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// ================================================================ //
// //
// File : arbdb.h //
// Purpose : external ARB DB interface //
// //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// ================================================================ //
#ifndef ARBDB_H
#define ARBDB_H
#ifndef ARBTOOLS_H
#include <arbtools.h>
#endif
#ifndef ARBDB_BASE_H
#include <arbdb_base.h>
#endif
#ifndef ARB_ERROR_H
#include <arb_error.h>
#endif
#ifndef _STDINT_H
#include <stdint.h>
#endif
#define GB_SYSTEM_FOLDER "__SYSTEM__"
#define GB_SYSTEM_KEY_DATA "@key_data"
#define GB_DEFAULT_ALIGNMENT "presets/use" // has to match ../WINDOW/aw_awar_defs.hxx@AWAR_DEFAULT_ALIGNMENT
// ---------------------
// simple types
typedef int GB_COMPRESSION_MASK;
// ------------------------------
// forward declare types
struct GB_NUMHASH;
struct GBS_regex;
struct GBS_string_matcher;
struct GBS_strstruct;
struct GEN_position;
struct DictData;
struct CharPtrArray;
struct StrArray;
struct ConstStrArray;
// -------------------
// constants
#define GB_USERFLAG_ANY 127 // maximum for gb_flag_types2::usr_ref
#define GB_USERFLAG_QUERY 1 // bit used for search&query (used on species, genes, experiments)
#define GB_USERFLAG_GHOSTNODE 1 // bit used by gbt_write_tree (only used on tree-nodes; so it does not clash with GB_USERFLAG_QUERY)
// --------------
// enums
enum GB_TYPES { // supported DB entry 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_base.hxx@sync_GB_TYPES_AW_VARIABLE_TYPE
GB_TYPE_MAX = 16,
GB_CREATE_CONTAINER = GB_DB,
GB_FIND = GB_NONE,
};
enum GB_SEARCH_TYPE {
SEARCH_BROTHER = 1, // [was: this_level]
SEARCH_CHILD = 2, // [was: down_level]
SEARCH_GRANDCHILD = 4, // [was: down_2_level]
SEARCH_NEXT_BROTHER = SEARCH_BROTHER+8, // [was: this_level|search_next]
SEARCH_CHILD_OF_NEXT = SEARCH_CHILD+8, // [was: down_level|search_next]
};
enum GB_UNDO_TYPE {
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
};
// -----------------------
// callback types
typedef long (*gb_hash_loop_type)(const char *key, long val, void *client_data);
typedef void (*gb_hash_const_loop_type)(const char *key, long val, void *client_data);
typedef int (*gbs_hash_compare_function) (const char *key0, long val0, const char *key1, long val1);
typedef const char* (*gb_export_sequence_cb)(GBDATA *gb_species, size_t *seq_len, GB_ERROR *error);
typedef GBDATA* (*GB_Link_Follower)(GBDATA *GB_root, GBDATA *GB_elem, const char *link);
typedef const char *(*gb_getenv_hook)(const char *varname);
// -----------------------
// GB_transaction
class GB_transaction : virtual Noncopyable {
GBDATA *ta_main;
bool ta_open; // is transaction open ?
GB_ERROR ta_err;
void init(GBDATA *gb_main, bool initial);
protected:
GB_transaction(GBDATA *gb_main, bool) { init(gb_main, true); }
public:
GB_transaction(GBDATA *gb_main) { init(gb_main, false); }
~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);')
ARB_ERROR close(ARB_ERROR& error); // abort transaction if error (e.g.: 'return ta.close(error);')
};
struct GB_initial_transaction : public GB_transaction {
GB_initial_transaction(GBDATA *gb_main) : GB_transaction(gb_main, true) {}
};
class GB_shell {
// initialize and cleanup module ARBDB
// No database usage is possible when no GB_shell exists!
public:
GB_shell();
~GB_shell();
static void ensure_inside();
static bool in_shell();
};
// --------------------------------------------
#if defined(DEBUG)
struct GB_SizeInfo {
long containers; // no of containers
long terminals; // no of terminals
long structure; // structure size
long data; // data size
long mem; // data memory size (compressed)
GB_SizeInfo() : containers(0), terminals(0), structure(0), data(0), mem(0) {}
void collect(GBDATA *gbd);
};
#endif
// --------------------------------------------
// include generated public prototypes
#include <ad_prot.h>
// to avoid arb-wide changes atm include some headers from CORE lib
#ifndef ARB_MSG_H
#include <arb_msg.h>
#endif
#ifndef ARB_STRING_H
#include <arb_string.h>
#endif
// ----------------------------------------------------
// const wrappers for functions from ad_prot.h
inline char *GBS_find_string(char *content, GB_CSTR key, int match_mode) {
return const_cast<char*>(GBS_find_string(const_cast<GB_CSTR>(content), key, match_mode));
}
// ---------------------------------
// error delivery functions
inline void GB_end_transaction_show_error(GBDATA *gbd, ARB_ERROR& error, void (*error_handler)(GB_ERROR)) {
GB_end_transaction_show_error(gbd, error.deliver(), error_handler);
}
inline ARB_ERROR GB_end_transaction(GBDATA *gbd, ARB_ERROR& error) {
return GB_end_transaction(gbd, error.deliver());
}
#else
#error arbdb.h included twice
#endif // ARBDB_H
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