ARB
Functions
ad_prot.h File Reference
#include <attributes.h>
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Functions

GBDATAEXP_get_experiment_data (GBDATA *gb_species)
 
GBDATAEXP_find_experiment_rel_exp_data (GBDATA *gb_experiment_data, const char *name)
 
GBDATAEXP_find_experiment (GBDATA *gb_species, const char *name)
 
GBDATAEXP_first_experiment_rel_exp_data (GBDATA *gb_experiment_data)
 
GBDATAEXP_next_experiment (GBDATA *gb_experiment)
 
GBDATAEXP_find_or_create_experiment_rel_exp_data (GBDATA *gb_experiment_data, const char *name)
 
bool GEN_is_genome_db (GBDATA *gb_main, int default_value)
 
GBDATAGEN_findOrCreate_gene_data (GBDATA *gb_species)
 
GBDATAGEN_find_gene_data (GBDATA *gb_species)
 
GBDATAGEN_expect_gene_data (GBDATA *gb_species)
 
GBDATAGEN_find_gene_rel_gene_data (GBDATA *gb_gene_data, const char *name)
 
GBDATAGEN_find_gene (GBDATA *gb_species, const char *name)
 
GBDATAGEN_expect_gene (GBDATA *gb_species, const char *name)
 
GBDATAGEN_create_nonexisting_gene (GBDATA *gb_species, const char *name)
 
GBDATAGEN_find_or_create_gene_rel_gene_data (GBDATA *gb_gene_data, const char *name)
 
GBDATAGEN_first_gene (GBDATA *gb_species)
 
GBDATAGEN_first_gene_rel_gene_data (GBDATA *gb_gene_data)
 
GBDATAGEN_next_gene (GBDATA *gb_gene)
 
GBDATAGEN_first_marked_gene (GBDATA *gb_species)
 
GBDATAGEN_next_marked_gene (GBDATA *gb_gene)
 
GEN_positionGEN_new_position (int parts, bool joinable)
 
void GEN_use_uncertainties (GEN_position *pos)
 
void GEN_free_position (GEN_position *pos)
 
GEN_positionGEN_read_position (GBDATA *gb_gene)
 
GB_ERROR GEN_write_position (GBDATA *gb_gene, const GEN_position *pos, long seqLength)
 
void GEN_sortAndMergeLocationParts (GEN_position *location)
 
const charGEN_origin_organism (GBDATA *gb_pseudo)
 
const charGEN_origin_gene (GBDATA *gb_pseudo)
 
bool GEN_is_pseudo_gene_species (GBDATA *gb_species)
 
GB_ERROR GEN_organism_not_found (GBDATA *gb_pseudo)
 
void GEN_add_pseudo_species_to_hash (GBDATA *gb_pseudo, GB_HASH *pseudo_hash)
 
GB_HASHGEN_create_pseudo_species_hash (GBDATA *gb_main, long additionalSize)
 
GBDATAGEN_find_pseudo_species (GBDATA *gb_main, const char *organism_name, const char *gene_name, const GB_HASH *pseudo_hash)
 
GBDATAGEN_find_origin_organism (GBDATA *gb_pseudo, const GB_HASH *organism_hash)
 
GBDATAGEN_find_origin_gene (GBDATA *gb_pseudo, const GB_HASH *organism_hash)
 
GBDATAGEN_first_pseudo_species (GBDATA *gb_main)
 
GBDATAGEN_next_pseudo_species (GBDATA *gb_species)
 
GBDATAGEN_first_marked_pseudo_species (GBDATA *gb_main)
 
bool GEN_is_organism (GBDATA *gb_species)
 
GBDATAGEN_find_organism (GBDATA *gb_main, const char *name)
 
GBDATAGEN_first_organism (GBDATA *gb_main)
 
GBDATAGEN_next_organism (GBDATA *gb_organism)
 
long GEN_get_organism_count (GBDATA *gb_main)
 
GBDATAGEN_first_marked_organism (GBDATA *gb_main)
 
GBDATAGEN_next_marked_organism (GBDATA *gb_organism)
 
charGEN_global_gene_identifier (GBDATA *gb_gene, GBDATA *gb_organism)
 
const charGB_get_db_path (GBDATA *gbd)
 
void GB_dump_db_path (GBDATA *gbd)
 
NOT4PERL void GB_dump (GBDATA *gbd)
 
NOT4PERL void GB_dump_no_limit (GBDATA *gbd)
 
GB_ERROR GB_fix_database (GBDATA *gb_main)
 
GBDATAGB_get_gb_main_during_cb (void)
 
NOT4PERL const void * GB_read_old_value (void)
 
long GB_read_old_size (void)
 
void GB_set_verbose (void)
 
void GB_set_next_main_idx (long idx)
 
GBDATAGB_open (const char *path, const char *opent)
 
GB_ERROR GBT_check_arb_file (const char *name) __ATTR__USERESULT
 
GB_CSTR GB_mapfile (GBDATA *gb_main)
 
GB_ERROR GB_save (GBDATA *gb, const char *path, const char *savetype)
 
GB_ERROR GB_create_parent_directory (const char *path)
 
GB_ERROR GB_create_directory (const char *path)
 
GB_ERROR GB_save_in_arbprop (GBDATA *gb, const char *path, const char *savetype)
 
const charGB_get_supported_compression_flags (bool verboose)
 
GB_ERROR GB_start_streamed_save_as (GBDATA *gbd, const char *path, const char *savetype, ArbDBWriter *&writer)
 
GB_ERROR GB_stream_save_part (ArbDBWriter *writer, GBDATA *from, GBDATA *till)
 
GB_ERROR GB_finish_stream_save (ArbDBWriter *&writer)
 
GB_ERROR GB_save_as (GBDATA *gbd, const char *path, const char *savetype)
 
GB_ERROR GB_delete_database (GB_CSTR filename)
 
GB_ERROR GB_save_quick_as (GBDATA *gbd, const char *path)
 
GB_ERROR GB_save_quick (GBDATA *gbd, const char *refpath)
 
void GB_disable_path (GBDATA *gbd, const char *path)
 
long GB_last_saved_clock (GBDATA *gb_main)
 
GB_ULONG GB_last_saved_time (GBDATA *gb_main)
 
void GB_flush_cache (GBDATA *gbd)
 
charGB_set_cache_size (GBDATA *gbd, size_t size)
 
GB_ERROR GBCMS_open (const char *path, long timeout, GBDATA *gb_main)
 
void GBCMS_shutdown (GBDATA *gbd)
 
bool GBCMS_accept_calls (GBDATA *gbd, bool wait_extra_time)
 
void GB_set_remote_action (GBDATA *gbd, bool in_action)
 
bool GB_inside_remote_action (GBDATA *gbd)
 
long GB_read_clients (GBDATA *gbd)
 
bool GB_is_server (GBDATA *gbd)
 
GBDATAGBCMC_find (GBDATA *gbd, const char *key, GB_TYPES type, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs)
 
GB_ERROR GB_tell_server_dont_wait (GBDATA *gbd)
 
GB_ERROR GB_install_pid (int mode)
 
bool GB_is_dictionary_compressed (GBDATA *gbd)
 
GB_CSTR GB_getcwd (void)
 
charGB_find_all_files (const char *dir, const char *mask, bool filename_only)
 
charGB_find_latest_file (const char *dir, const char *mask)
 
charGB_lib_file (bool warn_when_not_found, const char *libprefix, const char *filename)
 
charGB_property_file (bool warn_when_not_found, const char *filename)
 
void GBS_read_dir (StrArray &names, const char *dir, const char *mask)
 
const charGB_get_arb_revision_tag (void)
 
GB_HASHGBS_create_hash (long estimated_elements, GB_CASE case_sens)
 
GB_HASHGBS_create_dynaval_hash (long estimated_elements, GB_CASE case_sens, void(*freefun)(long))
 
void GBS_dynaval_free (long val)
 
void GBS_optimize_hash (const GB_HASH *hs)
 
charGBS_hashtab_2_string (const GB_HASH *hash)
 
long GBS_read_hash (const GB_HASH *hs, const char *key)
 
long GBS_write_hash (GB_HASH *hs, const char *key, long val)
 
long GBS_write_hash_no_strdup (GB_HASH *hs, char *key, long val)
 
long GBS_incr_hash (GB_HASH *hs, const char *key)
 
void GBS_free_hash (GB_HASH *hs)
 
void GBS_hash_do_loop (GB_HASH *hs, gb_hash_loop_type func, void *client_data)
 
void GBS_hash_do_const_loop (const GB_HASH *hs, gb_hash_const_loop_type func, void *client_data)
 
size_t GBS_hash_elements (const GB_HASH *hs)
 
const charGBS_hash_next_element_that (const GB_HASH *hs, const char *last_key, bool(*condition)(const char *key, long val, void *cd), void *cd)
 
void GBS_hash_do_sorted_loop (GB_HASH *hs, gb_hash_loop_type func, gbs_hash_compare_function sorter, void *client_data)
 
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)
 
int GBS_HCF_sortedByKey (const char *k0, long dummy_1x, const char *k1, long dummy_2x)
 
GB_NUMHASHGBS_create_numhash (size_t estimated_elements)
 
long GBS_read_numhash (GB_NUMHASH *hs, long key)
 
long GBS_write_numhash (GB_NUMHASH *hs, long key, long val)
 
void GBS_free_numhash (GB_NUMHASH *hs)
 
GB_HASHGBT_create_species_hash_sized (GBDATA *gb_main, long species_count)
 
GB_HASHGBT_create_species_hash (GBDATA *gb_main)
 
GB_HASHGBT_create_marked_species_hash (GBDATA *gb_main)
 
GB_HASHGBT_create_SAI_hash (GBDATA *gb_main)
 
GB_HASHGBT_create_organism_hash (GBDATA *gb_main)
 
GB_ERROR GB_create_index (GBDATA *gbd, const char *key, GB_CASE case_sens, long estimated_size) __ATTR__USERESULT
 
NOT4PERL void GB_dump_indices (GBDATA *gbd)
 
GB_ERROR GB_request_undo_type (GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT_TODO
 
GB_UNDO_TYPE GB_get_requested_undo_type (GBDATA *gb_main)
 
GB_ERROR GB_undo (GBDATA *gb_main, GB_UNDO_TYPE type) __ATTR__USERESULT
 
charGB_undo_info (GBDATA *gb_main, GB_UNDO_TYPE type)
 
GB_ERROR GB_set_undo_mem (GBDATA *gbd, long memsize)
 
NOT4PERL void GB_set_export_sequence_hook (gb_export_sequence_cb escb)
 
bool GB_supports_mapfile (void)
 
GBS_string_matcherGBS_compile_matcher (const char *search_expr, GB_CASE case_flag)
 
void GBS_free_matcher (GBS_string_matcher *matcher)
 
GB_CSTR GBS_find_string (GB_CSTR cont, GB_CSTR substr, int match_mode)
 
bool GBS_string_matches (const char *str, const char *expr, GB_CASE case_sens)
 
bool GBS_string_matches_regexp (const char *str, const GBS_string_matcher *expr)
 
charGBS_string_eval_in_env (const char *insource, const char *icommand, const GBL_call_env &callEnv)
 
charGBS_string_eval (const char *insource, const char *icommand)
 
double GB_log_fak (int n)
 
void GB_random_seed (unsigned seed)
 
int GB_random (int range)
 
GB_ERROR GB_optimize (GBDATA *gb_main)
 
GB_ERROR GBC_await_error (void)
 
GBDATAGB_find_sub_by_quark (GBDATA *father, GBQUARK key_quark, GBDATA *after, size_t skip_over)
 
GBDATAGB_find (GBDATA *gbd, const char *key, GB_SEARCH_TYPE gbs)
 
GBDATAGB_find_string (GBDATA *gbd, const char *key, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs)
 
NOT4PERL GBDATAGB_find_int (GBDATA *gbd, const char *key, long val, GB_SEARCH_TYPE gbs)
 
GBDATAGB_child (GBDATA *father)
 
GBDATAGB_nextChild (GBDATA *child)
 
GBDATAGB_entry (GBDATA *father, const char *key)
 
GBDATAGB_nextEntry (GBDATA *entry)
 
GBDATAGB_followingEntry (GBDATA *entry, size_t skip_over)
 
size_t GB_countEntries (GBDATA *father, const char *key)
 
GBDATAGB_brother (GBDATA *entry, const char *key)
 
const charGB_first_non_key_char (const char *str)
 
GBDATAGB_search (GBDATA *gbd, const char *fieldpath, GB_TYPES create)
 
GBDATAGB_searchOrCreate_string (GBDATA *gb_container, const char *fieldpath, const char *default_value)
 
GBDATAGB_searchOrCreate_int (GBDATA *gb_container, const char *fieldpath, long default_value)
 
GBDATAGB_searchOrCreate_float (GBDATA *gb_container, const char *fieldpath, float default_value)
 
long GB_number_of_marked_subentries (GBDATA *gbd)
 
GBDATAGB_first_marked (GBDATA *gbd, const char *keystring)
 
GBDATAGB_following_marked (GBDATA *gbd, const char *keystring, size_t skip_over)
 
GBDATAGB_next_marked (GBDATA *gbd, const char *keystring)
 
charGB_read_fp (FILE *in)
 
charGB_read_file (const char *path)
 
charGB_map_FILE (FILE *in, int writeable)
 
charGB_map_file (const char *path, int writeable)
 
GB_ULONG GB_time_of_day (void)
 
GB_ERROR GB_textprint (const char *path) __ATTR__USERESULT
 
GB_CSTR GB_getenvARB_XTERM (void)
 
GB_CSTR GB_getenvUSER (void)
 
GB_CSTR GB_getenvARBHOME (void)
 
GB_CSTR GB_getenvARBMACRO (void)
 
GB_CSTR GB_getenvARBMACROHOME (void)
 
GB_CSTR GB_getenvARB_GS (void)
 
GB_CSTR GB_getenvARB_PDFVIEW (void)
 
GB_CSTR GB_getenvDOCPATH (void)
 
GB_CSTR GB_getenvHTMLDOCPATH (void)
 
NOT4PERL gb_getenv_hook GB_install_getenv_hook (gb_getenv_hook hook)
 
GB_CSTR GB_getenv (const char *env)
 
bool GB_host_is_local (const char *hostname)
 
GB_ULONG GB_get_usable_memory (void)
 
NOT4PERL GB_ERROR GB_xcmd (const char *cmd, XCMD_TYPE exectype) __ATTR__USERESULT_TODO
 
GB_CSTR GB_append_suffix (const char *name, const char *suffix)
 
GB_CSTR GB_canonical_path (const char *anypath)
 
GB_CSTR GB_concat_path (GB_CSTR anypath_left, GB_CSTR anypath_right)
 
GB_CSTR GB_concat_full_path (const char *anypath_left, const char *anypath_right)
 
GB_CSTR GB_unfold_in_directory (const char *relative_directory, const char *path)
 
GB_CSTR GB_unfold_path (const char *pwd_envar, const char *path)
 
GB_CSTR GB_path_in_ARBHOME (const char *relative_path)
 
GB_CSTR GB_path_in_ARBLIB (const char *relative_path)
 
GB_CSTR GB_path_in_HOME (const char *relative_path)
 
GB_CSTR GB_path_in_arbprop (const char *relative_path)
 
GB_CSTR GB_path_in_ARBLIB (const char *relative_path_left, const char *anypath_right)
 
FILE * GB_fopen_tempfile (const char *filename, const char *fmode, char **res_fullname)
 
charGB_create_tempfile (const char *name)
 
charGB_unique_filename (const char *name_prefix, const char *suffix)
 
void GB_remove_on_exit (const char *filename)
 
void GB_split_full_path (const char *fullpath, char **res_dir, char **res_fullname, char **res_name_only, char **res_suffix)
 
charGBS_string_2_key (const char *str)
 
charGB_memdup (const char *source, size_t len)
 
GB_ERROR GB_check_key (const char *key) __ATTR__USERESULT
 
GB_ERROR GB_check_hkey (const char *key) __ATTR__USERESULT
 
charGBS_escape_string (const char *str, const char *chars_to_escape, char escape_char)
 
charGBS_unescape_string (const char *str, const char *escaped_chars, char escape_char)
 
charGBS_eval_env (GB_CSTR p)
 
long GBS_gcgchecksum (const char *seq)
 
uint32_t GB_checksum (const char *seq, long length, int ignore_case, const char *exclude)
 
uint32_t GBS_checksum (const char *seq, int ignore_case, const char *exclude)
 
size_t GBS_shorten_repeated_data (char *data)
 
charGBS_merge_tagged_strings (const char *s1, const char *tag1, const char *replace1, const char *s2, const char *tag2, const char *replace2)
 
charGBS_modify_tagged_string_with_ACI (const char *s, const char *dt, const char *tag, const char *aci, GBL_call_env &env)
 
charGB_read_as_tagged_string (GBDATA *gbd, const char *tagi)
 
void GBS_fwrite_string (const char *strngi, FILE *out)
 
charGBS_fconvert_string (char *buffer)
 
charGBS_replace_tabs_by_spaces (const char *text)
 
charGBS_trim (const char *str)
 
charGBS_log_action_to (const char *comment, const char *action, bool stamp)
 
const charGBS_funptr2readable (void *funptr, bool stripARBHOME)
 
DictDataGB_get_dictionary (GBDATA *gb_main, const char *key)
 
GB_ERROR GB_set_dictionary (GBDATA *gb_main, const char *key, const DictData *dd)
 
charGB_arbtcpdat_path (void)
 
const charGBS_scan_arb_tcp_param (const char *ipPort, const char *wantedParam)
 
const charGBS_nameserver_tag (const char *add_field)
 
const charGBS_ptserver_tag (int id)
 
const charGBS_read_arb_tcp (const char *env)
 
const char *const * GBS_get_arb_tcp_entries (const char *matching)
 
const charGBS_ptserver_logname (void)
 
void GBS_add_ptserver_logentry (const char *entry)
 
charGBS_ptserver_id_to_choice (int i, int showBuild)
 
const charGB_get_type_name (GBDATA *gbd)
 
float GB_atof (const char *str)
 
GB_BUFFER GB_give_buffer (size_t size)
 
GB_BUFFER GB_increase_buffer (size_t size)
 
NOT4PERL int GB_give_buffer_size (void)
 
GB_BUFFER GB_give_buffer2 (long size)
 
charGB_check_out_buffer (GB_CBUFFER buffer)
 
GB_BUFFER GB_give_other_buffer (GB_CBUFFER buffer, long size)
 
void GB_atexit (void(*exitfun)())
 
void GB_init_gb (void)
 
int GB_open_DBs (void)
 
void GB_close (GBDATA *gbd)
 
long GB_read_int (GBDATA *gbd)
 
int GB_read_byte (GBDATA *gbd)
 
GBDATAGB_read_pointer (GBDATA *gbd)
 
float GB_read_float (GBDATA *gbd)
 
long GB_read_count (GBDATA *gbd)
 
long GB_read_memuse (GBDATA *gbd)
 
long GB_calc_structure_size (GBDATA *gbd)
 
GB_CSTR GB_read_pntr (GBDATA *gbd)
 
GB_CSTR GB_read_char_pntr (GBDATA *gbd)
 
charGB_read_string (GBDATA *gbd)
 
size_t GB_read_string_count (GBDATA *gbd)
 
long GB_read_bits_count (GBDATA *gbd)
 
GB_CSTR GB_read_bits_pntr (GBDATA *gbd, char c_0, char c_1)
 
charGB_read_bits (GBDATA *gbd, char c_0, char c_1)
 
GB_CSTR GB_read_bytes_pntr (GBDATA *gbd)
 
long GB_read_bytes_count (GBDATA *gbd)
 
charGB_read_bytes (GBDATA *gbd)
 
GB_CUINT4GB_read_ints_pntr (GBDATA *gbd)
 
long GB_read_ints_count (GBDATA *gbd)
 
GB_UINT4GB_read_ints (GBDATA *gbd)
 
GB_CFLOATGB_read_floats_pntr (GBDATA *gbd)
 
float * GB_read_floats (GBDATA *gbd)
 
charGB_read_as_string (GBDATA *gbd)
 
bool GB_readable_as_string (GBDATA *gbd)
 
NOT4PERL uint8_t GB_read_lossless_byte (GBDATA *gbd, GB_ERROR &error)
 
NOT4PERL int32_t GB_read_lossless_int (GBDATA *gbd, GB_ERROR &error)
 
NOT4PERL float GB_read_lossless_float (GBDATA *gbd, GB_ERROR &error)
 
long GB_read_from_ints (GBDATA *gbd, long index)
 
double GB_read_from_floats (GBDATA *gbd, long index)
 
GB_ERROR GB_write_byte (GBDATA *gbd, int i)
 
GB_ERROR GB_write_int (GBDATA *gbd, long i)
 
GB_ERROR GB_write_pointer (GBDATA *gbd, GBDATA *pointer)
 
GB_ERROR GB_write_float (GBDATA *gbd, float f)
 
GB_ERROR GB_write_pntr (GBDATA *gbd, const char *s, size_t bytes_size, size_t stored_size)
 
GB_ERROR GB_write_string (GBDATA *gbd, const char *s)
 
GB_ERROR GB_write_bits (GBDATA *gbd, const char *bits, long size, const char *c_0)
 
GB_ERROR GB_write_bytes (GBDATA *gbd, const char *s, long size)
 
GB_ERROR GB_write_ints (GBDATA *gbd, const GB_UINT4 *i, long size)
 
GB_ERROR GB_write_floats (GBDATA *gbd, const float *f, long size)
 
GB_ERROR GB_write_autoconv_string (GBDATA *gbd, const char *val)
 
GB_ERROR GB_write_lossless_byte (GBDATA *gbd, uint8_t byte)
 
GB_ERROR GB_write_lossless_int (GBDATA *gbd, int32_t i)
 
GB_ERROR GB_write_lossless_float (GBDATA *gbd, float f)
 
int GB_read_security_write (GBDATA *gbd)
 
int GB_read_security_read (GBDATA *gbd)
 
int GB_read_security_delete (GBDATA *gbd)
 
GB_ERROR GB_write_security_write (GBDATA *gbd, unsigned long level)
 
GB_ERROR GB_write_security_read (GBDATA *gbd, unsigned long level)
 
GB_ERROR GB_write_security_delete (GBDATA *gbd, unsigned long level)
 
GB_ERROR GB_write_security_levels (GBDATA *gbd, unsigned long readlevel, unsigned long writelevel, unsigned long deletelevel)
 
void GB_change_my_security (GBDATA *gbd, int level)
 
GB_TYPES GB_read_type (GBDATA *gbd)
 
bool GB_is_container (GBDATA *gbd)
 
charGB_read_key (GBDATA *gbd)
 
GB_CSTR GB_read_key_pntr (GBDATA *gbd)
 
GBQUARK GB_find_existing_quark (GBDATA *gbd, const char *key)
 
GBQUARK GB_find_or_create_quark (GBDATA *gbd, const char *key)
 
GBQUARK GB_get_quark (GBDATA *gbd)
 
bool GB_has_key (GBDATA *gbd, const char *key)
 
long GB_read_clock (GBDATA *gbd)
 
GBDATAGB_get_father (GBDATA *gbd)
 
GBDATAGB_get_grandfather (GBDATA *gbd)
 
GBDATAGB_get_root (GBDATA *gbd)
 
bool GB_is_ancestor_of (GBDATA *gb_ancestor, GBDATA *gb_descendant)
 
GBDATAGB_create (GBDATA *father, const char *key, GB_TYPES type)
 
GBDATAGB_create_container (GBDATA *father, const char *key)
 
bool GB_allow_compression (GBDATA *gb_main, bool allow_compression)
 
GB_ERROR GB_delete (GBDATA *&source)
 
GB_ERROR GB_copy_dropProtectMarksAndTempstate (GBDATA *dest, GBDATA *source)
 
GB_ERROR GB_copy_dropMarksAndTempstate (GBDATA *dest, GBDATA *source)
 
GB_ERROR GB_copy_std (GBDATA *dest, GBDATA *source)
 
GB_ERROR GB_copy_overlay (GBDATA *dest, GBDATA *source)
 
GB_ERROR GB_copy_full (GBDATA *dest, GBDATA *source)
 
GBDATAGB_clone (GBDATA *gb_destCont, GBDATA *gb_source)
 
charGB_get_subfields (GBDATA *gbd)
 
GB_ERROR GB_set_temporary (GBDATA *gbd) __ATTR__USERESULT
 
GB_ERROR GB_clear_temporary (GBDATA *gbd)
 
bool GB_is_temporary (GBDATA *gbd)
 
bool GB_in_temporary_branch (GBDATA *gbd)
 
GB_ERROR GB_push_transaction (GBDATA *gbd)
 
GB_ERROR GB_pop_transaction (GBDATA *gbd)
 
GB_ERROR GB_begin_transaction (GBDATA *gbd)
 
GB_ERROR GB_no_transaction (GBDATA *gbd) __ATTR__USERESULT
 
GB_ERROR GB_abort_transaction (GBDATA *gbd)
 
GB_ERROR GB_commit_transaction (GBDATA *gbd)
 
GB_ERROR GB_end_transaction (GBDATA *gbd, GB_ERROR error)
 
void GB_end_transaction_show_error (GBDATA *gbd, GB_ERROR error, void(*error_handler)(GB_ERROR))
 
int GB_get_transaction_level (GBDATA *gbd)
 
GB_ERROR GB_release (GBDATA *gbd)
 
int GB_nsons (GBDATA *gbd)
 
void GB_disable_quicksave (GBDATA *gbd, const char *reason)
 
GB_ERROR GB_resort_data_base (GBDATA *gb_main, GBDATA **new_order_list, long listsize)
 
bool GB_user_flag (GBDATA *gbd, unsigned char user_bit)
 
void GB_raise_user_flag (GBDATA *gbd, unsigned char user_bit)
 
void GB_clear_user_flag (GBDATA *gbd, unsigned char user_bit)
 
void GB_write_user_flag (GBDATA *gbd, unsigned char user_bit, bool state)
 
void GB_write_flag (GBDATA *gbd, long flag)
 
int GB_read_flag (GBDATA *gbd)
 
void GB_touch (GBDATA *gbd)
 
char GB_type_2_char (GB_TYPES type)
 
void GB_print_debug_information (struct Unfixed_cb_parameter *, GBDATA *gb_main)
 
int GB_info (GBDATA *gbd)
 
long GB_number_of_subentries (GBDATA *gbd)
 
NOT4PERL charGB_command_interpreter_in_env (const char *str, const char *commands, const GBL_call_env &callEnv)
 
charGB_command_interpreter (const char *str, const char *commands, GBDATA *gb_main)
 

Function Documentation

GBDATA* EXP_get_experiment_data ( GBDATA gb_species)
GBDATA* EXP_find_experiment_rel_exp_data ( GBDATA gb_experiment_data,
const char name 
)
GBDATA* EXP_find_experiment ( GBDATA gb_species,
const char name 
)
GBDATA* EXP_first_experiment_rel_exp_data ( GBDATA gb_experiment_data)

Definition at line 27 of file adExperiment.cxx.

References GB_entry().

Referenced by first_experiment_in_range().

GBDATA* EXP_next_experiment ( GBDATA gb_experiment)

Definition at line 31 of file adExperiment.cxx.

References gb_assert, GB_has_key(), and GB_nextEntry().

Referenced by next_experiment_in_range().

GBDATA* EXP_find_or_create_experiment_rel_exp_data ( GBDATA gb_experiment_data,
const char name 
)

Definition at line 37 of file adExperiment.cxx.

References GBT_find_or_create_item_rel_item_data().

Referenced by experiment_create_handler().

bool GEN_is_genome_db ( GBDATA gb_main,
int  default_value 
)
GBDATA* GEN_findOrCreate_gene_data ( GBDATA gb_species)

Definition at line 44 of file adGene.cxx.

References gb_assert, GB_CREATE_CONTAINER, and GB_search().

Referenced by GEN_create_nonexisting_gene(), and NT_fix_gene_data().

GBDATA* GEN_find_gene_data ( GBDATA gb_species)
GBDATA* GEN_expect_gene_data ( GBDATA gb_species)
GBDATA* GEN_find_gene_rel_gene_data ( GBDATA gb_gene_data,
const char name 
)
GBDATA* GEN_find_gene ( GBDATA gb_species,
const char name 
)
GBDATA* GEN_expect_gene ( GBDATA gb_species,
const char name 
)

Definition at line 72 of file adGene.cxx.

References GBT_expect_item_rel_item_data(), and GEN_expect_gene_data().

GBDATA* GEN_create_nonexisting_gene ( GBDATA gb_species,
const char name 
)
GBDATA* GEN_find_or_create_gene_rel_gene_data ( GBDATA gb_gene_data,
const char name 
)
GBDATA* GEN_first_gene ( GBDATA gb_species)
GBDATA* GEN_first_gene_rel_gene_data ( GBDATA gb_gene_data)

Definition at line 134 of file adGene.cxx.

References GB_entry().

Referenced by first_gene_in_range(), GEN_root::GEN_root(), and NT_convert_gene_locations().

GBDATA* GEN_next_gene ( GBDATA gb_gene)
GBDATA* GEN_first_marked_gene ( GBDATA gb_species)

Definition at line 143 of file adGene.cxx.

References GB_first_marked(), and GEN_expect_gene_data().

Referenced by pd_get_the_gene_names(), and probe_match_event().

GBDATA* GEN_next_marked_gene ( GBDATA gb_gene)

Definition at line 146 of file adGene.cxx.

References GB_next_marked().

Referenced by next_gene_in_range(), pd_get_the_gene_names(), and probe_match_event().

GEN_position* GEN_new_position ( int  parts,
bool  joinable 
)
void GEN_use_uncertainties ( GEN_position pos)
void GEN_free_position ( GEN_position pos)
GEN_position* GEN_read_position ( GBDATA gb_gene)
GB_ERROR GEN_write_position ( GBDATA gb_gene,
const GEN_position pos,
long  seqLength 
)
void GEN_sortAndMergeLocationParts ( GEN_position location)
const char* GEN_origin_organism ( GBDATA gb_pseudo)
const char* GEN_origin_gene ( GBDATA gb_pseudo)
bool GEN_is_pseudo_gene_species ( GBDATA gb_species)
GB_ERROR GEN_organism_not_found ( GBDATA gb_pseudo)
void GEN_add_pseudo_species_to_hash ( GBDATA gb_pseudo,
GB_HASH pseudo_hash 
)
GB_HASH* GEN_create_pseudo_species_hash ( GBDATA gb_main,
long  additionalSize 
)
GBDATA* GEN_find_pseudo_species ( GBDATA gb_main,
const char organism_name,
const char gene_name,
const GB_HASH pseudo_hash 
)
GBDATA* GEN_find_origin_organism ( GBDATA gb_pseudo,
const GB_HASH organism_hash 
)
GBDATA* GEN_find_origin_gene ( GBDATA gb_pseudo,
const GB_HASH organism_hash 
)
GBDATA* GEN_first_pseudo_species ( GBDATA gb_main)
GBDATA* GEN_next_pseudo_species ( GBDATA gb_species)
GBDATA* GEN_first_marked_pseudo_species ( GBDATA gb_main)
bool GEN_is_organism ( GBDATA gb_species)
GBDATA* GEN_find_organism ( GBDATA gb_main,
const char name 
)
GBDATA* GEN_first_organism ( GBDATA gb_main)
GBDATA* GEN_next_organism ( GBDATA gb_organism)
long GEN_get_organism_count ( GBDATA gb_main)

Definition at line 766 of file adGene.cxx.

References GEN_first_organism(), and GEN_next_organism().

Referenced by GBT_create_organism_hash().

GBDATA* GEN_first_marked_organism ( GBDATA gb_main)
GBDATA* GEN_next_marked_organism ( GBDATA gb_organism)
char* GEN_global_gene_identifier ( GBDATA gb_gene,
GBDATA gb_organism 
)
const char* GB_get_db_path ( GBDATA gbd)
void GB_dump_db_path ( GBDATA gbd)

Definition at line 27 of file adTest.cxx.

References GB_get_db_path(), and GB_get_type_name().

Referenced by gb_fix_recursive(), and scanGbdByKey().

NOT4PERL void GB_dump ( GBDATA gbd)

Definition at line 186 of file adTest.cxx.

References dump_internal().

NOT4PERL void GB_dump_no_limit ( GBDATA gbd)

Definition at line 195 of file adTest.cxx.

References dump_internal(), and NULp.

GB_ERROR GB_fix_database ( GBDATA gb_main)

Definition at line 236 of file adTest.cxx.

References GB_begin_transaction(), GB_end_transaction(), and gb_fix_recursive().

GBDATA* GB_get_gb_main_during_cb ( void  )
NOT4PERL const void* GB_read_old_value ( void  )
long GB_read_old_size ( void  )
void GB_set_verbose ( void  )

Definition at line 31 of file ad_load.cxx.

Referenced by ARB_main(), and probe_read_data_base().

void GB_set_next_main_idx ( long  idx)

Definition at line 918 of file ad_load.cxx.

Referenced by ARB_main().

GBDATA* GB_open ( const char path,
const char opent 
)
GB_ERROR GBT_check_arb_file ( const char name)

Checks whether a file is an arb file (or ':')

Returns
NULp if it is an arb file

Definition at line 1369 of file ad_load.cxx.

References ARB_zfclose(), ARB_zfopen(), error(), gb_assert, GB_is_regularfile(), gb_read_in_uint32(), GBS_global_string(), has_ascii_db_id(), is_binary_db_id(), NULp, and ZFILE_AUTODETECT.

Referenced by check_argument_for_mode(), and detectArgType().

GB_CSTR GB_mapfile ( GBDATA gb_main)

Definition at line 101 of file ad_save_load.cxx.

References GB_MAIN(), gb_mapfile_name(), and GB_MAIN_TYPE::path.

Referenced by run_command().

GB_ERROR GB_save ( GBDATA gb,
const char path,
const char savetype 
)

save database

Parameters
gbdatabase root
pathfilename (if NULp -> use name stored in DB; otherwise store name in DB)
savetype
See also
GB_save_as()

Definition at line 803 of file ad_save_load.cxx.

References GB_MAIN(), and GB_save_as().

Referenced by ARB_main(), MG_save_cb(), NT_save_as_cb(), react_to_command(), and saveArb().

GB_ERROR GB_create_parent_directory ( const char path)
GB_ERROR GB_create_directory ( const char path)
GB_ERROR GB_save_in_arbprop ( GBDATA gb,
const char path,
const char savetype 
)

save database inside arb-properties-directory. Automatically creates subdirectories as needed.

Parameters
gbdatabase root
pathfilename (if NULp -> use name stored in DB)
savetype
See also
GB_save_as()

Definition at line 839 of file ad_save_load.cxx.

References ARB_strdup(), error(), GB_create_parent_directory(), GB_MAIN(), GB_path_in_arbprop(), and GB_save_as().

Referenced by AW_root::save_properties().

const char* GB_get_supported_compression_flags ( bool  verboose)
GB_ERROR GB_start_streamed_save_as ( GBDATA gbd,
const char path,
const char savetype,
ArbDBWriter *&  writer 
)

special save implementation for use in pipelines (e.g. silva) 'savetype' has contain 'a' (ascii) 'writer' has to be NULp (object will be constructed and assigned to)

Actual saving of data is triggered by GB_stream_save_part(). When done with saving part, call GB_finish_stream_save() - even in case of error!

Definition at line 1311 of file ad_save_load.cxx.

References gb_assert, GB_MAIN(), and ArbDBWriter::startSaveAs().

GB_ERROR GB_stream_save_part ( ArbDBWriter writer,
GBDATA from,
GBDATA till 
)

saves a part of the database.

save complete database: GB_stream_save_part(w, gb_main, gb_main);

save database in parts: GB_stream_save_part(w, gb_main, gb_some_container); forall (gb_some_sub_container) { // you may create/modify gb_some_sub_container here GB_stream_save_part(w, gb_some_sub_container, gb_some_sub_container); // you may delete/modify gb_some_sub_container here } GB_stream_save_part(w, gb_some_container, gb_main);

Note: gb_some_sub_container has to be a child of gb_some_container

Definition at line 1323 of file ad_save_load.cxx.

References GBDATA::as_container(), error(), GBDATA::is_container(), and ArbDBWriter::saveFromTill().

GB_ERROR GB_finish_stream_save ( ArbDBWriter *&  writer)

complete save-process started with GB_start_streamed_save_as() Has to be called (even if GB_start_streamed_save_as or GB_stream_save_part has returned an error!)

Definition at line 1349 of file ad_save_load.cxx.

References error(), ArbDBWriter::finishSave(), and NULp.

GB_ERROR GB_save_as ( GBDATA gbd,
const char path,
const char savetype 
)

Save whole database

Parameters
gbddatabase root
pathfilename (if NULp -> use name stored in DB)
savetype'a' ascii 'b' binary 'm' save mapfile (only together with binary)

'f' force saving even in disabled path to a different directory (out of order save) 'S' save to stdout (used in arb_2_ascii when saving to stdout; also useful for debugging)

Extra compression flags: 'z' stream through gzip/pigz 'B' stream through bzip2 'x' stream through xz

Definition at line 1362 of file ad_save_load.cxx.

References gb_assert, GB_MAIN(), NULp, RETURN_ERROR, and GB_MAIN_TYPE::save_as().

Referenced by ARB_main(), FINAL_TYPE< SEQTYPE >::ArbWriter(), calc_pvp(), FINAL_TYPE< SEQTYPE >::finish(), GB_save(), GB_save_in_arbprop(), main(), pd_export_pt_server(), and run_command().

GB_ERROR GB_delete_database ( GB_CSTR  filename)

Definition at line 1409 of file ad_save_load.cxx.

References error(), GB_await_error(), gb_remove_all_but_main(), GB_unlink(), and NULp.

Referenced by nt_delete_database().

GB_ERROR GB_save_quick_as ( GBDATA gbd,
const char path 
)

Definition at line 1502 of file ad_save_load.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::save_quick_as().

Referenced by MG_save_quick_result_cb(), and NT_save_quick_as_cb().

GB_ERROR GB_save_quick ( GBDATA gbd,
const char refpath 
)

Definition at line 1584 of file ad_save_load.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::save_quick().

Referenced by NT_save_quick_cb().

void GB_disable_path ( GBDATA gbd,
const char path 
)

Definition at line 1589 of file ad_save_load.cxx.

References GB_MAIN(), GBS_eval_env(), and NULp.

Referenced by GBT_open().

long GB_last_saved_clock ( GBDATA gb_main)

Definition at line 1594 of file ad_save_load.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::last_saved_transaction.

Referenced by nt_disconnect_from_db().

GB_ULONG GB_last_saved_time ( GBDATA gb_main)

Definition at line 1598 of file ad_save_load.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::last_saved_time.

Referenced by nt_disconnect_from_db().

void GB_flush_cache ( GBDATA gbd)

Definition at line 226 of file adcache.cxx.

References gb_uncache().

Referenced by GB_read_bits_pntr().

char* GB_set_cache_size ( GBDATA gbd,
size_t  size 
)
GB_ERROR GBCMS_open ( const char path,
long  timeout,
GBDATA gb_main 
)
void GBCMS_shutdown ( GBDATA gbd)
bool GBCMS_accept_calls ( GBDATA gbd,
bool  wait_extra_time 
)
void GB_set_remote_action ( GBDATA gbd,
bool  in_action 
)
bool GB_inside_remote_action ( GBDATA gbd)
long GB_read_clients ( GBDATA gbd)
bool GB_is_server ( GBDATA gbd)
GBDATA* GBCMC_find ( GBDATA gbd,
const char key,
GB_TYPES  type,
const char str,
GB_CASE  case_sens,
GB_SEARCH_TYPE  gbs 
)
GB_ERROR GB_tell_server_dont_wait ( GBDATA gbd)
GB_ERROR GB_install_pid ( int  mode)
bool GB_is_dictionary_compressed ( GBDATA gbd)
GB_CSTR GB_getcwd ( void  )
char* GB_find_all_files ( const char dir,
const char mask,
bool  filename_only 
)
char* GB_find_latest_file ( const char dir,
const char mask 
)
char* GB_lib_file ( bool  warn_when_not_found,
const char libprefix,
const char filename 
)
char* GB_property_file ( bool  warn_when_not_found,
const char filename 
)

Definition at line 204 of file adfile.cxx.

References GB_existing_file(), GB_lib_file(), GB_path_in_arbprop(), and result.

Referenced by GB_login().

void GBS_read_dir ( StrArray &  names,
const char dir,
const char mask 
)
const char* GB_get_arb_revision_tag ( void  )

retrieve arb revision tag (e.g. "14358@trunk") from ../lib/revision_info.txt File is generated by ../SOURCE_TOOLS/build_info.pl

Definition at line 304 of file adfile.cxx.

References GB_lib_file(), GB_read_file(), GBS_global_string_copy(), arb_test::nl(), and NULp.

Referenced by clientserver_error().

GB_HASH* GBS_create_hash ( long  estimated_elements,
GB_CASE  case_sens 
)

Create a hash

Parameters
estimated_elementsestimated number of elements added to hash (if you add more elements, hash will still work, but get slow)
case_sensGB_IGNORE_CASE or GB_MIND_CASE Uses linked lists to avoid collisions.

Definition at line 253 of file adhash.cxx.

References ARB_calloc(), GB_HASH::case_sens, GB_HASH::entries, GB_HASH::freefun, hash_size(), GB_HASH::nelem, NULp, and GB_HASH::size.

Referenced by an_get_prefix_hash(), arb_prm_primer(), aw_install_xkeys(), aw_question(), AW_xfig::AW_xfig(), AWT_translator::AWT_translator(), AWTC_pars_names(), ST_ML::calc_st_ml(), callDelay(), DI_MATRIX::compress(), ConsensusTree::ConsensusTree(), AW_xfig::create_gcs(), create_item_hash(), create_ref_hash(), MO_Liste::fill_marked_bakts(), g_bs_add_value_tag_to_hash(), gb_cache::gb_cache(), GB_DbScanner::GB_DbScanner(), gb_read_bin(), GB_remove_on_exit(), GBP_add_callback(), GBS_create_dynaval_hash(), GBS_merge_tagged_strings(), GBS_modify_tagged_string_with_ACI(), GBT_check_data(), GBT_link_tree_using_species_hash(), GDE_popup_filename_browser(), GEN_create_pseudo_species_hash(), GEN_testAndRemoveTranslations(), MO_Liste::get_all_species(), get_cached_taxonomy(), get_short(), getIcon(), BI_helix::initFromData(), AP_tree::mark_duplicates(), MatrixOrder::MatrixOrder(), mg_transfer_listed_species(), nt_add(), nt_add_partial(), nt_build_sai_string(), nt_create_configuration(), Package::Package(), PT_build_species_hash(), QUERY::search_duplicated_field_content(), Sondentopf::Sondentopf(), species_rename_join(), ST_Container::ST_Container(), AW_selection_list::to_hash(), and UniqueNameDetector::UniqueNameDetector().

GB_HASH* GBS_create_dynaval_hash ( long  estimated_elements,
GB_CASE  case_sens,
void(*)(long freefun 
)

like GBS_create_hash, but values stored in hash get freed using 'freefun' when hash gets destroyed

Definition at line 271 of file adhash.cxx.

References GB_HASH::freefun, and GBS_create_hash().

Referenced by aw_help_search(), QUERY::create_query_box(), DefinedCommands::DefinedCommands(), g_bs_get_string_of_tag_hash(), GBT_begin_rename_session(), get_cached_taxonomy(), and st_ml_check_sequence_quality().

void GBS_dynaval_free ( long  val)
void GBS_optimize_hash ( const GB_HASH hs)
char* GBS_hashtab_2_string ( const GB_HASH hash)
long GBS_read_hash ( const GB_HASH hs,
const char key 
)

Definition at line 395 of file adhash.cxx.

References find_hash_entry(), and gbs_hash_entry::val.

Referenced by an_find_shrt_prefix(), ap_mark_duplicates_rek(), arb_reduce_primer_len(), are_not_in_tree(), AW_window::at(), AW_window::at_ifdef(), aw_create_shell(), AW_forget_all_window_geometry(), aw_help_search(), aw_question(), aw_xkey_2_awkey(), AW_root::awar_no_error(), AWTC_create_numbered_suffix(), awtc_mark_hits(), callDelay(), AWT_translator::codon2aa(), AP_tree::colorize(), compare_hits(), QUERY::copy_selection_list_2_query_box(), AW_xfig::create_gcs(), ST_ML::find_node_by_name(), find_SAI_candidates(), find_species_candidates(), flush_cache_entry(), g_bs_add_value_tag_to_hash(), gb_write_key(), GBP_add_callback(), GBP_remove_callback(), GBT_check_alignment(), GBT_check_data(), GBT_commit_rename_session(), gbt_link_tree_to_hash_rek(), GBT_remove_leafs(), GBT_rename_species(), gbt_rename_tree_rek(), GDE_popup_filename_browser(), GEN_find_origin_organism(), GEN_read_pseudo_species_from_hash(), DefinedCommands::get(), ST_Container::get_cached_sonde(), get_cached_taxonomy(), ST_ML::get_color_string(), MatrixOrder::get_index(), MO_Liste::get_index_by_entry(), ST_ML::get_ml_vectors(), get_short(), SpecSetRegistry::get_species_index(), get_taxonomy(), get_taxonomy_string(), getHitInfo(), getIcon(), BI_helix::initFromData(), key2quark(), MERGE_sequences_simple(), MG_export_fields(), MG_transfer_one_species(), MP_mark_probes_in_tree(), UniqueNameDetector::name_known(), Package::not_defined(), nt_build_conf_marked(), nt_extract_configuration(), perform_query_cb(), ptpd_read_names(), QUERY::search_duplicated_field_content(), AW_root::search_remote_command(), species_rename_join(), st_ml_add_quality_string_to_species(), st_ml_add_sequence_part_to_stat(), and ST_ML::update_ml_likelihood().

long GBS_write_hash ( GB_HASH hs,
const char key,
long  val 
)

Definition at line 457 of file adhash.cxx.

References write_hash().

Referenced by UniqueNameDetector::add_name(), an_add_short(), an_remove_short(), ap_mark_duplicates_rek(), arb_reduce_primer_len(), aw_create_shell(), aw_help_search(), aw_question(), AW_xfig::AW_xfig(), AW_root::awar_float(), AW_root::awar_int(), AW_root::awar_pointer(), AW_root::awar_string(), build_taxonomy_rek(), ST_Container::cache_Sonde(), ST_ML::calc_st_ml(), callDelay(), CLEAR_QUERIED(), DI_MATRIX::compress(), ConsensusTree::ConsensusTree(), AW_xfig::create_gcs(), create_ref_hash(), AW_root::define_remote_command(), flush_cache_entry(), flush_taxonomy_cb(), GB_MAIN_TYPE::free_all_keys(), g_bs_add_value_tag_to_hash(), g_bs_read_tagged_hash(), gb_create_key(), GB_remove_on_exit(), gbcmc_read_keys(), GBP_add_callback(), GBP_remove_callback(), GBS_hash_do_sorted_loop(), GBT_add_item_to_hash(), GBT_check_alignment(), gbt_link_tree_to_hash_rek(), GBT_rename_species(), GDE_popup_filename_browser(), GEN_add_pseudo_species_to_hash(), Sondentopf::gen_color_hash(), get_cached_taxonomy(), get_short(), getIcon(), BI_helix::initFromData(), map_awXKey(), Package::mark_function_defined(), MERGE_sequences_simple(), MG_transfer_one_species(), nt_add(), nt_add_partial(), nt_build_conf_string_rek(), nt_build_sai_string(), NT_remove_species_in_tree_from_hash(), PT_build_species_hash(), MO_Liste::put_entry(), QUERY::search_duplicated_field_content(), DefinedCommands::set(), SET_QUERIED(), species_rename_join(), st_ml_add_sequence_part_to_stat(), AW_selection_list::to_hash(), and UniqueNameDetector::UniqueNameDetector().

long GBS_write_hash_no_strdup ( GB_HASH hs,
char key,
long  val 
)

Definition at line 462 of file adhash.cxx.

References write_hash().

Referenced by an_get_prefix_hash().

long GBS_incr_hash ( GB_HASH hs,
const char key 
)
void GBS_free_hash ( GB_HASH hs)

Definition at line 541 of file adhash.cxx.

References GB_HASH::entries, gb_assert, and GBS_erase_hash().

Referenced by ARB_main(), arb_prm_primer(), aw_uninstall_xkeys(), AWTC_pars_names(), KeySorter::bubble_sort(), ST_ML::calc_st_ml(), ST_ML::cleanup(), probe_struct_global::cleanup(), DI_MATRIX::compress(), QUERY::copy_selection_list_2_query_box(), AW_xfig::create_gcs(), exit_removal(), find_SAI_candidates(), find_species_candidates(), free_cached_taxonomy(), g_bs_free_hash_of_hashes(), g_bs_free_hash_of_hashes_elem(), g_bs_get_string_of_tag_hash(), GBT_check_data(), gbt_free_rename_session_data(), GBT_link_tree(), GBT_link_tree_using_species_hash(), GEN_testAndRemoveTranslations(), getIcon(), BI_helix::initFromData(), insert_all_species_into_tree(), AP_tree::mark_duplicates(), mark_gene_species_of_marked_genes(), mark_genes_of_marked_gene_species(), MERGE_sequences_simple(), mg_transfer_listed_species(), nt_add(), nt_add_partial(), NT_alltree_remove_leafs(), nt_build_sai_string(), nt_create_configuration(), nt_extract_configuration(), NT_pseudo_species_to_organism(), perform_query_cb(), QUERY::search_duplicated_field_content(), species_rename_join(), st_ml_check_sequence_quality(), AW_root_Motif::~AW_root_Motif(), AW_xfig::~AW_xfig(), AWT_translator::~AWT_translator(), ConsensusTree::~ConsensusTree(), QUERY::DbQuery::~DbQuery(), DefinedCommands::~DefinedCommands(), EG2PS_data::~EG2PS_data(), gb_cache::~gb_cache(), GB_DbScanner::~GB_DbScanner(), GB_MAIN_TYPE::~GB_MAIN_TYPE(), MatrixOrder::~MatrixOrder(), MO_Liste::~MO_Liste(), Package::~Package(), Sondentopf::~Sondentopf(), SpecSetRegistry::~SpecSetRegistry(), ST_Container::~ST_Container(), ST_ML::~ST_ML(), and UniqueNameDetector::~UniqueNameDetector().

void GBS_hash_do_loop ( GB_HASH hs,
gb_hash_loop_type  func,
void *  client_data 
)
void GBS_hash_do_const_loop ( const GB_HASH hs,
gb_hash_const_loop_type  func,
void *  client_data 
)
size_t GBS_hash_elements ( const GB_HASH hs)
const char* GBS_hash_next_element_that ( const GB_HASH hs,
const char last_key,
bool(*)(const char *key, long val, void *cd)  condition,
void *  cd 
)
void GBS_hash_do_sorted_loop ( GB_HASH hs,
gb_hash_loop_type  func,
gbs_hash_compare_function  sorter,
void *  client_data 
)

Definition at line 632 of file adhash.cxx.

References GBS_write_hash(), and get_sorted_hash_values().

Referenced by insert_all_species_into_tree().

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 
)
int GBS_HCF_sortedByKey ( const char k0,
long  dummy_1x,
const char k1,
long  dummy_2x 
)
GB_NUMHASH* GBS_create_numhash ( size_t  estimated_elements)
long GBS_read_numhash ( GB_NUMHASH hs,
long  key 
)
long GBS_write_numhash ( GB_NUMHASH hs,
long  key,
long  val 
)
void GBS_free_numhash ( GB_NUMHASH hs)

Definition at line 745 of file adhash.cxx.

References GB_NUMHASH::entries, and GBS_erase_numhash().

Referenced by aw_uninstall_xkeys(), and GB_MAIN_TYPE::~GB_MAIN_TYPE().

GB_HASH* GBT_create_species_hash_sized ( GBDATA gb_main,
long  species_count 
)
GB_HASH* GBT_create_species_hash ( GBDATA gb_main)
GB_HASH* GBT_create_marked_species_hash ( GBDATA gb_main)
GB_HASH* GBT_create_SAI_hash ( GBDATA gb_main)

Definition at line 44 of file adhashtools.cxx.

References create_item_hash(), GBT_first_SAI(), GBT_get_SAI_count(), and GBT_next_SAI().

Referenced by find_SAI_candidates().

GB_HASH* GBT_create_organism_hash ( GBDATA gb_main)
GB_ERROR GB_create_index ( GBDATA gbd,
const char key,
GB_CASE  case_sens,
long  estimated_size 
)
NOT4PERL void GB_dump_indices ( GBDATA gbd)
GB_ERROR GB_request_undo_type ( GBDATA gb_main,
GB_UNDO_TYPE  type 
)

Define how to undo DB changes.

This function should be called just before opening a transaction, otherwise its effect will be delayed.

Possible types are: GB_UNDO_UNDO enable undo GB_UNDO_NONE disable undo GB_UNDO_KILL disable undo and remove old undos !!

Note: if GB_request_undo_type returns an error, local undo type remains unchanged

Definition at line 718 of file adindex.cxx.

References _GBCMC_UNDOCOM_REQUEST_NOUNDO, _GBCMC_UNDOCOM_REQUEST_UNDO, error(), GB_MAIN(), GB_UNDO_KILL, GB_UNDO_NONE, gbcmc_send_undo_commands(), GB_MAIN_TYPE::is_client(), NULp, GB_MAIN_TYPE::requested_undo_type, and type.

Referenced by ARB_main(), FINAL_TYPE< SEQTYPE >::ArbWriter(), cleanup_ptserver_database(), GB_optimize(), GB_undo(), gbcms_talking_undo(), GBT_compress_sequence_tree2(), and NT_create_main_window().

GB_UNDO_TYPE GB_get_requested_undo_type ( GBDATA gb_main)

Definition at line 746 of file adindex.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::requested_undo_type.

Referenced by GB_optimize(), GB_undo(), and GBT_compress_sequence_tree2().

GB_ERROR GB_undo ( GBDATA gb_main,
GB_UNDO_TYPE  type 
)
char* GB_undo_info ( GBDATA gb_main,
GB_UNDO_TYPE  type 
)
GB_ERROR GB_set_undo_mem ( GBDATA gbd,
long  memsize 
)
NOT4PERL void GB_set_export_sequence_hook ( gb_export_sequence_cb  escb)

Definition at line 35 of file adlang1.cxx.

References gb_assert, and get_export_sequence.

Referenced by SEQIO::export_by_format(), and ExportFieldScanner::scanFields().

bool GB_supports_mapfile ( void  )

Definition at line 644 of file admap.cxx.

Referenced by pd_export_pt_server(), and run_command().

GBS_string_matcher* GBS_compile_matcher ( const char search_expr,
GB_CASE  case_flag 
)
void GBS_free_matcher ( GBS_string_matcher matcher)
GB_CSTR GBS_find_string ( GB_CSTR  cont,
GB_CSTR  substr,
int  match_mode 
)
bool GBS_string_matches ( const char str,
const char expr,
GB_CASE  case_sens 
)
bool GBS_string_matches_regexp ( const char str,
const GBS_string_matcher expr 
)
char* GBS_string_eval_in_env ( const char insource,
const char icommand,
const GBL_call_env callEnv 
)
char* GBS_string_eval ( const char insource,
const char icommand 
)
double GB_log_fak ( int  n)

Definition at line 21 of file admath.cxx.

References ARB_realloc(), gb_assert, max, and NULp.

Referenced by ap_calc_bootstrap_remark_sub().

void GB_random_seed ( unsigned  seed)

normally you should not use GB_random_seed. Use it only to reproduce some pseudo-random result (e.g. in unittests)

Definition at line 80 of file admath.cxx.

References gen, and RandomNumberGenerator::reseed().

int GB_random ( int  range)
GB_ERROR GB_optimize ( GBDATA gb_main)
GB_ERROR GBC_await_error ( void  )

Definition at line 245 of file adperl.cxx.

References GB_await_error().

GBDATA* GB_find_sub_by_quark ( GBDATA father,
GBQUARK  key_quark,
GBDATA after,
size_t  skip_over 
)
GBDATA* GB_find ( GBDATA gbd,
const char key,
GB_SEARCH_TYPE  gbs 
)
GBDATA* GB_find_string ( GBDATA gbd,
const char key,
const char str,
GB_CASE  case_sens,
GB_SEARCH_TYPE  gbs 
)
NOT4PERL GBDATA* GB_find_int ( GBDATA gbd,
const char key,
long  val,
GB_SEARCH_TYPE  gbs 
)

Definition at line 311 of file adquery.cxx.

References GB_CASE_UNDEFINED, gb_find_internal(), and GB_INT.

Referenced by gbcms_talking_find().

GBDATA* GB_child ( GBDATA father)
GBDATA* GB_nextChild ( GBDATA child)
GBDATA* GB_entry ( GBDATA father,
const char key 
)

Definition at line 334 of file adquery.cxx.

References GB_find(), and SEARCH_CHILD.

Referenced by ALI_translate_marked(), apply_command_to_alignment(), arb_prm_read(), awt_add_sequences_to_list(), awt_open_ACI_URL_with_item(), AWTC_pars_names(), AWTC_recreate_name(), AWTI_import_set_ali_and_type(), FieldReader::calc_value(), ColumnStat::calculate(), CheckedConsistencies::CheckedConsistencies(), cmpByKey(), collectKeysRegisteredInDatabase(), compress_sequence_tree(), concatenateFieldsCreateNewSpecies(), config_comment_changed_cb(), config_modified_cb(), count_field_occurrence(), create_nds_vars(), Data::Data(), FoundGroup::delete_from_DB(), delete_kept_ghostnodes(), delete_unused_changekeys(), DI_ENTRY::DI_ENTRY(), disexpectField(), do_hide_command_for_one_species(), do_mark_command_for_one_species(), ED4_getSaiColorString(), edit_SAI_description(), EXP_first_experiment_rel_exp_data(), expect_entry(), expectField(), export_tree_node_print_xml(), Itemfield_Selection::fill(), ALI_selection::fill(), EDB_root_bact::fill_data(), fillSelNamList(), find_group_name_entry(), find_or_create(), findAffectedKeys(), Structure3D::FindTypeOfRNA(), flush_taxonomy_if_new_group_cb(), GroupSearch::fold_found_groups(), CheckedConsistencies::forgetDoneChecks(), gb_convert_V2_to_V3(), gb_copy_explicit(), GB_countEntries(), gb_load_dictionary_data(), gb_load_key_data_and_dictionaries(), gb_load_single_key_data(), gb_resort_system_folder_to_top(), gb_save_dictionary_data(), gb_search_system_folder(), gbl_read_seq_sai_or_species(), GBT_add_data(), GBT_check_alignment(), GBT_check_data(), GBT_commit_rename_session(), GBT_convert_changekey(), GBT_count_alignments(), GBT_find_or_create(), GBT_find_sequence(), GBT_find_tree(), GBT_first_SAI(), GBT_first_SAI_rel_SAI_data(), GBT_first_species(), GBT_first_species_rel_species_data(), GBT_gen_accession_number(), GBT_get_alignment_names(), GBT_get_color_group(), GBT_get_colorset_names(), GBT_get_configuration_names(), GBT_get_item_count(), GBT_get_name(), GBT_is_partial(), GBT_read_tree_and_size(), gbt_read_tree_rek(), gbt_rename_alignment_of_item(), GBT_rename_species(), GBT_set_color_group(), GBT_size_of_tree(), GBT_tree_info_string(), gbt_write_tree(), gde_filter_weights(), GEN_create_nds_vars(), gen_extract_gene_2_pseudoSpecies(), GEN_first_gene(), GEN_first_gene_rel_gene_data(), GEN_is_genome_db(), GEN_is_organism(), GEN_make_node_text_init(), GEN_make_node_text_nds(), GEN_origin_gene(), GEN_origin_organism(), GEN_read_position(), GEN_root::GEN_root(), GEN_species_add_entry(), GEN_testAndRemoveTranslations(), GEN_write_position(), probe_input_data::get_acc(), get_cached_taxonomy(), probe_input_data::get_checksum(), probe_input_data::get_fullname(), probe_input_data::get_geneabspos(), Group::get_name(), RefEntries::RefSelector::get_refs(), ALI_ARBDB::get_SAI(), get_SAI_description(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), probe_input_data::get_shortname(), get_species_id(), probe_input_data::get_start(), probe_input_data::get_stop(), get_taxonomy(), get_tree_idx(), FoundGroup::get_tree_order(), PosGene::getName(), PosGene::getType(), group_awar_changed_cb(), group_is_folded(), group_set_folded(), ArbImporter::import_data(), NodeTextBuilder::init(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), KeySorter::KeySorter(), PHDATA::load(), main(), map_viewkey(), map_viewkeys(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), mark_gene_species_using_current_alignment(), MERGE_sequences_simple(), mergeSimilarSpecies(), MG_create_field_content(), MG_transfer_fields_info(), new_gbt_message_created_cb(), no_data_error(), nt_build_conf_string_rek(), NT_convert_gene_locations(), NT_count_different_chars(), NT_create_sai_from_pfold(), NT_del_mark_move_REF(), NT_fix_gene_data(), NT_format_all_alignments(), NT_importValidNames(), nt_rename_configuration(), nt_species_join(), NT_suggestValidNames(), parseCSV(), pd_get_the_gene_names(), pd_get_the_names(), PG_get_first_probe(), PG_initSpeciesMaps(), probe_input_data::preload_rel2abs(), probe_match_event(), PS_detect_probe_length(), PS_extract_probe_data(), PS_get_first_node(), PS_get_probe_for_path(), PS_print_paths(), PT_init_map(), PT_prepare_species_sequence(), read_tree_and_size_internal(), readACC(), remove_dup_colors(), remove_redundant_translation(), FoundGroup::rename_by_ACI(), DBwriter::renumberDuplicateGenes(), reorder_trees_cb(), GBT_config::saveAsOver(), ItemFieldShader::scan_value_range_cb(), SearchedTree::SearchedTree(), selected_config_changed_cb(), SequenceHandler::SequenceHandler(), set_SAI_group(), set_tree_idx(), show_all_changekeys(), species_rename_join(), SQ_evaluate(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), st_remove_entries(), AWT_graphic_tree::toggle_group(), trackAlignmentChanges(), translate_getInfo(), translate_removeInfo(), TranslateGeneToAminoAcidSequence(), translateSAItoColors(), tree_node_deleted_cb(), tree_read_byte(), tree_read_float(), tree_write_byte(), tree_write_float(), TREE_write_Newick(), TREE_write_XML(), UniqueNameDetector::UniqueNameDetector(), NodeTextBuilder::work(), write_entry(), SpecSetRegistry::write_node_information(), writeHistory(), and FieldTransfer::ItemClonedByRuleSet::~ItemClonedByRuleSet().

GBDATA* GB_nextEntry ( GBDATA entry)
GBDATA* GB_followingEntry ( GBDATA entry,
size_t  skip_over 
)

Definition at line 344 of file adquery.cxx.

References GB_FATHER(), GB_find_sub_by_quark(), and GB_get_quark().

size_t GB_countEntries ( GBDATA father,
const char key 
)

Definition at line 351 of file adquery.cxx.

References GB_entry(), and GB_nextEntry().

GBDATA* GB_brother ( GBDATA entry,
const char key 
)
const char* GB_first_non_key_char ( const char str)
GBDATA* GB_search ( GBDATA gbd,
const char fieldpath,
GB_TYPES  create 
)

Definition at line 531 of file adquery.cxx.

References GBDATA::expect_container(), and gb_search().

Referenced by alignment_vars_callback(), AliApplicable::apply_to_alignment(), ARB_main(), FINAL_TYPE< SEQTYPE >::ArbWriter(), AW_awar::AW_awar(), AW_forget_all_window_geometry(), AW_reactivate_all_questions(), awt_string_handler::awar_changed(), awar_updated_cb(), awt_create_CONFIG_selection_list(), awt_create_select_filter(), awt_create_select_filter_window_aw_cb(), AWT_default_protein_type(), AWT_modify_managed_configs(), awtc_nn_search_all_listed(), FieldSelDef::build_sel(), FieldReader::calc_value(), ED4_terminal::changed_by_database(), checkAndMergeFields(), CheckedConsistencies::CheckedConsistencies(), collectKeysRegisteredInDatabase(), compress_sequence_tree(), CON_export(), config_rename_handler(), create_nds_vars(), create_new_species(), create_ref_hash(), createDataFromConsensus(), createGroupFromSelected(), dbserver_container(), AP_pos_var::delete_aliEntry_from_SAI(), delete_unused_changekeys(), DI_create_matrix_variables(), ensure_trees_have_order(), AWT_configuration::erase_deleted_configs(), MacroRecorder::execute(), EXP_get_experiment_data(), experiment_rename_handler(), FastAligner_delete_temp_entries(), field_delete_cb(), filter_columnstat_SAIs(), filter_loadable_SAIs(), filter_posvar_SAI_for_ali(), find_or_create_error_container(), findOrCreate_configuration(), flush_taxonomy_cb(), CheckedConsistencies::forgetDoneChecks(), GB_clear_macro_error(), gb_convert_V2_to_V3(), GB_get_macro_error(), gb_load_single_key_data(), gb_read_ascii_beyond_header(), gb_search_system_folder(), GB_searchOrCreate_float(), GB_searchOrCreate_int(), GB_searchOrCreate_string(), gbs_build_replace_string(), GBT_add_data(), GBT_add_new_changekey_to_keypath(), GBT_colorset_root(), GBT_find_configuration(), GBT_get_changekey(), GBT_get_configuration_names(), GBT_open(), GBT_read_as_string(), GBT_read_char_pntr(), GBT_read_float(), GBT_read_int(), GBT_read_string(), GBT_read_tree_and_size(), GBT_searchOrCreate_itemfield_according_to_changekey(), gbt_wait_for_remote_action(), GBT_write_byte(), GBT_write_float(), GBT_write_int(), GBT_write_name_to_groupData(), GBT_write_string(), gbt_write_tree(), gbt_write_tree_nodes(), GEN_create_nds_vars(), GEN_expect_gene_data(), GEN_find_gene_data(), GEN_findOrCreate_gene_data(), GEN_make_node_text_init(), GEN_make_node_text_nds(), GEN_write_position(), gene_rename_handler(), get_addid(), AWT_configuration::get_config(), FINAL_TYPE< SEQTYPE >::get_first_field(), FoundGroup::get_name(), get_next_SAI_count(), GetDisplayInfo(), getKnownMacroClients(), group_species(), NodeTextBuilder::init(), ED4_root::init_alignment(), init_tmp_branch(), awt_input_handler::link_to(), AW_awar::make_global(), DbScanner::Map(), map_viewkeys(), mark_as_macro_executor(), MERGE_sequences_simple(), mg_check_field_cb(), MG_config_delete_cb(), MG_create_db_dependent_rename_awars(), MG_transfer_config(), MG_transfer_fields_info(), modify_fields_of_queried_cb(), SEC_structure_toggler::name(), nt_build_sai_string(), NT_create_alignment_vars(), NT_create_sai_from_pfold(), NT_deleteValidNames(), NT_fix_dict_compress(), NT_format_all_alignments(), NT_suggestValidNames(), pars_create_all_awars(), pd_get_the_gene_names(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), probe_match_event(), PT_prepare_data(), ALI_ARBDB::put_sequence(), ALI_ARBDB::put_sequence_string(), ArbImporter::read_data(), FieldTransfer::ReadRule::readFrom(), CheckedConsistencies::register_as_performed(), RegFieldSelection::registrate(), reorder_keys(), reorder_up_down(), AP_pos_var::save_aliEntry_to_SAI(), ItemFieldShader::scan_value_range_cb(), QUERY::search_duplicated_field_content(), SEC_db_interface::SEC_db_interface(), SEC_seq_data::SEC_seq_data(), SEC_structure_toggler::SEC_structure_toggler(), selectValidNameFromList(), AWT_configuration::set_config(), set_field_of_queried_cb(), set_protection_of_queried_cb(), setIntEntryToZero(), show_all_changekeys(), AWT_graphic_tree::show_ruler(), species_rename_cb(), species_rename_handler(), SQ_helix::SQ_calc_helix_layout(), SQ_physical_layout::SQ_calc_physical_layout(), SQ_ambiguities::SQ_count_ambiguities(), SQ_evaluate(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), SQ_remove_quality_entries(), transfer_field_of_listed_cb(), transfer_field_of_selected_cb(), transfer_single_field(), TreeAdmin::tree_append_remark(), TREE_install_update_callbacks(), tree_vars_callback(), wait_for_dbentry(), NodeTextBuilder::work(), writeStringToAlignment(), and FieldTransfer::WriteRule::writeTo().

GBDATA* GB_searchOrCreate_string ( GBDATA gb_container,
const char fieldpath,
const char default_value 
)
GBDATA* GB_searchOrCreate_int ( GBDATA gb_container,
const char fieldpath,
long  default_value 
)
GBDATA* GB_searchOrCreate_float ( GBDATA gb_container,
const char fieldpath,
float  default_value 
)
long GB_number_of_marked_subentries ( GBDATA gbd)
GBDATA* GB_first_marked ( GBDATA gbd,
const char keystring 
)
GBDATA* GB_following_marked ( GBDATA gbd,
const char keystring,
size_t  skip_over 
)
GBDATA* GB_next_marked ( GBDATA gbd,
const char keystring 
)
char* GB_read_fp ( FILE *  in)

like GB_read_file(), but works on already open file (useful together with GB_fopen_tempfile())

Note: File should be opened in text-mode (e.g. "rt")

Definition at line 271 of file adsocket.cxx.

References GBS_chrcat(), GBS_strclose(), and GBS_stropen().

Referenced by GB_read_file(), gbcms_sighup(), and read_export_format().

char* GB_read_file ( const char path)

read content of file 'path' into string (heap-copy)

if path is '-', read from STDIN

Returns
NULp in case of error (use GB_await_error() to get the message)

Definition at line 287 of file adsocket.cxx.

References GB_export_error(), GB_IO_error(), GB_read_fp(), GB_size_of_file(), GBS_eval_env(), NULp, and result.

Referenced by ARB_main(), aw_help_helpfile_changed_cb(), aw_help_search(), aw_ref_to_title(), AWT_show_file(), ed_submit_parse_event(), GB_get_arb_revision_tag(), AWT_configuration::Load(), main(), and RecordingMacro::RecordingMacro().

char* GB_map_FILE ( FILE *  in,
int  writeable 
)

Definition at line 323 of file adsocket.cxx.

References buffer, GB_export_error(), GB_export_errorf(), GB_size_of_FILE(), and NULp.

Referenced by GB_map_file(), and gb_recover_corrupt_file().

char* GB_map_file ( const char path,
int  writeable 
)

Definition at line 344 of file adsocket.cxx.

References buffer, GB_export_errorf(), GB_map_FILE(), and NULp.

Referenced by gb_map_mapfile(), and PTD_read_leafs_from_disk().

GB_ULONG GB_time_of_day ( void  )
GB_ERROR GB_textprint ( const char path)
GB_CSTR GB_getenvARB_XTERM ( void  )

Definition at line 493 of file adsocket.cxx.

References ARB_getenv_ignore_empty(), and NULp.

Referenced by AWT_console(), GB_getenv(), and GB_getenvARB_XCMD().

GB_CSTR GB_getenvUSER ( void  )
GB_CSTR GB_getenvARBHOME ( void  )

Definition at line 549 of file adsocket.cxx.

References EXIT_FAILURE, and getenv_existing_directory().

Referenced by GB_getenv(), GBS_funptr2readable(), readXmlTree(), and unitTesterDir().

GB_CSTR GB_getenvARBMACRO ( void  )
GB_CSTR GB_getenvARBMACROHOME ( void  )
GB_CSTR GB_getenvARB_GS ( void  )
GB_CSTR GB_getenvARB_PDFVIEW ( void  )

Definition at line 614 of file adsocket.cxx.

References GB_find_executable(), getenv_executable(), and NULp.

Referenced by aw_help_helpfile_changed_cb(), and GB_getenv().

GB_CSTR GB_getenvDOCPATH ( void  )
GB_CSTR GB_getenvHTMLDOCPATH ( void  )

Definition at line 633 of file adsocket.cxx.

References ARB_strdup(), GB_path_in_ARBLIB(), getenv_existing_directory(), and NULp.

Referenced by get_local_help_url().

NOT4PERL gb_getenv_hook GB_install_getenv_hook ( gb_getenv_hook  hook)

Definition at line 646 of file adsocket.cxx.

References getenv_hook.

Referenced by AW_unfold_path(), and ignore_arb_prop().

GB_CSTR GB_getenv ( const char env)
bool GB_host_is_local ( const char hostname)

Definition at line 693 of file adsocket.cxx.

References arb_assert, arb_gethostname(), ARB_strBeginsWith(), and ARB_stricmp().

Referenced by createCallOnSocketHost().

GB_ULONG GB_get_usable_memory ( void  )
NOT4PERL GB_ERROR GB_xcmd ( const char cmd,
XCMD_TYPE  exectype 
)
GB_CSTR GB_append_suffix ( const char name,
const char suffix 
)
GB_CSTR GB_canonical_path ( const char anypath)
GB_CSTR GB_concat_path ( GB_CSTR  anypath_left,
GB_CSTR  anypath_right 
)
GB_CSTR GB_concat_full_path ( const char anypath_left,
const char anypath_right 
)
GB_CSTR GB_unfold_in_directory ( const char relative_directory,
const char path 
)

Definition at line 1070 of file adsocket.cxx.

References GB_canonical_path(), GB_concat_full_path(), and is_absolute_path().

GB_CSTR GB_unfold_path ( const char pwd_envar,
const char path 
)
GB_CSTR GB_path_in_ARBHOME ( const char relative_path)
GB_CSTR GB_path_in_ARBLIB ( const char relative_path)
GB_CSTR GB_path_in_HOME ( const char relative_path)

Definition at line 1106 of file adsocket.cxx.

References GB_unfold_path().

Referenced by GB_getenvARB_PROP(), and GB_path_in_arb_temp().

GB_CSTR GB_path_in_arbprop ( const char relative_path)
GB_CSTR GB_path_in_ARBLIB ( const char relative_path_left,
const char anypath_right 
)

Definition at line 1112 of file adsocket.cxx.

References GB_concat_path(), and GB_path_in_ARBLIB().

FILE* GB_fopen_tempfile ( const char filename,
const char fmode,
char **  res_fullname 
)
char* GB_create_tempfile ( const char name)
char* GB_unique_filename ( const char name_prefix,
const char suffix 
)
void GB_remove_on_exit ( const char filename)
void GB_split_full_path ( const char fullpath,
char **  res_dir,
char **  res_fullname,
char **  res_name_only,
char **  res_suffix 
)
char* GBS_string_2_key ( const char str)
char* GB_memdup ( const char source,
size_t  len 
)
GB_ERROR GB_check_key ( const char key)
GB_ERROR GB_check_hkey ( const char key)
char* GBS_escape_string ( const char str,
const char chars_to_escape,
char  escape_char 
)

escape characters in 'str'

uses a special escape-method, which eliminates all 'chars_to_escape' completely from str (this makes further processing of the string more easy)

Parameters
strstring to escape
escape_charis the character used for escaping. For performance reasons it should be a character rarely used in 'str'.
chars_to_escapemay not contain 'A'-'Z' (these are used for escaping) and it may not be longer than 26 bytes
Returns
heap copy of escaped string

Inverse of GBS_unescape_string()

Definition at line 124 of file adstring.cxx.

References buffer, and gb_assert.

Referenced by colorDefChanged_callback(), insert_genes_of_organism(), and standard_list2file().

char* GBS_unescape_string ( const char str,
const char escaped_chars,
char  escape_char 
)

inverse of GB_escape_string() - for params see there

Definition at line 175 of file adstring.cxx.

References buffer, and gb_assert.

Referenced by colorDefTabNameChanged_callback(), parse_names_into_gene_struct(), and standard_file2list().

char* GBS_eval_env ( GB_CSTR  p)
long GBS_gcgchecksum ( const char seq)

Definition at line 247 of file adstring.cxx.

Referenced by gbl_gcgchecksum().

uint32_t GB_checksum ( const char seq,
long  length,
int  ignore_case,
const char exclude 
)
uint32_t GBS_checksum ( const char seq,
int  ignore_case,
const char exclude 
)
size_t GBS_shorten_repeated_data ( char data)

Definition at line 358 of file adstring.cxx.

References gb_assert, and orgLen.

Referenced by QUERY::DbQuery_update_list(), dump_internal(), QueryExpr::matches(), and SET_QUERIED().

char* GBS_merge_tagged_strings ( const char s1,
const char tag1,
const char replace1,
const char s2,
const char tag2,
const char replace2 
)
char* GBS_modify_tagged_string_with_ACI ( const char s,
const char dt,
const char tag,
const char aci,
GBL_call_env env 
)
char* GB_read_as_tagged_string ( GBDATA gbd,
const char tagi 
)
void GBS_fwrite_string ( const char strngi,
FILE *  out 
)

Definition at line 810 of file adstring.cxx.

Referenced by gb_write_one_child().

char* GBS_fconvert_string ( char buffer)

Definition at line 894 of file adstring.cxx.

References buffer, gb_assert, and NULp.

Referenced by gb_parse_ascii_rek().

char* GBS_replace_tabs_by_spaces ( const char text)

Definition at line 937 of file adstring.cxx.

References GBS_chrcat(), GBS_strclose(), and GBS_stropen().

Referenced by awt_aps_go(), and awt_aps_text_changed().

char* GBS_trim ( const char str)
char* GBS_log_action_to ( const char comment,
const char action,
bool  stamp 
)

concatenates 'comment' and 'action'. '
' is appended to existing 'comment' and/or 'action' (if missing).

Parameters
commentmay be NULp (=> result is 'action')
actionmay NOT be NULp
stamptrue -> prefix current timestamp in front of 'action'
Returns
heap copy of concatenation

Definition at line 990 of file adstring.cxx.

References dated_info(), GBS_chrcat(), GBS_strcat(), GBS_strclose(), and GBS_stropen().

Referenced by GBT_log_to_tree_remark(), ConsensusTreeBuilder::get_tree_remark(), nt_create_configuration(), EDB_root_bact::save_current_config(), TREE_load(), and TREE_write_Newick().

const char* GBS_funptr2readable ( void *  funptr,
bool  stripARBHOME 
)

Definition at line 1021 of file adstring.cxx.

References ARB_strBeginsWith(), and GB_getenvARBHOME().

Referenced by TypedDatabaseCallback::get_info().

DictData* GB_get_dictionary ( GBDATA gb_main,
const char key 
)
GB_ERROR GB_set_dictionary ( GBDATA gb_main,
const char key,
const DictData dd 
)
char* GB_arbtcpdat_path ( void  )

Definition at line 215 of file adtcp.cxx.

References GB_lib_file().

Referenced by awt_edit_arbtcpdat_cb(), and ArbTcpDat::update().

const char* GBS_scan_arb_tcp_param ( const char ipPort,
const char wantedParam 
)
const char* GBS_nameserver_tag ( const char add_field)

Definition at line 303 of file adtcp.cxx.

References ARB_strupper(), GBS_global_string_copy(), and RETURN_LOCAL_ALLOC.

Referenced by ARB_main(), and NameServerConnection::connect().

const char* GBS_ptserver_tag ( int  id)
const char* GBS_read_arb_tcp ( const char env)

Find an entry in the $ARBHOME/lib/arb_tcp.dat file

Be aware: GBS_read_arb_tcp returns a quite unusual string containing several string delimiters (0-characters). It contains all words (separated by space or tab in arb_tcp.dat) of the corresponding line in arb_tcp.dat. These words get concatenated (separated by 0 characters).

The first word (which matches the parameter env) is skipped. The second word (the socket info = "host:port") is returned directly as result. The third word is the server executable name. The fourth and following words are parameters to the executable.

To access these words follow this example:

const char *ipPort = GBS_read_arb_tcp(GBS_nameserver_tag(NULp)); if (ipPort) { const char *serverExe = strchr(ipPort, 0)+1; const char *para1 = strchr(serverExe, 0)+1; // always exists! const char *para2 = strchr(para1, 0)+1; if (para2[0]) { // para2 exists } } else { // handle error! }

see also GBS_read_arb_tcp_param() above

Returns NULp on error (which is exported in that case)

Definition at line 325 of file adtcp.cxx.

References error(), gb_assert, GB_export_error(), GB_getenvUSER(), GBS_global_string(), GBS_global_string_copy(), ArbTcpDat::get_entry(), ArbTcpDat::get_filename(), NULp, result, and ArbTcpDat::update().

Referenced by AP_probe_pt_look_for_server(), arb_look_and_kill_server(), arb_look_and_start_server(), ARB_main(), arb_start_server(), AW_select_nameserver(), NameServerConnection::connect(), gbcm_open_socket(), GBS_ptserver_id_to_choice(), MP_probe_pt_look_for_server(), pd_export_pt_server(), PD_probe_pt_look_for_server(), pd_query_pt_server(), run_command(), and sina_start().

const char* const* GBS_get_arb_tcp_entries ( const char matching)

returns a list of all matching non-user-specific entries found in arb_tcp.dat match is performed by GBS_string_matches (e.g. use "ARB_PT_SERVER*")

Definition at line 396 of file adtcp.cxx.

References error(), GB_export_error(), GB_MIND_CASE, GBS_string_matches(), ArbTcpDat::get_server_count(), ArbTcpDat::get_serverID(), id, NULp, and ArbTcpDat::update().

Referenced by AW_select_nameserver(), PT_selection::fill(), and pd_kill_pt_server().

const char* GBS_ptserver_logname ( void  )
void GBS_add_ptserver_logentry ( const char entry)

Definition at line 435 of file adtcp.cxx.

References GBS_ptserver_logname(), and NULp.

Referenced by enter_stage_1_build_tree(), pd_export_pt_server(), and run_command().

char* GBS_ptserver_id_to_choice ( int  i,
int  showBuild 
)
const char* GB_get_type_name ( GBDATA gbd)

Definition at line 66 of file arbdb.cxx.

References GB_TYPES_2_name(), and GBDATA::type().

Referenced by count_bases(), dump_internal(), GB_dump_db_path(), and gb_fix_recursive().

float GB_atof ( const char str)
GB_BUFFER GB_give_buffer ( size_t  size)
GB_BUFFER GB_increase_buffer ( size_t  size)

Definition at line 310 of file arbdb.cxx.

References alloc_buffer(), gb_local_data::buf1, gb_buffer::mem, NULp, and gb_buffer::size.

Referenced by gb_read_bin_rek_V2().

NOT4PERL int GB_give_buffer_size ( void  )

Definition at line 324 of file arbdb.cxx.

References gb_local_data::buf1, and gb_buffer::size.

Referenced by gb_read_bin_rek_V2().

GB_BUFFER GB_give_buffer2 ( long  size)

Definition at line 328 of file arbdb.cxx.

References gb_local_data::buf2, and give_buffer().

Referenced by GB_give_other_buffer(), gbcm_read_bin(), gbcm_write_bin(), and get_design_info().

char* GB_check_out_buffer ( GB_CBUFFER  buffer)
GB_BUFFER GB_give_other_buffer ( GB_CBUFFER  buffer,
long  size 
)
void GB_atexit ( void(*)()  exitfun)

Definition at line 396 of file arbdb.cxx.

References gb_local_data::atgbexit, gb_exitfun::exitfun, and gb_exitfun::next.

Referenced by GB_remove_on_exit().

void GB_init_gb ( void  )

Definition at line 506 of file arbdb.cxx.

References GB_shell::ensure_inside(), GBK_install_SIGSEGV_handler(), gbm_get_mem(), and gbm_init_mem().

Referenced by GB_login().

int GB_open_DBs ( void  )

Definition at line 516 of file arbdb.cxx.

References gb_local_data::open_dbs().

Referenced by aw_initstatus().

void GB_close ( GBDATA gbd)
long GB_read_int ( GBDATA gbd)

Definition at line 723 of file arbdb.cxx.

References GBDATA::as_entry(), GB_INT, GB_TEST_READ_NUM, gb_data_base_type_union::i, and GBENTRY::info.

Referenced by apply_command_to_alignment(), arb_prm_read(), AW_reactivate_all_questions(), AWTI_import_set_ali_and_type(), FieldReader::calc_value(), ED4_terminal::changed_by_database(), check_for_remote_command(), cmpByKey(), collectKeysRegisteredInDatabase(), create_nds_vars(), dump_internal(), ED4_alignment_length_changed(), ensure_trees_have_order(), Itemfield_Selection::fill(), gb_copy_explicit(), gb_find_value_equal(), GB_read_as_string(), GB_read_lossless_byte(), GB_read_lossless_int(), gb_write_one_child(), GBT_check_alignment(), GBT_get_color_group(), GBT_is_partial(), GBT_read_int(), GBT_read_tree_and_size(), gbt_read_tree_rek(), GBT_readOrCreate_int(), GBT_size_of_tree(), GBT_tree_info_string(), GEN_is_genome_db(), GEN_make_node_text_init(), GEN_make_node_text_nds(), GEN_read_position(), probe_input_data::get_checksum(), probe_input_data::get_geneabspos(), get_next_SAI_count(), probe_input_data::get_start(), probe_input_data::get_stop(), get_tree_idx(), FoundGroup::get_tree_order(), ED4_root::init_alignment(), KeySorter::KeySorter(), mark_as_macro_executor(), MG_transfer_fields_info(), NT_convert_gene_locations(), NT_format_all_alignments(), DB_scalable::read(), AW_awar::read_int(), read_tree_and_size_internal(), ItemFieldShader::scan_value_range_cb(), EDB_root_bact::search_sequence_data_rek(), SearchedTree::SearchedTree(), BoundActionTracker::set_recording(), ClientActionTracker::set_tracking_according_to(), show_all_changekeys(), SQ_evaluate(), SQ_mark_species(), SQ_pass2(), SQ_pass2_no_tree(), start_remote_command_for_application(), toggle_helix_for_SAI(), user_code_nr_changed_cb(), and NodeTextBuilder::work().

int GB_read_byte ( GBDATA gbd)
GBDATA* GB_read_pointer ( GBDATA gbd)
float GB_read_float ( GBDATA gbd)
long GB_read_count ( GBDATA gbd)
long GB_read_memuse ( GBDATA gbd)

Definition at line 756 of file arbdb.cxx.

References GBDATA::as_entry(), and GBENTRY::memsize().

Referenced by compress_sequence_tree().

long GB_calc_structure_size ( GBDATA gbd)
GB_CSTR GB_read_pntr ( GBDATA gbd)
GB_CSTR GB_read_char_pntr ( GBDATA gbd)

Definition at line 898 of file arbdb.cxx.

References GB_read_pntr(), GB_STRING, and GB_TEST_READ_PTR.

Referenced by ED4_root::add_to_selected(), alignTo(), alignToNextRelative(), apply_command_to_alignment(), arb_prm_read(), awt_add_sequences_to_list(), AWT_modify_managed_configs(), awt_open_ACI_URL_with_item(), PH_filter::calculate_column_homology(), calculateEndPosition(), CheckedConsistencies::CheckedConsistencies(), cmpByKey(), CON_export(), CON_insertSequences(), concatenateAlignments(), concatenateFieldsCreateNewSpecies(), config_modified_cb(), count_bases(), ImportTestData::countSpeciesAndData(), create_gene_species(), create_nds_vars(), db_updated_cb(), PH_display::display(), AP_sequence::do_lazy_load(), dump_internal(), ED4_getSaiColorString(), export_to_DB(), Itemfield_Selection::fill(), filter_columnstat_SAIs(), filter_posvar_SAI_for_ali(), findAffectedKeys(), Structure3D::FindTypeOfRNA(), g_b_put_sequences_in_container(), GB_command_interpreter_in_env(), gb_copy_explicit(), gb_find_value_equal(), GB_get_macro_error(), gb_index_find(), gb_load_key_data_and_dictionaries(), GB_read_lossless_byte(), GB_read_lossless_float(), GB_read_lossless_int(), GB_set_macro_error(), gb_uncompress_by_sequence(), gb_write_one_child(), GBT_check_alignment(), GBT_check_data(), GBT_commit_rename_session(), GBT_gen_accession_number(), GBT_get_alignment_names(), GBT_get_name(), GBT_read_char_pntr(), GBT_readOrCreate_char_pntr(), GBT_tree_info_string(), gbt_wait_for_remote_action(), gde_filter_weights(), gen_extract_gene_2_pseudoSpecies(), GEN_make_node_text_nds(), GEN_origin_gene(), GEN_origin_organism(), GEN_update_GENE_CONTENT(), probe_input_data::get_acc(), get_addid(), ST_ML::get_color_string(), AWT_configuration::get_config(), get_data_n_size(), probe_input_data::get_fullname(), Group::get_name(), FoundGroup::get_name(), RefEntries::RefSelector::get_refs(), get_SAI_description(), export_sequence_data::get_seq_data(), probe_input_data::get_shortname(), PosGene::getName(), PosGene::getType(), group_awar_changed_cb(), GBENTRY::index_check_in(), GBENTRY::index_check_out(), BI_helix::init(), BI_ecoli_ref::init(), insert_genes_of_organism(), is_named(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), main(), AW_awar::make_global(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), MG_create_db_dependent_rename_awars(), MG_create_remap(), SEC_structure_toggler::name(), new_gbt_message_created_cb(), no_data_error(), NT_convert_gene_locations(), NT_count_different_chars(), NT_format_all_alignments(), pd_get_the_gene_names(), pd_get_the_names(), PG_initSpeciesMaps(), PG_read_probe(), MostLikelySeq::print(), probe_design_event(), PS_extract_probe_data(), PS_get_probe_for_path(), PS_print_paths(), PT_init_map(), PT_prepare_species_sequence(), SequenceHandler::read_char_pntr(), AW_awar::read_char_pntr(), read_sequence_region(), readACC(), ReadArbdb(), ED4_root::remove_from_selected(), remove_redundant_translation(), DBwriter::renumberDuplicateGenes(), ED4_terminal::resolve_pointer_to_char_pntr(), run_command(), MostLikelySeq::set_sequence(), sina_start(), species_rename_cb(), species_rename_handler(), SQ_fetch_filtered_sequence(), st_ml_add_sequence_part_to_stat(), testDictionaryCompression(), trackAlignmentChanges(), translate_getInfo(), TranslateGeneToAminoAcidSequence(), translateSAItoColors(), UniqueNameDetector::UniqueNameDetector(), update_RangeList(), NodeTextBuilder::work(), and write_entry().

char* GB_read_string ( GBDATA gbd)

Definition at line 903 of file arbdb.cxx.

References GBDATA::as_entry(), GB_memdup(), GB_read_pntr(), GB_STRING, GB_TEST_READ_PTR, NULp, and GBENTRY::size().

Referenced by adaptCopiedAlignment(), ALI_translate_marked(), alignCompactedTo(), alignToNextRelative(), ARB_main(), awt_create_select_filter_window_aw_cb(), AWTC_pars_names(), AWTC_recreate_name(), ED4_terminal::changed_by_database(), compress_sequence_tree(), create_new_species(), Data::Data(), dot_missing_bases(), dot_sequence_by_consensus(), ED4_get_marked_from_menu(), ED4_pfold_set_SAI(), FastAligner_start(), fillSelNamList(), filter_posvar_SAI_for_ali(), CheckedConsistencies::forgetDoneChecks(), gb_cache_genome(), GB_read_as_string(), gb_set_compression(), GB_write_string(), gbl_read_seq_sai_or_species(), gbl_sequence(), GBT_read_string(), gbt_read_tree_rek(), GBT_readOrCreate_string(), gbt_wait_for_remote_action(), GEN_make_node_text_init(), GEN_make_node_text_nds(), get_helix_string(), ALI_ARBDB::get_SAI(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), get_taxonomy(), NodeTextBuilder::init(), insert_new_species_terminal(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), MERGE_sequences_simple(), MG_transfer_fields_info(), modsai_cb(), nt_build_sai_string(), NT_create_sai_from_pfold(), NT_del_mark_move_REF(), nt_species_join(), NT_suggestValidNames(), pars_create_all_awars(), parseCSV(), perform_block_operation_on_part_of_sequence(), perform_block_operation_on_whole_sequence(), primer_design_event_go(), primer_design_event_init(), probe_match_event(), PT_init_input_data(), PV_WriteTranslatedSequenceToDB(), react_to_command(), AW_awar::read_string(), read_tree_and_size_internal(), readCompactedSequence(), FoundGroup::rename_by_ACI(), reverseComplement(), SEC_seq_data::SEC_seq_data(), trackAlignmentChanges(), transfer_single_field(), TranslateGeneToAminoAcidSequence(), TreeAdmin::tree_append_remark(), TREE_write_Newick(), TREE_write_XML(), SpecSetRegistry::write_node_information(), and writeHistory().

size_t GB_read_string_count ( GBDATA gbd)
long GB_read_bits_count ( GBDATA gbd)
GB_CSTR GB_read_bits_pntr ( GBDATA gbd,
char  c_0,
char  c_1 
)
char* GB_read_bits ( GBDATA gbd,
char  c_0,
char  c_1 
)
GB_CSTR GB_read_bytes_pntr ( GBDATA gbd)
long GB_read_bytes_count ( GBDATA gbd)
char* GB_read_bytes ( GBDATA gbd)

Definition at line 968 of file arbdb.cxx.

References GBDATA::as_entry(), GB_memdup(), GB_read_bytes_pntr(), NULp, and GBENTRY::size().

Referenced by gb_read_dict_data().

GB_CUINT4* GB_read_ints_pntr ( GBDATA gbd)
long GB_read_ints_count ( GBDATA gbd)

Definition at line 1002 of file arbdb.cxx.

References GBDATA::as_entry(), GB_INTS, GB_TEST_READ_NUM, and GBENTRY::size().

Referenced by GB_read_from_ints().

GB_UINT4* GB_read_ints ( GBDATA gbd)

Definition at line 1007 of file arbdb.cxx.

References GBDATA::as_entry(), GB_memdup(), GB_read_ints_pntr(), NULp, and GBENTRY::size().

Referenced by ColumnStat::calculate().

GB_CFLOAT* GB_read_floats_pntr ( GBDATA gbd)
float* GB_read_floats ( GBDATA gbd)

Definition at line 1047 of file arbdb.cxx.

References GBDATA::as_entry(), GB_memdup(), GB_read_floats_pntr(), NULp, and GBENTRY::size().

char* GB_read_as_string ( GBDATA gbd)

reads basic db-field types and returns content as text.

See also
GB_write_autoconv_string
GB_readable_as_string

Definition at line 1054 of file arbdb.cxx.

References ARB_float_2_ascii(), ARB_strdup(), gb_assert, GB_BITS, GB_BYTE, GB_FLOAT, GB_INT, GB_read_bits(), GB_read_byte(), GB_read_float(), GB_read_int(), GB_read_string(), GB_STRING, GB_TYPE_readable_as_string(), GBS_global_string_copy(), NULp, and GBDATA::type().

Referenced by AWTC_pars_names(), AWTC_recreate_name(), FieldReader::calc_value(), checkAndMergeFields(), concatenateFieldsCreateNewSpecies(), count_bases(), create_new_species(), create_ref_hash(), createGroupFromSelected(), awt_string_handler::db_changed(), do_sth_with_species(), ED4_getSaiColorString(), ed_submit_info_event(), GB_command_interpreter_in_env(), gb_info(), GB_read_as_tagged_string(), gbs_build_replace_string(), GBT_convert_changekey(), GBT_read_as_string(), ED4_base::get_name_of_species(), get_species_id(), FINAL_TYPE< SEQTYPE >::get_target_data(), GetDisplayInfo(), group_species(), FilterDefinition::make_filter(), mergeSimilarSpecies(), MG_create_field_content(), MG_create_remap(), modify_fields_of_queried_cb(), perform_query_cb(), SequenceHandler::read_char_pntr(), SequenceHandler::read_string(), readFirstCompressedDataOf(), MultiFastaWriter::readString(), ItemFieldShader::scan_value_range_cb(), QUERY::search_duplicated_field_content(), set_field_of_queried_cb(), species_rename_join(), translateSAItoColors(), NodeTextBuilder::work(), and XML_recursive().

bool GB_readable_as_string ( GBDATA gbd)
NOT4PERL uint8_t GB_read_lossless_byte ( GBDATA gbd,
GB_ERROR error 
)

Reads an uint8_t previously written with GB_write_lossless_byte()

Parameters
gbdthe DB field
errorresult parameter (has to be NULp)
Returns
is undefined if error got set; contains read value otherwise

Definition at line 1087 of file arbdb.cxx.

References cannot_use_fun4entry(), gb_assert, GB_BYTE, GB_FLOAT, GB_have_error(), GB_incur_error(), GB_INT, GB_read_byte(), GB_read_char_pntr(), GB_read_float(), GB_read_int(), GB_STRING, result, and GBDATA::type().

NOT4PERL int32_t GB_read_lossless_int ( GBDATA gbd,
GB_ERROR error 
)

Reads an int32_t previously written with GB_write_lossless_int()

Parameters
gbdthe DB field
errorresult parameter (has to be NULp)
Returns
is undefined if error got set; contains read value otherwise

Definition at line 1122 of file arbdb.cxx.

References cannot_use_fun4entry(), gb_assert, GB_have_error(), GB_incur_error(), GB_INT, GB_read_char_pntr(), GB_read_int(), GB_STRING, result, and GBDATA::type().

NOT4PERL float GB_read_lossless_float ( GBDATA gbd,
GB_ERROR error 
)

Reads a float previously written with GB_write_lossless_float()

Parameters
gbdthe DB field
errorresult parameter (has to be NULp)
Returns
is undefined if error got set; contains read value otherwise

Definition at line 1149 of file arbdb.cxx.

References cannot_use_fun4entry(), gb_assert, GB_atof(), GB_FLOAT, GB_have_error(), GB_incur_error(), GB_read_char_pntr(), GB_read_float(), GB_STRING, result, and GBDATA::type().

long GB_read_from_ints ( GBDATA gbd,
long  index 
)

Definition at line 1180 of file arbdb.cxx.

References GB_read_ints_count(), GB_read_ints_pntr(), and NULp.

double GB_read_from_floats ( GBDATA gbd,
long  index 
)

Definition at line 1197 of file arbdb.cxx.

References GB_read_floats_count(), GB_read_floats_pntr(), and NULp.

GB_ERROR GB_write_byte ( GBDATA gbd,
int  i 
)
GB_ERROR GB_write_int ( GBDATA gbd,
long  i 
)
GB_ERROR GB_write_pointer ( GBDATA gbd,
GBDATA pointer 
)
GB_ERROR GB_write_float ( GBDATA gbd,
float  f 
)
GB_ERROR GB_write_pntr ( GBDATA gbd,
const char s,
size_t  bytes_size,
size_t  stored_size 
)
GB_ERROR GB_write_string ( GBDATA gbd,
const char s 
)

Definition at line 1385 of file arbdb.cxx.

References GBDATA::as_entry(), error(), gb_assert, GB_read_pntr(), GB_read_string(), GB_STRING, GB_TEST_NON_BUFFER, GB_TEST_WRITE, GB_write_pntr(), GBENTRY::memsize(), NULp, and GBENTRY::size().

Referenced by adaptCopiedAlignment(), ALI_realign_marked(), ALI_translate_marked(), alignCompactedTo(), alignToNextRelative(), EditedTerminal::apply(), ARB_main(), AW_awar::AW_awar(), awar_updated_cb(), AWT_modify_managed_configs(), awtc_nn_search_all_listed(), compress_sequence_tree(), CON_calc_max_freq(), CON_export(), concatenateAlignments(), concatenateFieldsCreateNewSpecies(), config_rename_handler(), create_ali_strEntry(), create_concatInfo_SAI(), create_gene_species(), create_nds_vars(), DB_create_string_field(), dot_sequence_by_consensus(), experiment_rename_handler(), g_b_create_master(), GB_clear_macro_error(), gb_convert_compression(), gb_copy_explicit(), gb_load_single_key_data(), gb_parse_ascii_rek(), gb_save_dictionary_data(), GB_searchOrCreate_string(), gb_set_compression(), GB_set_macro_error(), GB_write_autoconv_string(), GB_write_lossless_byte(), GB_write_lossless_float(), GB_write_lossless_int(), GBT_add_data(), GBT_commit_rename_session(), GBT_convert_changekey(), GBT_message(), GBT_remote_action_with_timeout(), GBT_remote_awar(), GBT_remote_read_awar(), GBT_rename_species(), GBT_write_group_name(), GBT_write_string(), gen_extract_gene_2_pseudoSpecies(), GEN_species_add_entry(), GEN_write_position(), gene_rename_handler(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), AW_awar::make_global(), MG_create_db_dependent_rename_awars(), modsai_cb(), NT_count_different_chars(), NT_create_sai_from_pfold(), NT_del_mark_move_REF(), nt_rename_configuration(), nt_species_join(), perform_block_operation_on_whole_sequence(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), probe_match_event(), ALI_ARBDB::put_SAI(), ALI_ARBDB::put_sequence(), ALI_ARBDB::put_sequence_string(), PV_WriteTranslatedSequenceToDB(), react_to_command(), ArbImporter::read_data(), readAndWrite(), CheckedConsistencies::register_as_performed(), DBwriter::renumberDuplicateGenes(), reverseComplement(), run_command(), AWT_configuration::set_config(), species_rename_handler(), SQ_pass2(), SQ_pass2_no_tree(), st_ml_add_quality_string_to_species(), trackAlignmentChanges(), transfer_single_field(), TreeAdmin::tree_append_remark(), FieldTransfer::unconvertedWrite(), write_entry(), ED4_terminal::write_sequence(), write_sequence_autoinc_alisize(), writeHistory(), DBwriter::writeSequence(), writeStringToAlignment(), writeToArb(), and FieldTransfer::ItemClonedByRuleSet::~ItemClonedByRuleSet().

GB_ERROR GB_write_bits ( GBDATA gbd,
const char bits,
long  size,
const char c_0 
)
GB_ERROR GB_write_bytes ( GBDATA gbd,
const char s,
long  size 
)
GB_ERROR GB_write_ints ( GBDATA gbd,
const GB_UINT4 i,
long  size 
)
GB_ERROR GB_write_floats ( GBDATA gbd,
const float *  f,
long  size 
)
GB_ERROR GB_write_autoconv_string ( GBDATA gbd,
const char val 
)

writes data to database field using automatic conversion. Warning: Conversion may cause silent data-loss! (e.g. writing "hello" to a numeric db-field results in zero content)

Writing back the unmodified(!) result of GB_read_as_string will not cause data loss.

Consider using the GB_write_lossless_...() functions below (and their counterparts GB_read_lossless_...()).

@@ refer to GBT_write_int_converted / GBT_write_float_converted

Definition at line 1477 of file arbdb.cxx.

References error(), GB_BITS, GB_BYTE, GB_FLOAT, GB_INT, GB_read_key_pntr(), GB_safe_atof(), GB_STRING, GB_write_bits(), GB_write_byte(), GB_write_float(), GB_write_int(), GB_write_string(), GBS_global_string(), and GBDATA::type().

Referenced by awt_string_handler::awar_changed(), FieldTransfer::convertAndWrite(), mg_check_field_cb(), modify_fields_of_queried_cb(), perform_block_operation_on_part_of_sequence(), set_field_of_queried_cb(), and SequenceHandler::write_string().

GB_ERROR GB_write_lossless_byte ( GBDATA gbd,
uint8_t  byte 
)

Writes an uint8_t to a database field capable to store any value w/o loss.

Returns
error otherwise The corresponding field filter is FIELD_FILTER_BYTE_WRITEABLE.

Definition at line 1502 of file arbdb.cxx.

References buffer, cannot_use_fun4entry(), GB_BYTE, GB_FLOAT, GB_INT, GB_STRING, GB_write_byte(), GB_write_float(), GB_write_int(), GB_write_string(), and GBDATA::type().

GB_ERROR GB_write_lossless_int ( GBDATA gbd,
int32_t  i 
)

Writes an int32_t to a database field capable to store any value w/o loss.

Returns
error otherwise The corresponding field filter is FIELD_FILTER_INT_WRITEABLE.

Definition at line 1521 of file arbdb.cxx.

References buffer, BUFSIZE, cannot_use_fun4entry(), gb_assert, GB_INT, GB_STRING, GB_write_int(), GB_write_string(), and GBDATA::type().

Referenced by FieldTransfer::convertAndWrite(), mark_action(), and mergeSimilarSpecies().

GB_ERROR GB_write_lossless_float ( GBDATA gbd,
float  f 
)

Writes a float to a database field capable to store any value w/o loss.

Returns
error otherwise The corresponding field filter is FIELD_FILTER_FLOAT_WRITEABLE.

Definition at line 1544 of file arbdb.cxx.

References buffer, BUFSIZE, cannot_use_fun4entry(), gb_assert, GB_FLOAT, GB_STRING, GB_write_float(), GB_write_string(), and GBDATA::type().

Referenced by FieldTransfer::convertAndWrite().

int GB_read_security_write ( GBDATA gbd)
int GB_read_security_read ( GBDATA gbd)

Definition at line 1574 of file arbdb.cxx.

References GB_GET_SECURITY_READ, and GB_test_transaction().

int GB_read_security_delete ( GBDATA gbd)

Definition at line 1578 of file arbdb.cxx.

References GB_GET_SECURITY_DELETE, and GB_test_transaction().

Referenced by ad_tree_set_security().

GB_ERROR GB_write_security_write ( GBDATA gbd,
unsigned long  level 
)
GB_ERROR GB_write_security_read ( GBDATA gbd,
unsigned long  level 
)
GB_ERROR GB_write_security_delete ( GBDATA gbd,
unsigned long  level 
)
GB_ERROR GB_write_security_levels ( GBDATA gbd,
unsigned long  readlevel,
unsigned long  writelevel,
unsigned long  deletelevel 
)
void GB_change_my_security ( GBDATA gbd,
int  level 
)
GB_TYPES GB_read_type ( GBDATA gbd)
bool GB_is_container ( GBDATA gbd)

Definition at line 1646 of file arbdb.cxx.

References GBDATA::is_container().

Referenced by gbs_build_replace_string(), and XML_recursive().

char* GB_read_key ( GBDATA gbd)
GB_CSTR GB_read_key_pntr ( GBDATA gbd)
GBQUARK GB_find_existing_quark ( GBDATA gbd,
const char key 
)
Returns
existing quark for 'key' (-1 if key is NULp, 0 if key is unknown)

Definition at line 1688 of file arbdb.cxx.

References GB_MAIN(), and key2quark().

Referenced by FoundGroup::delete_from_DB(), gb_find_internal(), GB_first_marked(), GB_following_marked(), and GB_has_key().

GBQUARK GB_find_or_create_quark ( GBDATA gbd,
const char key 
)
Returns
existing or newly created quark for 'key'

Definition at line 1693 of file arbdb.cxx.

References gb_find_or_create_quark(), and GB_MAIN().

Referenced by Dict::canDecompress(), GB_create_index(), FINAL_TYPE< SEQTYPE >::ItemQueryKey(), NT_fix_dict_compress(), and KeyInfo::testCompressed().

GBQUARK GB_get_quark ( GBDATA gbd)
bool GB_has_key ( GBDATA gbd,
const char key 
)
long GB_read_clock ( GBDATA gbd)
GBDATA* GB_get_father ( GBDATA gbd)
GBDATA* GB_get_grandfather ( GBDATA gbd)
GBDATA* GB_get_root ( GBDATA gbd)
bool GB_is_ancestor_of ( GBDATA gb_ancestor,
GBDATA gb_descendant 
)
GBDATA* GB_create ( GBDATA father,
const char key,
GB_TYPES  type 
)
GBDATA* GB_create_container ( GBDATA father,
const char key 
)

Create a new DB container

Parameters
fatherparent container
keyname of created container
Returns
  • created container
  • NULp on failure (error is exported then)
See also
GB_create()

Definition at line 1827 of file arbdb.cxx.

References GBDATA::expect_container(), gb_assert, GB_check_key(), gb_create_container(), GB_export_error(), GB_have_error(), GB_internal_errorf(), GB_test_transaction(), and NULp.

Referenced by FINAL_TYPE< SEQTYPE >::addSequence(), ARB_main(), concatenateFieldsCreateNewSpecies(), copy_SAI_cb(), copy_SAI_to_species_cb(), copy_tree_container(), create_data_entry(), create_gene_species(), create_nds_vars(), create_new_species(), DB_create_container(), experiment_copy_handler(), find_or_create(), findOrCreate_configuration(), gb_clone_explicit(), gb_convert_V2_to_V3(), GBT_add_data(), GBT_add_new_changekey_to_keypath(), GBT_create(), GBT_create_alignment(), GBT_find_or_create_item_rel_item_data(), GBT_rename_alignment(), gbt_rename_alignment_of_item(), gbt_write_tree_nodes(), GEN_create_nds_vars(), GEN_create_nonexisting_gene_rel_gene_data(), GEN_find_or_create_gene_rel_gene_data(), gene_copy_handler(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), MERGE_sequences_simple(), MG_copy_and_check_alignments(), MG_transfer_config(), MG_transfer_extended(), MG_transfer_one_species(), move_species_to_extended(), NT_create_sai_from_pfold(), NT_importValidNames(), nt_species_join(), ArbImporter::read_data(), species_copy_cb(), transfer_field_of_listed_cb(), transfer_tree(), tree_write_byte(), tree_write_float(), GroupBuilder::update_group(), and SpecSetRegistry::write_node_information().

bool GB_allow_compression ( GBDATA gb_main,
bool  allow_compression 
)

Definition at line 1895 of file arbdb.cxx.

References GB_MAIN_TYPE::compression_mask, and GB_MAIN().

Referenced by GB_delete(), and gbt_write_tree().

GB_ERROR GB_delete ( GBDATA *&  source)

delete a database entry. MAY(!) set source to NULp.

Definition at line 1904 of file arbdb.cxx.

References GB_MAIN_TYPE::call_pending_callbacks(), gb_flag_types::compressed_data, GBDATA::flags, GB_allow_compression(), gb_delete_entry(), GB_DELETED, GB_get_root(), GB_GET_SECURITY_DELETE, gb_main, GB_MAIN(), GB_read_key_pntr(), gb_set_compression(), GB_test_transaction(), gb_touch_entry(), GBS_global_string(), GB_MAIN_TYPE::get_transaction_level(), and NULp.

Referenced by ARB_main(), AW_awar::AW_awar(), AW_forget_all_window_geometry(), awtc_nn_search_all_listed(), calc_pvp(), compress_sequence_tree(), CON_export(), config_comment_changed_cb(), create_nds_vars(), AP_pos_var::delete_aliEntry_from_SAI(), FoundGroup::delete_from_DB(), delete_kept_ghostnodes(), delete_queried_species_cb(), delete_SAI_cb(), TreeAdmin::delete_tree_cb(), delete_unused_changekeys(), deleteDataOfKey(), edit_SAI_description(), AWT_configuration::erase_deleted_configs(), experiment_delete_cb(), export_to_DB(), FastAligner_delete_temp_entries(), field_delete_cb(), CheckedConsistencies::forgetDoneChecks(), gb_clone_explicit(), gb_load_key_data_and_dictionaries(), gb_save_dictionary_data(), gb_search_system_folder(), GBT_check_alignment(), GBT_convert_changekey(), GBT_rename_alignment(), gbt_rename_alignment_of_item(), GBT_rename_tree(), GBT_set_color_group(), gbt_write_tree(), gbt_write_tree_nodes(), GEN_create_nds_vars(), GEN_write_position(), gene_delete_cb(), ArbImporter::import_data(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), loadsave_colorset_cb(), MERGE_sequences_simple(), mg_check_field_cb(), MG_config_delete_cb(), MG_extended_delete_cb(), MG_transfer_one_species(), modify_fields_of_queried_cb(), move_species_to_extended(), new_gbt_message_created_cb(), NT_convert_gene_locations(), NT_create_sai_from_pfold(), NT_del_mark_move_REF(), nt_delete_configuration(), NT_delete_mark_all_cb(), NT_deleteValidNames(), NT_fix_gene_data(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), probe_match_event(), PT_prepare_data(), PT_prepare_species_sequence(), read_tree_and_size_internal(), SEC_structure_toggler::remove(), remove_dup_colors(), remove_redundant_translation(), AWT_graphic_tree::save_to_DB(), GBT_config::saveAsOver(), set_field_of_queried_cb(), set_SAI_group(), species_delete_cb(), species_rename_join(), SQ_remove_quality_entries(), st_remove_entries(), AWT_graphic_tree::toggle_group(), transfer_single_field(), transfer_tree(), translate_removeInfo(), tree_write_byte(), tree_write_float(), undo_entry(), SpecSetRegistry::write_node_information(), and FieldTransfer::ItemClonedByRuleSet::~ItemClonedByRuleSet().

GB_ERROR GB_copy_dropProtectMarksAndTempstate ( GBDATA dest,
GBDATA source 
)
GB_ERROR GB_copy_dropMarksAndTempstate ( GBDATA dest,
GBDATA source 
)

first attempt to fix traditional GB_copy_dropProtectMarksAndTempstate. As well NOT RECOMMENDED!

does correctly copy protection. clears marks + temporary state (see GB_copy_dropProtectMarksAndTempstate).

Will become obsolete!

Definition at line 2155 of file arbdb.cxx.

References CM_COPY_WITHPROTECT, and gb_copy_checked().

Referenced by ARB_main(), and MERGE_sequences_simple().

GB_ERROR GB_copy_std ( GBDATA dest,
GBDATA source 
)

recommended copy flavour: skips temp, preserves protection and marks. deletes other flags (e.g. query flag). sub-entries existing in 'dest' will not get overwritten.

Definition at line 2166 of file arbdb.cxx.

References CM_COPY_STANDARD, and gb_copy_checked().

GB_ERROR GB_copy_overlay ( GBDATA dest,
GBDATA source 
)

overlays 'dest' with 'source'. sub-entries existing in 'dest' will be overwritten! also applies to sub-containers.

Definition at line 2174 of file arbdb.cxx.

References CM_COPY_STANDARD, CM_OVERWRITE_EXISTING, and gb_copy_checked().

GB_ERROR GB_copy_full ( GBDATA dest,
GBDATA source 
)

complete copy (does also copy temporary entries)

Definition at line 2182 of file arbdb.cxx.

References CM_COPY_FULL, and gb_copy_checked().

GBDATA* GB_clone ( GBDATA gb_destCont,
GBDATA gb_source 
)

copy a clone of 'gb_source' into container 'gb_destCont' (like GB_copy_std would do).

Returns
pointer to clone (on success) or NULp (in which case an error MAY be exported).

Definition at line 2188 of file arbdb.cxx.

References GBDATA::as_container(), CM_COPY_STANDARD, error(), GBDATA::flags2, gb_flag_types2::folded_container, gb_assert, gb_clone_explicit(), GB_export_error(), GB_have_error(), GB_is_ancestor_of(), gb_unfold(), GBDATA::is_container(), and NULp.

char* GB_get_subfields ( GBDATA gbd)

Get all subfield names

Returns
all subfields of 'gbd' as ';'-separated heap-copy (first and last char of result is a ';')

Definition at line 2217 of file arbdb.cxx.

References ARB_alloc(), ARB_strdup(), GBDATA::as_container(), GBDATA::flags2, gb_flag_types2::folded_container, gb_assert, GB_child(), GB_nextChild(), GB_read_key_pntr(), gb_stpcpy(), GB_test_transaction(), gb_unfold(), GBDATA::is_container(), NULp, and result.

Referenced by checkAndMergeFields(), and create_new_species().

GB_ERROR GB_set_temporary ( GBDATA gbd)
GB_ERROR GB_clear_temporary ( GBDATA gbd)
bool GB_is_temporary ( GBDATA gbd)
bool GB_in_temporary_branch ( GBDATA gbd)
Returns
true, if 'gbd' is member of a temporary subtree, i.e. if GB_is_temporary(itself or any parent)

Definition at line 2307 of file arbdb.cxx.

References GB_get_father(), and GB_is_temporary().

Referenced by GB_create().

GB_ERROR GB_push_transaction ( GBDATA gbd)

start a transaction if no transaction is running. (otherwise only trace nested transactions)

recommended transaction usage:

1 GB_ERROR myFunc() {
2  GB_ERROR error = GB_push_transaction(gbd);
3  if (!error) {
4  error = ...;
5  }
6  return GB_end_transaction(gbd, error);
7 }
8 
9 void myFunc() {
10  GB_ERROR error = GB_push_transaction(gbd);
11  if (!error) {
12  error = ...;
13  }
14  GB_end_transaction_show_error(gbd, error, aw_message);
15 }
See also
GB_pop_transaction(), GB_end_transaction(), GB_begin_transaction()

Definition at line 2482 of file arbdb.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::push_transaction().

Referenced by alignCompactedTo(), AP_create_max_freq_window(), ARB_main(), awt_string_handler::awar_changed(), awt_create_2_filter_window(), awt_create_select_filter(), awt_create_select_filter_win(), awt_create_select_filter_window_aw_cb(), awt_create_select_filter_window_gb_cb(), awt_get_filter(), boundloc_changed_cb(), build_reverse_complement(), calculateEndPosition(), check_for_remote_command(), CON_calculate(), concatenateAlignments(), concatenateFieldsCreateNewSpecies(), count_mark_all_cb(), DbScanner::create(), create_gene_species(), ED4_root::create_hierarchy(), create_nds_vars(), QUERY::create_query_box(), QUERY::DbQuery_update_list(), di_autodetect_callback(), DI_create_matrix_variables(), DI_create_matrix_window(), dump_internal(), ED4_getSaiColorString(), executeKeystroke(), experiment_field_selection_list_rescan(), field_convert_commit_cb(), field_create_cb(), MO_Liste::fill_marked_bakts(), Structure3D::FindTypeOfRNA(), gb_info(), GB_print_debug_information(), GBT_begin_rename_session(), GBT_convert_changekey(), GBT_find_or_create_item_rel_item_data(), GBT_get_item_count(), GBT_install_message_handler(), GBT_mark_all(), GBT_mark_all_that(), GBT_message(), GBT_read_as_string(), GBT_read_char_pntr(), GBT_read_float(), GBT_read_int(), GBT_read_string(), GBT_readOrCreate_char_pntr(), GBT_readOrCreate_float(), GBT_readOrCreate_int(), GBT_readOrCreate_string(), GBT_write_byte(), GBT_write_float(), GBT_write_int(), GBT_write_string(), GEN_create_nds_vars(), GEN_create_nonexisting_gene_rel_gene_data(), GEN_find_or_create_gene_rel_gene_data(), gene_field_selection_list_rescan(), MO_Liste::get_all_species(), get_DB_state(), group_species(), GBENTRY::index_check_out(), launch_MapViewer_cb(), PHDATA::load(), ARB_seqtree_root::loadFromDB(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), mark_queried_cb(), MP_mark_probes_in_tree(), new_gbt_message_created_cb(), nt_changesecurity(), NT_reload_tree_event(), perform_query_cb(), popup_new_main_window(), probe_match_event(), PT_init_map(), AWT_canvas::push_transaction(), Aligner::run(), AW_root::save_properties(), GBT_config::saveAsOver(), ARB_seqtree_root::saveToDB(), AP_tree_root::saveToDB(), set_addid(), set_DB_state(), species_field_selection_list_rescan(), sq_calc_seq_quality_cb(), SQ_evaluate(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), SQ_remove_quality_entries(), st_ok_cb(), translateSAItoColors(), QUERY::unquery_all(), and ED4_terminal::write_sequence().

GB_ERROR GB_pop_transaction ( GBDATA gbd)

commit a transaction started with GB_push_transaction()

Definition at line 2512 of file arbdb.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::pop_transaction().

Referenced by alignCompactedTo(), AP_create_max_freq_window(), ARB_main(), awt_string_handler::awar_changed(), awt_create_2_filter_window(), awt_create_select_filter(), awt_create_select_filter_win(), awt_create_select_filter_window_aw_cb(), awt_create_select_filter_window_gb_cb(), awt_get_filter(), calculateEndPosition(), check_for_remote_command(), count_mark_all_cb(), DbScanner::create(), ED4_root::create_hierarchy(), create_nds_vars(), QUERY::create_query_box(), QUERY::DbQuery_update_list(), di_autodetect_callback(), DI_create_matrix_variables(), DI_create_matrix_window(), dump_internal(), ED4_getSaiColorString(), experiment_field_selection_list_rescan(), field_create_cb(), MO_Liste::fill_marked_bakts(), Structure3D::FindTypeOfRNA(), GB_end_transaction(), gb_info(), GB_print_debug_information(), GBT_get_item_count(), GBT_install_message_handler(), GBT_mark_all(), GBT_mark_all_that(), GBT_read_as_string(), GBT_read_char_pntr(), GBT_read_float(), GBT_read_int(), GBT_read_string(), GBT_readOrCreate_char_pntr(), GBT_readOrCreate_float(), GBT_readOrCreate_int(), GBT_readOrCreate_string(), gene_field_selection_list_rescan(), MO_Liste::get_all_species(), PHDATA::load(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), mark_queried_cb(), MP_mark_probes_in_tree(), new_gbt_message_created_cb(), nt_changesecurity(), NT_reload_tree_event(), perform_query_cb(), AWT_canvas::pop_transaction(), popup_new_main_window(), probe_match_event(), AW_root::save_properties(), species_field_selection_list_rescan(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), SQ_remove_quality_entries(), translateSAItoColors(), QUERY::unquery_all(), and ED4_terminal::write_sequence().

GB_ERROR GB_begin_transaction ( GBDATA gbd)

like GB_push_transaction(), but fails if there is already an transaction running.

See also
GB_commit_transaction() and GB_abort_transaction()

Definition at line 2516 of file arbdb.cxx.

References GB_MAIN_TYPE::begin_transaction(), and GB_MAIN().

Referenced by ARB_main(), FINAL_TYPE< SEQTYPE >::ArbWriter(), awtc_nn_search_all_listed(), ALI_ARBDB::begin_transaction(), config_rename_handler(), copy_rename_handler(), copy_SAI_cb(), copy_SAI_to_species_cb(), create_ali_handler(), create_new_species(), delete_queried_species_cb(), delete_SAI_cb(), di_calculate_tree_cb(), ED4_remove_faligner_entries(), ED4_timer(), ED4_undo_redo(), ED4_with_whole_block(), enter_stage_1_build_tree(), experiment_copy_handler(), experiment_create_handler(), experiment_rename_handler(), export_to_DB(), extended_rename_handler(), field_delete_cb(), fillSelNamList(), g_b_undo(), gb_create_dictionaries(), GB_fix_database(), GB_login(), gb_read_bin(), gbcms_talking_begin_transaction(), gbcms_talking_init_transaction(), GBT_remote_action_with_timeout(), GBT_remote_awar(), GBT_remote_read_awar(), gbt_wait_for_remote_action(), GEN_perform_command(), GEN_undo_cb(), gene_copy_handler(), gene_create_cb(), gene_rename_handler(), getArbFilter(), hide_field_cb(), ArbImporter::import_data(), insdel_event(), insdel_sai_event(), main(), mergeSimilarSpecies(), mg_check_field_cb(), MG_config_delete_cb(), MG_copy_and_check_alignments(), MG_extended_delete_cb(), MG_merge_tagged_field_cb(), MG_save_cb(), MG_save_quick_result_cb(), MG_transfer_config(), MG_transfer_extended(), mg_transfer_listed_species(), mg_transfer_selected_species(), MG_transfer_tree(), modify_fields_of_queried_cb(), move_species_to_extended(), nt_add_partial(), NT_count_different_chars(), NT_create_sai_from_pfold(), NT_database_optimization(), NT_deleteValidNames(), NT_importValidNames(), NT_suggestValidNames(), NTREE_move_tree_info(), ALI_ARBDB::open(), pars_start_cb(), pd_get_the_gene_names(), pd_get_the_names(), probe_read_data_base(), PT_init_input_data(), PT_prepare_data(), PV_WriteTranslatedSequenceToDB(), react_to_command(), rename_SAI_cb(), reorder_keys(), reorder_up_down(), resort_data_base(), GB_MAIN_TYPE::save_quick(), SEC_undo_cb(), selectValidNameFromList(), served(), set_field_of_queried_cb(), set_protection_of_queried_cb(), sina_start(), species_create_handler(), species_rename_join(), start_remote_command_for_application(), transfer_field_of_listed_cb(), transfer_field_of_selected_cb(), ScopedTransporter::transferAllIn(), transpro_event(), TreeAdmin::tree_copy_or_rename_cb(), wait_for_dbentry(), and writeToArb().

GB_ERROR GB_no_transaction ( GBDATA gbd)

Definition at line 2523 of file arbdb.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::no_transaction().

Referenced by run_command().

GB_ERROR GB_abort_transaction ( GBDATA gbd)

abort a running transaction, i.e. forget all changes made to DB inside the current transaction.

May be called instead of GB_pop_transaction() or GB_commit_transaction()

If a nested transactions got aborted, committing a surrounding transaction will silently abort it as well.

Definition at line 2527 of file arbdb.cxx.

References GB_MAIN_TYPE::abort_transaction(), and GB_MAIN().

Referenced by ARB_main(), awt_string_handler::awar_changed(), create_new_species(), delete_queried_species_cb(), enter_stage_1_build_tree(), GB_end_transaction(), gbcms_talking_begin_transaction(), gbcms_talking_init_transaction(), GBT_abort_rename_session(), ArbImporter::import_data(), nt_add_partial(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), and SQ_remove_quality_entries().

GB_ERROR GB_commit_transaction ( GBDATA gbd)
GB_ERROR GB_end_transaction ( GBDATA gbd,
GB_ERROR  error 
)

abort or commit transaction

@ param error

  • if NULp commit transaction
  • else abort transaction

always commits in no-transaction-mode

Returns
error or transaction error
See also
GB_push_transaction() for example

Definition at line 2549 of file arbdb.cxx.

References ASSERT_RESULT, error(), GB_abort_transaction(), GB_get_transaction_level(), GB_pop_transaction(), and NULp.

Referenced by ARB_main(), check_for_remote_command(), GB_transaction::close(), CON_calculate(), concatenateFieldsCreateNewSpecies(), config_rename_handler(), copy_rename_handler(), copy_SAI_cb(), copy_SAI_to_species_cb(), create_ali_handler(), create_gene_species(), create_new_species(), di_calculate_tree_cb(), experiment_copy_handler(), experiment_create_handler(), experiment_rename_handler(), extended_rename_handler(), fillSelNamList(), g_b_undo(), gb_create_dictionaries(), GB_end_transaction_show_error(), GB_fix_database(), GBT_commit_rename_session(), GBT_convert_changekey(), GBT_find_or_create_item_rel_item_data(), GBT_message(), GBT_remote_action_with_timeout(), GBT_remote_awar(), GBT_remote_read_awar(), gbt_wait_for_remote_action(), GBT_write_byte(), GBT_write_float(), GBT_write_int(), GBT_write_string(), GEN_create_nds_vars(), GEN_create_nonexisting_gene_rel_gene_data(), GEN_find_or_create_gene_rel_gene_data(), gene_copy_handler(), gene_rename_handler(), get_DB_state(), GBENTRY::index_check_out(), launch_MapViewer_cb(), ARB_seqtree_root::loadFromDB(), main(), mg_check_field_cb(), MG_transfer_config(), MG_transfer_extended(), mg_transfer_listed_species(), mg_transfer_selected_species(), MG_transfer_tree(), modify_fields_of_queried_cb(), NT_database_optimization(), NT_importValidNames(), NTREE_move_tree_info(), pars_start_cb(), pd_get_the_gene_names(), probe_read_data_base(), PT_init_map(), PT_prepare_data(), rename_SAI_cb(), resort_data_base(), Aligner::run(), GBT_config::saveAsOver(), ARB_seqtree_root::saveToDB(), AP_tree_root::saveToDB(), selectValidNameFromList(), set_addid(), set_DB_state(), species_create_handler(), sq_calc_seq_quality_cb(), SQ_evaluate(), st_ok_cb(), start_remote_command_for_application(), transfer_field_of_listed_cb(), transfer_field_of_selected_cb(), ScopedTransporter::transferAllIn(), TreeAdmin::tree_copy_or_rename_cb(), and writeToArb().

void GB_end_transaction_show_error ( GBDATA gbd,
GB_ERROR  error,
void(*)(GB_ERROR error_handler 
)
int GB_get_transaction_level ( GBDATA gbd)
Returns
transaction level <0 -> in no-transaction-mode (abort is impossible) 0 -> not in transaction 1 -> one single transaction 2, ... -> nested transactions

Definition at line 2578 of file arbdb.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::get_transaction_level().

Referenced by ALI_realign_marked(), aw_input(), GB_end_transaction(), nt_rename_configuration(), Aligner::run(), and AW_awar::set_temp_if_is_default().

GB_ERROR GB_release ( GBDATA gbd)
int GB_nsons ( GBDATA gbd)

return number of child entries

@@ does this work in clients ?

Definition at line 2624 of file arbdb.cxx.

References GBDATA::as_container(), GBCONTAINER::d, GBDATA::is_container(), and gb_data_list::size.

Referenced by resort_data_base().

void GB_disable_quicksave ( GBDATA gbd,
const char reason 
)

Disable quicksaving database

Parameters
gbdany DB node
reasonwhy quicksaving is not allowed

Definition at line 2635 of file arbdb.cxx.

References GB_MAIN().

Referenced by apply_command_to_alignment(), gb_convert_V2_to_V3(), GB_login(), GB_optimize(), GB_resort_data_base(), and GBT_compress_sequence_tree2().

GB_ERROR GB_resort_data_base ( GBDATA gb_main,
GBDATA **  new_order_list,
long  listsize 
)
bool GB_user_flag ( GBDATA gbd,
unsigned char  user_bit 
)
void GB_raise_user_flag ( GBDATA gbd,
unsigned char  user_bit 
)
void GB_clear_user_flag ( GBDATA gbd,
unsigned char  user_bit 
)
void GB_write_user_flag ( GBDATA gbd,
unsigned char  user_bit,
bool  state 
)

Definition at line 2753 of file arbdb.cxx.

References GB_clear_user_flag(), and GB_raise_user_flag().

Referenced by NT_create_config_after_import().

void GB_write_flag ( GBDATA gbd,
long  flag 
)