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/*! \file
* \brief
* Declares gmx::TrajectoryAnalysisSettings and gmx::TopologyInformation.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \inpublicapi
* \ingroup module_trajectoryanalysis
*/
#ifndef GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
#define GMX_TRAJECTORYANALYSIS_ANALYSISSETTINGS_H
-#include "../legacyheaders/typedefs.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/utility/common.h"
-#include "../options/timeunitmanager.h"
-#include "../utility/common.h"
+struct t_topology;
namespace gmx
{
*
* This class is used by trajectory analysis modules to inform the caller
* about the requirements they have on the input (e.g., whether a topology is
- * required, or whether PBC removal makes sense). It is also used to pass
+ * required, or whether PBC removal makes sense). It is also used to pass
* similar information back to the analysis module after parsing user input.
*
* Having this functionality as a separate class makes the
* TrajectoryAnalysisModule interface much cleaner, and also reduces the need to
* change existing code when new options are added.
*
+ * Methods in this class do not throw, except for the constructor, which may
+ * throw an std::bad_alloc.
+ *
+ * \todo
+ * Remove plain flags from the public interface.
+ *
* \inpublicapi
* \ingroup module_trajectoryanalysis
*/
* \see setRmPBC()
*/
efNoUserRmPBC = 1<<5,
- /*! \brief
- * Requests dumps of parsed and compiled selection trees.
- *
- * This flag is used by internal debugging tools to request
- * the selection trees dumping to stderr.
- */
- efDebugSelection = 1<<16,
};
//! Initializes default settings.
*
* Returns the value set with setPBC() and/or overridden by the user.
* The user-provided value can be accessed in
- * TrajectoryAnalysisModule::initOptionsDone(), and can be overridden
+ * TrajectoryAnalysisModule::optionsFinished(), and can be overridden
* with a call to setPBC().
*/
bool hasPBC() const;
private:
class Impl;
- PrivateImplPointer<Impl> _impl;
+ PrivateImplPointer<Impl> impl_;
friend class TrajectoryAnalysisRunnerCommon;
};
/*! \brief
* Topology information passed to a trajectory analysis module.
*
+ * This class is used to pass topology information to trajectory analysis
+ * modules and to manage memory for them. Having a single wrapper object
+ * instead of passing each item separately makes TrajectoryAnalysisModule
+ * interface simpler, and also reduces the need to change existing code if
+ * additional information is added.
+ *
+ * Methods in this class do not throw if not explicitly stated.
+ *
* \inpublicapi
* \ingroup module_trajectoryanalysis
*/
{
public:
//! Returns true if a topology file was loaded.
- bool hasTopology() const { return _top != NULL; }
+ bool hasTopology() const { return top_ != NULL; }
//! Returns true if a full topology file was loaded.
- bool hasFullTopology() const { return _bTop; }
+ bool hasFullTopology() const { return bTop_; }
//! Returns the loaded topology, or NULL if not loaded.
- t_topology *topology() const { return _top; }
+ t_topology *topology() const { return top_; }
//! Returns the ePBC field from the topology.
- int ePBC() const { return _ePBC; }
+ int ePBC() const { return ePBC_; }
/*! \brief
* Gets the configuration from the topology.
*
* (can be NULL, in which case it is not used).
* \param[out] box Box size from the topology file
* (can be NULL, in which case it is not used).
+ * \throws APIError if topology coordinates are not available and
+ * \p x is not NULL.
*
* If TrajectoryAnalysisSettings::efUseTopX has not been specified,
* \p x should be NULL.
~TopologyInformation();
//! The topology structure, or NULL if no topology loaded.
- t_topology *_top;
+ t_topology *top_;
//! true if full tpx file was loaded, false otherwise.
- bool _bTop;
+ bool bTop_;
//! Coordinates from the topology (can be NULL).
- rvec *_xtop;
+ rvec *xtop_;
//! The box loaded from the topology file.
- matrix _boxtop;
+ matrix boxtop_;
//! The ePBC field loaded from the topology file.
- int _ePBC;
+ int ePBC_;
GMX_DISALLOW_COPY_AND_ASSIGN(TopologyInformation);
+ /*! \brief
+ * Needed to initialize the data.
+ */
friend class TrajectoryAnalysisRunnerCommon;
};
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