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/*! \internal \file
* \brief
* Implements classes in analysismodule.h.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#include "gromacs/trajectoryanalysis/analysismodule.h"
+#include "gmxpre.h"
+
+#include "analysismodule.h"
#include <utility>
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
-#include "analysismodule-impl.h"
-
namespace gmx
{
+/********************************************************************
+ * TrajectoryAnalysisModule::Impl
+ */
+
+/*! \internal \brief
+ * Private implementation class for TrajectoryAnalysisModule.
+ *
+ * \ingroup module_trajectoryanalysis
+ */
+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;
+
+ //! Initializes analysis module data with given name and description.
+ Impl(const char *name, const char *description)
+ : name_(name), description_(description)
+ {
+ }
+
+ //! Name of the module.
+ std::string name_;
+ //! Description of the module.
+ std::string description_;
+ //! 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_;
+};
+
/********************************************************************
* TrajectoryAnalysisModuleData::Impl
*/
+/*! \internal \brief
+ * Private implementation class for TrajectoryAnalysisModuleData.
+ *
+ * \ingroup module_trajectoryanalysis
+ */
+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_;
+};
+
TrajectoryAnalysisModuleData::Impl::Impl(
- TrajectoryAnalysisModule *module,
+ TrajectoryAnalysisModule *module,
const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections)
- : _selections(selections)
+ 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)
{
- _handles.insert(std::make_pair(i->second, i->second->startData(opt)));
+ AnalysisDataHandle handle;
+ if (isInitialized(*i->second))
+ {
+ handle = i->second->startData(opt);
+ }
+ handles_.insert(std::make_pair(i->second, handle));
}
}
-TrajectoryAnalysisModuleData::Impl::~Impl()
+bool TrajectoryAnalysisModuleData::Impl::isInitialized(
+ const AnalysisData &data) const
{
+ for (int i = 0; i < data.dataSetCount(); ++i)
+ {
+ if (data.columnCount(i) > 0)
+ {
+ // If not all of the column counts are set, startData() in the
+ // constructor asserts, so that does not need to be checked here.
+ return true;
+ }
+ }
+ return false;
}
*/
TrajectoryAnalysisModuleData::TrajectoryAnalysisModuleData(
- TrajectoryAnalysisModule *module,
+ TrajectoryAnalysisModule *module,
const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections)
- : _impl(new Impl(module, opt, selections))
+ const SelectionCollection &selections)
+ : impl_(new Impl(module, opt, selections))
{
}
{
// FIXME: Call finishData() for all handles even if one throws
Impl::HandleContainer::iterator i;
- for (i = _impl->_handles.begin(); i != _impl->_handles.end(); ++i)
+ for (i = impl_->handles_.begin(); i != impl_->handles_.end(); ++i)
{
- i->second.finishData();
+ if (i->second.isValid())
+ {
+ i->second.finishData();
+ }
}
- _impl->_handles.clear();
+ impl_->handles_.clear();
}
AnalysisDataHandle
TrajectoryAnalysisModuleData::dataHandle(const AnalysisData &data)
{
- Impl::HandleContainer::const_iterator i = _impl->_handles.find(&data);
- GMX_RELEASE_ASSERT(i != _impl->_handles.end(),
+ Impl::HandleContainer::const_iterator i = impl_->handles_.find(&data);
+ GMX_RELEASE_ASSERT(i != impl_->handles_.end(),
"Data handle requested on unknown dataset");
return i->second;
}
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)
+ for (; i != selections.end(); ++i)
{
newSelections.push_back(parallelSelection(*i));
}
/********************************************************************
* TrajectoryAnalysisModuleDataBasic
*/
+
+namespace
+{
+
+/*! \brief
+ * Basic thread-local trajectory analysis data storage class.
+ *
+ * Most simple tools should only require data handles and selections to be
+ * thread-local, so this class implements just that.
+ *
+ * \ingroup module_trajectoryanalysis
+ */
+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);
+
+ virtual void finish();
+};
+
TrajectoryAnalysisModuleDataBasic::TrajectoryAnalysisModuleDataBasic(
- TrajectoryAnalysisModule *module,
+ TrajectoryAnalysisModule *module,
const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections)
+ const SelectionCollection &selections)
: TrajectoryAnalysisModuleData(module, opt, selections)
{
}
finishDataHandles();
}
+} // namespace
+
/********************************************************************
* TrajectoryAnalysisModule
*/
-TrajectoryAnalysisModule::TrajectoryAnalysisModule()
- : _impl(new Impl)
+TrajectoryAnalysisModule::TrajectoryAnalysisModule(const char *name,
+ const char *description)
+ : impl_(new Impl(name, description))
{
}
}
-void TrajectoryAnalysisModule::initOptionsDone(TrajectoryAnalysisSettings * /*settings*/)
+void TrajectoryAnalysisModule::optionsFinished(
+ Options * /*options*/,
+ TrajectoryAnalysisSettings * /*settings*/)
{
}
-void TrajectoryAnalysisModule::initAfterFirstFrame(const t_trxframe &/*fr*/)
+void TrajectoryAnalysisModule::initAfterFirstFrame(
+ const TrajectoryAnalysisSettings & /*settings*/,
+ const t_trxframe & /*fr*/)
{
}
TrajectoryAnalysisModuleDataPointer
TrajectoryAnalysisModule::startFrames(const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections)
+ const SelectionCollection &selections)
{
return TrajectoryAnalysisModuleDataPointer(
new TrajectoryAnalysisModuleDataBasic(this, opt, selections));
}
+const char *TrajectoryAnalysisModule::name() const
+{
+ return impl_->name_.c_str();
+}
+
+
+const char *TrajectoryAnalysisModule::description() const
+{
+ return impl_->description_.c_str();
+}
+
+
int TrajectoryAnalysisModule::datasetCount() const
{
- return _impl->_datasetNames.size();
+ return impl_->datasetNames_.size();
}
const std::vector<std::string> &TrajectoryAnalysisModule::datasetNames() const
{
- return _impl->_datasetNames;
+ return impl_->datasetNames_;
}
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(),
+ = 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
{
- Impl::DatasetContainer::const_iterator item = _impl->_datasets.find(name);
- if (item == _impl->_datasets.end())
+ Impl::DatasetContainer::const_iterator item = impl_->datasets_.find(name);
+ if (item == impl_->datasets_.end())
{
GMX_THROW(APIError("Unknown data set name"));
}
void TrajectoryAnalysisModule::registerBasicDataset(AbstractAnalysisData *data,
- const char *name)
+ const char *name)
{
+ GMX_RELEASE_ASSERT(data != NULL, "Attempting to register NULL data");
// TODO: Strong exception safety should be possible to implement.
- GMX_RELEASE_ASSERT(_impl->_datasets.find(name) == _impl->_datasets.end(),
+ GMX_RELEASE_ASSERT(impl_->datasets_.find(name) == impl_->datasets_.end(),
"Duplicate data set name registered");
- _impl->_datasets[name] = data;
- _impl->_datasetNames.push_back(name);
+ impl_->datasets_[name] = data;
+ impl_->datasetNames_.push_back(name);
}
void TrajectoryAnalysisModule::registerAnalysisDataset(AnalysisData *data,
- const char *name)
+ const char *name)
{
// TODO: Strong exception safety should be possible to implement.
registerBasicDataset(data, name);
- _impl->_analysisDatasets[name] = data;
+ impl_->analysisDatasets_[name] = data;
}
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff