"
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/file.h"
#include "gromacs/utility/messagestringcollector.h"
+#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "keywords.h"
-#include "parsetree.h"
+#include "poscalc.h"
+#include "scanner.h"
#include "selectioncollection-impl.h"
#include "selelem.h"
-#include "selhelp.h"
+#include "selmethod.h"
#include "symrec.h"
-#include "scanner.h"
-
using gmx::SelectionParserValue;
using gmx::SelectionParserValueList;
using gmx::SelectionParserValueListPointer;
char buf[1024];
va_list ap;
va_start(ap, fmt);
- vsprintf(buf, fmt, ap);
+ vsnprintf(buf, 1024, fmt, ap);
va_end(ap);
errors->append(buf);
}
/*!
* \param[in,out] sel Root of the selection element tree to initialize.
- * \param[in] scanner Scanner data structure.
- * \returns 0 on success, an error code on error.
*
* Propagates the \ref SEL_DYNAMIC flag from the children of \p sel to \p sel
* (if any child of \p sel is dynamic, \p sel is also marked as such).
* operation does not descend beyond such elements.
*/
void
-_gmx_selelem_update_flags(const SelectionTreeElementPointer &sel,
- yyscan_t scanner)
+_gmx_selelem_update_flags(const gmx::SelectionTreeElementPointer &sel)
{
bool bUseChildType = false;
bool bOnlySingleChildren;
while (child)
{
/* Update the child */
- _gmx_selelem_update_flags(child, scanner);
- /* Propagate the dynamic flag */
- sel->flags |= (child->flags & SEL_DYNAMIC);
+ _gmx_selelem_update_flags(child);
+ /* Propagate the dynamic and unsorted flags */
+ sel->flags |= (child->flags & (SEL_DYNAMIC | SEL_UNSORTED));
/* Propagate the type flag if necessary and check for problems */
if (bUseChildType)
{
if ((sel->flags & SEL_VALTYPEMASK)
&& !(sel->flags & child->flags & SEL_VALTYPEMASK))
{
- _gmx_selparser_error(scanner, "invalid combination of selection expressions");
- // FIXME: Use an exception.
- return;
+ // TODO: Recollect when this is triggered, and whether the type
+ // is appropriate.
+ GMX_THROW(gmx::InvalidInputError("Invalid combination of selection expressions"));
}
sel->flags |= (child->flags & SEL_VALTYPEMASK);
}
* Calls sel_datafunc() if one is specified for the method.
*/
void
-_gmx_selelem_init_method_params(const SelectionTreeElementPointer &sel,
- yyscan_t scanner)
+_gmx_selelem_init_method_params(const gmx::SelectionTreeElementPointer &sel,
+ yyscan_t scanner)
{
int nparams;
gmx_ana_selparam_t *orgparam;
* and calls _gmx_selelem_init_method_params();
*/
void
-_gmx_selelem_set_method(const SelectionTreeElementPointer &sel,
- gmx_ana_selmethod_t *method,
- yyscan_t scanner)
+_gmx_selelem_set_method(const gmx::SelectionTreeElementPointer &sel,
+ gmx_ana_selmethod_t *method,
+ yyscan_t scanner)
{
_gmx_selelem_set_vtype(sel, method->type);
sel->setName(method->name);
}
}
-/*!
- * \param[in] left Selection element for the left hand side.
- * \param[in] right Selection element for the right hand side.
- * \param[in] op String representation of the operator.
- * \param[in] scanner Scanner data structure.
- * \returns The created selection element.
- *
- * This function handles the creation of a gmx::SelectionTreeElement object for
- * arithmetic expressions.
- */
-SelectionTreeElementPointer
-_gmx_sel_init_arithmetic(const SelectionTreeElementPointer &left,
- const SelectionTreeElementPointer &right,
- char op, yyscan_t scanner)
+gmx::SelectionTreeElementPointer
+_gmx_sel_init_arithmetic(const gmx::SelectionTreeElementPointer &left,
+ const gmx::SelectionTreeElementPointer &right,
+ char op, yyscan_t /* scanner */)
{
SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_ARITHMETIC));
sel->v.type = REAL_VALUE;
buf[0] = op;
buf[1] = 0;
sel->setName(buf);
- sel->u.arith.opstr = strdup(buf);
+ sel->u.arith.opstr = gmx_strdup(buf);
sel->child = left;
sel->child->next = right;
return sel;
* comparison expressions.
*/
SelectionTreeElementPointer
-_gmx_sel_init_comparison(const SelectionTreeElementPointer &left,
- const SelectionTreeElementPointer &right,
+_gmx_sel_init_comparison(const gmx::SelectionTreeElementPointer &left,
+ const gmx::SelectionTreeElementPointer &right,
const char *cmpop, yyscan_t scanner)
{
gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
*/
SelectionTreeElementPointer
_gmx_sel_init_keyword(gmx_ana_selmethod_t *method,
- SelectionParserValueListPointer args,
+ gmx::SelectionParserValueListPointer args,
const char *rpost, yyscan_t scanner)
{
return init_keyword_internal(method, gmx::eStringMatchType_Auto, move(args),
SelectionTreeElementPointer
_gmx_sel_init_keyword_strmatch(gmx_ana_selmethod_t *method,
gmx::SelectionStringMatchType matchType,
- SelectionParserValueListPointer args,
+ gmx::SelectionParserValueListPointer args,
const char *rpost, yyscan_t scanner)
{
GMX_RELEASE_ASSERT(method->type == STR_VALUE,
* handling somewhere else (or sacrificing the simple syntax).
*/
SelectionTreeElementPointer
-_gmx_sel_init_method(gmx_ana_selmethod_t *method,
- SelectionParserParameterListPointer params,
+_gmx_sel_init_method(gmx_ana_selmethod_t *method,
+ gmx::SelectionParserParameterListPointer params,
const char *rpost, yyscan_t scanner)
{
gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
* selection modifiers.
*/
SelectionTreeElementPointer
-_gmx_sel_init_modifier(gmx_ana_selmethod_t *method,
- SelectionParserParameterListPointer params,
- const SelectionTreeElementPointer &sel, yyscan_t scanner)
+_gmx_sel_init_modifier(gmx_ana_selmethod_t *method,
+ gmx::SelectionParserParameterListPointer params,
+ const gmx::SelectionTreeElementPointer &sel,
+ yyscan_t scanner)
{
gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
char buf[128];
* evaluation of reference positions.
*/
SelectionTreeElementPointer
-_gmx_sel_init_position(const SelectionTreeElementPointer &expr,
+_gmx_sel_init_position(const gmx::SelectionTreeElementPointer &expr,
const char *type, yyscan_t scanner)
{
gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
SelectionTreeElementPointer sel(new SelectionTreeElement(SEL_GROUPREF));
_gmx_selelem_set_vtype(sel, GROUP_VALUE);
sel->setName(gmx::formatString("group \"%s\"", name));
- sel->u.gref.name = strdup(name);
+ sel->u.gref.name = gmx_strdup(name);
sel->u.gref.id = -1;
if (_gmx_sel_lexer_has_groups_set(scanner))
{
- gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
- sel->resolveIndexGroupReference(grps);
+ gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
+ gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
+ sel->resolveIndexGroupReference(grps, sc->gall.isize);
}
return sel;
if (_gmx_sel_lexer_has_groups_set(scanner))
{
- gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
- sel->resolveIndexGroupReference(grps);
+ gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
+ gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
+ sel->resolveIndexGroupReference(grps, sc->gall.isize);
}
return sel;
* made.
*/
SelectionTreeElementPointer
-_gmx_sel_init_variable_ref(const SelectionTreeElementPointer &sel)
+_gmx_sel_init_variable_ref(const gmx::SelectionTreeElementPointer &sel)
{
SelectionTreeElementPointer ref;
* gmx::SelectionTreeElement objects for selections.
*/
SelectionTreeElementPointer
-_gmx_sel_init_selection(const char *name,
- const SelectionTreeElementPointer &sel,
- yyscan_t scanner)
+_gmx_sel_init_selection(const char *name,
+ const gmx::SelectionTreeElementPointer &sel,
+ yyscan_t scanner)
{
- gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
- char buf[1024];
- sprintf(buf, "In selection '%s'", _gmx_sel_lexer_pselstr(scanner));
- gmx::MessageStringContext context(errors, buf);
-
if (sel->v.type != POS_VALUE)
{
/* FIXME: Better handling of this error */
root->setName(name);
}
/* Update the flags */
- _gmx_selelem_update_flags(root, scanner);
+ _gmx_selelem_update_flags(root);
+ gmx::ExceptionInitializer errors("Invalid index group reference(s)");
+ root->checkUnsortedAtoms(true, &errors);
+ if (errors.hasNestedExceptions())
+ {
+ GMX_THROW(gmx::InconsistentInputError(errors));
+ }
root->fillNameIfMissing(_gmx_sel_lexer_pselstr(scanner));
* element are both created.
*/
SelectionTreeElementPointer
-_gmx_sel_assign_variable(const char *name,
- const SelectionTreeElementPointer &expr,
- yyscan_t scanner)
+_gmx_sel_assign_variable(const char *name,
+ const gmx::SelectionTreeElementPointer &expr,
+ yyscan_t scanner)
{
gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
const char *pselstr = _gmx_sel_lexer_pselstr(scanner);
SelectionTreeElementPointer root;
- gmx::MessageStringCollector *errors = _gmx_sel_lexer_error_reporter(scanner);
- char buf[1024];
- sprintf(buf, "In selection '%s'", pselstr);
- gmx::MessageStringContext context(errors, buf);
-
- _gmx_selelem_update_flags(expr, scanner);
+ _gmx_selelem_update_flags(expr);
/* Check if this is a constant non-group value */
if (expr->type == SEL_CONST && expr->v.type != GROUP_VALUE)
{
/* If so, just assign the constant value to the variable */
sc->symtab->addVariable(name, expr);
- goto finish;
}
/* Check if we are assigning a variable to another variable */
- if (expr->type == SEL_SUBEXPRREF)
+ else if (expr->type == SEL_SUBEXPRREF)
{
/* If so, make a simple alias */
sc->symtab->addVariable(name, expr->child);
- goto finish;
}
- /* Create the root element */
- root.reset(new SelectionTreeElement(SEL_ROOT));
- root->setName(name);
- /* Create the subexpression element */
- root->child.reset(new SelectionTreeElement(SEL_SUBEXPR));
- root->child->setName(name);
- _gmx_selelem_set_vtype(root->child, expr->v.type);
- root->child->child = expr;
- /* Update flags */
- _gmx_selelem_update_flags(root, scanner);
- /* Add the variable to the symbol table */
- sc->symtab->addVariable(name, root->child);
-finish:
+ else
+ {
+ /* Create the root element */
+ root.reset(new SelectionTreeElement(SEL_ROOT));
+ root->setName(name);
+ /* Create the subexpression element */
+ root->child.reset(new SelectionTreeElement(SEL_SUBEXPR));
+ root->child->setName(name);
+ _gmx_selelem_set_vtype(root->child, expr->v.type);
+ root->child->child = expr;
+ /* Update flags */
+ _gmx_selelem_update_flags(root);
+ gmx::ExceptionInitializer errors("Invalid index group reference(s)");
+ root->checkUnsortedAtoms(true, &errors);
+ if (errors.hasNestedExceptions())
+ {
+ GMX_THROW(gmx::InconsistentInputError(errors));
+ }
+ /* Add the variable to the symbol table */
+ sc->symtab->addVariable(name, root->child);
+ }
srenew(sc->varstrs, sc->nvars + 1);
- sc->varstrs[sc->nvars] = strdup(pselstr);
+ sc->varstrs[sc->nvars] = gmx_strdup(pselstr);
++sc->nvars;
if (_gmx_sel_is_lexer_interactive(scanner))
{
* (if it was non-NULL) or the last element (if \p sel was NULL).
*/
SelectionTreeElementPointer
-_gmx_sel_append_selection(const SelectionTreeElementPointer &sel,
- SelectionTreeElementPointer last,
- yyscan_t scanner)
+_gmx_sel_append_selection(const gmx::SelectionTreeElementPointer &sel,
+ gmx::SelectionTreeElementPointer last,
+ yyscan_t scanner)
{
gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
return (int)sc->sel.size() == _gmx_sel_lexer_exp_selcount(scanner);
}
-
-/*!
- * \param[in] scanner Scanner data structure.
- */
-void
-_gmx_sel_handle_empty_cmd(yyscan_t scanner)
-{
- gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
- gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
- int i;
-
- if (!_gmx_sel_is_lexer_interactive(scanner))
- {
- return;
- }
-
- if (grps)
- {
- fprintf(stderr, "Available index groups:\n");
- gmx_ana_indexgrps_print(stderr, _gmx_sel_lexer_indexgrps(scanner), 0);
- }
- if (sc->nvars > 0 || !sc->sel.empty())
- {
- fprintf(stderr, "Currently provided selections:\n");
- for (i = 0; i < sc->nvars; ++i)
- {
- fprintf(stderr, " %s\n", sc->varstrs[i]);
- }
- for (i = 0; i < (int)sc->sel.size(); ++i)
- {
- fprintf(stderr, " %2d. %s\n", i+1, sc->sel[i]->selectionText());
- }
- }
-}
-
-/*!
- * \param[in] topic Topic for which help was requested, or NULL for general
- * help.
- * \param[in] scanner Scanner data structure.
- *
- * \p topic is freed by this function.
- */
-void
-_gmx_sel_handle_help_cmd(const SelectionParserValueListPointer &topic,
- yyscan_t scanner)
-{
- gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
-
- if (sc->rootHelp.get() == NULL)
- {
- sc->rootHelp = gmx::createSelectionHelpTopic();
- }
- gmx::HelpWriterContext context(&gmx::File::standardError(),
- gmx::eHelpOutputFormat_Console);
- gmx::HelpManager manager(*sc->rootHelp, context);
- try
- {
- SelectionParserValueList::const_iterator value;
- for (value = topic->begin(); value != topic->end(); ++value)
- {
- manager.enterTopic(value->stringValue());
- }
- }
- catch (const gmx::InvalidInputError &ex)
- {
- fprintf(stderr, "%s\n", ex.what());
- return;
- }
- manager.writeCurrentTopic();
-}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff