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/*! \file
* \brief
* Declares gmx::TrajectoryAnalysisModule and
* gmx::TrajectoryAnalysisModuleData.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \inpublicapi
* \ingroup module_trajectoryanalysis
*/
#include <string>
#include <vector>
-#include "../legacyheaders/typedefs.h"
+#include <boost/shared_ptr.hpp>
+
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/common.h"
-#include "../selection/selection.h" // For gmx::SelectionList
-#include "../utility/common.h"
-#include "../utility/uniqueptr.h"
+struct t_pbc;
+struct t_trxframe;
namespace gmx
{
*
* Thread-local storage of data handles and selections is implemented in this
* class; TrajectoryAnalysisModule instances can access the thread-local values
- * using dataHandle() and parallelSelection().
+ * in their TrajectoryAnalysisModule::analyzeFrame() method using dataHandle()
+ * and parallelSelection().
*
* \see TrajectoryAnalysisModule::startFrames()
* \see TrajectoryAnalysisModule::analyzeFrame()
/*! \brief
* Performs any finishing actions after all frames have been processed.
*
- * This function is called immediately before the destructor.
+ * \throws unspecified Implementation may throw exceptions to indicate
+ * errors.
+ *
+ * This function is called immediately before the destructor, after
+ * TrajectoryAnalysisModule::finishFrames().
+ * Derived classes should implement any final operations that need to
+ * be done after successful analysis.
* All implementations should call finishDataHandles().
*/
virtual void finish() = 0;
/*! \brief
* Returns a data handle for a given dataset.
*
- * Allowed data sets are those that have been registered with
+ * \param[in] data Analysis data object.
+ * \returns Data handle for \p data stored in this thread-local data.
+ *
+ * \p data should have previously been registered with
* TrajectoryAnalysisModule::registerAnalysisDataset().
+ * If \p data has zero columns in all data sets, the returned data
+ * handle is invalid.
+ *
+ * Does not throw.
*/
AnalysisDataHandle dataHandle(const AnalysisData &data);
/*! \brief
* Returns a selection that corresponds to the given selection.
+ *
+ * \param[in] selection Global selection object.
+ * \returns Selection object corresponding to this thread-local data.
+ *
+ * \p selection is the selection object that was obtained from
+ * SelectionOption. The return value is the corresponding selection
+ * in the selection collection with which this data object was
+ * constructed with.
+ *
+ * Does not throw.
*/
Selection parallelSelection(const Selection &selection);
/*! \brief
* Returns a set of selection that corresponds to the given selections.
+ *
+ * \throws std::bad_alloc if out of memory.
+ *
+ * Works as parallelSelection(), but for a list of selections at once.
+ *
+ * \see parallelSelection()
*/
SelectionList parallelSelections(const SelectionList &selections);
* \param[in] module Analysis module to use for data objects.
* \param[in] opt Data parallelization options.
* \param[in] selections Thread-local selection collection.
+ * \throws std::bad_alloc if out of memory.
+ * \throws unspecified Can throw any exception thrown by
+ * AnalysisData::startData().
*
* Calls AnalysisData::startData() on all data objects registered with
* TrajectoryAnalysisModule::registerAnalysisDataset() in \p module.
* The handles are accessible through dataHandle().
*/
- TrajectoryAnalysisModuleData(TrajectoryAnalysisModule *module,
+ TrajectoryAnalysisModuleData(TrajectoryAnalysisModule *module,
const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections);
+ const SelectionCollection &selections);
/*! \brief
* Calls finishData() on all data handles.
*
+ * \throws unspecified Can throw any exception thrown by
+ * AnalysisDataHandle::finishData().
+ *
* This function should be called from the implementation of finish()
* in all subclasses.
*/
private:
class Impl;
- PrivateImplPointer<Impl> _impl;
+ PrivateImplPointer<Impl> impl_;
};
//! Smart pointer to manage a TrajectoryAnalysisModuleData object.
-typedef gmx_unique_ptr<TrajectoryAnalysisModuleData>::type
- TrajectoryAnalysisModuleDataPointer;
+typedef boost::shared_ptr<TrajectoryAnalysisModuleData>
+ TrajectoryAnalysisModuleDataPointer;
/*! \brief
- * Base class for trajectory analysis methods.
+ * Base class for trajectory analysis modules.
*
* Trajectory analysis methods should derive from this class and override the
- * necessary virtual functions to implement initialization (initOptions(),
- * initOptionsDone(), initAnalysis(), initAfterFirstFrame()), per-frame analysis
+ * necessary virtual methods to implement initialization (initOptions(),
+ * optionsFinished(), initAnalysis(), initAfterFirstFrame()), per-frame analysis
* (analyzeFrame()), and final processing (finishFrames(), finishAnalysis(),
* writeOutput()).
*
* to the other methods. The default implementation of startFrames() can be
* used if only data handles and selections need to be thread-local.
*
+ * To get the full benefit from this class,
+ * \ref module_analysisdata "analysis data objects" and
+ * \ref module_selection "selections" should be used in the implementation.
+ * See the corresponding modules' documentation for details of how they work.
+ *
+ * Typical way of using AnalysisData in derived classes is to have the
+ * AnalysisData object as a member variable and register it using
+ * registerAnalysisDataset(). Analysis modules are initialized in
+ * initAnalysis() and the processing chain is initialized. If any of the
+ * modules is required, e.g., for post-processing in finishAnalysis(), it can
+ * be stored in a member variable. To add data to the data object in
+ * analyzeFrame(), a data handle is obtained using
+ * TrajectoryAnalysisModuleData::dataHandle().
+ *
+ * Typical way of using selections in derived classes is to have the required
+ * \ref Selection objects (or ::SelectionList objects) as member variables, and
+ * add the required selection options in initOptions(). These member variables
+ * can be accessed in initAnalysis() to get general information about the
+ * selections. In analyzeFrame(), these selection objects should not be used
+ * directly, but instead TrajectoryAnalysisModuleData::parallelSelection()
+ * should be used to obtain a selection object that works correctly also for
+ * parallel analysis.
+ *
+ * Derived classes should use exceptions to indicate errors in the virtual
+ * methods.
+ *
* \inpublicapi
* \ingroup module_trajectoryanalysis
*/
/*! \brief
* Initializes options understood by the module.
*
- * In addition to initializing the options, this function can also
- * provide information about its requirements using the \p settings
- * object; see TrajectoryAnalysisSettings for more details.
+ * \param[in,out] options Options object to add the options to.
+ * \param[in,out] settings Settings to pass to and from the module.
+ *
+ * This method is called first after the constructor, and it should
+ * add options understood by the module to \p options. Output values
+ * from options (including selections) should be stored in member
+ * variables.
+ *
+ * In addition to initializing the options, this method can also
+ * provide information about the module's requirements using the
+ * \p settings object; see TrajectoryAnalysisSettings for more details.
*
* If settings depend on the option values provided by the user, see
- * initOptionsDone().
+ * optionsFinished().
*/
- virtual Options &initOptions(TrajectoryAnalysisSettings *settings) = 0;
+ virtual void initOptions(Options *options,
+ TrajectoryAnalysisSettings *settings) = 0;
/*! \brief
* Called after all option values have been set.
*
+ * \param[in,out] options Options object in which options are stored.
+ * \param[in,out] settings Settings to pass to and from the module.
+ *
+ * This method is called after option values have been assigned (but
+ * interactive selection input has not yet been performed).
+ *
* If the module needs to change settings that affect topology loading
- * or selection initialization based on option values, this function
- * has to be overridden.
+ * (can be done using the \p settings object) or selection
+ * initialization (can be done using SelectionOptionInfo) based on
+ * option values, this method has to be overridden.
*
* The default implementation does nothing.
*/
- virtual void initOptionsDone(TrajectoryAnalysisSettings *settings);
+ virtual void optionsFinished(Options *options,
+ TrajectoryAnalysisSettings *settings);
/*! \brief
* Initializes the analysis.
*
+ * \param[in] settings Settings to pass to and from the module.
+ * \param[in] top Topology information.
+ *
* When this function is called, selections have been initialized based
* on user input, and a topology has been loaded if provided by the
* user. For dynamic selections, the selections have been evaluated to
* analyzeFrame() are always a subset of the selections provided here.
*/
virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
- const TopologyInformation &top) = 0;
+ const TopologyInformation &top) = 0;
/*! \brief
* Performs additional initialization after reading the first frame.
*
*
* The default implementation does nothing.
*/
- virtual void initAfterFirstFrame(const t_trxframe &fr);
+ virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
+ const t_trxframe &fr);
/*! \brief
* Starts the analysis of frames.
* \see TrajectoryAnalysisModuleData
*/
virtual TrajectoryAnalysisModuleDataPointer startFrames(
- const AnalysisDataParallelOptions &opt,
- const SelectionCollection &selections);
+ const AnalysisDataParallelOptions &opt,
+ const SelectionCollection &selections);
/*! \brief
* Analyzes a single frame.
*
* \param[in] pbc Periodic boundary conditions for \p fr.
* \param[in,out] pdata Data structure for frame-local data.
*
- * This function is called once for each frame to be analyzed,
- * and should analyze the positions provided in \p sel.
+ * This method is called once for each frame to be analyzed, and should
+ * analyze the positions provided in the selections. Data handles and
+ * selections should be obtained from the \p pdata structure.
*
- * For threaded analysis, this function is called asynchronously in
- * different threads to analyze different frames. The \p pdata
+ * For threaded analysis, this method is called asynchronously in
+ * different threads to analyze different frames. The \p pdata
* structure is one of the structures created with startFrames(),
* but no assumptions should be made about which of these data
- * structures is used. It is guaranteed that two instances of
+ * structures is used. It is guaranteed that two instances of
* analyzeFrame() are not running concurrently with the same \p pdata
* data structure.
* Any access to data structures not stored in \p pdata should be
*
* \param[in] pdata Data structure for thread-local data.
*
- * This function is called once for each call of startFrames(),
- * with the data structure returned by the corresponding startFrames().
+ * This method is called once for each call of startFrames(), with the
+ * data structure returned by the corresponding startFrames().
* The \p pdata object should be destroyed by the caller after this
* function has been called.
*
* You only need to override this method if you need custom
* operations to combine data from the frame-local data structures
- * to get the final result. In such cases, the data should be
+ * to get the final result. In such cases, the data should be
* aggregated in this function and stored in a member attribute.
*
* The default implementation does nothing.
/*! \brief
* Postprocesses data after frames have been read.
*
+ * \param[in] nframes Total number of frames processed.
+ *
* This function is called after all finishFrames() calls have been
* called.
+ * \p nframes will equal the number of calls to analyzeFrame() that
+ * have occurred.
*/
virtual void finishAnalysis(int nframes) = 0;
/*! \brief
*/
virtual void writeOutput() = 0;
+ /*! \brief
+ * Returns the name of the analysis module.
+ *
+ * Does not throw.
+ */
+ const char *name() const;
+ /*! \brief
+ * Returns short description for the analysis module.
+ *
+ * Does not throw.
+ */
+ const char *description() const;
/*! \brief
* Returns the number of datasets provided by the module.
+ *
+ * Does not throw.
*/
int datasetCount() const;
/*! \brief
- * Returns a vector with the names of the datasets.
+ * Returns a vector with the names of datasets provided by the module.
+ *
+ * Does not throw.
*/
const std::vector<std::string> &datasetNames() const;
/*! \brief
* Returns a pointer to the data set \p index.
*
* \param[in] index Data set to query for.
- * \returns A pointer to the data set, or NULL if \p index is not
- * valid.
+ * \returns Reference to the requested data set.
+ * \throws APIError if \p index is not valid.
+ *
+ * \p index should be >= 0 and < datasetCount().
*
* The return value is not const to allow callers to add modules to the
* data sets. However, the AbstractAnalysisData interface does not
* Returns a pointer to the data set with name \p name
*
* \param[in] name Data set to query for.
- * \returns A pointer to the data set, or NULL if \p name is not
- * recognized.
+ * \returns Reference to the requested data set.
+ * \throws APIError if \p name is not valid.
+ *
+ * \p name should be one of the names returned by datasetNames().
*
* The return value is not const to allow callers to add modules to the
* data sets. However, the AbstractAnalysisData interface does not
AbstractAnalysisData &datasetFromName(const char *name) const;
protected:
- //! Initializes the dataset registration mechanism.
- TrajectoryAnalysisModule();
+ /*! \brief
+ * Initializes the dataset registration mechanism.
+ *
+ * \param[in] name Name for the module.
+ * \param[in] description One-line description for the module.
+ * \throws std::bad_alloc if out of memory.
+ */
+ TrajectoryAnalysisModule(const char *name, const char *description);
/*! \brief
* Registers a dataset that exports data.
+ *
+ * \param data Data object to register.
+ * \param[in] name Name to register the dataset with.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * Registers \p data as a dataset that provides output from the
+ * analysis module. Callers for the module can access the dataset
+ * with datasetFromName() using \p name as an AbstractAnalysisData
+ * object. This allows them to add their own data modules to do extra
+ * processing.
+ *
+ * \p name must be unique across all calls within the same
+ * TrajectoryAnalysisModule instance.
*/
void registerBasicDataset(AbstractAnalysisData *data, const char *name);
/*! \brief
* Registers a parallelized dataset that exports data.
+ *
+ * \param data AnalysisData object to register.
+ * \param[in] name Name to register the dataset with.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * This method works as registerBasicDataset(), but additionally allows
+ * data handles for \p data to be accessed using
+ * TrajectoryAnalysisData.
+ *
+ * \see registerBasicDataset()
*/
void registerAnalysisDataset(AnalysisData *data, const char *name);
private:
class Impl;
- PrivateImplPointer<Impl> _impl;
+ PrivateImplPointer<Impl> impl_;
/*! \brief
* Needed to access the registered analysis data sets.
};
//! Smart pointer to manage a TrajectoryAnalysisModule.
-typedef gmx_unique_ptr<TrajectoryAnalysisModule>::type
- TrajectoryAnalysisModulePointer;
+typedef boost::shared_ptr<TrajectoryAnalysisModule>
+ TrajectoryAnalysisModulePointer;
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff