/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010-2018, The GROMACS development team.
+ * Copyright (c) 2019, 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.
* SelectionCollection::Impl
*/
-SelectionCollection::Impl::Impl()
- : debugLevel_(0), bExternalGroupsSet_(false), grps_(nullptr)
+SelectionCollection::Impl::Impl() : debugLevel_(0), bExternalGroupsSet_(false), grps_(nullptr)
{
- sc_.nvars = 0;
- sc_.varstrs = nullptr;
- sc_.top = nullptr;
+ sc_.nvars = 0;
+ sc_.varstrs = nullptr;
+ sc_.top = nullptr;
gmx_ana_index_clear(&sc_.gall);
- sc_.mempool = nullptr;
- sc_.symtab = std::make_unique<SelectionParserSymbolTable>();
+ sc_.mempool = nullptr;
+ sc_.symtab = std::make_unique<SelectionParserSymbolTable>();
gmx_ana_index_clear(&requiredAtoms_);
gmx_ana_selmethod_register_defaults(sc_.symtab.get());
}
}
-void
-SelectionCollection::Impl::clearSymbolTable()
+void SelectionCollection::Impl::clearSymbolTable()
{
sc_.symtab.reset();
}
*
* Handles line continuation, reading also the continuing line(s) in one call.
*/
-bool promptLine(TextInputStream *inputStream, TextWriter *statusWriter,
- std::string *line)
+bool promptLine(TextInputStream* inputStream, TextWriter* statusWriter, std::string* line)
{
if (statusWriter != nullptr)
{
* \p parserState until there is no more input, or until enough input is given
* (only in interactive mode).
*/
-int runParserLoop(yyscan_t scanner, _gmx_sel_yypstate *parserState,
- bool bInteractive)
+int runParserLoop(yyscan_t scanner, _gmx_sel_yypstate* parserState, bool bInteractive)
{
- int status = YYPUSH_MORE;
+ int status = YYPUSH_MORE;
do
{
YYSTYPE value;
break;
}
status = _gmx_sel_yypush_parse(parserState, token, &value, &location, scanner);
- }
- while (status == YYPUSH_MORE);
+ } while (status == YYPUSH_MORE);
_gmx_sel_lexer_rethrow_exception_if_occurred(scanner);
return status;
}
*
* Prints the available index groups and currently provided selections.
*/
-void printCurrentStatus(TextWriter *writer, gmx_ana_selcollection_t *sc,
- gmx_ana_indexgrps_t *grps, size_t firstSelection,
- int maxCount, const std::string &context, bool bFirst)
+void printCurrentStatus(TextWriter* writer,
+ gmx_ana_selcollection_t* sc,
+ gmx_ana_indexgrps_t* grps,
+ size_t firstSelection,
+ int maxCount,
+ const std::string& context,
+ bool bFirst)
{
if (grps != nullptr)
{
{
writer->writeString(formatString("%d selections", maxCount));
}
- writer->writeString(formatString("%s%s:\n",
- context.empty() ? "" : " ", context.c_str()));
- writer->writeString(formatString(
- "(one per line, <enter> for status/groups, 'help' for help%s)\n",
- maxCount < 0 ? ", Ctrl-D to end" : ""));
+ writer->writeString(formatString("%s%s:\n", context.empty() ? "" : " ", context.c_str()));
+ writer->writeString(
+ formatString("(one per line, <enter> for status/groups, 'help' for help%s)\n",
+ maxCount < 0 ? ", Ctrl-D to end" : ""));
if (!bFirst && (sc->nvars > 0 || sc->sel.size() > firstSelection))
{
writer->writeLine("Currently provided selections:");
}
for (size_t i = firstSelection; i < sc->sel.size(); ++i)
{
- writer->writeString(formatString(
- " %2d. %s\n",
- static_cast<int>(i - firstSelection + 1),
- sc->sel[i]->selectionText()));
+ writer->writeString(formatString(" %2d. %s\n", static_cast<int>(i - firstSelection + 1),
+ sc->sel[i]->selectionText()));
}
if (maxCount > 0)
{
- const int remaining
- = maxCount - static_cast<int>(sc->sel.size() - firstSelection);
- writer->writeString(formatString(
- "(%d more selection%s required)\n",
- remaining, remaining > 1 ? "s" : ""));
+ const int remaining = maxCount - static_cast<int>(sc->sel.size() - firstSelection);
+ writer->writeString(formatString("(%d more selection%s required)\n", remaining,
+ remaining > 1 ? "s" : ""));
}
}
}
* Initializes the selection help if not yet initialized, and finds the help
* topic based on words on the input line.
*/
-void printHelp(TextWriter *writer, gmx_ana_selcollection_t *sc,
- const std::string &line)
+void printHelp(TextWriter* writer, gmx_ana_selcollection_t* sc, const std::string& line)
{
if (sc->rootHelp.get() == nullptr)
{
manager.enterTopic(*value);
}
}
- catch (const InvalidInputError &ex)
+ catch (const InvalidInputError& ex)
{
writer->writeLine(ex.what());
return;
* Used internally to implement parseInteractive(), parseFromFile() and
* parseFromString().
*/
-SelectionList runParser(yyscan_t scanner, TextInputStream *inputStream,
- bool bInteractive, int maxnr, const std::string &context)
+SelectionList runParser(yyscan_t scanner,
+ TextInputStream* inputStream,
+ bool bInteractive,
+ int maxnr,
+ const std::string& context)
{
std::shared_ptr<void> scannerGuard(scanner, &_gmx_sel_free_lexer);
- gmx_ana_selcollection_t *sc = _gmx_sel_lexer_selcollection(scanner);
- gmx_ana_indexgrps_t *grps = _gmx_sel_lexer_indexgrps(scanner);
+ gmx_ana_selcollection_t* sc = _gmx_sel_lexer_selcollection(scanner);
+ gmx_ana_indexgrps_t* grps = _gmx_sel_lexer_indexgrps(scanner);
- size_t oldCount = sc->sel.size();
+ size_t oldCount = sc->sel.size();
{
- std::shared_ptr<_gmx_sel_yypstate> parserState(
- _gmx_sel_yypstate_new(), &_gmx_sel_yypstate_delete);
+ std::shared_ptr<_gmx_sel_yypstate> parserState(_gmx_sel_yypstate_new(), &_gmx_sel_yypstate_delete);
if (bInteractive)
{
- TextWriter *statusWriter = _gmx_sel_lexer_get_status_writer(scanner);
+ TextWriter* statusWriter = _gmx_sel_lexer_get_status_writer(scanner);
if (statusWriter != nullptr)
{
printCurrentStatus(statusWriter, sc, grps, oldCount, maxnr, context, true);
printCurrentStatus(statusWriter, sc, grps, oldCount, maxnr, context, false);
continue;
}
- if (startsWith(line, "help")
- && (line[4] == 0 || (std::isspace(line[4]) != 0)))
+ if (startsWith(line, "help") && (line[4] == 0 || (std::isspace(line[4]) != 0)))
{
printHelp(statusWriter, sc, line);
continue;
}
{
YYLTYPE location;
- status = _gmx_sel_yypush_parse(parserState.get(), 0, nullptr,
- &location, scanner);
+ status = _gmx_sel_yypush_parse(parserState.get(), 0, nullptr, &location, scanner);
}
// TODO: Remove added selections from the collection if parsing failed?
_gmx_sel_lexer_rethrow_exception_if_occurred(scanner);
-early_termination:
- GMX_RELEASE_ASSERT(status == 0,
- "Parser errors should have resulted in an exception");
+ early_termination:
+ GMX_RELEASE_ASSERT(status == 0, "Parser errors should have resulted in an exception");
}
else
{
int status = runParserLoop(scanner, parserState.get(), false);
- GMX_RELEASE_ASSERT(status == 0,
- "Parser errors should have resulted in an exception");
+ GMX_RELEASE_ASSERT(status == 0, "Parser errors should have resulted in an exception");
}
}
scannerGuard.reset();
int nr = sc->sel.size() - oldCount;
if (maxnr > 0 && nr != maxnr)
{
- std::string message
- = formatString("Too few selections provided; got %d, expected %d",
- nr, maxnr);
+ std::string message = formatString("Too few selections provided; got %d, expected %d", nr, maxnr);
GMX_THROW(InvalidInputError(message));
}
* the topology/maximum number of atoms set for the selection collection.
* Any issues are reported to \p errors.
*/
-void checkExternalGroups(const SelectionTreeElementPointer &root,
- int natoms,
- ExceptionInitializer *errors)
+void checkExternalGroups(const SelectionTreeElementPointer& root, int natoms, ExceptionInitializer* errors)
{
if (root->type == SEL_CONST && root->v.type == GROUP_VALUE)
{
{
root->checkIndexGroup(natoms);
}
- catch (const UserInputError &)
+ catch (const UserInputError&)
{
errors->addCurrentExceptionAsNested();
}
}
//! Checks whether the given topology properties are available.
-void checkTopologyProperties(const gmx_mtop_t *top,
- const SelectionTopologyProperties &props)
+void checkTopologyProperties(const gmx_mtop_t* top, const SelectionTopologyProperties& props)
{
if (top == nullptr)
{
if (props.hasAny())
{
- GMX_THROW(InconsistentInputError("Selection requires topology information, but none provided"));
+ GMX_THROW(InconsistentInputError(
+ "Selection requires topology information, but none provided"));
}
return;
}
if (props.needsMasses && !gmx_mtop_has_masses(top))
{
- GMX_THROW(InconsistentInputError("Selection requires mass information, but it is not available in the topology"));
+ GMX_THROW(InconsistentInputError(
+ "Selection requires mass information, but it is not available in the topology"));
}
}
-} // namespace
+} // namespace
-void SelectionCollection::Impl::resolveExternalGroups(
- const SelectionTreeElementPointer &root,
- ExceptionInitializer *errors)
+void SelectionCollection::Impl::resolveExternalGroups(const SelectionTreeElementPointer& root,
+ ExceptionInitializer* errors)
{
if (root->type == SEL_GROUPREF)
{
root->resolveIndexGroupReference(grps_, sc_.gall.isize);
}
- catch (const UserInputError &)
+ catch (const UserInputError&)
{
errors->addCurrentExceptionAsNested();
}
{
resolveExternalGroups(child, errors);
root->flags |= (child->flags & SEL_UNSORTED);
- child = child->next;
+ child = child->next;
}
}
bool SelectionCollection::Impl::areForcesRequested() const
{
- for (const auto &sel : sc_.sel)
+ for (const auto& sel : sc_.sel)
{
if (sel->hasFlag(gmx::efSelection_EvaluateForces))
{
SelectionTopologyProperties
-SelectionCollection::Impl::requiredTopologyPropertiesForPositionType(
- const std::string &post, bool forces) const
+SelectionCollection::Impl::requiredTopologyPropertiesForPositionType(const std::string& post, bool forces) const
{
SelectionTopologyProperties props;
if (!post.empty())
{
switch (PositionCalculationCollection::requiredTopologyInfoForType(post.c_str(), forces))
{
- case PositionCalculationCollection::RequiredTopologyInfo::None:
- break;
+ case PositionCalculationCollection::RequiredTopologyInfo::None: break;
case PositionCalculationCollection::RequiredTopologyInfo::Topology:
props.merge(SelectionTopologyProperties::topology());
break;
* SelectionCollection
*/
-SelectionCollection::SelectionCollection()
- : impl_(new Impl)
-{
-}
+SelectionCollection::SelectionCollection() : impl_(new Impl) {}
-SelectionCollection::~SelectionCollection()
-{
-}
+SelectionCollection::~SelectionCollection() {}
-void
-SelectionCollection::initOptions(IOptionsContainer *options,
- SelectionTypeOption selectionTypeOption)
+void SelectionCollection::initOptions(IOptionsContainer* options, SelectionTypeOption selectionTypeOption)
{
- const char * const debug_levels[]
- = { "no", "basic", "compile", "eval", "full" };
+ const char* const debug_levels[] = { "no", "basic", "compile", "eval", "full" };
- const char *const *postypes = PositionCalculationCollection::typeEnumValues;
+ const char* const* postypes = PositionCalculationCollection::typeEnumValues;
options->addOption(StringOption("selrpos")
- .enumValueFromNullTerminatedArray(postypes)
- .store(&impl_->rpost_).defaultValue(postypes[0])
- .description("Selection reference positions"));
+ .enumValueFromNullTerminatedArray(postypes)
+ .store(&impl_->rpost_)
+ .defaultValue(postypes[0])
+ .description("Selection reference positions"));
if (selectionTypeOption == IncludeSelectionTypeOption)
{
options->addOption(StringOption("seltype")
- .enumValueFromNullTerminatedArray(postypes)
- .store(&impl_->spost_).defaultValue(postypes[0])
- .description("Default selection output positions"));
+ .enumValueFromNullTerminatedArray(postypes)
+ .store(&impl_->spost_)
+ .defaultValue(postypes[0])
+ .description("Default selection output positions"));
}
else
{
}
GMX_RELEASE_ASSERT(impl_->debugLevel_ >= 0 && impl_->debugLevel_ <= 4,
"Debug level out of range");
- options->addOption(EnumIntOption("seldebug").hidden(impl_->debugLevel_ == 0)
- .enumValue(debug_levels).store(&impl_->debugLevel_)
- .description("Print out selection trees for debugging"));
+ options->addOption(EnumIntOption("seldebug")
+ .hidden(impl_->debugLevel_ == 0)
+ .enumValue(debug_levels)
+ .store(&impl_->debugLevel_)
+ .description("Print out selection trees for debugging"));
}
-void
-SelectionCollection::setReferencePosType(const char *type)
+void SelectionCollection::setReferencePosType(const char* type)
{
GMX_RELEASE_ASSERT(type != nullptr, "Cannot assign NULL position type");
// Check that the type is valid, throw if it is not.
- e_poscalc_t dummytype;
- int dummyflags;
+ e_poscalc_t dummytype;
+ int dummyflags;
PositionCalculationCollection::typeFromEnum(type, &dummytype, &dummyflags);
impl_->rpost_ = type;
}
-void
-SelectionCollection::setOutputPosType(const char *type)
+void SelectionCollection::setOutputPosType(const char* type)
{
GMX_RELEASE_ASSERT(type != nullptr, "Cannot assign NULL position type");
// Check that the type is valid, throw if it is not.
- e_poscalc_t dummytype;
- int dummyflags;
+ e_poscalc_t dummytype;
+ int dummyflags;
PositionCalculationCollection::typeFromEnum(type, &dummytype, &dummyflags);
impl_->spost_ = type;
}
-void
-SelectionCollection::setDebugLevel(int debugLevel)
+void SelectionCollection::setDebugLevel(int debugLevel)
{
impl_->debugLevel_ = debugLevel;
}
-void
-SelectionCollection::setTopology(gmx_mtop_t *top, int natoms)
+void SelectionCollection::setTopology(gmx_mtop_t* top, int natoms)
{
GMX_RELEASE_ASSERT(natoms > 0 || top != nullptr,
"The number of atoms must be given if there is no topology");
GMX_THROW(InconsistentInputError(errors));
}
}
- gmx_ana_selcollection_t *sc = &impl_->sc_;
+ gmx_ana_selcollection_t* sc = &impl_->sc_;
// Do this first, as it allocates memory, while the others don't throw.
gmx_ana_index_init_simple(&sc->gall, natoms);
sc->top = top;
}
-void
-SelectionCollection::setIndexGroups(gmx_ana_indexgrps_t *grps)
+void SelectionCollection::setIndexGroups(gmx_ana_indexgrps_t* grps)
{
GMX_RELEASE_ASSERT(grps == nullptr || !impl_->bExternalGroupsSet_,
"Can only set external groups once or clear them afterwards");
}
}
-SelectionTopologyProperties
-SelectionCollection::requiredTopologyProperties() const
+SelectionTopologyProperties SelectionCollection::requiredTopologyProperties() const
{
SelectionTopologyProperties props;
// These should not throw, because has been checked earlier.
props.merge(impl_->requiredTopologyPropertiesForPositionType(impl_->rpost_, false));
const bool forcesRequested = impl_->areForcesRequested();
- props.merge(impl_->requiredTopologyPropertiesForPositionType(impl_->spost_,
- forcesRequested));
+ props.merge(impl_->requiredTopologyPropertiesForPositionType(impl_->spost_, forcesRequested));
SelectionTreeElementPointer sel = impl_->sc_.root;
while (sel && !props.hasAll())
}
-bool
-SelectionCollection::requiresIndexGroups() const
+bool SelectionCollection::requiresIndexGroups() const
{
SelectionTreeElementPointer sel = impl_->sc_.root;
while (sel)
}
-SelectionList
-SelectionCollection::parseFromStdin(int count, bool bInteractive,
- const std::string &context)
+SelectionList SelectionCollection::parseFromStdin(int count, bool bInteractive, const std::string& context)
{
return parseInteractive(count, &StandardInputStream::instance(),
- bInteractive ? &TextOutputFile::standardError() : nullptr,
- context);
+ bInteractive ? &TextOutputFile::standardError() : nullptr, context);
}
namespace
{
//! Helper function to initialize status writer for interactive selection parsing.
-std::unique_ptr<TextWriter> initStatusWriter(TextOutputStream *statusStream)
+std::unique_ptr<TextWriter> initStatusWriter(TextOutputStream* statusStream)
{
std::unique_ptr<TextWriter> statusWriter;
if (statusStream != nullptr)
return statusWriter;
}
-} // namespace
+} // namespace
-SelectionList
-SelectionCollection::parseInteractive(int count,
- TextInputStream *inputStream,
- TextOutputStream *statusStream,
- const std::string &context)
+SelectionList SelectionCollection::parseInteractive(int count,
+ TextInputStream* inputStream,
+ TextOutputStream* statusStream,
+ const std::string& context)
{
yyscan_t scanner;
- const std::unique_ptr<TextWriter> statusWriter(
- initStatusWriter(statusStream));
- _gmx_sel_init_lexer(&scanner, &impl_->sc_, statusWriter.get(),
- count, impl_->bExternalGroupsSet_, impl_->grps_);
+ const std::unique_ptr<TextWriter> statusWriter(initStatusWriter(statusStream));
+ _gmx_sel_init_lexer(&scanner, &impl_->sc_, statusWriter.get(), count,
+ impl_->bExternalGroupsSet_, impl_->grps_);
return runParser(scanner, inputStream, true, count, context);
}
-SelectionList
-SelectionCollection::parseFromFile(const std::string &filename)
+SelectionList SelectionCollection::parseFromFile(const std::string& filename)
{
try
yyscan_t scanner;
TextInputFile file(filename);
// TODO: Exception-safe way of using the lexer.
- _gmx_sel_init_lexer(&scanner, &impl_->sc_, nullptr, -1,
- impl_->bExternalGroupsSet_,
- impl_->grps_);
+ _gmx_sel_init_lexer(&scanner, &impl_->sc_, nullptr, -1, impl_->bExternalGroupsSet_, impl_->grps_);
_gmx_sel_set_lex_input_file(scanner, file.handle());
return runParser(scanner, nullptr, false, -1, std::string());
}
- catch (GromacsException &ex)
+ catch (GromacsException& ex)
{
- ex.prependContext(formatString(
- "Error in parsing selections from file '%s'",
- filename.c_str()));
+ ex.prependContext(formatString("Error in parsing selections from file '%s'", filename.c_str()));
throw;
}
}
-SelectionList
-SelectionCollection::parseFromString(const std::string &str)
+SelectionList SelectionCollection::parseFromString(const std::string& str)
{
yyscan_t scanner;
- _gmx_sel_init_lexer(&scanner, &impl_->sc_, nullptr, -1,
- impl_->bExternalGroupsSet_,
- impl_->grps_);
+ _gmx_sel_init_lexer(&scanner, &impl_->sc_, nullptr, -1, impl_->bExternalGroupsSet_, impl_->grps_);
_gmx_sel_set_lex_input_str(scanner, str.c_str());
return runParser(scanner, nullptr, false, -1, std::string());
}
-void
-SelectionCollection::compile()
+void SelectionCollection::compile()
{
checkTopologyProperties(impl_->sc_.top, requiredTopologyProperties());
if (!impl_->bExternalGroupsSet_)
SelectionDataList::const_iterator iter;
for (iter = impl_->sc_.sel.begin(); iter != impl_->sc_.sel.end(); ++iter)
{
- const internal::SelectionData &sel = **iter;
+ const internal::SelectionData& sel = **iter;
if (sel.hasFlag(efSelection_OnlyAtoms))
{
if (!sel.hasOnlyAtoms())
{
std::string message = formatString(
- "Selection '%s' does not evaluate to individual atoms. "
- "This is not allowed in this context.",
- sel.selectionText());
+ "Selection '%s' does not evaluate to individual atoms. "
+ "This is not allowed in this context.",
+ sel.selectionText());
GMX_THROW(InvalidInputError(message));
}
if (sel.hasFlag(efSelection_OnlySorted))
if (!sel.hasSortedAtomIndices())
{
const std::string message = formatString(
- "Selection '%s' does not evaluate to atoms in an "
- "ascending (sorted) order. "
- "This is not allowed in this context.",
- sel.selectionText());
+ "Selection '%s' does not evaluate to atoms in an "
+ "ascending (sorted) order. "
+ "This is not allowed in this context.",
+ sel.selectionText());
GMX_THROW(InvalidInputError(message));
}
}
{
if (sel.posCount() == 0)
{
- std::string message = formatString(
- "Selection '%s' never matches any atoms.",
- sel.selectionText());
+ std::string message =
+ formatString("Selection '%s' never matches any atoms.", sel.selectionText());
GMX_THROW(InvalidInputError(message));
}
}
}
-void
-SelectionCollection::evaluate(t_trxframe *fr, t_pbc *pbc)
+void SelectionCollection::evaluate(t_trxframe* fr, t_pbc* pbc)
{
checkTopologyProperties(impl_->sc_.top, requiredTopologyProperties());
if (fr->bIndex)
if (!gmx_ana_index_contains(&g, &impl_->requiredAtoms_))
{
const std::string message = formatString(
- "Trajectory does not contain all atoms required for "
- "evaluating the provided selections.");
+ "Trajectory does not contain all atoms required for "
+ "evaluating the provided selections.");
GMX_THROW(InconsistentInputError(message));
}
}
if (fr->natoms <= maxAtomIndex)
{
const std::string message = formatString(
- "Trajectory has less atoms (%d) than what is required for "
- "evaluating the provided selections (atoms up to index %d "
- "are required).", fr->natoms, maxAtomIndex + 1);
+ "Trajectory has less atoms (%d) than what is required for "
+ "evaluating the provided selections (atoms up to index %d "
+ "are required).",
+ fr->natoms, maxAtomIndex + 1);
GMX_THROW(InconsistentInputError(message));
}
}
}
-void
-SelectionCollection::evaluateFinal(int nframes)
+void SelectionCollection::evaluateFinal(int nframes)
{
SelectionEvaluator evaluator;
evaluator.evaluateFinal(this, nframes);
}
-void
-SelectionCollection::printTree(FILE *fp, bool bValues) const
+void SelectionCollection::printTree(FILE* fp, bool bValues) const
{
SelectionTreeElementPointer sel = impl_->sc_.root;
while (sel)
}
-void
-SelectionCollection::printXvgrInfo(FILE *out) const
+void SelectionCollection::printXvgrInfo(FILE* out) const
{
- const gmx_ana_selcollection_t &sc = impl_->sc_;
+ const gmx_ana_selcollection_t& sc = impl_->sc_;
std::fprintf(out, "# Selections:\n");
for (int i = 0; i < sc.nvars; ++i)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff