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#ifndef GMX_TOPOLOGY_INDEX_H
#define GMX_TOPOLOGY_INDEX_H

#include <stdio.h>

#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"

struct t_atoms;
struct t_blocka;

void check_index(const char* gname, int n, int index[], const char* traj, int natoms);
/* Checks if any index is smaller than zero or larger than natoms,
 * if so a fatal_error is given with the gname (if gname=NULL, "Index" is used)
 * and traj (if traj=NULL, "the trajectory" is used).
 */

struct t_blocka* init_index(const char* gfile, char*** grpname);
/* Lower level routine than the next */

void rd_index(const char* statfile, int ngrps, int isize[], int* index[], char* grpnames[]);
/* Assume the group file is generated, so the
 * format need not be user-friendly. The format is:
 * nr of groups, total nr of atoms
 * for each group: name nr of element, elements.
 *
 * The function opens a file, reads ngrps groups, asks the
 * user for group numbers, and puts the resulting sizes in
 * isize, the int s in index and the names of
 * the groups in grpnames.
 *
 * It is also assumed, that when ngrps groups are requested
 * memory has been allocated for ngrps index arrays, and that
 * the dimension of the isize and grpnames arrays are ngrps.
 */

void get_index(const t_atoms* atoms, const char* fnm, int ngrps, int isize[], int* index[], char* grpnames[]);
/* Does the same as rd_index, but if the fnm pointer is NULL it
 * will not read from fnm, but it will make default index groups
 * for the atoms in *atoms.
 */

typedef struct
{
    int              maxframe;
    char**           grpname;
    struct t_blocka* clust;
    int*             inv_clust;
} t_cluster_ndx;

t_cluster_ndx* cluster_index(FILE* fplog, const char* ndx);


void write_index(const char* outf, struct t_blocka* b, char** gnames, gmx_bool bDuplicate, int natoms);
/* Writes index blocks to outf (writes an indexfile) */

/*! \brief
 * Add a new group with \p name to \p b.
 *
 * \param[in] b Block struct to add group to.
 * \param[in] gnames Names of groups.
 * \param[in] a Group to add to Block.
 * \param[in] name Group name.
 */
void add_grp(struct t_blocka* b, char*** gnames, gmx::ArrayRef<const int> a, const std::string& name);
/* Ads group a with name name to block b and namelist gnames */

void analyse(const t_atoms* atoms, struct t_blocka* gb, char*** gn, gmx_bool bASK, gmx_bool bVerb);
/* Makes index groups gb with names gn for atoms in atoms.
 * bASK=FALSE gives default groups.
 */

/*! \brief Look up a group in a list.
 *
 * \param[inout] s    The string to look up
 * \param[in] ngrps   The number of groups
 * \param[in] grpname The names of the groups
 * \return the group number or -1 if not found.
 */
int find_group(const char* s, int ngrps, char** grpname);


#endif
