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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
{
*
* \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.
};
//! 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.
* If settings depend on the option values provided by the user, see
* optionsFinished().
*/
- virtual void initOptions(Options *options,
+ virtual void initOptions(Options *options,
TrajectoryAnalysisSettings *settings) = 0;
/*! \brief
* Called after all option values have been set.
*
* The default implementation does nothing.
*/
- virtual void optionsFinished(Options *options,
+ 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.
*
};
//! Smart pointer to manage a TrajectoryAnalysisModule.
-typedef gmx_unique_ptr<TrajectoryAnalysisModule>::type
- TrajectoryAnalysisModulePointer;
+typedef boost::shared_ptr<TrajectoryAnalysisModule>
+ TrajectoryAnalysisModulePointer;
} // namespace gmx