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/*! \file
 * \internal \brief
 * Methods to get residue information during preprocessing.
 */
#ifndef GMX_GMXPREPROCESS_RESALL_H
#define GMX_GMXPREPROCESS_RESALL_H

#include <cstdio>

#include <filesystem>
#include <vector>

#include "gromacs/utility/arrayref.h"

class PreprocessingAtomTypes;

namespace gmx
{
class MDLogger;
}
struct PreprocessResidue;
struct t_symtab;

/*! \brief
 * Search for an entry in the rtp database.
 *
 * A mismatch of one character is allowed,
 * if there is only one nearly matching entry in the database,
 * a warning will be generated.
 *
 * \param[in] key The atomname to search for.
 * \param[in] rtpDBEntry Database with residue information.
 * \param[in] logger Logging object.
 * \returns The rtp residue name.
 */
std::string searchResidueDatabase(const std::string&                     key,
                                  gmx::ArrayRef<const PreprocessResidue> rtpDBEntry,
                                  const gmx::MDLogger&                   logger);

/*! \brief
 * Returns matching entry in database.
 *
 * \param[in] rtpname Name of the entry looked for.
 * \param[in] rtpDBEntry Database to search.
 * \throws If the name can not be found in the database.
 */
gmx::ArrayRef<const PreprocessResidue>::const_iterator
getDatabaseEntry(const std::string& rtpname, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry);

/*! \brief
 * Read atom types into database.
 *
 * \param[in] ffdir Force field directory.
 * \returns Atom type database.
 */
PreprocessingAtomTypes read_atype(const std::filesystem::path& ffdir);

/*! \brief
 * Read in database, append to exisiting.
 *
 * \param[in] resdb Name of database file.
 * \param[inout] rtpDBEntry Database to populate.
 * \param[inout] atype Atomtype information.
 * \param[inout] tab Symbol table for names.
 * \param[in] logger MDLogger interface.
 * \param[in] bAllowOverrideRTP If entries can be overwritten in the database.
 */
void readResidueDatabase(const std::filesystem::path&    resdb,
                         std::vector<PreprocessResidue>* rtpDBEntry,
                         PreprocessingAtomTypes*         atype,
                         t_symtab*                       tab,
                         const gmx::MDLogger&            logger,
                         bool                            bAllowOverrideRTP);

/*! \brief
 * Print out database.
 *
 * \param[in] out File to write to.
 * \param[in] rtpDBEntry Database to write out.
 * \param[in] atype Atom type information.
 */
void print_resall(FILE*                                  out,
                  gmx::ArrayRef<const PreprocessResidue> rtpDBEntry,
                  const PreprocessingAtomTypes&          atype);

#endif
