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1 /* ARB database interface.
2  *
3  * This file is generated by aisc_mkpt.
4  * Any changes you make here will be overwritten later!
5  */
7 #ifndef AD_PROT_H
8 #define AD_PROT_H
10 /* define ARB attributes: */
11 #ifndef ATTRIBUTES_H
12 # include <attributes.h>
13 #endif
16 /* adExperiment.cxx */
18 GBDATA *EXP_find_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name);
19 GBDATA *EXP_find_experiment(GBDATA *gb_species, const char *name);
20 GBDATA *EXP_first_experiment_rel_exp_data(GBDATA *gb_experiment_data);
21 GBDATA *EXP_next_experiment(GBDATA *gb_experiment);
22 GBDATA *EXP_find_or_create_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name);
24 /* adGene.cxx */
25 bool GEN_is_genome_db(GBDATA *gb_main, int default_value);
27 GBDATA *GEN_find_gene_data(GBDATA *gb_species);
28 GBDATA *GEN_expect_gene_data(GBDATA *gb_species);
29 GBDATA *GEN_find_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name);
30 GBDATA *GEN_find_gene(GBDATA *gb_species, const char *name);
31 GBDATA *GEN_expect_gene(GBDATA *gb_species, const char *name);
32 GBDATA *GEN_create_nonexisting_gene(GBDATA *gb_species, const char *name);
33 GBDATA *GEN_find_or_create_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name);
34 GBDATA *GEN_first_gene(GBDATA *gb_species);
36 GBDATA *GEN_next_gene(GBDATA *gb_gene);
37 GBDATA *GEN_first_marked_gene(GBDATA *gb_species);
39 GEN_position *GEN_new_position(int parts, bool joinable);
43 GB_ERROR GEN_write_position(GBDATA *gb_gene, const GEN_position *pos, long seqLength);
45 const char *GEN_origin_organism(GBDATA *gb_pseudo);
46 const char *GEN_origin_gene(GBDATA *gb_pseudo);
47 bool GEN_is_pseudo_gene_species(GBDATA *gb_species);
49 void GEN_add_pseudo_species_to_hash(GBDATA *gb_pseudo, GB_HASH *pseudo_hash);
51 GBDATA *GEN_find_pseudo_species(GBDATA *gb_main, const char *organism_name, const char *gene_name, const GB_HASH *pseudo_hash);
52 GBDATA *GEN_find_origin_organism(GBDATA *gb_pseudo, const GB_HASH *organism_hash);
53 GBDATA *GEN_find_origin_gene(GBDATA *gb_pseudo, const GB_HASH *organism_hash);
57 bool GEN_is_organism(GBDATA *gb_species);
58 GBDATA *GEN_find_organism(GBDATA *gb_main, const char *name);
60 GBDATA *GEN_next_organism(GBDATA *gb_organism);
64 char *GEN_global_gene_identifier(GBDATA *gb_gene, GBDATA *gb_organism);
66 /* adTest.cxx */
67 const char *GB_get_db_path(GBDATA *gbd);
68 void GB_dump_db_path(GBDATA *gbd);
69 NOT4PERL void GB_dump(GBDATA *gbd);
73 /* ad_cb.cxx */
75 NOT4PERL const void *GB_read_old_value(void);
76 long GB_read_old_size(void);
78 /* ad_load.cxx */
79 void GB_set_verbose(void);
80 void GB_set_next_main_idx(long idx);
81 GBDATA *GB_open(const char *path, const char *opent);
84 /* ad_save_load.cxx */
86 GB_ERROR GB_save(GBDATA *gb, const char *path, const char *savetype);
87 GB_ERROR GB_create_parent_directory(const char *path);
88 GB_ERROR GB_create_directory(const char *path);
89 GB_ERROR GB_save_in_arbprop(GBDATA *gb, const char *path, const char *savetype);
90 const char *GB_get_supported_compression_flags(bool verboose);
92 class ArbDBWriter;
94 GB_ERROR GB_start_streamed_save_as(GBDATA *gbd, const char *path, const char *savetype, ArbDBWriter*& writer);
97 GB_ERROR GB_save_as(GBDATA *gbd, const char *path, const char *savetype);
99 GB_ERROR GB_save_quick_as(GBDATA *gbd, const char *path);
100 GB_ERROR GB_save_quick(GBDATA *gbd, const char *refpath);
101 void GB_disable_path(GBDATA *gbd, const char *path);
105 /* adcache.cxx */
106 void GB_flush_cache(GBDATA *gbd);
107 char *GB_set_cache_size(GBDATA *gbd, size_t size);
109 /* adcomm.cxx */
110 GB_ERROR GBCMS_open(const char *path, long timeout, GBDATA *gb_main);
111 void GBCMS_shutdown(GBDATA *gbd);
112 bool GBCMS_accept_calls(GBDATA *gbd, bool wait_extra_time);
113 void GB_set_remote_action(GBDATA *gbd, bool in_action);
115 long GB_read_clients(GBDATA *gbd);
116 bool GB_is_server(GBDATA *gbd);
117 GBDATA *GBCMC_find(GBDATA *gbd, const char *key, GB_TYPES type, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs);
119 GB_ERROR GB_install_pid(int mode);
121 /* adcompr.cxx */
124 /* adfile.cxx */
125 GB_CSTR GB_getcwd(void);
126 char *GB_find_all_files(const char *dir, const char *mask, bool filename_only);
127 char *GB_find_latest_file(const char *dir, const char *mask);
128 char *GB_lib_file(bool warn_when_not_found, const char *libprefix, const char *filename);
129 char *GB_property_file(bool warn_when_not_found, const char *filename);
130 void GBS_read_dir(StrArray& names, const char *dir, const char *mask);
131 const char *GB_get_arb_revision_tag(void);
133 /* adhash.cxx */
134 GB_HASH *GBS_create_hash(long estimated_elements, GB_CASE case_sens);
135 GB_HASH *GBS_create_dynaval_hash(long estimated_elements, GB_CASE case_sens, void (*freefun)(long));
136 void GBS_dynaval_free(long val);
137 void GBS_optimize_hash(const GB_HASH *hs);
138 char *GBS_hashtab_2_string(const GB_HASH *hash);
139 long GBS_read_hash(const GB_HASH *hs, const char *key);
140 long GBS_write_hash(GB_HASH *hs, const char *key, long val);
141 long GBS_write_hash_no_strdup(GB_HASH *hs, char *key, long val);
142 long GBS_incr_hash(GB_HASH *hs, const char *key);
143 void GBS_free_hash(GB_HASH *hs);
144 void GBS_hash_do_loop(GB_HASH *hs, gb_hash_loop_type func, void *client_data);
145 void GBS_hash_do_const_loop(const GB_HASH *hs, gb_hash_const_loop_type func, void *client_data);
146 size_t GBS_hash_elements(const GB_HASH *hs);
147 const char *GBS_hash_next_element_that(const GB_HASH *hs, const char *last_key, bool (*condition)(const char *key, long val, void *cd), void *cd);
148 void GBS_hash_do_sorted_loop(GB_HASH *hs, gb_hash_loop_type func, gbs_hash_compare_function sorter, void *client_data);
149 void GBS_hash_do_const_sorted_loop(const GB_HASH *hs, gb_hash_const_loop_type func, gbs_hash_compare_function sorter, void *client_data);
150 int GBS_HCF_sortedByKey(const char *k0, long dummy_1x, const char *k1, long dummy_2x);
151 GB_NUMHASH *GBS_create_numhash(size_t estimated_elements);
152 long GBS_read_numhash(GB_NUMHASH *hs, long key);
153 long GBS_write_numhash(GB_NUMHASH *hs, long key, long val);
154 void GBS_free_numhash(GB_NUMHASH *hs);
156 /* adhashtools.cxx */
157 GB_HASH *GBT_create_species_hash_sized(GBDATA *gb_main, long species_count);
163 /* adindex.cxx */
164 GB_ERROR GB_create_index(GBDATA *gbd, const char *key, GB_CASE case_sens, long estimated_size) __ATTR__USERESULT;
165 NOT4PERL void GB_dump_indices(GBDATA *gbd);
170 GB_ERROR GB_set_undo_mem(GBDATA *gbd, long memsize);
172 /* adlang1.cxx */
175 /* admap.cxx */
176 bool GB_supports_mapfile(void);
178 /* admatch.cxx */
179 GBS_string_matcher *GBS_compile_matcher(const char *search_expr, GB_CASE case_flag);
180 void GBS_free_matcher(GBS_string_matcher *matcher);
181 GB_CSTR GBS_find_string(GB_CSTR cont, GB_CSTR substr, int match_mode);
182 bool GBS_string_matches(const char *str, const char *expr, GB_CASE case_sens);
183 bool GBS_string_matches_regexp(const char *str, const GBS_string_matcher *expr);
185  class GBL_call_env;
187 char *GBS_string_eval_in_env(const char *insource, const char *icommand, const GBL_call_env& callEnv);
188 char *GBS_string_eval(const char *insource, const char *icommand);
190 /* admath.cxx */
191 double GB_log_fak(int n);
192 void GB_random_seed(unsigned seed);
193 int GB_random(int range);
195 /* adoptimize.cxx */
198 /* adperl.cxx */
201 /* adquery.cxx */
202 GBDATA *GB_find_sub_by_quark(GBDATA *father, GBQUARK key_quark, GBDATA *after, size_t skip_over);
203 GBDATA *GB_find(GBDATA *gbd, const char *key, GB_SEARCH_TYPE gbs);
204 GBDATA *GB_find_string(GBDATA *gbd, const char *key, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs);
205 NOT4PERL GBDATA *GB_find_int(GBDATA *gbd, const char *key, long val, GB_SEARCH_TYPE gbs);
207 GBDATA *GB_nextChild(GBDATA *child);
208 GBDATA *GB_entry(GBDATA *father, const char *key);
209 GBDATA *GB_nextEntry(GBDATA *entry);
210 GBDATA *GB_followingEntry(GBDATA *entry, size_t skip_over);
211 size_t GB_countEntries(GBDATA *father, const char *key);
212 GBDATA *GB_brother(GBDATA *entry, const char *key);
213 const char *GB_first_non_key_char(const char *str);
214 GBDATA *GB_search(GBDATA *gbd, const char *fieldpath, GB_TYPES create);
215 GBDATA *GB_searchOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value);
216 GBDATA *GB_searchOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value);
217 GBDATA *GB_searchOrCreate_float(GBDATA *gb_container, const char *fieldpath, float default_value);
219 GBDATA *GB_first_marked(GBDATA *gbd, const char *keystring);
220 GBDATA *GB_following_marked(GBDATA *gbd, const char *keystring, size_t skip_over);
221 GBDATA *GB_next_marked(GBDATA *gbd, const char *keystring);
223 /* adsocket.cxx */
224 char *GB_read_fp(FILE *in);
225 char *GB_read_file(const char *path);
226 char *GB_map_FILE(FILE *in, int writeable);
227 char *GB_map_file(const char *path, int writeable);
229 GB_ERROR GB_textprint(const char *path) __ATTR__USERESULT;
231 GB_CSTR GB_getenvUSER(void);
240 GB_CSTR GB_getenv(const char *env);
241 bool GB_host_is_local(const char *hostname);
243 NOT4PERL GB_ERROR GB_xcmd(const char *cmd, XCMD_TYPE exectype) __ATTR__USERESULT_TODO;
244 GB_CSTR GB_append_suffix(const char *name, const char *suffix);
245 GB_CSTR GB_canonical_path(const char *anypath);
246 GB_CSTR GB_concat_path(GB_CSTR anypath_left, GB_CSTR anypath_right);
247 GB_CSTR GB_concat_full_path(const char *anypath_left, const char *anypath_right);
248 GB_CSTR GB_unfold_in_directory(const char *relative_directory, const char *path);
249 GB_CSTR GB_unfold_path(const char *pwd_envar, const char *path);
250 GB_CSTR GB_path_in_ARBHOME(const char *relative_path);
251 GB_CSTR GB_path_in_ARBLIB(const char *relative_path);
252 GB_CSTR GB_concat_path_in_ARBLIB(const char *relative_path_left, const char *anypath_right);
253 GB_CSTR GB_path_in_HOME(const char *relative_path);
254 GB_CSTR GB_path_in_arbprop(const char *relative_path);
255 FILE *GB_fopen_tempfile(const char *filename, const char *fmode, char **res_fullname);
256 char *GB_create_tempfile(const char *name);
257 char *GB_unique_filename(const char *name_prefix, const char *suffix);
258 void GB_remove_on_exit(const char *filename);
259 void GB_split_full_path(const char *fullpath, char **res_dir, char **res_fullname, char **res_name_only, char **res_suffix);
261 /* adstring.cxx */
262 char *GBS_string_2_key(const char *str);
263 char *GB_memdup(const char *source, size_t len);
264 GB_ERROR GB_check_key(const char *key) __ATTR__USERESULT;
265 GB_ERROR GB_check_hkey(const char *key) __ATTR__USERESULT;
266 char *GBS_escape_string(const char *str, const char *chars_to_escape, char escape_char);
267 char *GBS_unescape_string(const char *str, const char *escaped_chars, char escape_char);
268 char *GBS_eval_env(GB_CSTR p);
269 long GBS_gcgchecksum(const char *seq);
270 uint32_t GB_checksum(const char *seq, long length, int ignore_case, const char *exclude);
271 uint32_t GBS_checksum(const char *seq, int ignore_case, const char *exclude);
272 size_t GBS_shorten_repeated_data(char *data);
273 char *GBS_merge_tagged_strings(const char *s1, const char *tag1, const char *replace1, const char *s2, const char *tag2, const char *replace2);
274 char *GBS_modify_tagged_string_with_ACI(const char *s, const char *dt, const char *tag, const char *aci, GBL_call_env& env);
275 char *GB_read_as_tagged_string(GBDATA *gbd, const char *tagi);
276 void GBS_fwrite_string(const char *strngi, FILE *out);
277 char *GBS_fconvert_string(char *buffer);
278 char *GBS_replace_tabs_by_spaces(const char *text);
279 char *GBS_trim(const char *str);
280 char *GBS_log_action_to(const char *comment, const char *action, bool stamp);
281 const char *GBS_funptr2readable(void *funptr, bool stripARBHOME);
283 /* adsystem.cxx */
284 DictData *GB_get_dictionary(GBDATA *gb_main, const char *key);
285 GB_ERROR GB_set_dictionary(GBDATA *gb_main, const char *key, const DictData *dd);
287 /* adtcp.cxx */
288 char *GB_arbtcpdat_path(void);
289 const char *GBS_scan_arb_tcp_param(const char *ipPort, const char *wantedParam);
291 #ifdef UNIT_TESTS // UT_DIFF
292 #define TEST_SERVER_ID (-666)
293 #define TEST_GENESERVER_ID (-667)
294 #endif
296 const char *GBS_nameserver_tag(const char *add_field);
297 const char *GBS_ptserver_tag(int id);
298 const char *GBS_read_arb_tcp(const char *env);
299 const char *const *GBS_get_arb_tcp_entries(const char *matching);
300 const char *GBS_ptserver_logname(void);
301 void GBS_add_ptserver_logentry(const char *entry);
302 char *GBS_ptserver_id_to_choice(int i, int showBuild);
304 /* arbdb.cxx */
305 const char *GB_get_type_name(GBDATA *gbd);
306 float GB_atof(const char *str);
307 GB_BUFFER GB_give_buffer(size_t size);
308 GB_BUFFER GB_increase_buffer(size_t size);
309 NOT4PERL int GB_give_buffer_size(void);
310 GB_BUFFER GB_give_buffer2(long size);
313 void GB_atexit(void (*exitfun)());
314 void GB_init_gb(void);
315 int GB_open_DBs(void);
316 void GB_close(GBDATA *gbd);
317 long GB_read_int(GBDATA *gbd);
318 int GB_read_byte(GBDATA *gbd);
320 float GB_read_float(GBDATA *gbd);
321 long GB_read_count(GBDATA *gbd);
322 long GB_read_memuse(GBDATA *gbd);
326 char *GB_read_string(GBDATA *gbd);
327 size_t GB_read_string_count(GBDATA *gbd);
328 long GB_read_bits_count(GBDATA *gbd);
329 GB_CSTR GB_read_bits_pntr(GBDATA *gbd, char c_0, char c_1);
330 char *GB_read_bits(GBDATA *gbd, char c_0, char c_1);
332 long GB_read_bytes_count(GBDATA *gbd);
333 char *GB_read_bytes(GBDATA *gbd);
335 long GB_read_ints_count(GBDATA *gbd);
338 float *GB_read_floats(GBDATA *gbd);
339 char *GB_read_as_string(GBDATA *gbd);
340 bool GB_readable_as_string(GBDATA *gbd);
344 long GB_read_from_ints(GBDATA *gbd, long index);
345 double GB_read_from_floats(GBDATA *gbd, long index);
346 GB_ERROR GB_write_byte(GBDATA *gbd, int i);
347 GB_ERROR GB_write_int(GBDATA *gbd, long i);
348 GB_ERROR GB_write_pointer(GBDATA *gbd, GBDATA *pointer);
349 GB_ERROR GB_write_float(GBDATA *gbd, float f);
350 GB_ERROR GB_write_pntr(GBDATA *gbd, const char *s, size_t bytes_size, size_t stored_size);
351 GB_ERROR GB_write_string(GBDATA *gbd, const char *s);
352 GB_ERROR GB_write_bits(GBDATA *gbd, const char *bits, long size, const char *c_0);
353 GB_ERROR GB_write_bytes(GBDATA *gbd, const char *s, long size);
354 GB_ERROR GB_write_ints(GBDATA *gbd, const GB_UINT4 *i, long size);
355 GB_ERROR GB_write_floats(GBDATA *gbd, const float *f, long size);
356 GB_ERROR GB_write_autoconv_string(GBDATA *gbd, const char *val);
357 GB_ERROR GB_write_lossless_byte(GBDATA *gbd, uint8_t byte);
358 GB_ERROR GB_write_lossless_int(GBDATA *gbd, int32_t i);
361 int GB_read_security_read(GBDATA *gbd);
363 GB_ERROR GB_write_security_write(GBDATA *gbd, unsigned long level);
364 GB_ERROR GB_write_security_read(GBDATA *gbd, unsigned long level);
365 GB_ERROR GB_write_security_delete(GBDATA *gbd, unsigned long level);
366 GB_ERROR GB_write_security_levels(GBDATA *gbd, unsigned long readlevel, unsigned long writelevel, unsigned long deletelevel);
367 void GB_change_my_security(GBDATA *gbd, int level);
369 bool GB_is_container(GBDATA *gbd);
370 char *GB_read_key(GBDATA *gbd);
372 GBQUARK GB_find_existing_quark(GBDATA *gbd, const char *key);
373 GBQUARK GB_find_or_create_quark(GBDATA *gbd, const char *key);
375 bool GB_has_key(GBDATA *gbd, const char *key);
376 long GB_read_clock(GBDATA *gbd);
379 GBDATA *GB_get_root(GBDATA *gbd);
380 bool GB_is_ancestor_of(GBDATA *gb_ancestor, GBDATA *gb_descendant);
381 GBDATA *GB_create(GBDATA *father, const char *key, GB_TYPES type);
382 GBDATA *GB_create_container(GBDATA *father, const char *key);
383 bool GB_allow_compression(GBDATA *gb_main, bool allow_compression);
385 GB_ERROR GB_delete(GBDATA*& source);
388 GB_ERROR GB_copy_std(GBDATA *dest, GBDATA *source);
389 GB_ERROR GB_copy_overlay(GBDATA *dest, GBDATA *source);
390 GB_ERROR GB_copy_full(GBDATA *dest, GBDATA *source);
391 GBDATA *GB_clone(GBDATA *gb_destCont, GBDATA *gb_source);
392 char *GB_get_subfields(GBDATA *gbd);
395 bool GB_is_temporary(GBDATA *gbd);
396 bool GB_in_temporary_branch(GBDATA *gbd);
404 void GB_end_transaction_show_error(GBDATA *gbd, GB_ERROR error, void (*error_handler)(GB_ERROR));
407 int GB_nsons(GBDATA *gbd);
408 void GB_disable_quicksave(GBDATA *gbd, const char *reason);
409 GB_ERROR GB_resort_data_base(GBDATA *gb_main, GBDATA **new_order_list, long listsize);
410 bool GB_user_flag(GBDATA *gbd, unsigned char user_bit);
411 void GB_raise_user_flag(GBDATA *gbd, unsigned char user_bit);
412 void GB_clear_user_flag(GBDATA *gbd, unsigned char user_bit);
413 void GB_write_user_flag(GBDATA *gbd, unsigned char user_bit, bool state);
414 void GB_write_flag(GBDATA *gbd, long flag);
415 int GB_read_flag(GBDATA *gbd);
416 void GB_touch(GBDATA *gbd);
418 void GB_print_debug_information(struct Unfixed_cb_parameter *, GBDATA *gb_main);
419 int GB_info(GBDATA *gbd);
422 /* gb_aci.cxx */
423 NOT4PERL char *GB_command_interpreter_in_env(const char *str, const char *commands, const GBL_call_env& callEnv);
424 char *GB_command_interpreter(const char *str, const char *commands, GBDATA *gb_main);
426 #else
427 #error ad_prot.h included twice
428 #endif /* AD_PROT_H */
const char * GBS_ptserver_logname(void)
Definition: adtcp.cxx:425
GB_ERROR GB_begin_transaction(GBDATA *gbd)
Definition: arbdb.cxx:2528
GB_ERROR GB_check_key(const char *key) __ATTR__USERESULT
Definition: adstring.cxx:85
NOT4PERL const void * GB_read_old_value(void)
Definition: ad_cb.cxx:166
GB_HASH * GBT_create_marked_species_hash(GBDATA *gb_main)
Definition: adhashtools.cxx:40
GB_ERROR GB_copy_dropProtectMarksAndTempstate(GBDATA *dest, GBDATA *source)
Definition: arbdb.cxx:2152
GB_ERROR GBC_await_error(void)
Definition: adperl.cxx:245
void GBS_hash_do_const_sorted_loop(const GB_HASH *hs, gb_hash_const_loop_type func, gbs_hash_compare_function sorter, void *client_data)
Definition: adhash.cxx:641
NOT4PERL GBDATA * GB_find_int(GBDATA *gbd, const char *key, long val, GB_SEARCH_TYPE gbs)
Definition: adquery.cxx:311
void GB_dump_db_path(GBDATA *gbd)
Definition: adTest.cxx:27
const char * GB_ERROR
Definition: arb_core.h:25
long GEN_get_organism_count(GBDATA *gb_main)
Definition: adGene.cxx:756
GBS_string_matcher * GBS_compile_matcher(const char *search_expr, GB_CASE case_flag)
Definition: admatch.cxx:41
GB_ERROR GB_write_bits(GBDATA *gbd, const char *bits, long size, const char *c_0)
Definition: arbdb.cxx:1418
void GB_set_next_main_idx(long idx)
Definition: ad_load.cxx:918
GBDATA * GB_read_pointer(GBDATA *gbd)
Definition: arbdb.cxx:739
float * GB_read_floats(GBDATA *gbd)
Definition: arbdb.cxx:1053
NOT4PERL long GB_calc_structure_size(GBDATA *gbd)
GB_ERROR GB_commit_transaction(GBDATA *gbd)
Definition: arbdb.cxx:2551
char * GB_read_fp(FILE *in)
Definition: adsocket.cxx:271
const char * GBS_funptr2readable(void *funptr, bool stripARBHOME)
Definition: adstring.cxx:1007
void GB_remove_on_exit(const char *filename)
Definition: adsocket.cxx:1258
GB_ERROR GB_start_streamed_save_as(GBDATA *gbd, const char *path, const char *savetype, ArbDBWriter *&writer)
GB_ERROR GB_copy_full(GBDATA *dest, GBDATA *source)
Definition: arbdb.cxx:2190
GBDATA * GEN_next_gene(GBDATA *gb_gene)
Definition: adGene.cxx:138
GB_CSTR GB_path_in_arbprop(const char *relative_path)
Definition: adsocket.cxx:1166
bool GEN_is_organism(GBDATA *gb_species)
Definition: adGene.cxx:721
GBDATA * GEN_find_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name)
Definition: adGene.cxx:60
long GB_read_int(GBDATA *gbd)
Definition: arbdb.cxx:729
char * GB_read_key(GBDATA *gbd)
Definition: arbdb.cxx:1652
GBDATA * GB_child(GBDATA *father)
Definition: adquery.cxx:322
const char * GEN_origin_gene(GBDATA *gb_pseudo)
Definition: adGene.cxx:553
GB_ERROR GB_write_bytes(GBDATA *gbd, const char *s, long size)
Definition: arbdb.cxx:1434
GBDATA * GB_get_gb_main_during_cb(void)
Definition: ad_cb.cxx:142
bool GB_is_server(GBDATA *gbd)
Definition: adcomm.cxx:1697
long GBS_write_hash(GB_HASH *hs, const char *key, long val)
Definition: adhash.cxx:454
GB_ERROR GB_save(GBDATA *gb, const char *path, const char *savetype)
bool GB_is_temporary(GBDATA *gbd)
Definition: arbdb.cxx:2304
char * GBS_string_eval_in_env(const char *insource, const char *icommand, const GBL_call_env &callEnv)
Definition: admatch.cxx:493
GB_ERROR GB_write_string(GBDATA *gbd, const char *s)
Definition: arbdb.cxx:1387
void GEN_add_pseudo_species_to_hash(GBDATA *gb_pseudo, GB_HASH *pseudo_hash)
Definition: adGene.cxx:589
GB_ERROR GB_tell_server_dont_wait(GBDATA *gbd)
Definition: adcomm.cxx:1867
void GEN_free_position(GEN_position *pos)
Definition: adGene.cxx:195
GBDATA * GB_searchOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value)
Definition: adquery.cxx:546
GBDATA * GEN_find_gene(GBDATA *gb_species, const char *name)
Definition: adGene.cxx:64
int GB_info(GBDATA *gbd)
Definition: arbdb.cxx:2888
long GBS_incr_hash(GB_HASH *hs, const char *key)
Definition: adhash.cxx:467
GBDATA * GB_find(GBDATA *gbd, const char *key, GB_SEARCH_TYPE gbs)
Definition: adquery.cxx:295
char * GB_find_all_files(const char *dir, const char *mask, bool filename_only)
Definition: adfile.cxx:109
long GB_read_ints_count(GBDATA *gbd)
Definition: arbdb.cxx:1008
bool GB_readable_as_string(GBDATA *gbd)
Definition: arbdb.cxx:1080
NOT4PERL void GB_set_export_sequence_hook(gb_export_sequence_cb escb)
Definition: adlang1.cxx:35
void GBS_free_matcher(GBS_string_matcher *matcher)
Definition: admatch.cxx:94
GBDATA * GB_nextEntry(GBDATA *entry)
Definition: adquery.cxx:339
GB_ERROR GB_end_transaction(GBDATA *gbd, GB_ERROR error)
Definition: arbdb.cxx:2561
size_t GB_countEntries(GBDATA *father, const char *key)
Definition: adquery.cxx:351
bool GBCMS_accept_calls(GBDATA *gbd, bool wait_extra_time)
Definition: adcomm.cxx:1188
int(* gbs_hash_compare_function)(const char *key0, long val0, const char *key1, long val1)
Definition: arbdb.h:132
GBDATA * EXP_first_experiment_rel_exp_data(GBDATA *gb_experiment_data)
void GB_disable_quicksave(GBDATA *gbd, const char *reason)
Definition: arbdb.cxx:2647
GBDATA * GEN_findOrCreate_gene_data(GBDATA *gb_species)
Definition: adGene.cxx:44
long GBS_write_numhash(GB_NUMHASH *hs, long key, long val)
Definition: adhash.cxx:687
GB_ERROR GB_write_pntr(GBDATA *gbd, const char *s, size_t bytes_size, size_t stored_size)
Definition: arbdb.cxx:1344
const char * GB_get_type_name(GBDATA *gbd)
Definition: arbdb.cxx:72
GB_ERROR GB_delete_database(GB_CSTR filename)
void GB_end_transaction_show_error(GBDATA *gbd, GB_ERROR error, void(*error_handler)(GB_ERROR))
Definition: arbdb.cxx:2584
char * GB_read_as_string(GBDATA *gbd)
Definition: arbdb.cxx:1060
const char * GB_get_arb_revision_tag(void)
Definition: adfile.cxx:304
GB_ERROR GB_stream_save_part(ArbDBWriter *writer, GBDATA *from, GBDATA *till)
char * GB_read_as_tagged_string(GBDATA *gbd, const char *tagi)
Definition: adstring.cxx:776
size_t GBS_shorten_repeated_data(char *data)
Definition: adstring.cxx:357
long GB_read_bytes_count(GBDATA *gbd)
Definition: arbdb.cxx:969
GB_NUMHASH * GBS_create_numhash(size_t estimated_elements)
Definition: adhash.cxx:668
GB_HASH * GBS_create_dynaval_hash(long estimated_elements, GB_CASE case_sens, void(*freefun)(long))
Definition: adhash.cxx:271
GB_HASH * GBT_create_SAI_hash(GBDATA *gb_main)
Definition: adhashtools.cxx:44
char * GB_check_out_buffer(GB_CBUFFER buffer)
Definition: arbdb.cxx:350
char * GBS_string_eval(const char *insource, const char *icommand)
Definition: admatch.cxx:699
void GEN_sortAndMergeLocationParts(GEN_position *location)
Definition: adGene.cxx:487
Definition: arbdb.h:115
char * GBS_escape_string(const char *str, const char *chars_to_escape, char escape_char)
Definition: adstring.cxx:124
void GBS_free_hash(GB_HASH *hs)
Definition: adhash.cxx:538
GBDATA * GEN_find_organism(GBDATA *gb_main, const char *name)
Definition: adGene.cxx:728
char * GBS_string_2_key(const char *str)
Definition: adstring.cxx:52
int GB_open_DBs(void)
Definition: arbdb.cxx:522
GBDATA * GEN_expect_gene_data(GBDATA *gb_species)
Definition: adGene.cxx:54
long GBS_gcgchecksum(const char *seq)
Definition: adstring.cxx:246
GB_HASH * GBT_create_species_hash(GBDATA *gb_main)
Definition: adhashtools.cxx:36
void GEN_use_uncertainties(GEN_position *pos)
Definition: adGene.cxx:184
GB_ERROR GB_create_parent_directory(const char *path)
char * GBS_replace_tabs_by_spaces(const char *text)
Definition: adstring.cxx:923
uint32_t GB_checksum(const char *seq, long length, int ignore_case, const char *exclude)
Definition: adstring.cxx:319
bool GB_allow_compression(GBDATA *gb_main, bool allow_compression)
Definition: arbdb.cxx:1896
NOT4PERL gb_getenv_hook GB_install_getenv_hook(gb_getenv_hook hook)
Definition: adsocket.cxx:699
long(* gb_hash_loop_type)(const char *key, long val, void *client_data)
Definition: arbdb.h:130
void GBCMS_shutdown(GBDATA *gbd)
Definition: adcomm.cxx:247
long GB_read_bits_count(GBDATA *gbd)
Definition: arbdb.cxx:921
GB_ERROR GB_fix_database(GBDATA *gb_main)
Definition: adTest.cxx:237
char * GBS_ptserver_id_to_choice(int i, int showBuild)
Definition: adtcp.cxx:447
GBDATA * GB_get_grandfather(GBDATA *gbd)
Definition: arbdb.cxx:1728
GB_CSTR GB_getenvARB_GS(void)
Definition: adsocket.cxx:640
Definition: seq_search.cxx:34
GBDATA * GB_get_father(GBDATA *gbd)
Definition: arbdb.cxx:1722
GB_CSTR GB_canonical_path(const char *anypath)
Definition: adsocket.cxx:1000
GB_ERROR GB_push_transaction(GBDATA *gbd)
Definition: arbdb.cxx:2494
FILE * seq
Definition: rns.c:46
long GBS_write_hash_no_strdup(GB_HASH *hs, char *key, long val)
Definition: adhash.cxx:459
GB_CSTR GB_getenvARBHOME(void)
Definition: adsocket.cxx:579
unsigned long GB_ULONG
Definition: arbdb_base.h:42
#define NOT4PERL
Definition: arbdb_base.h:23
GB_CSTR GBS_find_string(GB_CSTR cont, GB_CSTR substr, int match_mode)
Definition: admatch.cxx:103
GB_ERROR GB_delete(GBDATA *&source)
Definition: arbdb.cxx:1916
char * GB_read_bytes(GBDATA *gbd)
Definition: arbdb.cxx:974
GB_ERROR GB_release(GBDATA *gbd)
Definition: arbdb.cxx:2600
char * GBS_modify_tagged_string_with_ACI(const char *s, const char *dt, const char *tag, const char *aci, GBL_call_env &env)
Definition: adstring.cxx:747
GB_BUFFER GB_give_other_buffer(GB_CBUFFER buffer, long size)
Definition: arbdb.cxx:363
GBDATA * EXP_next_experiment(GBDATA *gb_experiment)
NOT4PERL void GB_dump_indices(GBDATA *gbd)
char * GB_set_cache_size(GBDATA *gbd, size_t size)
Definition: adcache.cxx:294
const char * GBS_hash_next_element_that(const GB_HASH *hs, const char *last_key, bool(*condition)(const char *key, long val, void *cd), void *cd)
Definition: adhash.cxx:574
Definition: arbdb.h:107
POS_TREE1 * father
Definition: probe_tree.h:39
void GB_change_my_security(GBDATA *gbd, int level)
Definition: arbdb.cxx:1627
GB_ERROR GB_check_hkey(const char *key) __ATTR__USERESULT
Definition: adstring.cxx:92
static FullNameMap names
void GB_raise_user_flag(GBDATA *gbd, unsigned char user_bit)
Definition: arbdb.cxx:2755
GBDATA * EXP_find_experiment(GBDATA *gb_species, const char *name)
unsigned int GB_UINT4
Definition: arbdb_base.h:37
bool GB_user_flag(GBDATA *gbd, unsigned char user_bit)
Definition: arbdb.cxx:2750
GBDATA * GBCMC_find(GBDATA *gbd, const char *key, GB_TYPES type, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs)
Definition: adcomm.cxx:1725
GB_CSTR GB_read_bytes_pntr(GBDATA *gbd)
Definition: arbdb.cxx:964
GB_ERROR GB_write_lossless_byte(GBDATA *gbd, uint8_t byte)
Definition: arbdb.cxx:1504
GB_ERROR GB_optimize(GBDATA *gb_main)
GB_ERROR GB_clear_temporary(GBDATA *gbd)
Definition: arbdb.cxx:2295
size_t GB_read_string_count(GBDATA *gbd)
Definition: arbdb.cxx:916
char * GB_memdup(const char *source, size_t len)
Definition: adstring.cxx:56
NOT4PERL void GB_dump_no_limit(GBDATA *gbd)
Definition: adTest.cxx:196
GB_ERROR GB_write_security_levels(GBDATA *gbd, unsigned long readlevel, unsigned long writelevel, unsigned long deletelevel)
Definition: arbdb.cxx:1615
GB_HASH * GEN_create_pseudo_species_hash(GBDATA *gb_main, long additionalSize)
Definition: adGene.cxx:599
AliDataPtr after(AliDataPtr data, size_t pos)
Definition: insdel.cxx:593
GBDATA * GEN_first_pseudo_species(GBDATA *gb_main)
Definition: adGene.cxx:684
GBDATA * GB_create_container(GBDATA *father, const char *key)
Definition: arbdb.cxx:1829
char * GB_create_tempfile(const char *name)
Definition: adsocket.cxx:1222
long GB_read_count(GBDATA *gbd)
Definition: arbdb.cxx:758
GB_TYPES GB_read_type(GBDATA *gbd)
Definition: arbdb.cxx:1643
GB_ERROR GB_finish_stream_save(ArbDBWriter *&writer)
const char * GBS_read_arb_tcp(const char *env)
Definition: adtcp.cxx:325
void GB_random_seed(unsigned seed)
Definition: admath.cxx:80
GB_ERROR GB_install_pid(int mode)
Definition: adcomm.cxx:1957
GB_CSTR GB_read_key_pntr(GBDATA *gbd)
Definition: arbdb.cxx:1656
GBDATA * GEN_find_or_create_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name)
Definition: adGene.cxx:100
GB_ERROR GB_set_undo_mem(GBDATA *gbd, long memsize)
Definition: adindex.cxx:833
const char * GBS_scan_arb_tcp_param(const char *ipPort, const char *wantedParam)
Definition: adtcp.cxx:275
long GB_read_memuse(GBDATA *gbd)
Definition: arbdb.cxx:762
char * GB_property_file(bool warn_when_not_found, const char *filename)
Definition: adfile.cxx:204
GBDATA * GB_create(GBDATA *father, const char *key, GB_TYPES type)
Definition: arbdb.cxx:1781
long GB_read_old_size(void)
Definition: ad_cb.cxx:183
char * GB_map_FILE(FILE *in, int writeable)
Definition: adsocket.cxx:323
GBDATA * GEN_first_marked_gene(GBDATA *gb_species)
Definition: adGene.cxx:143
NOT4PERL int32_t GB_read_lossless_int(GBDATA *gbd, GB_ERROR &error)
Definition: arbdb.cxx:1128
GB_CSTR GB_read_pntr(GBDATA *gbd)
Definition: arbdb.cxx:877
long GB_number_of_subentries(GBDATA *gbd)
Definition: arbdb.cxx:2892
const char * GB_first_non_key_char(const char *str)
Definition: adquery.cxx:416
void GBS_hash_do_const_loop(const GB_HASH *hs, gb_hash_const_loop_type func, void *client_data)
Definition: adhash.cxx:559
int GB_read_security_write(GBDATA *gbd)
Definition: arbdb.cxx:1572
NOT4PERL float GB_read_lossless_float(GBDATA *gbd, GB_ERROR &error)
Definition: arbdb.cxx:1155
GB_BUFFER GB_give_buffer(size_t size)
Definition: arbdb.cxx:311
void GBS_fwrite_string(const char *strngi, FILE *out)
Definition: adstring.cxx:807
char * GB_find_latest_file(const char *dir, const char *mask)
Definition: adfile.cxx:152
GB_ERROR GB_save_as(GBDATA *gbd, const char *path, const char *savetype)
NOT4PERL uint8_t GB_read_lossless_byte(GBDATA *gbd, GB_ERROR &error)
Definition: arbdb.cxx:1093
long GBS_read_numhash(GB_NUMHASH *hs, long key)
Definition: adhash.cxx:679
char * GBS_trim(const char *str)
Definition: adstring.cxx:947
bool GB_is_ancestor_of(GBDATA *gb_ancestor, GBDATA *gb_descendant)
Definition: arbdb.cxx:1744
char * GB_get_subfields(GBDATA *gbd)
Definition: arbdb.cxx:2225
GBDATA * GB_clone(GBDATA *gb_destCont, GBDATA *gb_source)
Definition: arbdb.cxx:2196
void GB_disable_path(GBDATA *gbd, const char *path)
void GB_atexit(void(*exitfun)())
Definition: arbdb.cxx:402
GBDATA * GEN_next_marked_organism(GBDATA *gb_organism)
Definition: adGene.cxx:773
char * GB_map_file(const char *path, int writeable)
Definition: adsocket.cxx:344
static void error(const char *msg)
Definition: mkptypes.cxx:96
GBDATA * GB_get_root(GBDATA *gbd)
Definition: arbdb.cxx:1740
GB_ERROR GB_abort_transaction(GBDATA *gbd)
Definition: arbdb.cxx:2539
char * GB_read_bits(GBDATA *gbd, char c_0, char c_1)
Definition: arbdb.cxx:958
FILE * GB_fopen_tempfile(const char *filename, const char *fmode, char **res_fullname)
Definition: adsocket.cxx:1176
GB_CSTR GB_path_in_ARBHOME(const char *relative_path)
Definition: adsocket.cxx:1149
void GB_set_remote_action(GBDATA *gbd, bool in_action)
Definition: adcomm.cxx:1656
void GB_flush_cache(GBDATA *gbd)
Definition: adcache.cxx:226
GBQUARK GB_find_or_create_quark(GBDATA *gbd, const char *key)
Definition: arbdb.cxx:1695
GB_CSTR GB_mapfile(GBDATA *gb_main)
GBDATA * GB_searchOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value)
Definition: adquery.cxx:569
GB_ULONG GB_time_of_day(void)
Definition: adsocket.cxx:357
void GBS_hash_do_sorted_loop(GB_HASH *hs, gb_hash_loop_type func, gbs_hash_compare_function sorter, void *client_data)
Definition: adhash.cxx:629
bool GB_inside_remote_action(GBDATA *gbd)
Definition: adcomm.cxx:1668
const char * GEN_origin_organism(GBDATA *gb_pseudo)
Definition: adGene.cxx:549
size_t GBS_hash_elements(const GB_HASH *hs)
Definition: adhash.cxx:570
GB_ERROR GB_write_lossless_int(GBDATA *gbd, int32_t i)
Definition: arbdb.cxx:1523
float GB_read_float(GBDATA *gbd)
Definition: arbdb.cxx:744
char * GB_undo_info(GBDATA *gb_main, GB_UNDO_TYPE type)
Definition: adindex.cxx:806
long GB_read_clients(GBDATA *gbd)
Definition: adcomm.cxx:1682
GB_UINT4 * GB_read_ints(GBDATA *gbd)
Definition: arbdb.cxx:1013
Definition: adsocket.cxx:686
int GB_random(int range)
Definition: admath.cxx:88
GB_CSTR GB_getenvDOCPATH(void)
Definition: adsocket.cxx:676
GBDATA * GEN_find_gene_data(GBDATA *gb_species)
Definition: adGene.cxx:50
GB_ERROR GB_set_dictionary(GBDATA *gb_main, const char *key, const DictData *dd)
Definition: adsystem.cxx:295
GBDATA * GEN_next_organism(GBDATA *gb_organism)
Definition: adGene.cxx:745
GBDATA * GB_find_sub_by_quark(GBDATA *father, GBQUARK key_quark, GBDATA *after, size_t skip_over)
Definition: adquery.cxx:174
bool GB_is_container(GBDATA *gbd)
Definition: arbdb.cxx:1648
GB_ERROR GEN_write_position(GBDATA *gb_gene, const GEN_position *pos, long seqLength)
Definition: adGene.cxx:325
void GBS_dynaval_free(long val)
Definition: adhash.cxx:278
GBQUARK GB_get_quark(GBDATA *gbd)
Definition: arbdb.cxx:1703
NOT4PERL GB_ERROR GB_xcmd(const char *cmd, XCMD_TYPE exectype) __ATTR__USERESULT_TODO
Definition: adsocket.cxx:906
const char *(* gb_getenv_hook)(const char *varname)
Definition: arbdb.h:138
GB_ERROR GBCMS_open(const char *path, long timeout, GBDATA *gb_main)
Definition: adcomm.cxx:198
int GB_read_flag(GBDATA *gbd)
Definition: arbdb.cxx:2796
double GB_log_fak(int n)
Definition: admath.cxx:21
GB_ERROR GB_copy_std(GBDATA *dest, GBDATA *source)
Definition: arbdb.cxx:2174
GB_CSTR GB_path_in_ARBLIB(const char *relative_path)
Definition: adsocket.cxx:1156
GB_ERROR GB_write_security_write(GBDATA *gbd, unsigned long level)
Definition: arbdb.cxx:1584
Definition: arbdb.h:99
GBDATA * GB_followingEntry(GBDATA *entry, size_t skip_over)
Definition: adquery.cxx:344
int GB_nsons(GBDATA *gbd)
Definition: arbdb.cxx:2636
GB_ERROR GB_pop_transaction(GBDATA *gbd)
Definition: arbdb.cxx:2524
GB_CSTR GB_getcwd(void)
Definition: adfile.cxx:24
char * GBS_log_action_to(const char *comment, const char *action, bool stamp)
Definition: adstring.cxx:976
bool GB_has_key(GBDATA *gbd, const char *key)
Definition: arbdb.cxx:1707
void GBS_read_dir(StrArray &names, const char *dir, const char *mask)
Definition: adfile.cxx:213
GB_ERROR GB_save_quick_as(GBDATA *gbd, const char *path)
GBDATA * GB_following_marked(GBDATA *gbd, const char *keystring, size_t skip_over)
Definition: adquery.cxx:663
GBDATA * GB_brother(GBDATA *entry, const char *key)
Definition: adquery.cxx:361
GB_CUINT4 * GB_read_ints_pntr(GBDATA *gbd)
Definition: arbdb.cxx:979
GB_ERROR GB_write_float(GBDATA *gbd, float f)
Definition: arbdb.cxx:1281
GB_ERROR GB_save_in_arbprop(GBDATA *gb, const char *path, const char *savetype)
Definition: arb_core.h:30
GB_ERROR GB_write_security_read(GBDATA *gbd, unsigned long level)
Definition: arbdb.cxx:1595
void GBS_free_numhash(GB_NUMHASH *hs)
Definition: adhash.cxx:742
GB_ERROR GBT_check_arb_file(const char *name) __ATTR__USERESULT
Definition: ad_load.cxx:1369
GB_ERROR GB_create_index(GBDATA *gbd, const char *key, GB_CASE case_sens, long estimated_size) __ATTR__USERESULT
Definition: adindex.cxx:117
GB_ERROR GB_write_int(GBDATA *gbd, long i)
Definition: arbdb.cxx:1250
void(* gb_hash_const_loop_type)(const char *key, long val, void *client_data)
Definition: arbdb.h:131
void GB_init_gb(void)
Definition: arbdb.cxx:512
void GB_print_debug_information(struct Unfixed_cb_parameter *, GBDATA *gb_main)
Definition: arbdb.cxx:2814
void GBS_hash_do_loop(GB_HASH *hs, gb_hash_loop_type func, void *client_data)
Definition: adhash.cxx:545
long GB_last_saved_clock(GBDATA *gb_main)
GBDATA * GEN_next_pseudo_species(GBDATA *gb_species)
Definition: adGene.cxx:691
long int flag
Definition: f2c.h:39
char * GBS_unescape_string(const char *str, const char *escaped_chars, char escape_char)
Definition: adstring.cxx:175
GB_CSTR GB_getenv(const char *env)
Definition: adsocket.cxx:709
GB_CSTR GB_append_suffix(const char *name, const char *suffix)
Definition: adsocket.cxx:984
GB_CSTR GB_concat_full_path(const char *anypath_left, const char *anypath_right)
Definition: adsocket.cxx:1103
const char *(* gb_export_sequence_cb)(GBDATA *gb_species, size_t *seq_len, GB_ERROR *error)
Definition: arbdb.h:134
long GB_number_of_marked_subentries(GBDATA *gbd)
Definition: adquery.cxx:635
char * GB_unique_filename(const char *name_prefix, const char *suffix)
Definition: adsocket.cxx:1233
Definition: adindex.cxx:755
char * GB_lib_file(bool warn_when_not_found, const char *libprefix, const char *filename)
Definition: adfile.cxx:198
GEN_position * GEN_new_position(int parts, bool joinable)
Definition: adGene.cxx:155
const float GB_CFLOAT
Definition: arbdb_base.h:43
GB_ERROR GB_set_temporary(GBDATA *gbd) __ATTR__USERESULT
Definition: arbdb.cxx:2282
int GB_read_security_read(GBDATA *gbd)
Definition: arbdb.cxx:1576
int GB_read_security_delete(GBDATA *gbd)
Definition: arbdb.cxx:1580
double GB_read_from_floats(GBDATA *gbd, long index)
Definition: arbdb.cxx:1203
const char *const * GBS_get_arb_tcp_entries(const char *matching)
Definition: adtcp.cxx:390
GB_ULONG GB_get_usable_memory(void)
Definition: adsocket.cxx:865
GB_CSTR GB_concat_path(GB_CSTR anypath_left, GB_CSTR anypath_right)
Definition: adsocket.cxx:1069
GBDATA * GEN_create_nonexisting_gene(GBDATA *gb_species, const char *name)
Definition: adGene.cxx:96
char * GEN_global_gene_identifier(GBDATA *gb_gene, GBDATA *gb_organism)
Definition: adGene.cxx:783
GB_ULONG GB_last_saved_time(GBDATA *gb_main)
GBDATA * EXP_find_or_create_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name)
char * GBS_hashtab_2_string(const GB_HASH *hash)
Definition: adhash.cxx:368
GB_CSTR GB_unfold_in_directory(const char *relative_directory, const char *path)
Definition: adsocket.cxx:1123
GBDATA * GB_open(const char *path, const char *opent)
Definition: ad_load.cxx:1363
void GB_write_flag(GBDATA *gbd, long flag)
Definition: arbdb.cxx:2773
GB_UNDO_TYPE GB_get_requested_undo_type(GBDATA *gb_main)
Definition: adindex.cxx:749
GBDATA * GB_searchOrCreate_float(GBDATA *gb_container, const char *fieldpath, float default_value)
Definition: adquery.cxx:591
GBDATA * GEN_find_origin_organism(GBDATA *gb_pseudo, const GB_HASH *organism_hash)
Definition: adGene.cxx:643
GB_BUFFER GB_increase_buffer(size_t size)
Definition: arbdb.cxx:316
const char * GBS_nameserver_tag(const char *add_field)
Definition: adtcp.cxx:303
void GB_write_user_flag(GBDATA *gbd, unsigned char user_bit, bool state)
Definition: arbdb.cxx:2765
GBDATA * GB_next_marked(GBDATA *gbd, const char *keystring)
Definition: adquery.cxx:670
GB_CSTR GB_getenvUSER(void)
Definition: adsocket.cxx:545
void GB_touch(GBDATA *gbd)
Definition: arbdb.cxx:2802
GB_CSTR GB_path_in_HOME(const char *relative_path)
Definition: adsocket.cxx:1163
GBQUARK GB_find_existing_quark(GBDATA *gbd, const char *key)
Definition: arbdb.cxx:1690
GB_ERROR GB_write_ints(GBDATA *gbd, const GB_UINT4 *i, long size)
Definition: arbdb.cxx:1439
Definition: attributes.h:58
int GB_read_byte(GBDATA *gbd)
Definition: arbdb.cxx:734
char * GB_read_string(GBDATA *gbd)
Definition: arbdb.cxx:909
GB_ERROR GB_write_byte(GBDATA *gbd, int i)
Definition: arbdb.cxx:1238
GB_BUFFER GB_give_buffer2(long size)
Definition: arbdb.cxx:334
GB_ERROR GB_textprint(const char *path) __ATTR__USERESULT
Definition: adsocket.cxx:363
GB_ERROR GB_copy_dropMarksAndTempstate(GBDATA *dest, GBDATA *source)
Definition: arbdb.cxx:2163
Definition: adsocket.cxx:659
GB_ERROR GB_write_security_delete(GBDATA *gbd, unsigned long level)
Definition: arbdb.cxx:1605
GB_CSTR GB_concat_path_in_ARBLIB(const char *relative_path_left, const char *anypath_right)
Definition: adsocket.cxx:1159
char * GB_arbtcpdat_path(void)
Definition: adtcp.cxx:215
uint32_t GBS_checksum(const char *seq, int ignore_case, const char *exclude)
Definition: adstring.cxx:352
float GB_atof(const char *str)
Definition: arbdb.cxx:190
const char * GB_get_db_path(GBDATA *gbd)
Definition: adTest.cxx:14
char * GBS_fconvert_string(char *buffer)
Definition: adstring.cxx:880
void GB_clear_user_flag(GBDATA *gbd, unsigned char user_bit)
Definition: arbdb.cxx:2760
int GBS_HCF_sortedByKey(const char *k0, long dummy_1x, const char *k1, long dummy_2x)
Definition: adhash.cxx:653
GBDATA * GB_find_string(GBDATA *gbd, const char *key, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs)
Definition: adquery.cxx:302
NOT4PERL int GB_give_buffer_size(void)
Definition: arbdb.cxx:330
long GB_read_clock(GBDATA *gbd)
Definition: arbdb.cxx:1714
char * GBS_eval_env(GB_CSTR p)
Definition: adstring.cxx:212
void GB_split_full_path(const char *fullpath, char **res_dir, char **res_fullname, char **res_name_only, char **res_suffix)
Definition: adsocket.cxx:1268
NOT4PERL void GB_dump(GBDATA *gbd)
Definition: adTest.cxx:187
GBDATA * GEN_first_gene(GBDATA *gb_species)
Definition: adGene.cxx:130
GB_ERROR GB_write_floats(GBDATA *gbd, const float *f, long size)
Definition: arbdb.cxx:1457
GBDATA * EXP_get_experiment_data(GBDATA *gb_species)
bool GB_host_is_local(const char *hostname)
Definition: adsocket.cxx:746
Definition: adsocket.cxx:593
GB_CSTR GB_read_bits_pntr(GBDATA *gbd, char c_0, char c_1)
Definition: arbdb.cxx:926
GB_HASH * GBT_create_organism_hash(GBDATA *gb_main)
Definition: adhashtools.cxx:48
GB_ERROR GB_write_lossless_float(GBDATA *gbd, float f)
Definition: arbdb.cxx:1546
GBDATA * EXP_find_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name)
long GB_read_from_ints(GBDATA *gbd, long index)
Definition: arbdb.cxx:1186
GB_ERROR GB_test_delete_possible(GBDATA *gb_obj)
Definition: arbdb.cxx:1904
GB_HASH * GBT_create_species_hash_sized(GBDATA *gb_main, long species_count)
Definition: adhashtools.cxx:32
char * GB_command_interpreter(const char *str, const char *commands, GBDATA *gb_main)
Definition: gb_aci.cxx:453
GBDATA * GEN_expect_gene(GBDATA *gb_species, const char *name)
Definition: adGene.cxx:72
void GB_set_verbose(void)
Definition: ad_load.cxx:31
NOT4PERL char * GB_command_interpreter_in_env(const char *str, const char *commands, const GBL_call_env &callEnv)
Definition: gb_aci.cxx:361
Definition: arbdb.h:62
GB_ERROR GB_no_transaction(GBDATA *gbd) __ATTR__USERESULT
Definition: arbdb.cxx:2535
int GB_get_transaction_level(GBDATA *gbd)
Definition: arbdb.cxx:2590
GB_ERROR GB_request_undo_type(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT_TODO
Definition: adindex.cxx:721
const char * GB_CBUFFER
Definition: arbdb_base.h:27
GBDATA * GB_nextChild(GBDATA *child)
Definition: adquery.cxx:326
GBDATA * GB_first_marked(GBDATA *gbd, const char *keystring)
Definition: adquery.cxx:655
bool GBS_string_matches_regexp(const char *str, const GBS_string_matcher *expr)
Definition: admatch.cxx:269
bool GB_is_dictionary_compressed(GBDATA *gbd)
Definition: adcompr.cxx:869
GB_CFLOAT * GB_read_floats_pntr(GBDATA *gbd)
Definition: arbdb.cxx:1019
void GBS_add_ptserver_logentry(const char *entry)
Definition: adtcp.cxx:429
GB_CSTR GB_read_char_pntr(GBDATA *gbd)
Definition: arbdb.cxx:904
GBDATA * gb_main
Definition: adname.cxx:32
GB_ERROR GB_resort_data_base(GBDATA *gb_main, GBDATA **new_order_list, long listsize)
Definition: arbdb.cxx:2655
Definition: attributes.h:103
GB_ERROR GEN_organism_not_found(GBDATA *gb_pseudo)
Definition: adGene.cxx:565
char * GBS_merge_tagged_strings(const char *s1, const char *tag1, const char *replace1, const char *s2, const char *tag2, const char *replace2)
Definition: adstring.cxx:710
GBDATA * GEN_next_marked_gene(GBDATA *gb_gene)
Definition: adGene.cxx:146
bool GBS_string_matches(const char *str, const char *expr, GB_CASE case_sens)
Definition: admatch.cxx:193
GBDATA * GEN_first_marked_organism(GBDATA *gb_main)
Definition: adGene.cxx:767
const char * GBS_ptserver_tag(int id)
Definition: adtcp.cxx:312
GBDATA * GB_search(GBDATA *gbd, const char *fieldpath, GB_TYPES create)
Definition: adquery.cxx:531
GBDATA * GEN_first_organism(GBDATA *gb_main)
Definition: adGene.cxx:739
GB_CSTR GB_getenvARB_XTERM(void)
Definition: adsocket.cxx:523
DictData * GB_get_dictionary(GBDATA *gb_main, const char *key)
Definition: adsystem.cxx:279
bool GEN_is_genome_db(GBDATA *gb_main, int default_value)
Definition: adGene.cxx:20
GEN_position * GEN_read_position(GBDATA *gb_gene)
Definition: adGene.cxx:250
const char * GB_get_supported_compression_flags(bool verboose)
size_t length
const unsigned int GB_CUINT4
Definition: arbdb_base.h:40
GB_ERROR GB_write_pointer(GBDATA *gbd, GBDATA *pointer)
Definition: arbdb.cxx:1269
GB_CSTR GB_unfold_path(const char *pwd_envar, const char *path)
Definition: adsocket.cxx:1132
bool GEN_is_pseudo_gene_species(GBDATA *gb_species)
Definition: adGene.cxx:558
Definition: adsocket.cxx:628
GBDATA * GEN_first_marked_pseudo_species(GBDATA *gb_main)
Definition: adGene.cxx:711
GB_ERROR GB_copy_overlay(GBDATA *dest, GBDATA *source)
Definition: arbdb.cxx:2182
const char * GB_CSTR
Definition: arbdb_base.h:25
char GB_type_2_char(GB_TYPES type)
Definition: arbdb.cxx:2809
Definition: arbdb_base.h:30
char * GB_BUFFER
Definition: arbdb_base.h:26
GBDATA * GEN_first_gene_rel_gene_data(GBDATA *gb_gene_data)
Definition: adGene.cxx:134
long GBS_read_hash(const GB_HASH *hs, const char *key)
Definition: adhash.cxx:392
GBDATA * GB_entry(GBDATA *father, const char *key)
Definition: adquery.cxx:334
GB_ERROR GB_create_directory(const char *path)
GB_ERROR GB_save_quick(GBDATA *gbd, const char *refpath)
bool GB_supports_mapfile(void)
Definition: admap.cxx:644
GBDATA * GEN_find_pseudo_species(GBDATA *gb_main, const char *organism_name, const char *gene_name, const GB_HASH *pseudo_hash)
Definition: adGene.cxx:613
void GB_close(GBDATA *gbd)
Definition: arbdb.cxx:655
void GBS_optimize_hash(const GB_HASH *hs)
Definition: adhash.cxx:316
GB_HASH * GBS_create_hash(long estimated_elements, GB_CASE case_sens)
Definition: adhash.cxx:253
GBDATA * GEN_find_origin_gene(GBDATA *gb_pseudo, const GB_HASH *organism_hash)
Definition: adGene.cxx:666
char * GB_read_file(const char *path)
Definition: adsocket.cxx:287
bool GB_in_temporary_branch(GBDATA *gbd)
Definition: arbdb.cxx:2310
GB_ERROR GB_write_autoconv_string(GBDATA *gbd, const char *val)
Definition: arbdb.cxx:1479
GB_write_int const char s
Definition: AW_awar.cxx:154