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/*! \file
 * \brief
 * Declares gmx::TopologyInformation.
 *
 * \author Teemu Murtola <teemu.murtola@gmail.com>
 * \author Mark Abraham <mark.j.abraham@gmail.com>
 * \inlibraryapi
 * \ingroup module_trajectoryanalysis
 */
#ifndef GMX_TRAJECTORYANALYSIS_TOPOLOGYINFORMATION_H
#define GMX_TRAJECTORYANALYSIS_TOPOLOGYINFORMATION_H

#include <memory>
#include <string>
#include <vector>

#include "gromacs/math/vectypes.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/classhelpers.h"

//! Forward declaration
typedef struct gmx_rmpbc *gmx_rmpbc_t;

namespace gmx
{

template<typename T> class ArrayRef;

class TopologyInformation;
class TrajectoryAnalysisRunnerCommon;

/*! \libinternal
 * \brief Topology information available to a trajectory analysis module.
 *
 * This class is used to provide 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.
 *
 * It is intended that eventually most clients of this class will be
 * analysis tools ported to the new analysis framework, but we will
 * use this infrastructure also from the legacy analysis tools during
 * the transition period. That will make it easier to put those tools
 * under tests, and eventually port them.
 *
 * Methods in this class do not throw if not explicitly stated.
 *
 * The main data content is constant once loaded, but some content is
 * constructed only when required (e.g. atoms_ and
 * expandedTopology_). Their data members are mutable, so that the
 * lazy construction idiom works properly. Some clients wish to modify
 * the t_atoms, so there is an efficient mechanism for them to get a
 * copy they can modify without disturbing this class. (The
 * implementation releases the cached lazily constructed atoms_, but
 * from the point of view of the caller, that is a copy.) The getters
 * and copy functions are const for callers, which correctly expresses
 * that the topology information is not being changed, merely copied
 * and presented in a different form.
 *
 * \ingroup module_trajectoryanalysis
 */
class TopologyInformation
{
    public:
        //! Returns true if a topology file was loaded.
        bool hasTopology() const { return hasLoadedMtop_; }
        //! Returns true if a full topology file was loaded.
        bool hasFullTopology() const { return bTop_; }
        /*! \brief Builder function to fill the contents of
         * TopologyInformation in \c topInfo from \c filename.
         *
         * Different tools require, might need, would benefit from, or
         * do not need topology information. This functions implements
         * the two-phase construction that is currently needed to
         * support that.
         *
         * Any coordinate or run input file format will work, but the
         * kind of data available from the getter methods afterwards
         * will vary. For example, the mtop() available after reading
         * a plain structure file will have a single molecule block and
         * molecule type, regardless of contents.
         *
         * After reading, this object can return many kinds of primary
         * and derived data structures to its caller.
         *
         * \todo This should throw upon error but currently does
         * not. */
        void fillFromInputFile(const std::string &filename);
        /*! \brief Returns the loaded topology, or nullptr if not loaded. */
        gmx_mtop_t *mtop() const { return mtop_.get(); }
        //! Returns the loaded topology fully expanded, or nullptr if no topology is available.
        const gmx_localtop_t *expandedTopology() const;
        /*! \brief Returns a read-only handle to the fully expanded
         * atom data arrays, which might be valid but empty if no
         * topology is available. */
        const t_atoms *atoms() const;
        /*! \brief Copies the fully expanded atom data arrays, which
         * might be valid but empty if no topology is available. */
        AtomsDataPtr copyAtoms() const;
        //! Returns the ePBC field from the topology.
        int ePBC() const { return ePBC_; }
        /*! \brief
         * Gets the configuration positions from the topology file.
         *
         * If TrajectoryAnalysisSettings::efUseTopX has not been specified,
         * this method should not be called.
         *
         * \throws  APIError if topology position coordinates are not available
         */
        ArrayRef<const RVec> x() const;
        /*! \brief
         * Gets the configuration velocities from the topology file.
         *
         * If TrajectoryAnalysisSettings::efUseTopV has not been specified,
         * this method should not be called.
         *
         * \throws  APIError if topology velocity coordinates are not available
         */
        ArrayRef<const RVec> v() const;
        /*! \brief
         * Gets the configuration box from the topology file.
         *
         * \param[out] box   Box size from the topology file, must not be nullptr.
         */
        void getBox(matrix box) const;
        /*! \brief Returns a name for the topology.
         *
         * If a full topology was read from a a file, returns the name
         * it contained, otherwise the empty string. */
        const char *name() const;

        TopologyInformation();
        ~TopologyInformation();

    private:
        //! The topology structure, or nullptr if no topology loaded.
        std::unique_ptr<gmx_mtop_t> mtop_;
        //! Whether a topology has been loaded.
        bool hasLoadedMtop_;
        //! The fully expanded topology structure, nullptr if not yet constructed.
        mutable ExpandedTopologyPtr      expandedTopology_;
        //! The fully expanded atoms data structure, nullptr if not yet constructed.
        mutable AtomsDataPtr             atoms_;
        //! true if full tpx file was loaded, false otherwise.
        bool                             bTop_;
        //! Position coordinates from the topology (can be nullptr).
        std::vector<RVec>                xtop_;
        //! Velocity coordinates from the topology (can be nullptr).
        std::vector<RVec>                vtop_;
        //! The box loaded from the topology file.
        matrix                           boxtop_ {};
        //! The ePBC field loaded from the topology file.
        int                              ePBC_;

        // TODO This type is probably movable if we need that.
        GMX_DISALLOW_COPY_AND_ASSIGN(TopologyInformation);

        /*! \brief
         * Needed to initialize the data.
         */
        friend class TrajectoryAnalysisRunnerCommon;
};

//! Convenience overload useful for implementing legacy tools.
gmx_rmpbc_t gmx_rmpbc_init(const gmx::TopologyInformation &topInfo);

} // namespace gmx

#endif
