Changeset 8285

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Timestamp:
08/12/11 18:05:33 (6 months ago)
Author:
westram
Message:
  • automatic changes to generated headers caused by [8284]
Location:
trunk
Files:
6 modified

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Unmodified
Added
Removed

  • trunk/ARBDB/ad_prot.h

    r8253 r8285  
    1313#endif 
    1414 
     15 
     16/* adExperiment.cxx */ 
     17GBDATA *EXP_get_experiment_data(GBDATA *gb_species); 
     18GBDATA *EXP_find_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name); 
     19GBDATA *EXP_find_experiment(GBDATA *gb_species, const char *name); 
     20GBDATA *EXP_expect_experiment(GBDATA *gb_species, const char *name); 
     21GBDATA *EXP_first_experiment_rel_exp_data(GBDATA *gb_experiment_data); 
     22GBDATA *EXP_next_experiment(GBDATA *gb_experiment); 
     23GBDATA *EXP_find_or_create_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name); 
     24 
     25/* adGene.cxx */ 
     26bool GEN_is_genome_db(GBDATA *gb_main, int default_value); 
     27GBDATA *GEN_findOrCreate_gene_data(GBDATA *gb_species); 
     28GBDATA *GEN_find_gene_data(GBDATA *gb_species); 
     29GBDATA *GEN_expect_gene_data(GBDATA *gb_species); 
     30GBDATA *GEN_find_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name); 
     31GBDATA *GEN_find_gene(GBDATA *gb_species, const char *name); 
     32GBDATA *GEN_create_nonexisting_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name); 
     33GBDATA *GEN_create_nonexisting_gene(GBDATA *gb_species, const char *name); 
     34GBDATA *GEN_find_or_create_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name); 
     35GBDATA *GEN_find_or_create_gene(GBDATA *gb_species, const char *name); 
     36GBDATA *GEN_first_gene(GBDATA *gb_species); 
     37GBDATA *GEN_first_gene_rel_gene_data(GBDATA *gb_gene_data); 
     38GBDATA *GEN_next_gene(GBDATA *gb_gene); 
     39GBDATA *GEN_first_marked_gene(GBDATA *gb_species); 
     40GBDATA *GEN_next_marked_gene(GBDATA *gb_gene); 
     41GEN_position *GEN_new_position(int parts, bool joinable); 
     42void GEN_use_uncertainties(GEN_position *pos); 
     43void GEN_free_position(GEN_position *pos); 
     44GEN_position *GEN_read_position(GBDATA *gb_gene); 
     45GB_ERROR GEN_write_position(GBDATA *gb_gene, const GEN_position *pos); 
     46void GEN_sortAndMergeLocationParts(GEN_position *location); 
     47const char *GEN_origin_organism(GBDATA *gb_pseudo); 
     48const char *GEN_origin_gene(GBDATA *gb_pseudo); 
     49bool GEN_is_pseudo_gene_species(GBDATA *gb_species); 
     50GB_ERROR GEN_organism_not_found(GBDATA *gb_pseudo); 
     51GBDATA *GEN_read_pseudo_species_from_hash(GB_HASH *pseudo_hash, const char *organism_name, const char *gene_name); 
     52void GEN_add_pseudo_species_to_hash(GBDATA *gb_pseudo, GB_HASH *pseudo_hash); 
     53GB_HASH *GEN_create_pseudo_species_hash(GBDATA *gb_main, int additionalSize); 
     54GBDATA *GEN_find_pseudo_species(GBDATA *gb_main, const char *organism_name, const char *gene_name, GB_HASH *pseudo_hash); 
     55GBDATA *GEN_find_origin_organism(GBDATA *gb_pseudo, GB_HASH *organism_hash); 
     56GBDATA *GEN_find_origin_gene(GBDATA *gb_pseudo, GB_HASH *organism_hash); 
     57GBDATA *GEN_first_pseudo_species(GBDATA *gb_main); 
     58GBDATA *GEN_first_pseudo_species_rel_species_data(GBDATA *gb_species_data); 
     59GBDATA *GEN_next_pseudo_species(GBDATA *gb_species); 
     60GBDATA *GEN_first_marked_pseudo_species(GBDATA *gb_main); 
     61GBDATA *GEN_next_marked_pseudo_species(GBDATA *gb_species); 
     62bool GEN_is_organism(GBDATA *gb_species); 
     63GBDATA *GEN_find_organism(GBDATA *gb_main, const char *name); 
     64GBDATA *GEN_first_organism(GBDATA *gb_main); 
     65GBDATA *GEN_next_organism(GBDATA *gb_organism); 
     66long GEN_get_organism_count(GBDATA *gb_main); 
     67GBDATA *GEN_first_marked_organism(GBDATA *gb_main); 
     68GBDATA *GEN_next_marked_organism(GBDATA *gb_organism); 
     69char *GEN_global_gene_identifier(GBDATA *gb_gene, GBDATA *gb_organism); 
    1570 
    1671/* adTest.cxx */ 
    … …  
    3893GB_ERROR GB_save_quick(GBDATA *gb, const char *refpath); 
    3994void GB_disable_path(GBDATA *gbd, const char *path); 
     95 
     96/* adcache.cxx */ 
     97char *GB_set_cache_size(GBDATA *gbd, size_t size); 
    4098 
    4199/* adcomm.cxx */ 
    … …  
    50108GB_ERROR GB_install_pid(int mode); 
    51109const char *GB_date_string(void); 
     110 
     111/* adcompr.cxx */ 
     112bool GB_is_dictionary_compressed(GBDATA *gbd); 
     113 
     114/* adfile.cxx */ 
     115GB_CSTR GB_getcwd(void); 
     116char *GB_find_all_files(const char *dir, const char *mask, bool filename_only); 
     117char *GB_find_latest_file(const char *dir, const char *mask); 
     118const char *GB_existing_file(const char *file, bool warn_when_not_found); 
     119char *GB_lib_file(bool warn_when_not_found, const char *libprefix, const char *filename); 
     120char *GB_property_file(bool warn_when_not_found, const char *filename); 
     121void GBS_read_dir(StrArray &names, const char *dir, const char *mask); 
     122bool GB_test_textfile_difflines(const char *file1, const char *file2, int expected_difflines, int special_mode); 
     123size_t GB_test_mem_equal(const unsigned char *buf1, const unsigned char *buf2, size_t common); 
     124bool GB_test_files_equal(const char *file1, const char *file2); 
     125void GBT_transform_names(StrArray &dest, const StrArray &source, char *transform (const char *, void *), void *client_data); 
    52126 
    53127/* adhash.cxx */ 
    … …  
    81155void GBS_free_numhash(GB_NUMHASH *hs); 
    82156 
    83 /* adcache.cxx */ 
    84 char *GB_set_cache_size(GBDATA *gbd, size_t size); 
    85  
    86157/* adhashtools.cxx */ 
    87158void GBT_add_item_to_hash(GBDATA *gb_item, GB_HASH *item_hash); 
    … …  
    92163GB_HASH *GBT_create_organism_hash(GBDATA *gb_main); 
    93164 
     165/* adindex.cxx */ 
     166GB_ERROR GB_create_index(GBDATA *gbd, const char *key, GB_CASE case_sens, long estimated_size) __ATTR__USERESULT; 
     167NOT4PERL void GB_dump_indices(GBDATA *gbd); 
     168GB_ERROR GB_request_undo_type(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT_TODO; 
     169GB_UNDO_TYPE GB_get_requested_undo_type(GBDATA *gb_main); 
     170GB_ERROR GB_undo(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT; 
     171char *GB_undo_info(GBDATA *gb_main, GB_UNDO_TYPE type); 
     172GB_ERROR GB_set_undo_mem(GBDATA *gbd, long memsize); 
     173 
    94174/* adlang1.cxx */ 
    95175NOT4PERL void GB_set_export_sequence_hook(gb_export_sequence_cb escb); 
    … …  
    105185NOT4PERL void *GB_recalloc(void *ptr, unsigned int oelem, unsigned int nelem, unsigned int elsize); 
    106186void GB_memerr(void); 
     187 
     188/* admap.cxx */ 
     189bool GB_supports_mapfile(void); 
    107190 
    108191/* admatch.cxx */ 
    … …  
    130213/* adperl.cxx */ 
    131214GB_ERROR GBC_await_error(void); 
     215 
     216/* adquery.cxx */ 
     217const char *GB_get_GBDATA_path(GBDATA *gbd); 
     218GBDATA *GB_find_sub_by_quark(GBDATA *father, GBQUARK key_quark, GBDATA *after, size_t skip_over); 
     219NOT4PERL GBDATA *GB_find_subcontent_by_quark(GBDATA *father, GBQUARK key_quark, GB_TYPES type, const char *val, GB_CASE case_sens, GBDATA *after, size_t skip_over); 
     220GBDATA *GB_find(GBDATA *gbd, const char *key, GB_SEARCH_TYPE gbs); 
     221GBDATA *GB_find_string(GBDATA *gbd, const char *key, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs); 
     222NOT4PERL GBDATA *GB_find_int(GBDATA *gbd, const char *key, long val, GB_SEARCH_TYPE gbs); 
     223GBDATA *GB_child(GBDATA *father); 
     224GBDATA *GB_nextChild(GBDATA *child); 
     225GBDATA *GB_entry(GBDATA *father, const char *key); 
     226GBDATA *GB_nextEntry(GBDATA *entry); 
     227GBDATA *GB_followingEntry(GBDATA *entry, size_t skip_over); 
     228GBDATA *GB_brother(GBDATA *entry, const char *key); 
     229char *GB_first_non_key_char(const char *str); 
     230GBDATA *GB_search(GBDATA *gbd, const char *fieldpath, GB_TYPES create); 
     231GBDATA *GB_searchOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value); 
     232GBDATA *GB_searchOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value); 
     233GBDATA *GB_searchOrCreate_float(GBDATA *gb_container, const char *fieldpath, double default_value); 
     234GBDATA *GB_search_last_son(GBDATA *gbd); 
     235long GB_number_of_marked_subentries(GBDATA *gbd); 
     236GBDATA *GB_first_marked(GBDATA *gbd, const char *keystring); 
     237GBDATA *GB_following_marked(GBDATA *gbd, const char *keystring, size_t skip_over); 
     238GBDATA *GB_next_marked(GBDATA *gbd, const char *keystring); 
     239char *GB_command_interpreter(GBDATA *gb_main, const char *str, const char *commands, GBDATA *gbd, const char *default_tree_name); 
     240 
     241/* adsocket.cxx */ 
     242void GB_usleep(long usec); 
     243char *GB_read_fp(FILE *in); 
     244char *GB_read_file(const char *path); 
     245char *GB_map_FILE(FILE *in, int writeable); 
     246char *GB_map_file(const char *path, int writeable); 
     247GB_ULONG GB_time_of_day(void); 
     248long GB_last_saved_clock(GBDATA *gb_main); 
     249GB_ULONG GB_last_saved_time(GBDATA *gb_main); 
     250GB_ERROR GB_textprint(const char *path) __ATTR__USERESULT; 
     251GB_ERROR GB_xterm(void) __ATTR__USERESULT; 
     252GB_ERROR GB_xcmd(const char *cmd, bool background, bool wait_only_if_error) __ATTR__USERESULT_TODO; 
     253char *GB_executable(GB_CSTR exe_name); 
     254char *GB_find_executable(GB_CSTR description_of_executable, ...) __ATTR__SENTINEL; 
     255void GB_setenv(const char *var, const char *value); 
     256GB_CSTR GB_getenvARB_XTERM(void); 
     257GB_CSTR GB_getenvARB_XCMD(void); 
     258GB_CSTR GB_getenvUSER(void); 
     259GB_CSTR GB_getenvHOME(void); 
     260GB_CSTR GB_getenvARBHOME(void); 
     261GB_CSTR GB_getenvARBMACRO(void); 
     262GB_CSTR GB_getenvARBMACROHOME(void); 
     263GB_CSTR GB_getenvARBCONFIG(void); 
     264GB_CSTR GB_getenvPATH(void); 
     265GB_CSTR GB_getenvARB_GS(void); 
     266GB_CSTR GB_getenvARB_PDFVIEW(void); 
     267GB_CSTR GB_getenvARB_TEXTEDIT(void); 
     268GB_CSTR GB_getenvDOCPATH(void); 
     269GB_CSTR GB_getenvHTMLDOCPATH(void); 
     270NOT4PERL gb_getenv_hook GB_install_getenv_hook(gb_getenv_hook hook); 
     271GB_CSTR GB_getenv(const char *env); 
     272bool GB_host_is_local(const char *hostname); 
     273GB_ULONG GB_get_physical_memory(void); 
     274GB_CSTR GB_append_suffix(const char *name, const char *suffix); 
     275GB_CSTR GB_canonical_path(const char *anypath); 
     276GB_CSTR GB_concat_path(GB_CSTR anypath_left, GB_CSTR anypath_right); 
     277GB_CSTR GB_concat_full_path(const char *anypath_left, const char *anypath_right); 
     278GB_CSTR GB_unfold_path(const char *pwd_envar, const char *path); 
     279GB_CSTR GB_path_in_ARBHOME(const char *relative_path); 
     280GB_CSTR GB_path_in_ARBLIB(const char *relative_path); 
     281GB_CSTR GB_path_in_arbprop(const char *relative_path); 
     282GB_CSTR GB_path_in_ARBHOME(const char *relative_path_left, const char *anypath_right); 
     283GB_CSTR GB_path_in_ARBLIB(const char *relative_path_left, const char *anypath_right); 
     284FILE *GB_fopen_tempfile(const char *filename, const char *fmode, char **res_fullname); 
     285char *GB_create_tempfile(const char *name); 
     286char *GB_unique_filename(const char *name_prefix, const char *suffix); 
     287void GB_remove_on_exit(const char *filename); 
     288void GB_split_full_path(const char *fullpath, char **res_dir, char **res_fullname, char **res_name_only, char **res_suffix); 
    132289 
    133290/* adstring.cxx */ 
    … …  
    158315char *GBS_trim(const char *str); 
    159316char *GBS_log_dated_action_to(const char *comment, const char *action); 
    160  
    161 /* adfile.cxx */ 
    162 GB_CSTR GB_getcwd(void); 
    163 char *GB_find_all_files(const char *dir, const char *mask, bool filename_only); 
    164 char *GB_find_latest_file(const char *dir, const char *mask); 
    165 const char *GB_existing_file(const char *file, bool warn_when_not_found); 
    166 char *GB_lib_file(bool warn_when_not_found, const char *libprefix, const char *filename); 
    167 char *GB_property_file(bool warn_when_not_found, const char *filename); 
    168 void GBS_read_dir(StrArray &names, const char *dir, const char *mask); 
    169 bool GB_test_textfile_difflines(const char *file1, const char *file2, int expected_difflines, int special_mode); 
    170 size_t GB_test_mem_equal(const unsigned char *buf1, const unsigned char *buf2, size_t common); 
    171 bool GB_test_files_equal(const char *file1, const char *file2); 
    172 void GBT_transform_names(StrArray &dest, const StrArray &source, char *transform (const char *, void *), void *client_data); 
    173317 
    174318/* adsystem.cxx */ 
    … …  
    326470long GB_number_of_subentries(GBDATA *gbd); 
    327471 
    328 /* adExperiment.cxx */ 
    329 GBDATA *EXP_get_experiment_data(GBDATA *gb_species); 
    330 GBDATA *EXP_find_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name); 
    331 GBDATA *EXP_find_experiment(GBDATA *gb_species, const char *name); 
    332 GBDATA *EXP_expect_experiment(GBDATA *gb_species, const char *name); 
    333 GBDATA *EXP_first_experiment_rel_exp_data(GBDATA *gb_experiment_data); 
    334 GBDATA *EXP_next_experiment(GBDATA *gb_experiment); 
    335 GBDATA *EXP_find_or_create_experiment_rel_exp_data(GBDATA *gb_experiment_data, const char *name); 
    336  
    337 /* adGene.cxx */ 
    338 bool GEN_is_genome_db(GBDATA *gb_main, int default_value); 
    339 GBDATA *GEN_findOrCreate_gene_data(GBDATA *gb_species); 
    340 GBDATA *GEN_find_gene_data(GBDATA *gb_species); 
    341 GBDATA *GEN_expect_gene_data(GBDATA *gb_species); 
    342 GBDATA *GEN_find_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name); 
    343 GBDATA *GEN_find_gene(GBDATA *gb_species, const char *name); 
    344 GBDATA *GEN_create_nonexisting_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name); 
    345 GBDATA *GEN_create_nonexisting_gene(GBDATA *gb_species, const char *name); 
    346 GBDATA *GEN_find_or_create_gene_rel_gene_data(GBDATA *gb_gene_data, const char *name); 
    347 GBDATA *GEN_find_or_create_gene(GBDATA *gb_species, const char *name); 
    348 GBDATA *GEN_first_gene(GBDATA *gb_species); 
    349 GBDATA *GEN_first_gene_rel_gene_data(GBDATA *gb_gene_data); 
    350 GBDATA *GEN_next_gene(GBDATA *gb_gene); 
    351 GBDATA *GEN_first_marked_gene(GBDATA *gb_species); 
    352 GBDATA *GEN_next_marked_gene(GBDATA *gb_gene); 
    353 GEN_position *GEN_new_position(int parts, bool joinable); 
    354 void GEN_use_uncertainties(GEN_position *pos); 
    355 void GEN_free_position(GEN_position *pos); 
    356 GEN_position *GEN_read_position(GBDATA *gb_gene); 
    357 GB_ERROR GEN_write_position(GBDATA *gb_gene, const GEN_position *pos); 
    358 void GEN_sortAndMergeLocationParts(GEN_position *location); 
    359 const char *GEN_origin_organism(GBDATA *gb_pseudo); 
    360 const char *GEN_origin_gene(GBDATA *gb_pseudo); 
    361 bool GEN_is_pseudo_gene_species(GBDATA *gb_species); 
    362 GB_ERROR GEN_organism_not_found(GBDATA *gb_pseudo); 
    363 GBDATA *GEN_read_pseudo_species_from_hash(GB_HASH *pseudo_hash, const char *organism_name, const char *gene_name); 
    364 void GEN_add_pseudo_species_to_hash(GBDATA *gb_pseudo, GB_HASH *pseudo_hash); 
    365 GB_HASH *GEN_create_pseudo_species_hash(GBDATA *gb_main, int additionalSize); 
    366 GBDATA *GEN_find_pseudo_species(GBDATA *gb_main, const char *organism_name, const char *gene_name, GB_HASH *pseudo_hash); 
    367 GBDATA *GEN_find_origin_organism(GBDATA *gb_pseudo, GB_HASH *organism_hash); 
    368 GBDATA *GEN_find_origin_gene(GBDATA *gb_pseudo, GB_HASH *organism_hash); 
    369 GBDATA *GEN_first_pseudo_species(GBDATA *gb_main); 
    370 GBDATA *GEN_first_pseudo_species_rel_species_data(GBDATA *gb_species_data); 
    371 GBDATA *GEN_next_pseudo_species(GBDATA *gb_species); 
    372 GBDATA *GEN_first_marked_pseudo_species(GBDATA *gb_main); 
    373 GBDATA *GEN_next_marked_pseudo_species(GBDATA *gb_species); 
    374 bool GEN_is_organism(GBDATA *gb_species); 
    375 GBDATA *GEN_find_organism(GBDATA *gb_main, const char *name); 
    376 GBDATA *GEN_first_organism(GBDATA *gb_main); 
    377 GBDATA *GEN_next_organism(GBDATA *gb_organism); 
    378 long GEN_get_organism_count(GBDATA *gb_main); 
    379 GBDATA *GEN_first_marked_organism(GBDATA *gb_main); 
    380 GBDATA *GEN_next_marked_organism(GBDATA *gb_organism); 
    381 char *GEN_global_gene_identifier(GBDATA *gb_gene, GBDATA *gb_organism); 
    382  
    383 /* adcompr.cxx */ 
    384 bool GB_is_dictionary_compressed(GBDATA *gbd); 
    385  
    386 /* adindex.cxx */ 
    387 GB_ERROR GB_create_index(GBDATA *gbd, const char *key, GB_CASE case_sens, long estimated_size) __ATTR__USERESULT; 
    388 NOT4PERL void GB_dump_indices(GBDATA *gbd); 
    389 GB_ERROR GB_request_undo_type(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT_TODO; 
    390 GB_UNDO_TYPE GB_get_requested_undo_type(GBDATA *gb_main); 
    391 GB_ERROR GB_undo(GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT; 
    392 char *GB_undo_info(GBDATA *gb_main, GB_UNDO_TYPE type); 
    393 GB_ERROR GB_set_undo_mem(GBDATA *gbd, long memsize); 
    394  
    395 /* admap.cxx */ 
    396 bool GB_supports_mapfile(void); 
    397  
    398 /* adquery.cxx */ 
    399 const char *GB_get_GBDATA_path(GBDATA *gbd); 
    400 GBDATA *GB_find_sub_by_quark(GBDATA *father, GBQUARK key_quark, GBDATA *after, size_t skip_over); 
    401 NOT4PERL GBDATA *GB_find_subcontent_by_quark(GBDATA *father, GBQUARK key_quark, GB_TYPES type, const char *val, GB_CASE case_sens, GBDATA *after, size_t skip_over); 
    402 GBDATA *GB_find(GBDATA *gbd, const char *key, GB_SEARCH_TYPE gbs); 
    403 GBDATA *GB_find_string(GBDATA *gbd, const char *key, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs); 
    404 NOT4PERL GBDATA *GB_find_int(GBDATA *gbd, const char *key, long val, GB_SEARCH_TYPE gbs); 
    405 GBDATA *GB_child(GBDATA *father); 
    406 GBDATA *GB_nextChild(GBDATA *child); 
    407 GBDATA *GB_entry(GBDATA *father, const char *key); 
    408 GBDATA *GB_nextEntry(GBDATA *entry); 
    409 GBDATA *GB_followingEntry(GBDATA *entry, size_t skip_over); 
    410 GBDATA *GB_brother(GBDATA *entry, const char *key); 
    411 char *GB_first_non_key_char(const char *str); 
    412 GBDATA *GB_search(GBDATA *gbd, const char *fieldpath, GB_TYPES create); 
    413 GBDATA *GB_searchOrCreate_string(GBDATA *gb_container, const char *fieldpath, const char *default_value); 
    414 GBDATA *GB_searchOrCreate_int(GBDATA *gb_container, const char *fieldpath, long default_value); 
    415 GBDATA *GB_searchOrCreate_float(GBDATA *gb_container, const char *fieldpath, double default_value); 
    416 GBDATA *GB_search_last_son(GBDATA *gbd); 
    417 long GB_number_of_marked_subentries(GBDATA *gbd); 
    418 GBDATA *GB_first_marked(GBDATA *gbd, const char *keystring); 
    419 GBDATA *GB_following_marked(GBDATA *gbd, const char *keystring, size_t skip_over); 
    420 GBDATA *GB_next_marked(GBDATA *gbd, const char *keystring); 
    421 char *GB_command_interpreter(GBDATA *gb_main, const char *str, const char *commands, GBDATA *gbd, const char *default_tree_name); 
    422  
    423 /* adsocket.cxx */ 
    424 void GB_usleep(long usec); 
    425 char *GB_read_fp(FILE *in); 
    426 char *GB_read_file(const char *path); 
    427 char *GB_map_FILE(FILE *in, int writeable); 
    428 char *GB_map_file(const char *path, int writeable); 
    429 GB_ULONG GB_time_of_day(void); 
    430 long GB_last_saved_clock(GBDATA *gb_main); 
    431 GB_ULONG GB_last_saved_time(GBDATA *gb_main); 
    432 GB_ERROR GB_textprint(const char *path) __ATTR__USERESULT; 
    433 GB_ERROR GB_xterm(void) __ATTR__USERESULT; 
    434 GB_ERROR GB_xcmd(const char *cmd, bool background, bool wait_only_if_error) __ATTR__USERESULT_TODO; 
    435 char *GB_executable(GB_CSTR exe_name); 
    436 char *GB_find_executable(GB_CSTR description_of_executable, ...) __ATTR__SENTINEL; 
    437 void GB_setenv(const char *var, const char *value); 
    438 GB_CSTR GB_getenvARB_XTERM(void); 
    439 GB_CSTR GB_getenvARB_XCMD(void); 
    440 GB_CSTR GB_getenvUSER(void); 
    441 GB_CSTR GB_getenvHOME(void); 
    442 GB_CSTR GB_getenvARBHOME(void); 
    443 GB_CSTR GB_getenvARBMACRO(void); 
    444 GB_CSTR GB_getenvARBMACROHOME(void); 
    445 GB_CSTR GB_getenvARBCONFIG(void); 
    446 GB_CSTR GB_getenvPATH(void); 
    447 GB_CSTR GB_getenvARB_GS(void); 
    448 GB_CSTR GB_getenvARB_PDFVIEW(void); 
    449 GB_CSTR GB_getenvARB_TEXTEDIT(void); 
    450 GB_CSTR GB_getenvDOCPATH(void); 
    451 GB_CSTR GB_getenvHTMLDOCPATH(void); 
    452 NOT4PERL gb_getenv_hook GB_install_getenv_hook(gb_getenv_hook hook); 
    453 GB_CSTR GB_getenv(const char *env); 
    454 bool GB_host_is_local(const char *hostname); 
    455 GB_ULONG GB_get_physical_memory(void); 
    456 GB_CSTR GB_append_suffix(const char *name, const char *suffix); 
    457 GB_CSTR GB_canonical_path(const char *anypath); 
    458 GB_CSTR GB_concat_path(GB_CSTR anypath_left, GB_CSTR anypath_right); 
    459 GB_CSTR GB_concat_full_path(const char *anypath_left, const char *anypath_right); 
    460 GB_CSTR GB_unfold_path(const char *pwd_envar, const char *path); 
    461 GB_CSTR GB_path_in_ARBHOME(const char *relative_path); 
    462 GB_CSTR GB_path_in_ARBLIB(const char *relative_path); 
    463 GB_CSTR GB_path_in_arbprop(const char *relative_path); 
    464 GB_CSTR GB_path_in_ARBHOME(const char *relative_path_left, const char *anypath_right); 
    465 GB_CSTR GB_path_in_ARBLIB(const char *relative_path_left, const char *anypath_right); 
    466 FILE *GB_fopen_tempfile(const char *filename, const char *fmode, char **res_fullname); 
    467 char *GB_create_tempfile(const char *name); 
    468 char *GB_unique_filename(const char *name_prefix, const char *suffix); 
    469 void GB_remove_on_exit(const char *filename); 
    470 void GB_split_full_path(const char *fullpath, char **res_dir, char **res_fullname, char **res_name_only, char **res_suffix); 
    471  
    472472#else 
    473473#error ad_prot.h included twice 

  • trunk/ARBDB/ad_t_prot.h

    r8037 r8285  
    2929NOT4PERL GB_ERROR GBT_determine_T_or_U(GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target); 
    3030NOT4PERL void GBT_reverseComplementNucSequence(char *seq, long length, char T_or_U); 
     31 
     32/* adali.cxx */ 
     33int GBT_count_alignments(GBDATA *gb_main); 
     34GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name); 
     35void GBT_get_alignment_names(ConstStrArray &names, GBDATA *gbd); 
     36GB_ERROR GBT_check_alignment_name(const char *alignment_name); 
     37GBDATA *GBT_create_alignment(GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type); 
     38NOT4PERL GB_ERROR GBT_check_alignment(GBDATA *gb_main, GBDATA *preset_alignment, GB_HASH *species_name_hash); 
     39GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest, int copy, int dele); 
     40NOT4PERL GBDATA *GBT_add_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type) __ATTR__DEPRECATED_TODO("better use GBT_create_sequence_data()"); 
     41NOT4PERL GBDATA *GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write); 
     42GB_ERROR GBT_write_sequence(GBDATA *gb_data, const char *ali_name, long ali_len, const char *sequence); 
     43GBDATA *GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name); 
     44int GBT_is_partial(GBDATA *gb_species, int default_value, int define_if_undef); 
     45GBDATA *GBT_read_sequence(GBDATA *gb_species, const char *aliname); 
     46char *GBT_get_default_alignment(GBDATA *gb_main); 
     47GB_ERROR GBT_set_default_alignment(GBDATA *gb_main, const char *alignment_name); 
     48GBDATA *GBT_get_alignment(GBDATA *gb_main, const char *aliname); 
     49long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname); 
     50GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len); 
     51int GBT_get_alignment_aligned(GBDATA *gb_main, const char *aliname); 
     52char *GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname); 
     53GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname); 
     54bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name); 
     55NOT4PERL char *GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length); 
     56char *GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator); 
    3157 
    3258/* adcolumns.cxx */ 
    … …  
    162188char *GBT_existing_tree(GBDATA *gb_main, const char *tree_name); 
    163189 
    164 /* adali.cxx */ 
    165 int GBT_count_alignments(GBDATA *gb_main); 
    166 GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name); 
    167 void GBT_get_alignment_names(ConstStrArray &names, GBDATA *gbd); 
    168 GB_ERROR GBT_check_alignment_name(const char *alignment_name); 
    169 GBDATA *GBT_create_alignment(GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type); 
    170 NOT4PERL GB_ERROR GBT_check_alignment(GBDATA *gb_main, GBDATA *preset_alignment, GB_HASH *species_name_hash); 
    171 GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest, int copy, int dele); 
    172 NOT4PERL GBDATA *GBT_add_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type) __ATTR__DEPRECATED_TODO("better use GBT_create_sequence_data()"); 
    173 NOT4PERL GBDATA *GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write); 
    174 GB_ERROR GBT_write_sequence(GBDATA *gb_data, const char *ali_name, long ali_len, const char *sequence); 
    175 GBDATA *GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name); 
    176 int GBT_is_partial(GBDATA *gb_species, int default_value, int define_if_undef); 
    177 GBDATA *GBT_read_sequence(GBDATA *gb_species, const char *aliname); 
    178 char *GBT_get_default_alignment(GBDATA *gb_main); 
    179 GB_ERROR GBT_set_default_alignment(GBDATA *gb_main, const char *alignment_name); 
    180 GBDATA *GBT_get_alignment(GBDATA *gb_main, const char *aliname); 
    181 long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname); 
    182 GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len); 
    183 int GBT_get_alignment_aligned(GBDATA *gb_main, const char *aliname); 
    184 char *GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname); 
    185 GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname); 
    186 bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name); 
    187 NOT4PERL char *GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length); 
    188 char *GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator); 
    189  
    190190#else 
    191191#error ad_t_prot.h included twice 

  • trunk/ARBDB/gb_prot.h

    r8258 r8285  
    1313#endif 
    1414 
    15  
    16 /* ad_load.cxx */ 
    17 GB_ERROR gb_read_ascii(const char *path, GBCONTAINER *gbd); 
    18 long gb_read_bin_rek(FILE *in, GBCONTAINER *gbd, long nitems, long version, long reversed); 
    19 long gb_recover_corrupt_file(GBCONTAINER *gbd, FILE *in, GB_ERROR recovery_reason); 
    20 long gb_read_bin_rek_V2(FILE *in, GBCONTAINER *gbd, long nitems, long version, long reversed, long deep); 
    21 GBDATA *gb_search_system_folder_rek(GBDATA *gbd); 
    22 void gb_search_system_folder(GBDATA *gb_main); 
    23 long gb_read_bin(FILE *in, GBCONTAINER *gbd, int diff_file_allowed); 
    24 GB_MAIN_IDX gb_make_main_idx(GB_MAIN_TYPE *Main); 
    25 void gb_release_main_idx(GB_MAIN_TYPE *Main); 
    26 GB_ERROR gb_login_remote(GB_MAIN_TYPE *Main, const char *path, const char *opent); 
    27  
    28 /* ad_save_load.cxx */ 
    29 char *gb_findExtension(char *path); 
    30 GB_CSTR gb_oldQuicksaveName(GB_CSTR path, int nr); 
    31 GB_CSTR gb_quicksaveName(GB_CSTR path, int nr); 
    32 GB_CSTR gb_mapfile_name(GB_CSTR path); 
    33 GB_CSTR gb_overwriteName(GB_CSTR path); 
    34 GB_CSTR gb_reffile_name(GB_CSTR path); 
    35 GB_ERROR gb_delete_reference(const char *master); 
    36 GB_ERROR gb_create_reference(const char *master); 
    37 GB_ERROR gb_add_reference(const char *master, const char *changes); 
    38 GB_ERROR gb_remove_all_but_main(GB_MAIN_TYPE *Main, const char *path); 
    39 long gb_ascii_2_bin(const char *source, GBDATA *gbd); 
    40 GB_BUFFER gb_bin_2_ascii(GBDATA *gbd); 
    41 long gb_read_in_long(FILE *in, long reversed); 
    42 long gb_read_number(FILE *in); 
    43 void gb_put_number(long i, FILE *out); 
    44 long gb_read_bin_error(FILE *in, GBDATA *gbd, const char *text); 
    45 long gb_write_out_long(long data, FILE *out); 
    46 int gb_is_writeable(gb_header_list *header, GBDATA *gbd, long version, long diff_save); 
    47 int gb_write_bin_sub_containers(FILE *out, GBCONTAINER *gbc, long version, long diff_save, int is_root); 
    48 long gb_write_bin_rek(FILE *out, GBDATA *gbd, long version, long diff_save, long index_of_master_file); 
    49 int gb_write_bin(FILE *out, GBDATA *gbd, long version); 
    50 char *gb_full_path(const char *path); 
    51 GB_ERROR gb_check_saveable(GBDATA *gbd, const char *path, const char *flags); 
    52  
    53 /* adcomm.cxx */ 
    54 GB_ERROR gbcm_unfold_client(GBCONTAINER *gbd, long deep, long index_pos) __ATTR__USERESULT; 
    55 GB_ERROR gbcmc_begin_sendupdate(GBDATA *gbd); 
    56 GB_ERROR gbcmc_end_sendupdate(GBDATA *gbd); 
    57 GB_ERROR gbcmc_sendupdate_create(GBDATA *gbd); 
    58 GB_ERROR gbcmc_sendupdate_delete(GBDATA *gbd); 
    59 GB_ERROR gbcmc_sendupdate_update(GBDATA *gbd, int send_headera); 
    60 GB_ERROR gbcmc_begin_transaction(GBDATA *gbd); 
    61 GB_ERROR gbcmc_init_transaction(GBCONTAINER *gbd); 
    62 GB_ERROR gbcmc_commit_transaction(GBDATA *gbd); 
    63 GB_ERROR gbcmc_abort_transaction(GBDATA *gbd); 
    64 GB_ERROR gbcms_add_to_delete_list(GBDATA *gbd); 
    65 long gbcmc_key_alloc(GBDATA *gbd, const char *key); 
    66 GB_ERROR gbcmc_send_undo_commands(GBDATA *gbd, enum gb_undo_commands command) __ATTR__USERESULT; 
    67 char *gbcmc_send_undo_info_commands(GBDATA *gbd, enum gb_undo_commands command); 
    68 GB_ERROR gbcm_login(GBCONTAINER *gb_main, const char *loginname); 
    69 GBCM_ServerResult gbcmc_close(gbcmc_comm *link); 
    70 GB_ERROR gbcm_logout(GB_MAIN_TYPE *Main, const char *loginname); 
    71  
    72 /* adhash.cxx */ 
    73 size_t gbs_get_a_prime(size_t above_or_equal_this); 
    74  
    75 /* adcache.cxx */ 
    76 void gb_init_cache(GB_MAIN_TYPE *Main); 
    77 void gb_destroy_cache(GB_MAIN_TYPE *Main); 
    78 char *gb_read_cache(GBDATA *gbd); 
    79 void gb_free_cache(GB_MAIN_TYPE *Main, GBDATA *gbd); 
    80 char *gb_alloc_cache_index(GBDATA *gbd, size_t size); 
    81 void gb_flush_cache(GBDATA *gbd); 
    82  
    83 /* adlang1.cxx */ 
    84 void gbl_install_standard_commands(GBDATA *gb_main); 
    85  
    86 /* admalloc.cxx */ 
    87 void gbm_flush_mem(void); 
    88 void gbm_init_mem(void); 
    89 void gbm_debug_mem(void); 
    90  
    91 /* adoptimize.cxx */ 
    92 GB_ERROR gb_convert_V2_to_V3(GBDATA *gb_main); 
    93 char *gb_uncompress_by_dictionary(GBDATA *gbd, GB_CSTR s_source, long size, long *new_size); 
    94 char *gb_compress_by_dictionary(GB_DICTIONARY *dict, GB_CSTR s_source, long size, long *msize, int last_flag, int search_backward, int search_forward); 
    95 GB_ERROR gb_create_dictionaries(GB_MAIN_TYPE *Main, long maxmem); 
    96  
    97 /* adstring.cxx */ 
    98 void gbs_uppercase(char *str); 
    99 void gbs_memcopy(char *dest, const char *source, long len); 
    100 char *gbs_add_path(char *path, char *name); 
    101  
    102 /* adfile.cxx */ 
    103 GB_ERROR gb_scan_directory(char *basename, gb_scandir *sd) __ATTR__USERESULT_TODO; 
    104  
    105 /* adsystem.cxx */ 
    106 GB_ERROR gb_load_dictionary_data(GBDATA *gb_main, const char *key, char **dict_data, long *size); 
    107 GB_DICTIONARY *gb_create_dict(GBDATA *gb_dict); 
    108 void gb_system_key_changed_cb(GBDATA *gbd, int *cl, GB_CB_TYPE type); 
    109 void gb_system_master_changed_cb(GBDATA *gbd, int *cl, GB_CB_TYPE type); 
    110 void gb_load_single_key_data(GBDATA *gb_main, GBQUARK q); 
    111 GB_ERROR gb_save_dictionary_data(GBDATA *gb_main, const char *key, const char *dict, int size); 
    112 GB_ERROR gb_load_key_data_and_dictionaries(GBDATA *gb_main) __ATTR__USERESULT; 
    113  
    114 /* arbdb.cxx */ 
    115 GBDATA *gb_remembered_db(void); 
    116 GB_ERROR gb_unfold(GBCONTAINER *gbd, long deep, int index_pos); 
    117 void gb_close_unclosed_DBs(void); 
    118 int gb_read_nr(GBDATA *gbd); 
    119 GB_ERROR gb_write_compressed_pntr(GBDATA *gbd, const char *s, long memsize, long stored_size); 
    120 int gb_get_compression_mask(GB_MAIN_TYPE *Main, GBQUARK key, int gb_type); 
    121 GB_ERROR gb_security_error(GBDATA *gbd) __ATTR__USERESULT; 
    122 GB_CSTR gb_read_key_pntr(GBDATA *gbd); 
    123 GBQUARK gb_key_2_existing_quark(GB_MAIN_TYPE *Main, const char *key); 
    124 GBQUARK gb_key_2_quark(GB_MAIN_TYPE *Main, const char *key); 
    125 GBDATA *gb_create(GBDATA *father, const char *key, GB_TYPES type); 
    126 GBDATA *gb_create_container(GBDATA *father, const char *key); 
    127 void gb_rename(GBCONTAINER *gbc, const char *new_key); 
    128 GB_ERROR gb_delete_force(GBDATA *source); 
    129 GB_ERROR gb_set_compression(GBDATA *source); 
    130 GB_ERROR gb_init_transaction(GBCONTAINER *gbd); 
    131 void gb_add_changed_callback_list(GBDATA *gbd, gb_transaction_save *old, GB_CB_TYPE gbtype, GB_CB func, int *clientdata); 
    132 void gb_add_delete_callback_list(GBDATA *gbd, gb_transaction_save *old, GB_CB func, int *clientdata); 
    133 GB_ERROR gb_do_callback_list(GB_MAIN_TYPE *Main); 
    134 GB_MAIN_TYPE *gb_get_main_during_cb(void); 
    135 GB_CSTR gb_read_pntr_ts(GBDATA *gbd, gb_transaction_save *ts); 
    136 int gb_info(GBDATA *gbd, int deep); 
    13715 
    13816/* ad_core.cxx */ 
    … …  
    17250GB_ERROR gb_commit_transaction_local_rek(GBDATA *gbd, long mode, int *pson_created); 
    17351 
     52/* ad_load.cxx */ 
     53GB_ERROR gb_read_ascii(const char *path, GBCONTAINER *gbd); 
     54long gb_read_bin_rek(FILE *in, GBCONTAINER *gbd, long nitems, long version, long reversed); 
     55long gb_recover_corrupt_file(GBCONTAINER *gbd, FILE *in, GB_ERROR recovery_reason); 
     56long gb_read_bin_rek_V2(FILE *in, GBCONTAINER *gbd, long nitems, long version, long reversed, long deep); 
     57GBDATA *gb_search_system_folder_rek(GBDATA *gbd); 
     58void gb_search_system_folder(GBDATA *gb_main); 
     59long gb_read_bin(FILE *in, GBCONTAINER *gbd, int diff_file_allowed); 
     60GB_MAIN_IDX gb_make_main_idx(GB_MAIN_TYPE *Main); 
     61void gb_release_main_idx(GB_MAIN_TYPE *Main); 
     62GB_ERROR gb_login_remote(GB_MAIN_TYPE *Main, const char *path, const char *opent); 
     63 
     64/* ad_save_load.cxx */ 
     65char *gb_findExtension(char *path); 
     66GB_CSTR gb_oldQuicksaveName(GB_CSTR path, int nr); 
     67GB_CSTR gb_quicksaveName(GB_CSTR path, int nr); 
     68GB_CSTR gb_mapfile_name(GB_CSTR path); 
     69GB_CSTR gb_overwriteName(GB_CSTR path); 
     70GB_CSTR gb_reffile_name(GB_CSTR path); 
     71GB_ERROR gb_delete_reference(const char *master); 
     72GB_ERROR gb_create_reference(const char *master); 
     73GB_ERROR gb_add_reference(const char *master, const char *changes); 
     74GB_ERROR gb_remove_all_but_main(GB_MAIN_TYPE *Main, const char *path); 
     75long gb_ascii_2_bin(const char *source, GBDATA *gbd); 
     76GB_BUFFER gb_bin_2_ascii(GBDATA *gbd); 
     77long gb_read_in_long(FILE *in, long reversed); 
     78long gb_read_number(FILE *in); 
     79void gb_put_number(long i, FILE *out); 
     80long gb_read_bin_error(FILE *in, GBDATA *gbd, const char *text); 
     81long gb_write_out_long(long data, FILE *out); 
     82int gb_is_writeable(gb_header_list *header, GBDATA *gbd, long version, long diff_save); 
     83int gb_write_bin_sub_containers(FILE *out, GBCONTAINER *gbc, long version, long diff_save, int is_root); 
     84long gb_write_bin_rek(FILE *out, GBDATA *gbd, long version, long diff_save, long index_of_master_file); 
     85int gb_write_bin(FILE *out, GBDATA *gbd, long version); 
     86char *gb_full_path(const char *path); 
     87GB_ERROR gb_check_saveable(GBDATA *gbd, const char *path, const char *flags); 
     88 
     89/* adcache.cxx */ 
     90void gb_init_cache(GB_MAIN_TYPE *Main); 
     91void gb_destroy_cache(GB_MAIN_TYPE *Main); 
     92char *gb_read_cache(GBDATA *gbd); 
     93void gb_free_cache(GB_MAIN_TYPE *Main, GBDATA *gbd); 
     94char *gb_alloc_cache_index(GBDATA *gbd, size_t size); 
     95void gb_flush_cache(GBDATA *gbd); 
     96 
     97/* adcomm.cxx */ 
     98GB_ERROR gbcm_unfold_client(GBCONTAINER *gbd, long deep, long index_pos) __ATTR__USERESULT; 
     99GB_ERROR gbcmc_begin_sendupdate(GBDATA *gbd); 
     100GB_ERROR gbcmc_end_sendupdate(GBDATA *gbd); 
     101GB_ERROR gbcmc_sendupdate_create(GBDATA *gbd); 
     102GB_ERROR gbcmc_sendupdate_delete(GBDATA *gbd); 
     103GB_ERROR gbcmc_sendupdate_update(GBDATA *gbd, int send_headera); 
     104GB_ERROR gbcmc_begin_transaction(GBDATA *gbd); 
     105GB_ERROR gbcmc_init_transaction(GBCONTAINER *gbd); 
     106GB_ERROR gbcmc_commit_transaction(GBDATA *gbd); 
     107GB_ERROR gbcmc_abort_transaction(GBDATA *gbd); 
     108GB_ERROR gbcms_add_to_delete_list(GBDATA *gbd); 
     109long gbcmc_key_alloc(GBDATA *gbd, const char *key); 
     110GB_ERROR gbcmc_send_undo_commands(GBDATA *gbd, enum gb_undo_commands command) __ATTR__USERESULT; 
     111char *gbcmc_send_undo_info_commands(GBDATA *gbd, enum gb_undo_commands command); 
     112GB_ERROR gbcm_login(GBCONTAINER *gb_main, const char *loginname); 
     113GBCM_ServerResult gbcmc_close(gbcmc_comm *link); 
     114GB_ERROR gbcm_logout(GB_MAIN_TYPE *Main, const char *loginname); 
     115 
    174116/* adcompr.cxx */ 
    175117gb_compress_tree *gb_build_uncompress_tree(const unsigned char *data, long short_flag, char **end); 
    … …  
    191133GB_CBUFFER gb_uncompress_data(GBDATA *gbd, GB_CBUFFER source, long size); 
    192134 
     135/* adfile.cxx */ 
     136GB_ERROR gb_scan_directory(char *basename, gb_scandir *sd) __ATTR__USERESULT_TODO; 
     137 
     138/* adhash.cxx */ 
     139size_t gbs_get_a_prime(size_t above_or_equal_this); 
     140 
    193141/* adindex.cxx */ 
    194142char *gb_index_check_in(GBDATA *gbd); 
    … …  
    204152void gb_check_in_undo_delete(GB_MAIN_TYPE *Main, GBDATA *gbd, int deep); 
    205153 
     154/* adlang1.cxx */ 
     155void gbl_install_standard_commands(GBDATA *gb_main); 
     156 
     157/* admalloc.cxx */ 
     158void gbm_flush_mem(void); 
     159void gbm_init_mem(void); 
     160void gbm_debug_mem(void); 
     161 
    206162/* admap.cxx */ 
    207163GB_ERROR gb_save_mapfile(GB_MAIN_TYPE *Main, GB_CSTR path); 
    … …  
    209165GBDATA *gb_map_mapfile(const char *path); 
    210166int gb_isMappedMemory(void *mem); 
     167 
     168/* adoptimize.cxx */ 
     169GB_ERROR gb_convert_V2_to_V3(GBDATA *gb_main); 
     170char *gb_uncompress_by_dictionary(GBDATA *gbd, GB_CSTR s_source, long size, long *new_size); 
     171char *gb_compress_by_dictionary(GB_DICTIONARY *dict, GB_CSTR s_source, long size, long *msize, int last_flag, int search_backward, int search_forward); 
     172GB_ERROR gb_create_dictionaries(GB_MAIN_TYPE *Main, long maxmem); 
    211173 
    212174/* adquery.cxx */ 
    … …  
    236198long gbcm_read_long(int socket); 
    237199 
     200/* adstring.cxx */ 
     201void gbs_uppercase(char *str); 
     202void gbs_memcopy(char *dest, const char *source, long len); 
     203char *gbs_add_path(char *path, char *name); 
     204 
     205/* adsystem.cxx */ 
     206GB_ERROR gb_load_dictionary_data(GBDATA *gb_main, const char *key, char **dict_data, long *size); 
     207GB_DICTIONARY *gb_create_dict(GBDATA *gb_dict); 
     208void gb_system_key_changed_cb(GBDATA *gbd, int *cl, GB_CB_TYPE type); 
     209void gb_system_master_changed_cb(GBDATA *gbd, int *cl, GB_CB_TYPE type); 
     210void gb_load_single_key_data(GBDATA *gb_main, GBQUARK q); 
     211GB_ERROR gb_save_dictionary_data(GBDATA *gb_main, const char *key, const char *dict, int size); 
     212GB_ERROR gb_load_key_data_and_dictionaries(GBDATA *gb_main) __ATTR__USERESULT; 
     213 
     214/* arbdb.cxx */ 
     215GBDATA *gb_remembered_db(void); 
     216GB_ERROR gb_unfold(GBCONTAINER *gbd, long deep, int index_pos); 
     217void gb_close_unclosed_DBs(void); 
     218int gb_read_nr(GBDATA *gbd); 
     219GB_ERROR gb_write_compressed_pntr(GBDATA *gbd, const char *s, long memsize, long stored_size); 
     220int gb_get_compression_mask(GB_MAIN_TYPE *Main, GBQUARK key, int gb_type); 
     221GB_ERROR gb_security_error(GBDATA *gbd) __ATTR__USERESULT; 
     222GB_CSTR gb_read_key_pntr(GBDATA *gbd); 
     223GBQUARK gb_key_2_existing_quark(GB_MAIN_TYPE *Main, const char *key); 
     224GBQUARK gb_key_2_quark(GB_MAIN_TYPE *Main, const char *key); 
     225GBDATA *gb_create(GBDATA *father, const char *key, GB_TYPES type); 
     226GBDATA *gb_create_container(GBDATA *father, const char *key); 
     227void gb_rename(GBCONTAINER *gbc, const char *new_key); 
     228GB_ERROR gb_delete_force(GBDATA *source); 
     229GB_ERROR gb_set_compression(GBDATA *source); 
     230GB_ERROR gb_init_transaction(GBCONTAINER *gbd); 
     231void gb_add_changed_callback_list(GBDATA *gbd, gb_transaction_save *old, GB_CB_TYPE gbtype, GB_CB func, int *clientdata); 
     232void gb_add_delete_callback_list(GBDATA *gbd, gb_transaction_save *old, GB_CB func, int *clientdata); 
     233GB_ERROR gb_do_callback_list(GB_MAIN_TYPE *Main); 
     234GB_MAIN_TYPE *gb_get_main_during_cb(void); 
     235GB_CSTR gb_read_pntr_ts(GBDATA *gbd, gb_transaction_save *ts); 
     236int gb_info(GBDATA *gbd, int deep); 
     237 
    238238#else 
    239239#error gb_prot.h included twice 

  • trunk/NTREE/nt_cb.hxx

    r7891 r8285  
    2020#include <aw_base.hxx> 
    2121#endif 
    22  
    23 class AW_window; 
    2422class AWT_canvas; 
    2523 

  • trunk/NTREE/nt_internal.h

    r7891 r8285  
    1212 
    1313 
    14 /* NT_cb.cxx */ 
     14/* AP_consensus.cxx */ 
    1515 
    16 #ifndef ARBDB_BASE_H 
    17 #include <arbdb_base.h> 
    18 #endif 
    1916#ifndef AW_BASE_HXX 
    2017#include <aw_base.hxx> 
    2118#endif 
    2219 
    23 class AW_window; 
    24 class AWT_canvas; 
    25  
    26 void NT_delete_mark_all_cb(void *, AWT_canvas *ntw); 
    27 AW_window *NT_open_select_tree_window(AW_root *awr, char *awar_tree); 
    28 void NT_select_last_tree(AW_window *aww, char *awar_tree); 
    29 AW_window *NT_open_select_alignment_window(AW_root *awr); 
    30 void NT_system_cb(AW_window *aww, AW_CL cl_command, AW_CL cl_auto_help_file); 
    31 void NT_system_in_xterm_cb(AW_window *aww, AW_CL cl_command, AW_CL cl_auto_help_file); 
    32  
    33 /* AP_consensus.cxx */ 
    3420AW_window *AP_open_con_expert_window(AW_root *aw_root); 
    3521AW_window *AP_open_consensus_window(AW_root *aw_root); 
    … …  
    4329AW_window *AP_open_cprofile_window(AW_root *aw_root); 
    4430 
     31/* AP_pos_var_pars.cxx */ 
     32void AP_calc_pos_var_pars(AW_window *aww); 
     33AW_window *AP_open_pos_var_pars_window(AW_root *root); 
     34 
    4535/* ColumnStat_2_gnuplot.cxx */ 
    4636AW_window *NT_create_colstat_2_gnuplot_window(AW_root *root); 
    4737 
    48 /* AP_pos_var_pars.cxx */ 
    49 void AP_calc_pos_var_pars(AW_window *aww); 
    50 AW_window *AP_open_pos_var_pars_window(AW_root *root); 
     38/* NT_cb.cxx */ 
     39 
     40#ifndef ARBDB_BASE_H 
     41#include <arbdb_base.h> 
     42#endif 
     43#ifndef AW_BASE_HXX 
     44#include <aw_base.hxx> 
     45#endif 
     46class AWT_canvas; 
     47 
     48void NT_delete_mark_all_cb(void *, AWT_canvas *ntw); 
     49AW_window *NT_open_select_tree_window(AW_root *awr, char *awar_tree); 
     50void NT_select_last_tree(AW_window *aww, char *awar_tree); 
     51AW_window *NT_open_select_alignment_window(AW_root *awr); 
     52void NT_system_cb(AW_window *aww, AW_CL cl_command, AW_CL cl_auto_help_file); 
     53void NT_system_in_xterm_cb(AW_window *aww, AW_CL cl_command, AW_CL cl_auto_help_file); 
    5154 
    5255/* NT_concatenate.cxx */ 

  • trunk/PROBE/pt_prototypes.h

    r8246 r8285  
    1919ARB_ERROR enter_stage_1_build_tree(PT_main *, char *tname) __ATTR__USERESULT; 
    2020ARB_ERROR enter_stage_3_load_tree(PT_main *, const char *tname) __ATTR__USERESULT; 
     21 
     22/* PT_debug.cxx */ 
     23void PT_dump_tree_statistics(void); 
     24void PT_dump_POS_TREE_recursive(POS_TREE *IF_DEBUG (pt), const char *IF_DEBUG (prefix)); 
     25void PT_dump_POS_TREE(POS_TREE *IF_DEBUG (node)); 
    2126 
    2227/* PT_etc.cxx */ 
    … …  
    109114ARB_ERROR PTD_read_leafs_from_disk(const char *fname, POS_TREE **pnode) __ATTR__USERESULT; 
    110115 
    111 /* PT_debug.cxx */ 
    112 void PT_dump_tree_statistics(void); 
    113 void PT_dump_POS_TREE_recursive(POS_TREE *IF_DEBUG (pt), const char *IF_DEBUG (prefix)); 
    114 void PT_dump_POS_TREE(POS_TREE *IF_DEBUG (node)); 
    115  
    116116/* probe_tree.h */ 
    117117template <typename T >int PT_forwhole_chain(POS_TREE *node, T func);