root/branches/stable_5.0/ARBDB/arbdb.h

#ifndef ARBDB_H
#define ARBDB_H

#ifndef _STDINT_H
#include <stdint.h>
#endif

#ifndef ARBDB_BASE_H
#include <arbdb_base.h>
#endif

#ifndef ARB_ASSERT_H
#include <arb_assert.h>
#endif
#define gb_assert(bed) arb_assert(bed)

#define NOT4PERL
/* function definitions starting with NOT4PERL are not included into the ARB-perl-interface */

#define GB_PATH_MAX 1024
#define GBS_GLOBAL_STRING_SIZE 64000

#define GB_KEY_LEN_MAX  64 /* max. length of a key (a whole key path may be longer) */
#define GB_KEY_LEN_MIN  2

#define GBUSE(a) a=a

typedef char *MALLOC_T;

typedef unsigned long GB_ULONG;

/* 4 Bytes */
typedef unsigned int GB_UINT4;
typedef const unsigned int GB_CUINT4;
typedef const float GB_CFLOAT;

/* ---------------------------------------- need some stuff if adlocal.h is not included */

#ifndef ADLOCAL_H

typedef void (*GB_CB)(GBDATA *,int *clientdata, GB_CB_TYPE gbtype);

#if defined(DEBUG)
#define MEMORY_TEST 1
#else
#define MEMORY_TEST 0
#endif


#if (MEMORY_TEST==1)

typedef char                        *GB_REL_STRING;
typedef struct gb_data_base_type    *GB_REL_GBDATA;
typedef struct gb_data_base_type2   *GB_REL_CONTAINER;

#else

typedef long GB_REL_STRING;       /* relative address */
typedef long GB_REL_GBDATA;       /* relative address */
typedef long GB_REL_CONTAINER;    /* relative address */

#endif /*MEMORY_TEST==1*/

struct gb_main_type;
typedef struct gb_main_type *GB_MAIN_TYPE;

typedef struct gbs_hash_struct  GB_HASH;
typedef struct gbs_hashi_struct GB_HASHI;

struct GBS_regex;
struct GBS_string_matcher;

typedef struct GBS_regex          GBS_REGEX;
typedef struct GBS_string_matcher GBS_MATCHER;

struct gb_flag_types {      /* public flags */
    unsigned int        type:4;
    unsigned int        security_delete:3;
    unsigned int        security_write:3;
    unsigned int        security_read:3;
    unsigned int        compressed_data: 1;
    unsigned int        unused: 1;  /* last bit saved */
    unsigned int        user_flags:8;
    unsigned int        temporary:1;    /* ==1 -> don't save entry */
    unsigned int        saved_flags:8;
};

struct gb_flag_types2 {     /* private flags */
    unsigned int        intern0: 16;
    unsigned int        intern1: 16;
};



/********************* public ******************/

struct GBS_strstruct;
struct DictData;

typedef int GBQUARK;

/*********** Undo ***********/
typedef enum {
    GB_UNDO_NONE,   /* no undo */
    GB_UNDO_KILL,   /* no undo and delete all old undos */
    GB_UNDO_UNDO,   /* normal undo -> deleted all redoes */
    GB_UNDO_REDO,   /* moves to UNDO_REDO */
    GB_UNDO_UNDO_REDO   /* internal makes undo redoable */
}   GB_UNDO_TYPE;

typedef enum { GB_IGNORE_CASE = 0 , GB_MIND_CASE = 1, GB_CASE_UNDEFINED = 2 } GB_CASE;

struct gb_transaction_save;

#endif /*ADLOCAL_H*/

// --------------------------------------------------------------------------------

typedef int GB_COMPRESSION_MASK;

typedef enum gb_key_types {
    GB_NONE        = 0,
    GB_BIT         = 1,
    GB_BYTE        = 2,
    GB_INT         = 3,
    GB_FLOAT       = 4,
    GB_POINTER     = 5, // not savable! only allowed in temporary entries
    GB_BITS        = 6,
    // 7 is unused
    GB_BYTES       = 8,
    GB_INTS        = 9,
    GB_FLOATS      = 10,
    GB_LINK        = 11,
    GB_STRING      = 12,
    GB_STRING_SHRT = 13,                            /* used automatically during save */
    // 14 is unused
    GB_DB          = 15,

    // keep GB_TYPES consistent with AW_VARIABLE_TYPE
    // see ../WINDOW/aw_root.hxx@sync_GB_TYPES_AW_VARIABLE_TYPE
    
    GB_TYPE_MAX = 16

} GB_TYPES;

enum gb_search_enum {
    GB_FIND = 0,
    GB_CREATE_CONTAINER = GB_DB /* create other types: use GB_TYPES */
};

#define GB_TYPE_2_CHAR "-bcif-B-CIFlSS-%"

enum gb_search_types {
    this_level = 1,
    down_level = 2,
    down_2_level = 4,
    search_next = 8 /* search after item : this_level,down_level*/
};
/********************* public end ******************/

/********************* client/server ******************/
struct gbcmc_comm {
    int socket;
    char    *unix_name;
    char    *error;
};


/********************* database ******************/

#define SIZOFINTERN 10

struct gb_extern_data {
    GB_REL_STRING rel_data; /* Typ: (char *) */
    long    memsize;
    long    size;
};

struct GB_INTern_strings {
    char    data[SIZOFINTERN];
    unsigned char memsize;
    unsigned char size;
};

struct GB_INTern {
    char    data[SIZOFINTERN];
};

union gb_data_base_type_union {
    int32_t                   i;
    void                     *ptr;
    struct GB_INTern_strings  istr;
    struct GB_INTern          in;
    struct gb_extern_data     ex;
};

struct gb_callback;
struct gb_db_extended {
    long    creation_date;
    long    update_date;
    struct gb_callback      *callback;
    struct gb_transaction_save  *old;
};

struct gb_data_base_type {
    long                           server_id;
    GB_REL_CONTAINER               rel_father; /* Typ: (struct gb_data_base_type2 *) */
    struct gb_db_extended         *ext;
    long                           index;
    struct gb_flag_types           flags;
    struct gb_flag_types2          flags2;
    union gb_data_base_type_union  info;
    int                            cache_index; /* should be a member of gb_db_extended */
};

/*********** Alignment ***********/

typedef enum
{
    GB_AT_UNKNOWN,
    GB_AT_RNA,      /* Nucleotide sequence (U) */
    GB_AT_DNA,      /* Nucleotide sequence (T) */
    GB_AT_AA,       /* AminoAcid */

} GB_alignment_type;

/*********** Sort ***********/


#ifdef __cplusplus
extern "C" {
#endif

    typedef long (*GB_MERGE_SORT)(void *, void *, char *cd);
    /*#define GB_MERGE_SORT long (*)(void *, void *, char *cd )*/

#ifdef __cplusplus
}
#endif

struct GBL_command_table;

#ifdef __cplusplus
extern "C" {
#endif

    typedef GBDATA* (*GB_Link_Follower)(GBDATA *GB_root,GBDATA *GB_elem,const char *link);
    typedef int (*gbs_hash_compare_function) (const char *key0, long val0, const char *key1, long val1);
    typedef int (*gb_compare_function)(const void *p0, const void *p1, void *client_data);
    typedef long (*gb_hash_loop_type)(const char *key, long val, void *client_data);
    typedef void (*gb_warning_func_type)(const char *msg);
    typedef void (*gb_information_func_type)(const char *msg);
    typedef int (*gb_status_func_type)(double val);
    typedef int (*gb_status_func2_type)(const char *val);
    typedef void (*gb_error_handler_type)(const char *msg);
    typedef const char* (*gb_export_sequence_cb)(GBDATA *gb_species, size_t *seq_len, GB_ERROR *error);

#ifdef __cplusplus
}
#endif

#if defined(__GNUG__) || defined(__cplusplus)
extern "C" {
#endif

# define P_(s) s

#include <ad_prot.h>
#ifdef ADLOCAL_H
#include <ad_lpro.h>
#endif /*ADLOCAL_H*/

#undef P_

#if defined(__GNUG__) || defined(__cplusplus)
}
#endif

#ifdef __cplusplus

#ifndef ARBTOOLS_H
#include <arbtools.h>
#endif

// --------------------------------------------------------------------------------
// some const wrappers:

inline char *GBS_find_string(char *str, GB_CSTR key, int match_mode) {
    return const_cast<char*>(GBS_find_string(const_cast<GB_CSTR>(str), key, match_mode));
}

// --------------------------------------------------------------------------------

struct gb_data_base_type2;
class GB_transaction : Noncopyable {
    GBDATA *ta_main;
    bool      ta_open;          // is transaction open ?
    GB_ERROR  ta_err;

public:
    GB_transaction(GBDATA *gb_main);
    ~GB_transaction();

    bool ok() const { return ta_open && !ta_err; } // ready to work on DB? 
    GB_ERROR close(GB_ERROR error); // abort transaction if error (e.g.: 'return ta.close(error);')
};

int GB_info(struct gb_data_base_type2 *gbd);

#endif /*__cplusplus*/

#define GB_INLINE inline

#else
#error "arbdb.h included twice"
#endif /*ARBDB_H*/