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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 "../selection/selection.h" // For gmx::SelectionList
-#include "../utility/common.h"
-#include "../utility/uniqueptr.h"
+#include "gromacs/selection/selection.h" // For gmx::SelectionList
+#include "gromacs/utility/common.h"
+
+struct t_pbc;
+struct t_trxframe;
namespace gmx
{
*
* \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.
*/
* 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.
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 modules.
*
* Trajectory analysis methods should derive from this class and override the
* necessary virtual methods to implement initialization (initOptions(),
- * initOptionsDone(), initAnalysis(), initAfterFirstFrame()), per-frame analysis
+ * optionsFinished(), initAnalysis(), initAfterFirstFrame()), per-frame analysis
* (analyzeFrame()), and final processing (finishFrames(), finishAnalysis(),
* writeOutput()).
*
/*! \brief
* Initializes options understood by the module.
*
+ * \param[in,out] options Options object to add the options to.
* \param[in,out] settings Settings to pass to and from the module.
- * \returns Reference to options that are accepted by the module.
*
- * Typical implementation returns a reference to a member variable
- * after first adding necessary options to that object. Output values
+ * 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.
*
* \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
*
* The default implementation does nothing.
*/
- virtual void initOptionsDone(TrajectoryAnalysisSettings *settings);
+ virtual void optionsFinished(Options *options,
+ TrajectoryAnalysisSettings *settings);
/*! \brief
* Initializes the analysis.
*
* 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.
*
*/
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.
*
/*! \brief
* Initializes the dataset registration mechanism.
*
- * \throws std::bad_alloc if out of memory.
+ * \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();
+ TrajectoryAnalysisModule(const char *name, const char *description);
/*! \brief
* Registers a dataset that exports data.
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