/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, 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.
*/
class TrajectoryAnalysisModule::Impl
{
- public:
- //! Container that associates a data set with its name.
- typedef std::map<std::string, AbstractAnalysisData *> DatasetContainer;
- //! Container that associates a AnalysisData object with its name.
- typedef std::map<std::string, AnalysisData *> AnalysisDatasetContainer;
-
- //! List of registered data set names.
- std::vector<std::string> datasetNames_;
- /*! \brief
- * Keeps all registered data sets.
- *
- * This container also includes datasets from \a analysisDatasets_.
- */
- DatasetContainer datasets_;
- //! Keeps registered AnalysisData objects.
- AnalysisDatasetContainer analysisDatasets_;
+public:
+ //! Container that associates a data set with its name.
+ typedef std::map<std::string, AbstractAnalysisData*> DatasetContainer;
+ //! Container that associates a AnalysisData object with its name.
+ typedef std::map<std::string, AnalysisData*> AnalysisDatasetContainer;
+
+ //! List of registered data set names.
+ std::vector<std::string> datasetNames_;
+ /*! \brief
+ * Keeps all registered data sets.
+ *
+ * This container also includes datasets from \a analysisDatasets_.
+ */
+ DatasetContainer datasets_;
+ //! Keeps registered AnalysisData objects.
+ AnalysisDatasetContainer analysisDatasets_;
};
/********************************************************************
*/
class TrajectoryAnalysisModuleData::Impl
{
- public:
- //! Container that associates a data handle to its AnalysisData object.
- typedef std::map<const AnalysisData *, AnalysisDataHandle>
- HandleContainer;
-
- //! \copydoc TrajectoryAnalysisModuleData::TrajectoryAnalysisModuleData()
- Impl(TrajectoryAnalysisModule *module,
- const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections);
-
- //! Checks whether the given AnalysisData has been initialized.
- bool isInitialized(const AnalysisData &data) const;
-
- //! Keeps a data handle for each AnalysisData object.
- HandleContainer handles_;
- //! Stores thread-local selections.
- const SelectionCollection &selections_;
+public:
+ //! Container that associates a data handle to its AnalysisData object.
+ typedef std::map<const AnalysisData*, AnalysisDataHandle> HandleContainer;
+
+ //! \copydoc TrajectoryAnalysisModuleData::TrajectoryAnalysisModuleData()
+ Impl(TrajectoryAnalysisModule* module,
+ const AnalysisDataParallelOptions& opt,
+ const SelectionCollection& selections);
+
+ //! Checks whether the given AnalysisData has been initialized.
+ bool isInitialized(const AnalysisData& data) const;
+
+ //! Keeps a data handle for each AnalysisData object.
+ HandleContainer handles_;
+ //! Stores thread-local selections.
+ const SelectionCollection& selections_;
};
-TrajectoryAnalysisModuleData::Impl::Impl(
- TrajectoryAnalysisModule *module,
- const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections)
- : selections_(selections)
+TrajectoryAnalysisModuleData::Impl::Impl(TrajectoryAnalysisModule* module,
+ const AnalysisDataParallelOptions& opt,
+ const SelectionCollection& selections) :
+ selections_(selections)
{
TrajectoryAnalysisModule::Impl::AnalysisDatasetContainer::const_iterator i;
- for (i = module->impl_->analysisDatasets_.begin();
- i != module->impl_->analysisDatasets_.end(); ++i)
+ for (i = module->impl_->analysisDatasets_.begin(); i != module->impl_->analysisDatasets_.end(); ++i)
{
AnalysisDataHandle handle;
if (isInitialized(*i->second))
}
}
-bool TrajectoryAnalysisModuleData::Impl::isInitialized(
- const AnalysisData &data) const
+bool TrajectoryAnalysisModuleData::Impl::isInitialized(const AnalysisData& data) const
{
for (int i = 0; i < data.dataSetCount(); ++i)
{
* TrajectoryAnalysisModuleData
*/
-TrajectoryAnalysisModuleData::TrajectoryAnalysisModuleData(
- TrajectoryAnalysisModule *module,
- const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections)
- : impl_(new Impl(module, opt, selections))
+TrajectoryAnalysisModuleData::TrajectoryAnalysisModuleData(TrajectoryAnalysisModule* module,
+ const AnalysisDataParallelOptions& opt,
+ const SelectionCollection& selections) :
+ impl_(new Impl(module, opt, selections))
{
}
-TrajectoryAnalysisModuleData::~TrajectoryAnalysisModuleData()
-{
-}
+TrajectoryAnalysisModuleData::~TrajectoryAnalysisModuleData() {}
void TrajectoryAnalysisModuleData::finishDataHandles()
}
-AnalysisDataHandle
-TrajectoryAnalysisModuleData::dataHandle(const AnalysisData &data)
+AnalysisDataHandle TrajectoryAnalysisModuleData::dataHandle(const AnalysisData& data)
{
Impl::HandleContainer::const_iterator i = impl_->handles_.find(&data);
- GMX_RELEASE_ASSERT(i != impl_->handles_.end(),
- "Data handle requested on unknown dataset");
+ GMX_RELEASE_ASSERT(i != impl_->handles_.end(), "Data handle requested on unknown dataset");
return i->second;
}
-Selection TrajectoryAnalysisModuleData::parallelSelection(const Selection &selection)
+Selection TrajectoryAnalysisModuleData::parallelSelection(const Selection& selection)
{
// TODO: Implement properly.
return selection;
}
-SelectionList
-TrajectoryAnalysisModuleData::parallelSelections(const SelectionList &selections)
+SelectionList TrajectoryAnalysisModuleData::parallelSelections(const SelectionList& selections)
{
// TODO: Consider an implementation that does not allocate memory every time.
- SelectionList newSelections;
+ SelectionList newSelections;
newSelections.reserve(selections.size());
SelectionList::const_iterator i = selections.begin();
for (; i != selections.end(); ++i)
*/
class TrajectoryAnalysisModuleDataBasic : public TrajectoryAnalysisModuleData
{
- public:
- /*! \brief
- * Initializes thread-local storage for data handles and selections.
- *
- * \param[in] module Analysis module to use for data objects.
- * \param[in] opt Data parallelization options.
- * \param[in] selections Thread-local selection collection.
- */
- TrajectoryAnalysisModuleDataBasic(TrajectoryAnalysisModule *module,
- const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections);
-
- void finish() override;
+public:
+ /*! \brief
+ * Initializes thread-local storage for data handles and selections.
+ *
+ * \param[in] module Analysis module to use for data objects.
+ * \param[in] opt Data parallelization options.
+ * \param[in] selections Thread-local selection collection.
+ */
+ TrajectoryAnalysisModuleDataBasic(TrajectoryAnalysisModule* module,
+ const AnalysisDataParallelOptions& opt,
+ const SelectionCollection& selections);
+
+ void finish() override;
};
-TrajectoryAnalysisModuleDataBasic::TrajectoryAnalysisModuleDataBasic(
- TrajectoryAnalysisModule *module,
- const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections)
- : TrajectoryAnalysisModuleData(module, opt, selections)
+TrajectoryAnalysisModuleDataBasic::TrajectoryAnalysisModuleDataBasic(TrajectoryAnalysisModule* module,
+ const AnalysisDataParallelOptions& opt,
+ const SelectionCollection& selections) :
+ TrajectoryAnalysisModuleData(module, opt, selections)
{
}
-void
-TrajectoryAnalysisModuleDataBasic::finish()
+void TrajectoryAnalysisModuleDataBasic::finish()
{
finishDataHandles();
}
-} // namespace
+} // namespace
/********************************************************************
* TrajectoryAnalysisModule
*/
-TrajectoryAnalysisModule::TrajectoryAnalysisModule()
- : impl_(new Impl())
-{
-}
+TrajectoryAnalysisModule::TrajectoryAnalysisModule() : impl_(new Impl()) {}
-TrajectoryAnalysisModule::~TrajectoryAnalysisModule()
-{
-}
+TrajectoryAnalysisModule::~TrajectoryAnalysisModule() {}
-void TrajectoryAnalysisModule::optionsFinished(
- TrajectoryAnalysisSettings * /*settings*/)
-{
-}
+void TrajectoryAnalysisModule::optionsFinished(TrajectoryAnalysisSettings* /*settings*/) {}
-void TrajectoryAnalysisModule::initAfterFirstFrame(
- const TrajectoryAnalysisSettings & /*settings*/,
- const t_trxframe & /*fr*/)
+void TrajectoryAnalysisModule::initAfterFirstFrame(const TrajectoryAnalysisSettings& /*settings*/,
+ const t_trxframe& /*fr*/)
{
}
-TrajectoryAnalysisModuleDataPointer
-TrajectoryAnalysisModule::startFrames(const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections)
+TrajectoryAnalysisModuleDataPointer TrajectoryAnalysisModule::startFrames(const AnalysisDataParallelOptions& opt,
+ const SelectionCollection& selections)
{
- return TrajectoryAnalysisModuleDataPointer(
- new TrajectoryAnalysisModuleDataBasic(this, opt, selections));
+ return TrajectoryAnalysisModuleDataPointer(new TrajectoryAnalysisModuleDataBasic(this, opt, selections));
}
-void TrajectoryAnalysisModule::finishFrames(TrajectoryAnalysisModuleData * /*pdata*/)
-{
-}
+void TrajectoryAnalysisModule::finishFrames(TrajectoryAnalysisModuleData* /*pdata*/) {}
int TrajectoryAnalysisModule::datasetCount() const
}
-const std::vector<std::string> &TrajectoryAnalysisModule::datasetNames() const
+const std::vector<std::string>& TrajectoryAnalysisModule::datasetNames() const
{
return impl_->datasetNames_;
}
-AbstractAnalysisData &TrajectoryAnalysisModule::datasetFromIndex(int index) const
+AbstractAnalysisData& TrajectoryAnalysisModule::datasetFromIndex(int index) const
{
if (index < 0 || index >= datasetCount())
{
GMX_THROW(APIError("Out of range data set index"));
}
- Impl::DatasetContainer::const_iterator item
- = impl_->datasets_.find(impl_->datasetNames_[index]);
- GMX_RELEASE_ASSERT(item != impl_->datasets_.end(),
- "Inconsistent data set names");
+ Impl::DatasetContainer::const_iterator item = impl_->datasets_.find(impl_->datasetNames_[index]);
+ GMX_RELEASE_ASSERT(item != impl_->datasets_.end(), "Inconsistent data set names");
return *item->second;
}
-AbstractAnalysisData &TrajectoryAnalysisModule::datasetFromName(const char *name) const
+AbstractAnalysisData& TrajectoryAnalysisModule::datasetFromName(const char* name) const
{
Impl::DatasetContainer::const_iterator item = impl_->datasets_.find(name);
if (item == impl_->datasets_.end())
}
-void TrajectoryAnalysisModule::registerBasicDataset(AbstractAnalysisData *data,
- const char *name)
+void TrajectoryAnalysisModule::registerBasicDataset(AbstractAnalysisData* data, const char* name)
{
GMX_RELEASE_ASSERT(data != nullptr, "Attempting to register NULL data");
// TODO: Strong exception safety should be possible to implement.
}
-void TrajectoryAnalysisModule::registerAnalysisDataset(AnalysisData *data,
- const char *name)
+void TrajectoryAnalysisModule::registerAnalysisDataset(AnalysisData* data, const char* name)
{
// TODO: Strong exception safety should be possible to implement.
registerBasicDataset(data, name);
void TrajectoryAnalysisModule::finishFrameSerial(int frameIndex)
{
Impl::AnalysisDatasetContainer::const_iterator data;
- for (data = impl_->analysisDatasets_.begin();
- data != impl_->analysisDatasets_.end();
- ++data)
+ for (data = impl_->analysisDatasets_.begin(); data != impl_->analysisDatasets_.end(); ++data)
{
data->second->finishFrameSerial(frameIndex);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff