ARB
arbdb.h
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1 // ================================================================ //
2 // //
3 // File : arbdb.h //
4 // Purpose : external ARB DB interface //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // ================================================================ //
10 
11 #ifndef ARBDB_H
12 #define ARBDB_H
13 
14 #ifndef ARBTOOLS_H
15 #include <arbtools.h>
16 #endif
17 #ifndef ARBDB_BASE_H
18 #include <arbdb_base.h>
19 #endif
20 #ifndef ARB_ERROR_H
21 #include <arb_error.h>
22 #endif
23 #ifndef _STDINT_H
24 #include <stdint.h>
25 #endif
26 
27 #define GB_SYSTEM_FOLDER "__SYSTEM__"
28 #define GB_SYSTEM_KEY_DATA "@key_data"
29 
30 #define GB_DEFAULT_ALIGNMENT "presets/use" // has to match ../WINDOW/aw_awar_defs.hxx@AWAR_DEFAULT_ALIGNMENT
31 
32 // ---------------------
33 // simple types
34 
35 typedef int GB_COMPRESSION_MASK;
36 
37 // ------------------------------
38 // forward declare types
39 
40 struct GB_NUMHASH;
41 
42 struct GBS_regex;
43 struct GBS_string_matcher;
44 struct GBS_strstruct;
45 struct GEN_position;
46 struct DictData;
47 struct CharPtrArray;
48 struct StrArray;
49 struct ConstStrArray;
50 
51 // -------------------
52 // constants
53 
54 #define GB_USERFLAG_ANY 127 // maximum for gb_flag_types2::usr_ref
55 #define GB_USERFLAG_QUERY 1 // bit used for search&query (used on species, genes, experiments)
56 #define GB_USERFLAG_WASMARKED 2 // bit used to temp. store marks
57 #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)
58 
59 // --------------
60 // enums
61 
62 enum GB_TYPES { // supported DB entry types
63  GB_NONE = 0,
64  GB_BIT = 1,
65  GB_BYTE = 2,
66  GB_INT = 3,
67  GB_FLOAT = 4,
68  GB_POINTER = 5, // not savable! only allowed in temporary entries
69  GB_BITS = 6,
70  // 7 is unused
71  GB_BYTES = 8,
72  GB_INTS = 9,
73  GB_FLOATS = 10,
74  GB_OBSOLETE = 11, // former GB_LINK (stay backward compatible until arb 6.2 or later)
75  GB_STRING = 12,
76  GB_STRING_SHRT = 13, // used automatically during save
77  // 14 is unused
78  GB_DB = 15,
79 
80  // keep GB_TYPES consistent with AW_VARIABLE_TYPE
81  // see ../WINDOW/aw_base.hxx@sync_GB_TYPES_AW_VARIABLE_TYPE
82 
84 
87 
88 };
89 
96  return type == GB_STRING || type == GB_BYTE || type == GB_INT || type == GB_FLOAT || type == GB_BITS;
97 }
98 
100  SEARCH_BROTHER = 1, // [was: this_level]
101  SEARCH_CHILD = 2, // [was: down_level]
102  SEARCH_GRANDCHILD = 4, // [was: down_2_level]
103  SEARCH_NEXT_BROTHER = SEARCH_BROTHER+8, // [was: this_level|search_next]
104  SEARCH_CHILD_OF_NEXT = SEARCH_CHILD+8, // [was: down_level|search_next]
105 };
106 
108  GB_UNDO_NONE, // no undo
109  GB_UNDO_KILL, // no undo and delete all old undos
110  GB_UNDO_UNDO, // normal undo -> deleted all redoes
111  GB_UNDO_REDO, // moves to UNDO_REDO
112  GB_UNDO_UNDO_REDO // internal makes undo redoable
113 };
114 
115 enum XCMD_TYPE {
116  // internal (use public values below):
117  _XCMD__ASYNC = 1, // run asynchronous (otherwise wait for finish)
118  _XCMD__WAITKEY = 2, // always wait for keypress (otherwise only in case of error!)
119 
120  // public:
125 };
126 
127 // -----------------------
128 // callback types
129 
130 typedef long (*gb_hash_loop_type)(const char *key, long val, void *client_data);
131 typedef void (*gb_hash_const_loop_type)(const char *key, long val, void *client_data);
132 typedef int (*gbs_hash_compare_function) (const char *key0, long val0, const char *key1, long val1);
133 
134 typedef const char* (*gb_export_sequence_cb)(GBDATA *gb_species, size_t *seq_len, GB_ERROR *error);
135 
136 typedef GBDATA* (*GB_Link_Follower)(GBDATA *GB_root, GBDATA *GB_elem, const char *link);
137 
138 typedef const char *(*gb_getenv_hook)(const char *varname);
139 
140 // -----------------------
141 // GB_transaction
142 
143 class GB_transaction : virtual Noncopyable {
144  GBDATA *ta_main;
145  bool ta_open; // is transaction open ?
146  GB_ERROR ta_err;
147 
148  void init(GBDATA *gb_main, bool initial);
149 protected:
150  GB_transaction(GBDATA *gb_main, bool) { init(gb_main, true); }
151 public:
152  GB_transaction(GBDATA *gb_main) { init(gb_main, false); }
153  ~GB_transaction();
154 
155  bool ok() const { return ta_open && !ta_err; } // ready to work on DB?
156  GB_ERROR close(GB_ERROR error); // abort transaction if error (e.g.: 'return ta.close(error);')
157  ARB_ERROR close(ARB_ERROR& error); // abort transaction if error (e.g.: 'return ta.close(error);')
158 };
159 
162 };
163 
164 class GB_shell {
165  // initialize and cleanup module ARBDB
166  // No database usage is possible when no GB_shell exists!
167 public:
168  GB_shell();
169  ~GB_shell();
170 
171  static void ensure_inside();
172  static bool in_shell();
173 };
174 
175 // --------------------------
176 // GB_securityLevel
177 
178 class GB_securityLevel : virtual Noncopyable {
179  // changes global security level until destruction of this.
180  // intended to be used as auto-variable.
181 
182  GBDATA *gbdata;
183  int previous_level;
184 
185  int whats_my_security() const;
186  void change_my_security(int level);
187 
188 public:
189  GBDATA *get_gbd() const { return gbdata; } // internal use only
190 
191  int previous() const { return previous_level; }
192  int current() const { return whats_my_security(); }
193 
194  GB_securityLevel(GBDATA *gbd, int level) :
195  gbdata(gbd),
196  previous_level(current())
197  {
198  change_my_security(level);
199  }
201  change_my_security(previous());
202  }
203 
204 };
205 struct GB_topSecurityLevel : public GB_securityLevel { // derived from Noncopyable
206  // raise security level to top (allow everything).
207  // Note: the highest user-level is 6
209  GB_securityLevel(gbd, 7)
210  {}
211 };
212 struct GB_previousSecurityLevel : public GB_securityLevel { // derived from Noncopyable
213  // temporarily lower security again (while another GB_securityLevel is active).
215  GB_securityLevel(active.get_gbd(), active.previous())
216  {}
217 };
218 
219 // --------------------------------------------
220 
221 #if defined(DEBUG)
222 struct GB_SizeInfo {
223  long containers; // no of containers
224  long terminals; // no of terminals
225  long structure; // structure size
226  long data; // data size
227  long mem; // data memory size (compressed)
228 
229  GB_SizeInfo() : containers(0), terminals(0), structure(0), data(0), mem(0) {}
230 
231  void collect(GBDATA *gbd);
232 };
233 #endif
234 
235 // --------------------------------------------
236 // include generated public prototypes
237 
238 #include <ad_prot.h>
239 
240 // to avoid arb-wide changes atm include some headers from CORE lib
241 #ifndef ARB_MEM_H
242 #include <arb_mem.h>
243 #endif
244 #ifndef ARB_MSG_H
245 #include <arb_msg.h>
246 #endif
247 #ifndef ARB_STRING_H
248 #include <arb_string.h>
249 #endif
250 
251 // ----------------------------------------------------
252 // const wrappers for functions from ad_prot.h
253 
254 inline char *GBS_find_string(char *content, GB_CSTR key, int match_mode) {
255  return const_cast<char*>(GBS_find_string(const_cast<GB_CSTR>(content), key, match_mode));
256 }
257 
258 // ---------------------------------
259 // error delivery functions
260 
261 inline void GB_end_transaction_show_error(GBDATA *gbd, ARB_ERROR& error, void (*error_handler)(GB_ERROR)) {
262  GB_end_transaction_show_error(gbd, error.deliver(), error_handler);
263 }
265  return GB_end_transaction(gbd, error.deliver());
266 }
267 
268 
269 #else
270 #error arbdb.h included twice
271 #endif // ARBDB_H
const char * GB_ERROR
Definition: arb_core.h:25
GB_TYPES type
bool GB_TYPE_readable_as_string(GB_TYPES type)
Definition: arbdb.h:90
Definition: arbdb.h:65
Definition: arbdb.h:69
~GB_securityLevel()
Definition: arbdb.h:200
long
Definition: AW_awar.cxx:154
int(* gbs_hash_compare_function)(const char *key0, long val0, const char *key1, long val1)
Definition: arbdb.h:132
bool ok() const
Definition: arbdb.h:155
int current() const
Definition: arbdb.h:192
XCMD_TYPE
Definition: arbdb.h:115
GB_topSecurityLevel(GBDATA *gbd)
Definition: arbdb.h:208
long(* gb_hash_loop_type)(const char *key, long val, void *client_data)
Definition: arbdb.h:130
char * GBS_find_string(char *content, GB_CSTR key, int match_mode)
Definition: arbdb.h:254
GB_UNDO_TYPE
Definition: arbdb.h:107
GB_initial_transaction(GBDATA *gb_main)
Definition: arbdb.h:161
GB_transaction(GBDATA *gb_main, bool)
Definition: arbdb.h:150
Definition: arbdb.h:67
Definition: arbdb.h:78
GB_ERROR deliver() const
Definition: arb_error.h:114
#define true
Definition: ureadseq.h:14
~GB_shell()
Definition: arbdb.cxx:451
Definition: arbdb.h:64
GB_shell()
Definition: arbdb.cxx:447
static void ensure_inside()
Definition: arbdb.cxx:456
static void error(const char *msg)
Definition: mkptypes.cxx:96
int previous() const
Definition: arbdb.h:191
ARB_ERROR GB_end_transaction(GBDATA *gbd, ARB_ERROR &error)
Definition: arbdb.h:264
GB_previousSecurityLevel(const GB_securityLevel &active)
Definition: arbdb.h:214
GB_securityLevel(GBDATA *gbd, int level)
Definition: arbdb.h:194
GB_SEARCH_TYPE
Definition: arbdb.h:99
Definition: arbdb.h:86
static bool in_shell()
Definition: arbdb.cxx:458
void(* gb_hash_const_loop_type)(const char *key, long val, void *client_data)
Definition: arbdb.h:131
Definition: arbdb.h:72
Definition: arbdb.h:63
GB_ERROR close(GB_ERROR error)
Definition: arbdbpp.cxx:32
aisc_com * link
GB_transaction(GBDATA *gb_main)
Definition: arbdb.h:152
int GB_COMPRESSION_MASK
Definition: arbdb.h:35
GB_TYPES
Definition: arbdb.h:62
GBDATA * get_gbd() const
Definition: arbdb.h:189
GBDATA * gb_main
Definition: adname.cxx:33
Definition: arbdb.h:71
void GB_end_transaction_show_error(GBDATA *gbd, ARB_ERROR &error, void(*error_handler)(GB_ERROR))
Definition: arbdb.h:261
const char * GB_CSTR
Definition: arbdb_base.h:25
Definition: arbdb.h:66