ad_prot.h File Reference

#include <attributes.h>

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Functions
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)
GBDATA *	EXP_next_experiment (GBDATA *gb_experiment)
GBDATA *	EXP_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)
GBDATA *	GEN_findOrCreate_gene_data (GBDATA *gb_species)
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)
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)
GBDATA *	GEN_next_gene (GBDATA *gb_gene)
GBDATA *	GEN_first_marked_gene (GBDATA *gb_species)
GBDATA *	GEN_next_marked_gene (GBDATA *gb_gene)
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)
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)
NOT4PERL void	GB_dump (GBDATA *gbd)
NOT4PERL void	GB_dump_no_limit (GBDATA *gbd)
GB_ERROR	GB_fix_database (GBDATA *gb_main)
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)
void	GB_set_next_main_idx (long idx)
GBDATA *	GB_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 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)
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)
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)
void	GBS_read_dir (StrArray &names, const char *dir, const char *mask)
const char *	GB_get_arb_revision_tag (void)
GB_HASH *	GBS_create_hash (long estimated_elements, GB_CASE case_sens)
GB_HASH *	GBS_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)
char *	GBS_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 char *	GBS_hash_next_element_that (const GB_HASH *hs, const char *last_key, bool(*condition)(const char *key, long val, void *cd), void *cd)
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_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)
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)
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) __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
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)
bool	GB_supports_mapfile (void)
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)
void	GB_random_seed (unsigned seed)
int	GB_random (int range)
GB_ERROR	GB_optimize (GBDATA *gb_main)
GB_ERROR	GBC_await_error (void)
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)
GBDATA *	GB_child (GBDATA *father)
GBDATA *	GB_nextChild (GBDATA *child)
GBDATA *	GB_entry (GBDATA *father, const char *key)
GBDATA *	GB_nextEntry (GBDATA *entry)
GBDATA *	GB_followingEntry (GBDATA *entry, size_t skip_over)
size_t	GB_countEntries (GBDATA *father, const char *key)
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)
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)
char *	GB_read_file (const char *path)
char *	GB_map_FILE (FILE *in, int writeable)
char *	GB_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_concat_path_in_ARBLIB (const char *relative_path_left, const char *anypath_right)
GB_CSTR	GB_path_in_HOME (const char *relative_path)
GB_CSTR	GB_path_in_arbprop (const char *relative_path)
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) __ATTR__USERESULT
GB_ERROR	GB_check_hkey (const char *key) __ATTR__USERESULT
char *	GBS_escape_string (const char *str, const char *chars_to_escape, char escape_char)
char *	GBS_unescape_string (const char *str, const char *escaped_chars, char escape_char)
char *	GBS_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)
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)
char *	GBS_fconvert_string (char *buffer)
char *	GBS_replace_tabs_by_spaces (const char *text)
char *	GBS_trim (const char *str)
char *	GBS_log_action_to (const char *comment, const char *action, bool stamp)
const char *	GBS_funptr2readable (void *funptr, bool stripARBHOME)
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)
const char *	GBS_scan_arb_tcp_param (const char *ipPort, const char *wantedParam)
const char *	GBS_nameserver_tag (const char *add_field)
const char *	GBS_ptserver_tag (int id)
const char *	GBS_read_arb_tcp (const char *env)
const char *const *	GBS_get_arb_tcp_entries (const char *matching)
const char *	GBS_ptserver_logname (void)
void	GBS_add_ptserver_logentry (const char *entry)
char *	GBS_ptserver_id_to_choice (int i, int showBuild)
const char *	GB_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)
char *	GB_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)
GBDATA *	GB_read_pointer (GBDATA *gbd)
float	GB_read_float (GBDATA *gbd)
long	GB_read_count (GBDATA *gbd)
long	GB_read_memuse (GBDATA *gbd)
NOT4PERL long	GB_calc_structure_size (GBDATA *gbd)
GB_CSTR	GB_read_pntr (GBDATA *gbd)
GB_CSTR	GB_read_char_pntr (GBDATA *gbd)
char *	GB_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)
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)
GB_CUINT4 *	GB_read_ints_pntr (GBDATA *gbd)
long	GB_read_ints_count (GBDATA *gbd)
GB_UINT4 *	GB_read_ints (GBDATA *gbd)
GB_CFLOAT *	GB_read_floats_pntr (GBDATA *gbd)
float *	GB_read_floats (GBDATA *gbd)
char *	GB_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)
char *	GB_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)
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)
bool	GB_allow_compression (GBDATA *gb_main, bool allow_compression)
GB_ERROR	GB_test_delete_possible (GBDATA *gb_obj)
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)
GBDATA *	GB_clone (GBDATA *gb_destCont, GBDATA *gb_source)
char *	GB_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 char *	GB_command_interpreter_in_env (const char *str, const char *commands, const GBL_call_env &callEnv)
char *	GB_command_interpreter (const char *str, const char *commands, GBDATA *gb_main)

Function Documentation

GBDATA* EXP_get_experiment_data

(

GBDATA *

gb_species

)

Definition at line 15 of file adExperiment.cxx.

References GB_CREATE_CONTAINER, and GB_search().

Referenced by EXP_find_experiment(), EXP_get_first_experiment_data(), EXP_get_next_experiment_data(), and get_current_experiment_data().

GBDATA* EXP_find_experiment_rel_exp_data	(	GBDATA *	gb_experiment_data,
		const char *	name
	)

Definition at line 19 of file adExperiment.cxx.

References GBT_find_item_rel_item_data().

Referenced by EXP_find_experiment(), experiment_copy_handler(), experiment_create_handler(), and experiment_rename_handler().

GBDATA* EXP_find_experiment	(	GBDATA *	gb_species,
		const char *	name
	)

Definition at line 22 of file adExperiment.cxx.

References EXP_find_experiment_rel_exp_data(), and EXP_get_experiment_data().

Referenced by EXP_item_type_species_selector::current(), EXP_find_experiment_by_id(), and EXP_get_current_experiment().

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
	)

Definition at line 20 of file adGene.cxx.

References assert_or_exit, error(), GB_await_error(), GB_create(), GB_entry(), GB_INT, GB_read_int(), GB_write_int(), GBK_terminatef(), GENOM_DB_TYPE, and NULp.

Referenced by create_primer_design_window(), create_probe_admin_window(), create_probe_design_window(), expect_used_in_genome_db(), GBT_commit_rename_session(), GEN_is_organism(), ArbImporter::import_data(), MERGE_create_main_window(), mg_transfer_listed_species(), mg_transfer_selected_species(), NT_import_sequences(), NT_repair_DB(), pd_export_pt_server(), CheckedConsistencies::perform_item_checks(), popup_new_main_window(), primer_design_event_init(), probe_design_event(), and probe_match_event().

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

)

Definition at line 50 of file adGene.cxx.

References GB_FIND, and GB_search().

Referenced by gbl_findgene(), GEN_find_gene(), GEN_root::GEN_root(), NT_convert_gene_locations(), NT_fix_gene_data(), and probe_match_event().

GBDATA* GEN_expect_gene_data

(

GBDATA *

gb_species

)

Definition at line 54 of file adGene.cxx.

References gb_assert, GB_FIND, and GB_search().

Referenced by GEN_expect_gene(), GEN_first_gene(), GEN_first_marked_gene(), GEN_get_first_gene_data(), GEN_get_local_gene_data(), GEN_get_next_gene_data(), and get_current_gene_data().

GBDATA* GEN_find_gene_rel_gene_data	(	GBDATA *	gb_gene_data,
		const char *	name
	)

Definition at line 60 of file adGene.cxx.

References GBT_find_item_rel_item_data().

Referenced by GEN_create_nonexisting_gene_rel_gene_data(), GEN_find_gene(), gene_copy_handler(), gene_create_cb(), and gene_rename_handler().

GBDATA* GEN_find_gene	(	GBDATA *	gb_species,
		const char *	name
	)

Definition at line 64 of file adGene.cxx.

References GEN_find_gene_data(), GEN_find_gene_rel_gene_data(), and NULp.

Referenced by GEN_item_type_species_selector::current(), gen_find_gene_by_id(), GEN_find_origin_gene(), GEN_get_current_gene(), primer_design_event_init(), and probe_match_event().

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
	)

Definition at line 96 of file adGene.cxx.

References GEN_create_nonexisting_gene_rel_gene_data(), and GEN_findOrCreate_gene_data().

GBDATA* GEN_find_or_create_gene_rel_gene_data	(	GBDATA *	gb_gene_data,
		const char *	name
	)

Definition at line 100 of file adGene.cxx.

References error(), GB_create_container(), GB_end_transaction(), GB_export_error(), GB_find_string(), GB_get_father(), GB_IGNORE_CASE, GB_push_transaction(), GBT_write_string(), NULp, and SEARCH_GRANDCHILD.

Referenced by gene_create_cb().

GBDATA* GEN_first_gene

(

GBDATA *

gb_species

)

Definition at line 130 of file adGene.cxx.

References GB_entry(), and GEN_expect_gene_data().

Referenced by do_hide_command_for_one_species(), do_mark_command_for_one_species(), insert_genes_of_organism(), mark_organisms_with_marked_genes(), and probe_match_event().

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

)

Definition at line 138 of file adGene.cxx.

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

Referenced by do_hide_command_for_one_species(), do_mark_command_for_one_species(), GEN_root::GEN_root(), insert_genes_of_organism(), mark_organisms_with_marked_genes(), next_gene_in_range(), NT_convert_gene_locations(), and probe_match_event().

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
	)

Definition at line 155 of file adGene.cxx.

References ARB_calloc(), GEN_position::complement, gb_assert, GEN_position::joinable, lastFreedPosition, NULp, GEN_position::parts, GEN_position::start_pos, GEN_position::start_uncertain, GEN_position::stop_pos, and GEN_position::stop_uncertain.

Referenced by Location::create_GEN_position(), LocationEditor::create_GEN_position_from_fields(), GEN_read_position(), and NT_convert_gene_locations().

void GEN_use_uncertainties

(

GEN_position *

pos

)

Definition at line 184 of file adGene.cxx.

References GEN_position::complement, GEN_position::parts, GEN_position::start_uncertain, and GEN_position::stop_uncertain.

Referenced by Location::create_GEN_position(), LocationEditor::create_GEN_position_from_fields(), GEN_read_position(), gene_changed_cb(), and NT_convert_gene_locations().

void GEN_free_position

(

GEN_position *

pos

)

Definition at line 195 of file adGene.cxx.

References GEN_position::start_pos.

Referenced by GBT_read_gene_sequence_and_length(), GEN_read_position(), loadPositions4gene(), NT_convert_gene_locations(), primer_design_event_init(), scan_gene_positions(), LocationEditor::set_pos(), GEN_position_mem_handler::~GEN_position_mem_handler(), and LocationEditor::~LocationEditor().

GEN_position* GEN_read_position

(

GBDATA *

gb_gene

)

Definition at line 250 of file adGene.cxx.

References GEN_position::complement, error(), gb_assert, GB_entry(), GB_export_error(), GB_read_int(), GBS_global_string(), GEN_free_position(), GEN_new_position(), GEN_use_uncertainties(), NULp, parseCSV(), parsePositions(), CharPtrArray::reserve(), GEN_position::start_pos, GEN_position::start_uncertain, GEN_position::stop_pos, and GEN_position::stop_uncertain.

Referenced by GBT_read_gene_sequence_and_length(), gene_changed_cb(), loadPositions4gene(), PosGene::PosGene(), primer_design_event_init(), and scan_gene_positions().

GB_ERROR GEN_write_position	(	GBDATA *	gb_gene,
		const GEN_position *	pos,
		long	seqLength
	)

Definition at line 325 of file adGene.cxx.

References GBS_strstruct::cat(), GEN_position::complement, error(), gb_assert, GB_await_error(), GB_delete(), GB_entry(), GB_get_grandfather(), GB_INT, GB_read_count(), GB_search(), GB_STRING, GB_write_int(), GB_write_string(), GBS_global_string(), GBT_find_sequence(), GENOM_ALIGNMENT, GBS_strstruct::get_data(), GEN_position::joinable, length, NULp, GEN_position::parts, GBS_strstruct::put(), start, GEN_position::start_pos, GEN_position::start_uncertain, GEN_position::stop_pos, and GEN_position::stop_uncertain.

Referenced by boundloc_changed_cb(), gene_create_cb(), NT_convert_gene_locations(), and DBwriter::writeFeature().

void GEN_sortAndMergeLocationParts

(

GEN_position *

location

)

Definition at line 487 of file adGene.cxx.

References cmp_location_parts(), GEN_position::complement, NULp, GEN_position::parts, GEN_position::start_pos, GEN_position::stop_pos, and swap.

Referenced by GBT_read_gene_sequence_and_length(), and scan_gene_positions().

const char* GEN_origin_organism

(

GBDATA *

gb_pseudo

)

Definition at line 549 of file adGene.cxx.

References GB_entry(), GB_read_char_pntr(), and NULp.

Referenced by GEN_add_pseudo_species_to_hash(), GEN_find_origin_organism(), GEN_find_pseudo_species(), GEN_is_pseudo_gene_species(), GEN_organism_not_found(), GEN_species_name_changed_cb(), MG_create_field_content(), and MG_transfer_one_species().

const char* GEN_origin_gene

(

GBDATA *

gb_pseudo

)

Definition at line 553 of file adGene.cxx.

References GB_entry(), GB_read_char_pntr(), and NULp.

Referenced by GEN_add_pseudo_species_to_hash(), GEN_find_origin_gene(), GEN_find_pseudo_species(), GEN_species_name_changed_cb(), and MG_create_field_content().

bool GEN_is_pseudo_gene_species

(

GBDATA *

gb_species

)

Definition at line 558 of file adGene.cxx.

References GEN_origin_organism().

Referenced by apply_to_origin(), GEN_find_origin_gene(), GEN_find_origin_organism(), GEN_first_marked_pseudo_species(), GEN_first_pseudo_species(), GEN_mark_organism_or_corresponding_organism(), GEN_next_marked_pseudo_species(), GEN_next_pseudo_species(), GEN_organism_not_found(), GEN_species_name_changed_cb(), MG_create_field_content(), MG_export_fields(), MG_transfer_one_species(), MG_update_example(), and relink_pseudo_species_to_organisms().

GB_ERROR GEN_organism_not_found

(

GBDATA *

gb_pseudo

)

Definition at line 565 of file adGene.cxx.

References gb_assert, GB_export_errorf(), GBT_get_name_or_description(), GEN_find_origin_organism(), GEN_is_pseudo_gene_species(), GEN_origin_organism(), and NULp.

Referenced by GEN_mark_organism_or_corresponding_organism().

void GEN_add_pseudo_species_to_hash	(	GBDATA *	gb_pseudo,
		GB_HASH *	pseudo_hash
	)

Definition at line 589 of file adGene.cxx.

References gb_assert, GBS_write_hash(), GEN_origin_gene(), GEN_origin_organism(), and pseudo_species_hash_key().

Referenced by GEN_create_pseudo_species_hash(), and gen_extract_gene_2_pseudoSpecies().

GB_HASH* GEN_create_pseudo_species_hash	(	GBDATA *	gb_main,
		long	additionalSize
	)

Definition at line 599 of file adGene.cxx.

References GB_IGNORE_CASE, GBS_create_hash(), GBT_get_species_count(), GEN_add_pseudo_species_to_hash(), GEN_first_pseudo_species(), and GEN_next_pseudo_species().

Referenced by EG2PS_data::EG2PS_data().

GBDATA* GEN_find_pseudo_species	(	GBDATA *	gb_main,
		const char *	organism_name,
		const char *	gene_name,
		const GB_HASH *	pseudo_hash
	)

Definition at line 613 of file adGene.cxx.

References GEN_first_pseudo_species(), GEN_next_pseudo_species(), GEN_origin_gene(), GEN_origin_organism(), and GEN_read_pseudo_species_from_hash().

Referenced by auto_select_pseudo_species(), and gen_extract_gene_2_pseudoSpecies().

GBDATA* GEN_find_origin_organism	(	GBDATA *	gb_pseudo,
		const GB_HASH *	organism_hash
	)

Definition at line 643 of file adGene.cxx.

References gb_assert, GB_get_father(), GBS_read_hash(), GBT_find_species_rel_species_data(), GEN_is_pseudo_gene_species(), GEN_origin_organism(), and NULp.

Referenced by apply_to_origin(), GEN_find_origin_gene(), GEN_mark_organism_or_corresponding_organism(), GEN_organism_not_found(), MG_create_field_content(), and relink_pseudo_species_to_organisms().

GBDATA* GEN_find_origin_gene	(	GBDATA *	gb_pseudo,
		const GB_HASH *	organism_hash
	)

Definition at line 666 of file adGene.cxx.

References gb_assert, GEN_find_gene(), GEN_find_origin_organism(), GEN_is_pseudo_gene_species(), GEN_origin_gene(), and NULp.

Referenced by apply_to_origin(), mark_gene_species_of_marked_genes(), mark_genes_of_marked_gene_species(), and MG_create_field_content().

GBDATA* GEN_first_pseudo_species

(

GBDATA *

gb_main

)

Definition at line 684 of file adGene.cxx.

References GBT_first_species(), GEN_is_pseudo_gene_species(), and GEN_next_pseudo_species().

Referenced by GBT_commit_rename_session(), GEN_create_pseudo_species_hash(), GEN_find_pseudo_species(), mark_gene_species(), mark_gene_species_of_marked_genes(), mark_gene_species_using_current_alignment(), and mark_genes_of_marked_gene_species().

GBDATA* GEN_next_pseudo_species

(

GBDATA *

gb_species

)

Definition at line 691 of file adGene.cxx.

References GBT_next_species(), and GEN_is_pseudo_gene_species().

Referenced by GBT_commit_rename_session(), GEN_create_pseudo_species_hash(), GEN_find_pseudo_species(), GEN_first_pseudo_species(), mark_gene_species(), mark_gene_species_of_marked_genes(), mark_gene_species_using_current_alignment(), and mark_genes_of_marked_gene_species().

GBDATA* GEN_first_marked_pseudo_species

(

GBDATA *

gb_main

)

Definition at line 711 of file adGene.cxx.

References GBT_first_marked_species(), GEN_is_pseudo_gene_species(), and GEN_next_marked_pseudo_species().

Referenced by EXP_get_first_experiment_data(), and GEN_get_first_gene_data().

bool GEN_is_organism

(

GBDATA *

gb_species

)

Definition at line 721 of file adGene.cxx.

References gb_assert, GB_entry(), GB_get_root(), GEN_is_genome_db(), and GENOM_ALIGNMENT.

Referenced by gbl_findgene(), GEN_find_organism(), GEN_first_marked_organism(), GEN_first_organism(), GEN_mark_organism_or_corresponding_organism(), GEN_next_marked_organism(), and GEN_next_organism().

GBDATA* GEN_find_organism	(	GBDATA *	gb_main,
		const char *	name
	)

Definition at line 728 of file adGene.cxx.

References GBT_find_species(), GEN_is_organism(), and NULp.

Referenced by EXP_find_experiment_by_id(), gen_find_gene_by_id(), GEN_get_first_gene_data(), get_selected_organism(), MG_transfer_one_species(), and GEN_graphic::reinit_gen_root().

GBDATA* GEN_first_organism

(

GBDATA *

gb_main

)

Definition at line 739 of file adGene.cxx.

References GBT_first_species(), GEN_is_organism(), and GEN_next_organism().

Referenced by GBT_create_organism_hash(), GEN_get_first_gene_data(), GEN_get_organism_count(), GEN_perform_command(), get_first_organism(), mark_organisms(), mark_organisms_with_marked_genes(), NT_convert_gene_locations(), and pd_get_the_gene_names().

GBDATA* GEN_next_organism

(

GBDATA *

gb_organism

)

Definition at line 745 of file adGene.cxx.

References GBT_next_species(), and GEN_is_organism().

Referenced by GBT_create_organism_hash(), GEN_first_organism(), GEN_get_next_gene_data(), GEN_get_organism_count(), GEN_perform_command(), get_next_organism(), mark_organisms(), mark_organisms_with_marked_genes(), NT_convert_gene_locations(), and pd_get_the_gene_names().

long GEN_get_organism_count

(

GBDATA *

gb_main

)

Definition at line 756 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

)

Definition at line 767 of file adGene.cxx.

References GBT_first_marked_species(), GEN_is_organism(), and GEN_next_marked_organism().

Referenced by EXP_get_first_experiment_data(), GEN_get_first_gene_data(), GEN_perform_command(), and get_first_organism().

GBDATA* GEN_next_marked_organism

(

GBDATA *

gb_organism

)

Definition at line 773 of file adGene.cxx.

References GBT_next_marked_species(), and GEN_is_organism().

Referenced by EXP_get_next_experiment_data(), GEN_first_marked_organism(), GEN_get_next_gene_data(), GEN_perform_command(), and get_next_organism().

char* GEN_global_gene_identifier	(	GBDATA *	gb_gene,
		GBDATA *	gb_organism
	)

Definition at line 783 of file adGene.cxx.

References gb_assert, GB_get_grandfather(), GBS_global_string_copy(), and GBT_get_name_or_description().

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

const char* GB_get_db_path

(

GBDATA *

gbd

)

Definition at line 14 of file adTest.cxx.

References GB_FATHER(), GB_KEY(), GBS_global_string_copy(), NULp, and RETURN_LOCAL_ALLOC.

Referenced by deleteDataOfKey(), dump_internal(), error_with_dbentry(), gb_alloc_cache_index(), GB_dump_db_path(), gb_recover_corrupt_file(), gb_transactable_type(), gb_uncompress_by_dictionary(), gb_write_bin_rek(), GB_write_int(), gb_write_one_child(), and FINAL_TYPE< SEQTYPE >::get_name().

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 187 of file adTest.cxx.

References dump_internal().

NOT4PERL void GB_dump_no_limit

(

GBDATA *

gbd

)

Definition at line 196 of file adTest.cxx.

References dump_internal(), and NULp.

GB_ERROR GB_fix_database

(

GBDATA *

gb_main

)

Definition at line 237 of file adTest.cxx.

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

GBDATA* GB_get_gb_main_during_cb

(

void

)

Definition at line 142 of file ad_cb.cxx.

References GB_CB_DELETE, gb_get_main_during_cb(), GB_inside_callback(), gb_main, GB_MAIN_TYPE::gb_main(), and NULp.

Referenced by flush_taxonomy_cb().

NOT4PERL const void* GB_read_old_value

(

void

)

Definition at line 166 of file ad_cb.cxx.

References GB_export_error(), GB_GETDATA_TS(), gb_read_pntr_ts(), gb_triggered_callback::gbd, NULp, and gb_triggered_callback::old.

Referenced by ED4_terminal::changed_by_database(), and ED4_sequence_terminal::deleted_from_database().

long GB_read_old_size

(

void

)

Definition at line 183 of file ad_cb.cxx.

References GB_export_error(), GB_GETSIZE_TS(), and gb_triggered_callback::old.

Referenced by ED4_terminal::changed_by_database(), and ED4_sequence_terminal::deleted_from_database().

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
	)

Definition at line 1363 of file ad_load.cxx.

References GB_getenvUSER(), and GB_login().

Referenced by ARB_main(), ArbImporter::ArbImporter(), FINAL_TYPE< SEQTYPE >::ArbWriter(), calc_pvp(), check_socket_available(), export_newick(), export_seq_data(), GBT_open(), main(), ALI_ARBDB::open(), AP_main::open(), PH_root::open(), openArb(), probe_read_data_base(), run_command(), run_server(), and save_tree_as_newick().

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 102 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

gb	database root
path	filename (if NULp -> use name stored in DB; otherwise store name in DB)
savetype

See also

GB_save_as()

Definition at line 804 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

)

Definition at line 816 of file ad_save_load.cxx.

References error(), GB_create_directory(), GB_is_directory(), GB_split_full_path(), and NULp.

Referenced by GB_create_directory(), GB_fopen_tempfile(), and GB_save_in_arbprop().

GB_ERROR GB_create_directory

(

const char *

path

)

Definition at line 827 of file ad_save_load.cxx.

References error(), GB_create_parent_directory(), GB_failedTo_error(), GB_IO_error(), GB_is_directory(), and NULp.

Referenced by AW_create_fileselection_awars(), create_new_mask_cb(), GB_create_parent_directory(), getenv_autodirectory(), LoadMenus(), and scan_existing_input_masks().

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

gb	database root
path	filename (if NULp -> use name stored in DB)
savetype

See also

GB_save_as()

Definition at line 840 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

)

Definition at line 955 of file ad_save_load.cxx.

References GBS_strstruct::cat(), gb_assert, GBS_static_string(), GBS_strstruct::get_data(), and SUPPORTED_COMPRESSION_FLAGS.

Referenced by ARB_main(), and AWT_insert_DBcompression_selector().

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 1320 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 1332 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 1358 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

gbd	database root
path	filename (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 1371 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 1418 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 1511 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 1593 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 1598 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 1603 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 1607 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
	)

Definition at line 294 of file adcache.cxx.

References gb_cache::big_data_min_size, GB_MAIN_TYPE::cache, GB_MAIN(), gb_cache::max_data_size, and NULp.

Referenced by startup_sequence_cb().

GB_ERROR GBCMS_open	(	const char *	path,
		long	timeout,
		GBDATA *	gb_main
	)

Definition at line 198 of file adcomm.cxx.

References GBDATA::as_container(), ASSERT_RESULT, error(), gb_main, gb_server_data::gb_main, GB_MAIN(), gbcm_open_socket(), gbcmc_close(), gbcmc_open(), gbcms_sighup(), GBS_global_string(), gb_server_data::hso, INSTALL_SIGHANDLER, MAX_QUEUE_LEN, NULp, GB_MAIN_TYPE::server_data, gb_server_data::timeout, and gb_server_data::unix_name.

Referenced by run_server(), and startup_dbserver().

void GBCMS_shutdown

(

GBDATA *

gbd

)

Definition at line 247 of file adcomm.cxx.

References GB_MAIN(), gb_server_data::hso, Socinf::next, GB_MAIN_TYPE::server_data, gb_server_data::soci, Socinf::socket, and gb_server_data::unix_name.

Referenced by nt_disconnect_from_db(), and run_server().

bool GBCMS_accept_calls	(	GBDATA *	gbd,
		bool	wait_extra_time
	)

Definition at line 1188 of file adcomm.cxx.

References error(), FD_SET_TYPE, g_bcms_delete_Socinf(), GB_MAIN(), gbcm_logout(), GBCM_SERVER_ABORTED, GBCM_SERVER_OK, gbcms_talking(), GB_MAIN_TYPE::get_transaction_level(), gb_server_data::hso, Socinf::next, gb_server_data::nsoc, NULp, GB_MAIN_TYPE::server_data, gb_server_data::soci, Socinf::socket, gb_server_data::timeout, and gb_server_data::wait_for_new_request.

Referenced by serve_db_interrupt(), and served().

void GB_set_remote_action	(	GBDATA *	gbd,
		bool	in_action
	)

Definition at line 1656 of file adcomm.cxx.

References gb_assert, GB_MAIN(), gb_server_data::inside_remote_action, GB_MAIN_TYPE::is_server(), and GB_MAIN_TYPE::server_data.

Referenced by check_for_remote_command().

bool GB_inside_remote_action

(

GBDATA *

gbd

)

Definition at line 1668 of file adcomm.cxx.

References gb_assert, GB_MAIN(), gb_server_data::inside_remote_action, GB_MAIN_TYPE::is_server(), and GB_MAIN_TYPE::server_data.

Referenced by GB_resort_data_base().

long GB_read_clients

(

GBDATA *

gbd

)

Definition at line 1682 of file adcomm.cxx.

References GB_MAIN(), GB_MAIN_TYPE::is_server(), gb_server_data::nsoc, and GB_MAIN_TYPE::server_data.

Referenced by gb_create_header_array(), GB_create_index(), GB_resort_data_base(), gb_resort_system_folder_to_top(), MERGE_create_main_window(), nt_create_all_awars(), nt_disconnect_from_db(), NT_exit(), NT_restart(), server_main_loop(), and startup_dbserver().

bool GB_is_server

(

GBDATA *

gbd

)

Definition at line 1697 of file adcomm.cxx.

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

Referenced by check_for_remote_command(), dump_internal(), make_macro_recording_tracker(), MERGE_create_main_window(), and startup_mainwindow_and_dbserver().

GBDATA* GBCMC_find	(	GBDATA *	gbd,
		const char *	key,
		GB_TYPES	type,
		const char *	str,
		GB_CASE	case_sens,
		GB_SEARCH_TYPE	gbs
	)

Definition at line 1725 of file adcomm.cxx.

References GB_MAIN_TYPE::c_link, CLIENT_RECEIVE_ERROR, CLIENT_SEND_ERROR, error(), gb_assert, GB_export_error(), GB_export_errorf(), GB_INT, GB_MAIN(), GB_NONE, GB_STRING, GBCM_COMMAND_FIND, GBCM_COMMAND_FIND_ERG, gbcm_read_flush(), gbcm_read_two(), gbcm_write_flush(), gbcm_write_long(), gbcm_write_string(), gbcm_write_two(), gbcmc_unfold_list(), GBS_read_numhash(), invalid_use_in_server(), GB_MAIN_TYPE::is_server(), NULp, GB_MAIN_TYPE::remote_hash, result, GBDATA::server_id, and gbcmc_comm::socket.

Referenced by find_sub_sub_by_quark().

GB_ERROR GB_tell_server_dont_wait

(

GBDATA *

gbd

)

Definition at line 1867 of file adcomm.cxx.

References GB_MAIN_TYPE::c_link, CLIENT_SEND_ERROR, GB_MAIN(), GBCM_COMMAND_DONT_WAIT, gbcm_write_two(), GB_MAIN_TYPE::is_server(), NULp, GBDATA::server_id, and gbcmc_comm::socket.

Referenced by DI_timer(), and ED4_timer().

GB_ERROR GB_install_pid

(

int

mode

)

Definition at line 1957 of file adcomm.cxx.

References error(), gb_assert, GB_await_error(), GB_fopen_tempfile(), GB_getenv(), GB_getenvUSER(), GB_is_privatefile(), GBS_global_string(), GBS_global_string_copy(), and NULp.

Referenced by ARB_main(), aw_initstatus(), and GB_login().

bool GB_is_dictionary_compressed

(

GBDATA *

gbd

)

Definition at line 869 of file adcompr.cxx.

References GBDATA::as_entry(), gb_flag_types::compressed_data, GBENTRY::data(), error(), GBDATA::flags, GB_COMPRESSION_DICTIONARY, GB_COMPRESSION_HUFFMANN, GB_COMPRESSION_LAST, GB_COMPRESSION_RUNLENGTH, GB_COMPRESSION_SEQUENCE, GB_COMPRESSION_SORTBYTES, GB_COMPRESSION_TAGS_SIZE_MAX, GB_export_errorf(), GB_internal_error(), GB_read_key_pntr(), gb_uncompress_by_sequence(), gb_uncompress_equal_bytes(), gb_uncompress_huffmann(), gb_uncompress_longs(), GBDATA::is_entry(), NULp, and GBENTRY::uncompressed_size().

Referenced by deleteDataOfKey(), readFirstCompressedDataOf(), and testDictionaryCompression().

GB_CSTR GB_getcwd

(

void

)

Definition at line 24 of file adfile.cxx.

References ARB_PATH_MAX, NULp, and RETURN_ONETIME_ALLOC.

Referenced by AW_get_selected_fullname(), expand_symbolic_directories(), gb_full_path(), GB_getenvHOME(), and GB_unfold_path().

char* GB_find_all_files	(	const char *	dir,
		const char *	mask,
		bool	filename_only
	)

Definition at line 109 of file adfile.cxx.

References ARB_PATH_MAX, ARB_strdup(), buffer, GB_IGNORE_CASE, GBS_compile_matcher(), GBS_free_matcher(), GBS_global_string_copy(), GBS_string_matches_regexp(), NULp, and result.

Referenced by get_overlay_files().

char* GB_find_latest_file	(	const char *	dir,
		const char *	mask
	)

Definition at line 152 of file adfile.cxx.

References ARB_PATH_MAX, buffer, GB_IGNORE_CASE, GBS_compile_matcher(), GBS_free_matcher(), GBS_string_matches_regexp(), NULp, and result.

Referenced by startup_gui().

char* GB_lib_file	(	bool	warn_when_not_found,
		const char *	libprefix,
		const char *	filename
	)

Definition at line 198 of file adfile.cxx.

References GB_concat_path_in_ARBLIB(), and GB_existing_file().

Referenced by find_data_file(), GB_arbtcpdat_path(), GB_get_arb_revision_tag(), GB_property_file(), and GetImageFile().

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
	)

Definition at line 213 of file adfile.cxx.

References ARB_strdup(), gb_assert, GB_canonical_path(), GB_clear_error(), GB_concat_path(), GB_export_errorf(), GB_have_error(), GB_is_directory(), GB_is_readablefile(), GB_MIND_CASE, GB_string_comparator(), GBS_compile_matcher(), GBS_free_matcher(), GBS_global_string_copy(), GBS_string_matches_regexp(), and NULp.

Referenced by AWTC_create_submission_window(), ArbImporter::detect_format(), ArbImporter::import_data(), StorableSelectionList::load(), and LoadMenus().

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_elements	estimated number of elements added to hash (if you add more elements, hash will still work, but get slow)
case_sens	GB_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(), 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(), SpeciesSpace::SpeciesSpace(), 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

)

Definition at line 278 of file adhash.cxx.

Referenced by aw_help_search(), DefinedCommands::DefinedCommands(), g_bs_get_string_of_tag_hash(), GBT_begin_rename_session(), get_cached_taxonomy(), and DefinedCommands::set().

void GBS_optimize_hash

(

const GB_HASH *

hs

)

Definition at line 316 of file adhash.cxx.

References ARB_calloc(), GB_HASH::case_sens, GB_HASH::entries, GB_CALC_HASH_INDEX, gbs_get_a_prime(), gbs_hash_entry::key, GB_HASH::nelem, gbs_hash_entry::next, and GB_HASH::size.

Referenced by an_add_short(), GBP_add_callback(), get_short(), and MG_export_fields().

char* GBS_hashtab_2_string

(

const GB_HASH *

hash

)

Definition at line 368 of file adhash.cxx.

References GBS_hash_do_const_loop(), gbs_hash_to_strstruct(), and GBS_strstruct::release().

Referenced by GEN_testAndRemoveTranslations().

long GBS_read_hash	(	const GB_HASH *	hs,
		const char *	key
	)

Definition at line 392 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(), SpeciesSpace::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 454 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(), 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(), SpeciesSpace::SpeciesSpace(), 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 459 of file adhash.cxx.

References write_hash().

Referenced by an_get_prefix_hash().

long GBS_incr_hash	(	GB_HASH *	hs,
		const char *	key
	)

Definition at line 467 of file adhash.cxx.

References ARB_strdup(), delete_from_list(), GB_HASH::entries, find_hash_entry(), gbm_get_mem(), GBM_HASH_INDEX, gbs_hash_entry::key, GB_HASH::nelem, gbs_hash_entry::next, result, and gbs_hash_entry::val.

Referenced by arb_prm_primer(), AWTC_pars_names(), flush_cache_entry(), GBT_check_data(), gbt_scan_db_rek(), GEN_testAndRemoveTranslations(), and MG_export_fields().

void GBS_free_hash

(

GB_HASH *

hs

)

Definition at line 538 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(), 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(), SpeciesSpace::~SpeciesSpace(), 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
	)

Definition at line 545 of file adhash.cxx.

References delete_from_list(), GB_HASH::entries, gbs_hash_entry::next, GB_HASH::size, and gbs_hash_entry::val.

Referenced by arb_prm_primer(), ST_ML::calc_st_ml(), g_bs_free_hash_of_hashes(), BI_helix::initFromData(), insert_all_species_into_tree(), nt_add(), and AW_xfig::~AW_xfig().

void GBS_hash_do_const_loop	(	const GB_HASH *	hs,
		gb_hash_const_loop_type	func,
		void *	client_data
	)

Definition at line 559 of file adhash.cxx.

References GB_HASH::entries, gbs_hash_entry::next, and GB_HASH::size.

Referenced by AW_root::apply_focus_policy(), arb_prm_primer(), AW_forget_all_window_geometry(), aw_update_all_window_geometry_awars(), QUERY::DbQuery_update_list(), AW_root::dont_save_awars_with_default_value(), exit_removal(), GBS_hashtab_2_string(), GBT_check_data(), GBT_scan_db(), BI_helix::initFromData(), nt_add_partial(), AW_root::unlink_awars_from_DB(), and gb_cache::~gb_cache().

size_t GBS_hash_elements

(

const GB_HASH *

hs

)

Definition at line 570 of file adhash.cxx.

References GB_HASH::nelem.

Referenced by AWT_translator::AWT_translator(), QUERY::copy_selection_list_2_query_box(), find_SAI_candidates(), find_species_candidates(), gb_create_key(), insert_all_species_into_tree(), nt_add(), nt_extract_configuration(), and perform_query_cb().

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
	)

Definition at line 574 of file adhash.cxx.

References GB_HASH::entries, find_hash_entry(), gbs_hash_entry::key, gbs_hash_entry::next, NULp, GB_HASH::size, gbs_hash_entry::val, and while().

Referenced by tree_of_cached_taxonomy().

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 629 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
	)

Definition at line 641 of file adhash.cxx.

References get_sorted_hash_values().

Referenced by g_bs_get_string_of_tag_hash(), g_bs_read_tagged_hash(), nt_build_sai_string(), and gb_cache::~gb_cache().

int GBS_HCF_sortedByKey	(	const char *	k0,
		long	dummy_1x,
		const char *	k1,
		long	dummy_2x
	)

Definition at line 653 of file adhash.cxx.

Referenced by g_bs_get_string_of_tag_hash(), g_bs_read_tagged_hash(), nt_build_sai_string(), and gb_cache::~gb_cache().

GB_NUMHASH* GBS_create_numhash

(

size_t

estimated_elements

)

Definition at line 668 of file adhash.cxx.

References ARB_calloc(), GB_NUMHASH::entries, hash_size(), GB_NUMHASH::nelem, and GB_NUMHASH::size.

Referenced by aw_install_xkeys(), and GB_MAIN_TYPE::login_remote().

long GBS_read_numhash	(	GB_NUMHASH *	hs,
		long	key
	)

Definition at line 679 of file adhash.cxx.

References GB_NUMHASH::entries, gbs_numhash_index(), numhash_entry::next, and GB_NUMHASH::size.

Referenced by aw_xkey_2_awkey(), gbcmc_begin_transaction(), GBCMC_find(), and gbcmc_unfold_list().

long GBS_write_numhash	(	GB_NUMHASH *	hs,
		long	key,
		long	val
	)

Definition at line 687 of file adhash.cxx.

References GB_NUMHASH::entries, gb_assert, gbm_free_mem(), gbm_get_mem(), GBM_HASH_INDEX, gbs_numhash_index(), numhash_entry::key, GB_NUMHASH::nelem, numhash_entry::next, GB_NUMHASH::size, and numhash_entry::val.

Referenced by gb_pre_delete_entry(), gbcm_read_bin(), gbcmc_end_sendupdate(), gbcmc_init_transaction(), and map_awXKey().

void GBS_free_numhash

(

GB_NUMHASH *

hs

)

Definition at line 742 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
	)

Definition at line 32 of file adhashtools.cxx.

References create_item_hash(), GBT_first_species(), and GBT_next_species().

Referenced by GBT_create_species_hash(), and MERGE_sequences_simple().

GB_HASH* GBT_create_species_hash

(

GBDATA *

gb_main

)

Definition at line 36 of file adhashtools.cxx.

References GBT_create_species_hash_sized(), and GBT_get_species_count().

Referenced by find_species_candidates(), GBT_begin_rename_session(), GBT_link_tree(), mark_nontree_cb(), mg_transfer_listed_species(), and NT_alltree_remove_leafs().

GB_HASH* GBT_create_marked_species_hash

(

GBDATA *

gb_main

)

Definition at line 40 of file adhashtools.cxx.

References create_item_hash(), GBT_first_marked_species(), GBT_get_species_count(), and GBT_next_marked_species().

Referenced by mark_nontree_cb(), nt_add(), and nt_extract_configuration().

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

)

Definition at line 48 of file adhashtools.cxx.

References create_item_hash(), GEN_first_organism(), GEN_get_organism_count(), and GEN_next_organism().

Referenced by mark_gene_species_of_marked_genes(), mark_genes_of_marked_gene_species(), mg_transfer_listed_species(), and NT_pseudo_species_to_organism().

GB_ERROR GB_create_index	(	GBDATA *	gbd,
		const char *	key,
		GB_CASE	case_sens,
		long	estimated_size
	)

Definition at line 117 of file adindex.cxx.

References GBDATA::as_container(), gb_index_files::case_sens, error(), GB_find_or_create_quark(), GB_find_sub_by_quark(), GB_GBM_INDEX, GB_INDEX_FIND, GB_read_clients(), GBCONTAINER_IFS(), gbm_get_mem(), gbs_get_a_prime(), gb_index_files::hash_table_size, GBDATA::is_entry(), gb_index_files::key, gb_index_files::nr_of_elements, NULp, RETURN_ERROR, SET_GB_INDEX_FILES_ENTRIES(), SET_GB_INDEX_FILES_NEXT(), and SET_GBCONTAINER_IFS().

Referenced by gb_load_key_data_and_dictionaries(), and GBT_open().

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 721 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 749 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
	)

Definition at line 755 of file adindex.cxx.

References _GBCMC_UNDOCOM_REDO, _GBCMC_UNDOCOM_UNDO, ASSERT_NO_ERROR, error(), g_b_undo(), GB_get_requested_undo_type(), GB_internal_error(), GB_MAIN(), GB_request_undo_type(), GB_UNDO_REDO, GB_UNDO_UNDO, GB_UNDO_UNDO_REDO, gbcmc_send_undo_commands(), GB_MAIN_TYPE::is_client(), NULp, g_b_undo_mgr::r, g_b_undo_mgr::u, and GB_MAIN_TYPE::undo.

Referenced by ED4_undo_redo(), gbcms_talking_undo(), GEN_undo_cb(), NT_undo_cb(), and SEC_undo_cb().

char* GB_undo_info	(	GBDATA *	gb_main,
		GB_UNDO_TYPE	type
	)

Definition at line 806 of file adindex.cxx.

References _GBCMC_UNDOCOM_INFO_REDO, _GBCMC_UNDOCOM_INFO_UNDO, g_b_undo_info(), GB_export_error(), GB_MAIN(), GB_UNDO_REDO, GB_UNDO_UNDO, gbcmc_send_undo_info_commands(), GB_MAIN_TYPE::is_client(), NULp, g_b_undo_mgr::r, g_b_undo_mgr::u, and GB_MAIN_TYPE::undo.

Referenced by gbcms_talking_undo().

GB_ERROR GB_set_undo_mem	(	GBDATA *	gbd,
		long	memsize
	)

Definition at line 833 of file adindex.cxx.

References _GBCMC_UNDOCOM_SET_MEM, g_b_check_undo_size(), GB_export_errorf(), GB_MAIN(), gbcmc_send_undo_commands(), GB_MAIN_TYPE::is_client(), g_b_undo_mgr::max_size_of_all_undos, NULp, and GB_MAIN_TYPE::undo.

Referenced by gbcms_talking_undo().

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
	)

Definition at line 41 of file admatch.cxx.

References ARB_strdup(), GBS_string_matcher::case_flag, error(), GB_export_error(), GB_MIND_CASE, GBS_compile_regexpr(), GBS_free_matcher(), GBS_global_string(), GBS_unwrap_regexpr(), NULp, GBS_string_matcher::regexpr, SM_ANY, SM_INVALID, SM_REGEXPR, SM_WILDCARDED, GBS_string_matcher::type, and GBS_string_matcher::wildexpr.

Referenced by GB_find_all_files(), GB_find_latest_file(), and GBS_read_dir().

void GBS_free_matcher

(

GBS_string_matcher *

matcher

)

Definition at line 94 of file admatch.cxx.

References GBS_free_regexpr(), GBS_string_matcher::regexpr, and GBS_string_matcher::wildexpr.

Referenced by GB_find_all_files(), GB_find_latest_file(), GBS_compile_matcher(), and GBS_read_dir().

GB_CSTR GBS_find_string	(	GB_CSTR	cont,
		GB_CSTR	substr,
		int	match_mode
	)

Definition at line 103 of file admatch.cxx.

References NULp.

Referenced by aw_help_helpfile_changed_cb(), AW_openURL(), AW_xfig::AW_xfig(), export_species_using_form(), GBS_eval_env(), GBS_string_eval_in_env(), GBS_string_matches(), and transfer_single_field().

bool GBS_string_matches	(	const char *	str,
		const char *	expr,
		GB_CASE	case_sens
	)

Definition at line 193 of file admatch.cxx.

References ARB_strchrnul(), ARB_strpartdup(), GB_IGNORE_CASE, GBS_find_string(), and s.

Referenced by aw_help_helpfile_changed_cb(), AW_help_popup(), aw_ref_to_title(), AW_server_callback(), ArbImporter::detect_format(), fieldContainsAlignment(), filter_columnstat_SAIs(), gb_find_value_equal(), gb_index_find(), GB_login(), GBS_get_arb_tcp_entries(), GBS_string_matches_regexp(), gde_filter_weights(), ArbImporter::read_data(), ArbImporter::read_line(), and write_entry().

bool GBS_string_matches_regexp	(	const char *	str,
		const GBS_string_matcher *	expr
	)

Definition at line 269 of file admatch.cxx.

References GBS_string_matcher::case_flag, gb_assert, GBS_regmatch_compiled(), GBS_string_matches(), NULp, GBS_string_matcher::regexpr, SM_ANY, SM_INVALID, SM_REGEXPR, SM_WILDCARDED, GBS_string_matcher::type, and GBS_string_matcher::wildexpr.

Referenced by GB_find_all_files(), GB_find_latest_file(), and GBS_read_dir().

char* GBS_string_eval_in_env	(	const char *	insource,
		const char *	icommand,
		const GBL_call_env &	callEnv
	)

Definition at line 493 of file admatch.cxx.

References ARB_strdup(), ARB_strpartdup(), GBS_strstruct::cat(), command, GBS_strstruct::empty(), GBS_strstruct::erase(), error(), gb_assert, GB_export_error(), gbs_build_replace_string(), gbs_compress_command(), GBS_find_string(), GBS_global_string(), GBS_MWILD, GBS_SEP, GBS_SET, GBS_WILD, GBS_strstruct::get_data(), GBS_strstruct::ncat(), NULp, GBL_IMPL::print_trace(), GBS_strstruct::release(), GBS_strstruct::swap_content(), GBL_IMPL::traceACI, and GBL_IMPL::traceIndent.

Referenced by ed_submit_info_event(), export_species_using_form(), GB_command_interpreter_in_env(), gbl_srt(), gbs_build_replace_string(), GBS_string_eval(), ArbImporter::read_data(), and ExportFieldScanner::scanFields().

char* GBS_string_eval	(	const char *	insource,
		const char *	icommand
	)

Definition at line 699 of file admatch.cxx.

References GBS_string_eval_in_env(), and NULp.

Referenced by ARB_main(), aw_help_helpfile_changed_cb(), aw_help_search(), AW_reactivate_all_advices(), aw_ref_to_title(), awt_create_filter_awars(), awt_create_select_filter(), awtc_delete_names_file(), awtc_remove_arb_acc(), ColumnStat::ColumnStat(), CommandOutput::CommandOutput(), create_itemfield_selection_button(), ed_submit_parse_event(), export_format_single(), export_to_DB(), File_selection::File_selection(), ALI_selection::fill(), ArbImporter::import_data(), NameInformation::NameInformation(), ArbImporter::next_file(), ParseMenus(), pd_export_pt_server(), read_export_format(), RefEntries::refresh_result_cb(), ColumnStat::refresh_sai_selection_list(), tree_vars_callback(), type2id(), AW_awar::update(), update_default_treename_cb(), and update_rulesAwar().

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

)

Definition at line 88 of file admath.cxx.

References gen, and RandomNumberGenerator::get_rand().

Referenced by AWTC_generate_random_name(), AP_filter::enable_bootstrap(), filter_seq(), gb_make_main_idx(), GBT_create_unique_item_identifier(), get_random(), and AP_tree_edge::mixTree().

GB_ERROR GB_optimize

(

GBDATA *

gb_main

)

Definition at line 2556 of file adoptimize.cxx.

References ASSERT_NO_ERROR, error(), gb_create_dictionaries(), GB_disable_quicksave(), GB_get_requested_undo_type(), GB_get_usable_memory(), GB_MAIN(), GB_request_undo_type(), GB_UNDO_KILL, and NULp.

Referenced by NT_database_optimization().

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
	)

Definition at line 174 of file adquery.cxx.

References after(), GBDATA::expect_container(), find_sub_by_quark(), GB_MIND_CASE, GB_NONE, and NULp.

Referenced by GB_create_index(), GB_followingEntry(), GB_nextEntry(), and FINAL_TYPE< SEQTYPE >::get_first_field().

GBDATA* GB_find	(	GBDATA *	gbd,
		const char *	key,
		GB_SEARCH_TYPE	gbs
	)

Definition at line 295 of file adquery.cxx.

References GB_CASE_UNDEFINED, gb_find_internal(), GB_NONE, and NULp.

Referenced by filter_posvar_SAI_for_ali(), GB_brother(), GB_child(), GB_entry(), GB_nextChild(), gbcms_talking_find(), GBT_expect_item_rel_item_data(), main(), MultiFastaWriter::readData(), MultiFastaWriter::readString(), and sina_start().

GBDATA* GB_find_string	(	GBDATA *	gbd,
		const char *	key,
		const char *	str,
		GB_CASE	case_sens,
		GB_SEARCH_TYPE	gbs
	)

Definition at line 302 of file adquery.cxx.

References gb_find_internal(), and GB_STRING.

Referenced by apply_command_to_alignment(), applyToItemFoundByKey(), arb_prm_read(), concatenateAlignments(), config_rename_handler(), gb_load_dictionary_data(), gb_load_single_key_data(), gb_save_dictionary_data(), gbcms_talking_find(), GBT_check_data(), GBT_create_alignment(), GBT_find_configuration(), GBT_find_item_rel_item_data(), GBT_get_alignment(), GBT_get_changekey(), GEN_find_or_create_gene_rel_gene_data(), get_global_alignments(), ALI_ARBDB::get_SAI(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), mg_check_field_cb(), MG_config_delete_cb(), MG_transfer_config(), ALI_ARBDB::put_sequence(), ALI_ARBDB::put_sequence_string(), PV_WriteTranslatedSequenceToDB(), set_protection_of_queried_cb(), test_GB_find_string(), test_GB_find_string_indexed(), and transfer_field_of_listed_cb().

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

)

Definition at line 322 of file adquery.cxx.

References GB_find(), NULp, and SEARCH_CHILD.

Referenced by AW_forget_all_window_geometry(), AW_reactivate_all_questions(), awt_add_sequences_to_list(), ColumnStat::calculate(), count_elements(), FoundGroup::delete_from_DB(), deleteDataOfKey(), dump_internal(), ed_submit_info_event(), ensure_trees_have_order(), AWT_configuration::erase_deleted_configs(), gb_convert_compression(), gb_copy_explicit(), gb_fix_recursive(), GB_get_subfields(), gb_resort_system_folder_to_top(), gb_search_system_folder_rek(), gb_set_compression(), gb_uncache(), gb_write_childs(), gbl_read_seq_sai_or_species(), GBT_check_alignment(), GBT_get_tree_names(), gbt_scan_db_rek(), gbt_scan_db_start(), gbt_write_tree_nodes(), FINAL_TYPE< SEQTYPE >::get_first_field(), get_first_tree(), get_max_tree_idx(), get_tree_behind_idx(), get_tree_infrontof_idx(), get_tree_with_idx(), getKnownMacroClients(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), iterate(), KeySorter::KeySorter(), nds_delete_database_entries(), NT_create_sai_from_pfold(), NT_fix_gene_data(), nt_species_join(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), readFirstCompressedDataOf(), EDB_root_bact::search_sequence_data_rek(), set_parents_with_only_temp_childs_temp(), split_alignment(), testDictionaryCompression(), UniqueNameDetector::UniqueNameDetector(), and XML_recursive().

GBDATA* GB_nextChild

(

GBDATA *

child

)

Definition at line 326 of file adquery.cxx.

References GB_find(), NULp, and SEARCH_NEXT_BROTHER.

Referenced by AW_forget_all_window_geometry(), AW_reactivate_all_questions(), awt_add_sequences_to_list(), ColumnStat::calculate(), count_elements(), FoundGroup::delete_from_DB(), deleteDataOfKey(), dump_internal(), ed_submit_info_event(), ensure_trees_have_order(), AWT_configuration::erase_deleted_configs(), gb_convert_compression(), gb_copy_explicit(), gb_fix_recursive(), GB_get_subfields(), gb_resort_system_folder_to_top(), gb_search_system_folder_rek(), gb_set_compression(), gb_uncache(), gb_write_childs(), gbl_read_seq_sai_or_species(), GBT_check_alignment(), GBT_get_tree_names(), gbt_scan_db_rek(), gbt_scan_db_start(), gbt_write_tree_nodes(), FINAL_TYPE< SEQTYPE >::get_first_field(), get_max_tree_idx(), get_next_tree(), get_tree_behind_idx(), get_tree_infrontof_idx(), get_tree_with_idx(), getKnownMacroClients(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), iterate(), FINAL_TYPE< SEQTYPE >::iterate(), KeySorter::KeySorter(), nds_delete_database_entries(), NT_create_sai_from_pfold(), nt_species_join(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), readFirstCompressedDataOf(), EDB_root_bact::search_sequence_data_rek(), set_parents_with_only_temp_childs_temp(), split_alignment(), testDictionaryCompression(), UniqueNameDetector::UniqueNameDetector(), and XML_recursive().

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(), 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(), get_SAI_id(), 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(), nds_delete_database_entries(), nds_maintain_viewkeys(), 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(), split_alignment(), 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

)

Definition at line 339 of file adquery.cxx.

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

Referenced by apply_command_to_alignment(), CheckedConsistencies::CheckedConsistencies(), collectKeysRegisteredInDatabase(), compress_sequence_tree(), dbserver_entry(), delete_unused_changekeys(), EXP_next_experiment(), Itemfield_Selection::fill(), ALI_selection::fill(), fillSelNamList(), findAffectedKeys(), flush_taxonomy_if_new_group_cb(), GroupSearch::fold_found_groups(), CheckedConsistencies::forgetDoneChecks(), gb_copy_explicit(), GB_countEntries(), gb_load_key_data_and_dictionaries(), GBT_check_data(), GBT_count_alignments(), GBT_get_alignment_names(), GBT_get_colorset_names(), GBT_get_configuration_names(), GBT_next_SAI(), GBT_next_species(), gbt_rename_alignment_of_item(), GBT_write_byte(), GBT_write_float(), GBT_write_int(), GBT_write_string(), gbt_write_tree(), GEN_create_nds_vars(), GEN_make_node_text_init(), GEN_next_gene(), GEN_testAndRemoveTranslations(), get_cached_taxonomy(), NodeTextBuilder::init(), map_viewkeys(), MERGE_sequences_simple(), MG_transfer_fields_info(), nds_delete_database_entries(), nds_maintain_viewkeys(), new_gbt_message_created_cb(), NT_format_all_alignments(), NT_suggestValidNames(), PG_get_next_probe(), PS_get_next_node(), read_tree_and_size_internal(), remove_dup_colors(), DBwriter::renumberDuplicateGenes(), and show_all_changekeys().

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
	)

Definition at line 361 of file adquery.cxx.

References GB_find(), and SEARCH_BROTHER.

Referenced by arb_prm_read(), awt_create_select_filter_window_aw_cb(), ALI_ARBDB::get_SAI(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), ALI_ARBDB::put_sequence(), and ALI_ARBDB::put_sequence_string().

const char* GB_first_non_key_char

(

const char *

str

)

Definition at line 416 of file adquery.cxx.

References keychar_table::first_non_key_character().

Referenced by GBT_add_new_changekey_to_keypath(), GEN_make_node_text_init(), NodeTextBuilder::init(), and FINAL_TYPE< SEQTYPE >::ItemQueryKey().

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_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(), nds_delete_database_entries(), nds_maintain_viewkeys(), 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
	)

Definition at line 546 of file adquery.cxx.

References error(), gb_assert, GB_await_error(), GB_clear_error(), gb_expect_type(), GB_export_error(), GB_FIND, GB_have_error(), GB_search(), GB_STRING, GB_write_string(), and NULp.

Referenced by dbserver_entry(), GB_set_macro_error(), GBT_readOrCreate_char_pntr(), GBT_readOrCreate_string(), GEN_create_nds_vars(), and nds_maintain_viewkeys().

GBDATA* GB_searchOrCreate_int	(	GBDATA *	gb_container,
		const char *	fieldpath,
		long	default_value
	)

Definition at line 569 of file adquery.cxx.

References error(), gb_assert, GB_await_error(), gb_expect_type(), GB_export_error(), GB_FIND, GB_have_error(), GB_INT, GB_search(), GB_write_int(), and NULp.

Referenced by announce_recording(), check_for_remote_command(), create_macro_variables(), GBT_readOrCreate_int(), GEN_create_nds_vars(), AWT_graphic_tree::handle_command(), nds_maintain_viewkeys(), EDB_root_bact::search_sequence_data_rek(), set_DB_state(), set_intEntry_to(), set_keep_ghostnodes(), BoundActionTracker::set_recording(), start_remote_command_for_application(), and toggle_helix_for_SAI().

GBDATA* GB_searchOrCreate_float	(	GBDATA *	gb_container,
		const char *	fieldpath,
		float	default_value
	)

Definition at line 591 of file adquery.cxx.

References error(), gb_assert, GB_await_error(), gb_expect_type(), GB_export_error(), GB_FIND, GB_FLOAT, GB_have_error(), GB_search(), GB_write_float(), and NULp.

Referenced by GBT_readOrCreate_float(), and AWT_graphic_tree::handle_command().

long GB_number_of_marked_subentries

(

GBDATA *

gbd

)

Definition at line 635 of file adquery.cxx.

References GBDATA::as_container(), GBCONTAINER::d, flags, GB_DATA_LIST_HEADER(), GB_DELETED, GBCONTAINER_MAIN(), GBDATA::is_container(), gb_data_list::nheader, gb_user::userbit, and GB_MAIN_TYPE::users.

Referenced by GBT_count_marked_species(), and GBT_mark_all().

GBDATA* GB_first_marked	(	GBDATA *	gbd,
		const char *	keystring
	)

Definition at line 655 of file adquery.cxx.

References GBDATA::expect_container(), GB_find_existing_quark(), gb_search_marked(), GB_test_transaction(), and NULp.

Referenced by first_experiment_in_range(), first_gene_in_range(), GBT_first_marked_species(), GBT_first_marked_species_rel_species_data(), GEN_first_marked_gene(), and get_first_SAI().

GBDATA* GB_following_marked	(	GBDATA *	gbd,
		const char *	keystring,
		size_t	skip_over
	)

Definition at line 663 of file adquery.cxx.

References GB_FATHER(), GB_find_existing_quark(), gb_search_marked(), GB_test_transaction(), GBDATA::index, and NULp.

Referenced by GB_next_marked().

GBDATA* GB_next_marked	(	GBDATA *	gbd,
		const char *	keystring
	)

Definition at line 670 of file adquery.cxx.

References GB_following_marked().

Referenced by GBT_next_marked_species(), GEN_next_marked_gene(), get_next_SAI(), and next_experiment_in_range().

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_strstruct::put(), and GBS_strstruct::release_memfriendly().

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

)

Definition at line 357 of file adsocket.cxx.

References NULp.

Referenced by config_modified_cb(), ArbDBWriter::finishSave(), nt_disconnect_from_db(), and GB_MAIN_TYPE::save_quick().

GB_ERROR GB_textprint

(

const char *

path

)

Definition at line 363 of file adsocket.cxx.

References command, error(), GB_failedTo_error(), GBK_singlequote(), GBK_system(), GBS_eval_env(), and GBS_global_string().

Referenced by export_nds_cb().

GB_CSTR GB_getenvARB_XTERM

(

void

)

Definition at line 523 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

)

Definition at line 545 of file adsocket.cxx.

References ARB_getenv_ignore_empty(), and NULp.

Referenced by GB_getenv(), GB_install_pid(), GB_open(), GB_unique_filename(), gbcms_sighup(), GBS_read_arb_tcp(), init_local_com_struct(), MP_init_local_com_struct(), and NT_create_trackAliChanges_Awars().

GB_CSTR GB_getenvARBHOME

(

void

)

Definition at line 579 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

)

Definition at line 593 of file adsocket.cxx.

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

Referenced by fullMacroname(), GB_getenv(), and GBT_relativeMacroname().

GB_CSTR GB_getenvARBMACROHOME

(

void

)

Definition at line 628 of file adsocket.cxx.

References GB_path_in_arbprop(), and getenv_autodirectory().

Referenced by fullMacroname(), GB_getenv(), GBT_relativeMacroname(), and RecordingMacro::RecordingMacro().

GB_CSTR GB_getenvARB_GS

(

void

)

Definition at line 640 of file adsocket.cxx.

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

Referenced by aw_help_helpfile_changed_cb(), awt_aps_go(), canvas_to_printer(), and GB_getenv().

GB_CSTR GB_getenvARB_PDFVIEW

(

void

)

Definition at line 659 of file adsocket.cxx.

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

Referenced by aw_help_helpfile_changed_cb(), and GB_getenv().

GB_CSTR GB_getenvDOCPATH

(

void

)

Definition at line 676 of file adsocket.cxx.

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

Referenced by aw_help_edit_help(), aw_help_search(), GB_getenv(), get_full_qualified_help_file_name(), and get_local_help_url().

GB_CSTR GB_getenvHTMLDOCPATH

(

void

)

Definition at line 686 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 699 of file adsocket.cxx.

References getenv_hook.

Referenced by AW_unfold_path(), and ignore_arb_prop().

GB_CSTR GB_getenv

(

const char *

env

)

Definition at line 709 of file adsocket.cxx.

References ARB_getenv_ignore_empty(), GB_getenvARB_GS(), GB_getenvARB_PDFVIEW(), GB_getenvARB_PROP(), GB_getenvARB_XCMD(), GB_getenvARB_XTERM(), GB_getenvARBCONFIG(), GB_getenvARBHOME(), GB_getenvARBMACRO(), GB_getenvARBMACROHOME(), GB_getenvDOCPATH(), GB_getenvHOME(), GB_getenvUSER(), getenv_hook, and result.

Referenced by aed_start_naligning(), arb_start_server(), detect_sina_version(), enter_stage_1_build_tree(), GB_get_usable_memory(), GB_install_pid(), GB_unfold_path(), GB_xcmd(), gbcms_sighup(), GBS_eval_env(), ignore_arb_prop(), printFile(), and show_soft_link().

bool GB_host_is_local

(

const char *

hostname

)

Definition at line 746 of file adsocket.cxx.

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

Referenced by createCallOnSocketHost().

GB_ULONG GB_get_usable_memory

(

void

)

Definition at line 865 of file adsocket.cxx.

References gb_assert, GB_getenv(), GB_informationf(), GB_warningf(), GBK_terminate(), GBS_readable_size(), get_physical_memory(), and parse_env_mem_definition().

Referenced by ARB_main(), enter_stage_1_build_tree(), GB_optimize(), pars_check_size(), and primer_design_event_go().

NOT4PERL GB_ERROR GB_xcmd	(	const char *	cmd,
		XCMD_TYPE	exectype
	)

Definition at line 906 of file adsocket.cxx.

References _XCMD__ASYNC, _XCMD__WAITKEY, BUFSIZE, GBS_strstruct::cat(), gb_assert, GB_getenv(), GB_getenvARB_XCMD(), GBK_doublequote(), GBK_singlequote(), GBK_system(), GBS_strstruct::get_data(), GBS_strstruct::put(), and XCMD_SYNC_WAITKEY.

Referenced by AWT_system_in_console_cb(), colstat_2_gnuplot_cb(), pd_query_pt_server(), readXmlTree(), and sina_start().

GB_CSTR GB_append_suffix	(	const char *	name,
		const char *	suffix
	)

Definition at line 984 of file adsocket.cxx.

References ARB_PATH_MAX, GBS_global_string_to_buffer(), result, and use_other_path_buf().

Referenced by copyMoveRuleset_cb(), export_filename_changed_cb(), export_format_multiple(), filename_changed_cb(), and update_format_description_and_suffix().

GB_CSTR GB_canonical_path

(

const char *

anypath

)

Definition at line 1000 of file adsocket.cxx.

References ARB_PATH_MAX, gb_assert, GB_concat_path(), GB_export_error(), GB_export_errorf(), GB_getenvHOME(), GB_split_full_path(), GBS_global_string(), GBS_reuse_buffer(), NULp, path_toggle, result, and use_other_path_buf().

Referenced by File_selection::filename_changed(), GB_concat_full_path(), GB_unfold_in_directory(), GB_unfold_path(), GBS_read_dir(), and read_export_format().

GB_CSTR GB_concat_path	(	GB_CSTR	anypath_left,
		GB_CSTR	anypath_right
	)

Definition at line 1069 of file adsocket.cxx.

References GBS_global_string_to_buffer(), NULp, result, and use_other_path_buf().

Referenced by copyMoveRuleset_cb(), export_filename_changed_cb(), export_format_multiple(), GB_canonical_path(), GB_concat_full_path(), GB_concat_path_in_ARBHOME(), GB_concat_path_in_ARBLIB(), GB_fopen_tempfile(), GB_path_in_arb_temp(), GBS_read_dir(), update_format_description_and_suffix(), and XFER_getFullFTS().

GB_CSTR GB_concat_full_path	(	const char *	anypath_left,
		const char *	anypath_right
	)

Definition at line 1103 of file adsocket.cxx.

References gb_assert, GB_canonical_path(), GB_concat_path(), and result.

Referenced by AW_get_selected_fullname(), File_selection::filename_changed(), flagDir(), GB_unfold_in_directory(), GB_unfold_path(), mutexDir(), runDir(), and unitTesterDir().

GB_CSTR GB_unfold_in_directory	(	const char *	relative_directory,
		const char *	path
	)

Definition at line 1123 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
	)

Definition at line 1132 of file adsocket.cxx.

References gb_assert, GB_canonical_path(), GB_concat_full_path(), GB_getcwd(), GB_getenv(), is_absolute_path(), and is_name_of_envvar().

Referenced by AW_unfold_path(), GB_path_in_ARBHOME(), GB_path_in_arbprop(), and GB_path_in_HOME().

GB_CSTR GB_path_in_ARBHOME

(

const char *

relative_path

)

Definition at line 1149 of file adsocket.cxx.

References GB_unfold_path().

Referenced by develDocPath(), GB_concat_path_in_ARBHOME(), GBT_macro_execute(), get_full_qualified_help_file_name(), read_export_format(), and ArbImporter::read_format().

GB_CSTR GB_path_in_ARBLIB

(

const char *

relative_path

)

Definition at line 1156 of file adsocket.cxx.

References GB_concat_path_in_ARBHOME().

Referenced by AWTC_create_submission_window(), create_export_awars(), create_import_awars(), ED4_create_modsai_window(), GB_concat_path_in_ARBLIB(), GB_getenvARBMACRO(), GB_getenvDOCPATH(), GB_getenvHTMLDOCPATH(), GBS_ptserver_logname(), GBT_open(), ignore_arb_prop(), inputMaskDir(), LoadMenus(), NDS_popup_select_srtaci_window(), NT_importValidNames(), RecordingMacro::RecordingMacro(), and startup_gui().

GB_CSTR GB_concat_path_in_ARBLIB	(	const char *	relative_path_left,
		const char *	anypath_right
	)

Definition at line 1159 of file adsocket.cxx.

References GB_concat_path(), and GB_path_in_ARBLIB().

Referenced by AW_get_pixmapPath(), AW_xfig::AW_xfig(), create_modify_fields_window(), GB_lib_file(), and namesFilename().

GB_CSTR GB_path_in_HOME

(

const char *

relative_path

)

Definition at line 1163 of file adsocket.cxx.

References GB_unfold_path().

Referenced by GB_getenvARB_PROP(), GB_path_in_arb_temp(), and save_messagebox_content_to().

GB_CSTR GB_path_in_arbprop

(

const char *

relative_path

)

Definition at line 1166 of file adsocket.cxx.

References GB_unfold_path().

Referenced by create_awars(), create_export_awars(), create_import_awars(), detectProperties(), ED4_create_search_awars(), GB_getenvARBCONFIG(), GB_getenvARBMACROHOME(), GB_property_file(), GB_save_in_arbprop(), ED4_root::generate_window(), initXferAwars(), inputMaskDir(), LoadMenus(), startup_gui(), and XFER_getFullFTS().

FILE* GB_fopen_tempfile	(	const char *	filename,
		const char *	fmode,
		char **	res_fullname
	)

Definition at line 1176 of file adsocket.cxx.

References ARB_strdup(), error(), GB_concat_path(), GB_create_parent_directory(), GB_export_error(), GB_IO_error(), GB_PATH_TMP, GBS_global_string(), and NULp.

Referenced by awt_aps_go(), colstat_2_gnuplot_cb(), GB_create_tempfile(), GB_install_pid(), gbcms_sighup(), gbl_exec(), PH_create_ml_multiline_SAI(), and sina_start().

char* GB_create_tempfile

(

const char *

name

)

Definition at line 1222 of file adsocket.cxx.

References GB_fopen_tempfile().

Referenced by ad_move_tree_info(), aw_help_search(), aw_help_show_external_format(), awt_aps_go(), canvas_to_printer(), export_format_single(), ArbImporter::next_file(), preCreateTempfile(), and update_exportTest_result_cb().

char* GB_unique_filename	(	const char *	name_prefix,
		const char *	suffix
	)

Definition at line 1233 of file adsocket.cxx.

References GB_getenvUSER(), and GBS_global_string_copy().

Referenced by ad_move_tree_info(), aw_help_search(), aw_help_show_external_format(), awt_aps_go(), canvas_to_printer(), colstat_2_gnuplot_cb(), export_format_single(), gbl_exec(), ArbImporter::next_file(), PH_create_ml_multiline_SAI(), and sina_start().

void GB_remove_on_exit

(

const char *

filename

)

Definition at line 1258 of file adsocket.cxx.

References exit_removal(), GB_atexit(), GB_MIND_CASE, GBS_create_hash(), and GBS_write_hash().

Referenced by ad_move_tree_info(), aw_help_search(), PH_create_ml_multiline_SAI(), and sina_start().

void GB_split_full_path	(	const char *	fullpath,
		char **	res_dir,
		char **	res_fullname,
		char **	res_name_only,
		char **	res_suffix
	)

Definition at line 1268 of file adsocket.cxx.

References ARB_strdup(), ARB_strpartdup(), gb_assert, and NULp.

Referenced by askCopyMoveRuleset_cb(), aw_help_show_external_format(), awt_aps_go(), copyMoveRuleset_cb(), export_filename_changed_cb(), export_format_multiple(), filename_changed_cb(), GB_canonical_path(), GB_create_parent_directory(), SelectedDatabase::get_dir(), SEQIO::get_exportFormat_evalForm(), SelectedDatabase::get_mask(), getNameOnly(), nt_start_2nd_arb(), ExportFieldScanner::scanFields(), set_suffix(), and update_format_description_and_suffix().

char* GBS_string_2_key

(

const char *

str

)

Definition at line 52 of file adstring.cxx.

References GBS_string_2_key_with_exclusions().

Referenced by aw_question(), aws_init_localized(), awt_create_load_box(), AWT_create_mask_submenu(), create_calltexe_window(), create_save_box_for_selection_lists(), createCopy_table_handler(), current_changed_cb(), export_to_DB(), ID_checker::fromText(), gb_fix_recursive(), GB_read_as_tagged_string(), GBS_merge_tagged_strings(), GBS_modify_tagged_string_with_ACI(), GDE_create_filename_browser_window(), GDE_makeawarname_in(), AW_window_menu_modes_opengl::init(), AW_window_menu_modes::init(), AW_window_menu::init(), AW_window_simple_menu::init(), AW_window_message::init(), name2ID(), ArbImporter::read_data(), sai_transtab_awar(), and trackAlignmentChanges().

char* GB_memdup	(	const char *	source,
		size_t	len
	)

Definition at line 56 of file adstring.cxx.

Referenced by gb_convert_compression(), GB_read_bits(), GB_read_bytes(), GB_read_floats(), GB_read_ints(), and GB_read_string().

GB_ERROR GB_check_key

(

const char *

key

)

Definition at line 85 of file adstring.cxx.

References check_key().

Referenced by aw_question(), field_create_cb(), GB_create(), GB_create_container(), GBT_add_data(), GBT_check_alignment_name(), GBT_check_tree_name(), and gcman_specific_awarname().

GB_ERROR GB_check_hkey

(

const char *

key

)

Definition at line 92 of file adstring.cxx.

References check_key(), EMPTY_KEY_NOT_ALLOWED, gb_assert, and NULp.

Referenced by add_field_cb(), AW_awar::AW_awar(), check_data_path(), FieldTransfer::WriteRule::check_hkey(), field_create_cb(), GBT_add_data(), gbt_scan_db_rek(), gcman_specific_awarname(), and prepare_and_get_selected_itemfield().

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

str	string to escape
escape_char	is the character used for escaping. For performance reasons it should be a character rarely used in 'str'.
chars_to_escape	may 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

)

Definition at line 212 of file adstring.cxx.

References ARB_strpartdup(), GBS_strstruct::cat(), error(), GB_export_error(), GB_getenv(), GBS_find_string(), GBS_global_string(), GBS_strstruct::ncat(), NULp, and GBS_strstruct::release_memfriendly().

Referenced by aw_modal_file_selection(), AWT_create_ascii_print_window(), create_print_awars(), GB_disable_path(), GB_getenvPATH(), GB_read_file(), GB_textprint(), and getenv_autodirectory().

long GBS_gcgchecksum

(

const char *

seq

)

Definition at line 246 of file adstring.cxx.

Referenced by gbl_gcgchecksum().

uint32_t GB_checksum	(	const char *	seq,
		long	length,
		int	ignore_case,
		const char *	exclude
	)

Definition at line 319 of file adstring.cxx.

References crctab, length, and tab().

Referenced by AW_advice(), calcSequenceChecksum(), ChecksumCollector::checksum(), GBS_checksum(), and PT_prepare_species_sequence().

uint32_t GBS_checksum	(	const char *	seq,
		int	ignore_case,
		const char *	exclude
	)

Definition at line 352 of file adstring.cxx.

References GB_checksum().

Referenced by adaptCopiedAlignment(), awt_create_select_filter_win(), concatenateFieldsCreateNewSpecies(), export_to_DB(), gbl_checksum(), GBT_gen_accession_number(), gen_extract_gene_2_pseudoSpecies(), CommandOutput::has_checksum(), pd_get_the_gene_names(), pd_get_the_names(), ArbImporter::read_data(), trackAlignmentChanges(), and ED4_terminal::write_sequence().

size_t GBS_shorten_repeated_data

(

char *

data

)

Definition at line 357 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
	)

Definition at line 710 of file adstring.cxx.

References ARB_strdup(), g_bs_convert_string_to_tagged_hash_with_delete(), g_bs_free_hash_of_hashes(), g_bs_get_string_of_tag_hash(), GB_MIND_CASE, GBS_create_hash(), GBS_string_2_key(), NULp, and result.

Referenced by MG_merge_tagged_field_cb().

char* GBS_modify_tagged_string_with_ACI	(	const char *	s,
		const char *	dt,
		const char *	tag,
		const char *	aci,
		GBL_call_env &	env
	)

Definition at line 747 of file adstring.cxx.

References ARB_strdup(), error(), g_bs_convert_string_to_tagged_hash_with_rewrite(), g_bs_free_hash_of_hashes(), g_bs_get_string_of_tag_hash(), GB_export_error(), GB_MIND_CASE, GBS_create_hash(), GBS_string_2_key(), NULp, and result.

Referenced by modify_fields_of_queried_cb().

char* GB_read_as_tagged_string	(	GBDATA *	gbd,
		const char *	tagi
	)

Definition at line 776 of file adstring.cxx.

References TextRef::copy(), GB_read_as_string(), GBS_string_2_key(), TaggedContentParser::get_content(), TaggedContentParser::get_tag(), TaggedContentParser::has_part(), TaggedContentParser::has_tag(), TextRef::icompare(), TaggedContentParser::next(), and NULp.

Referenced by mg_check_field_cb().

void GBS_fwrite_string	(	const char *	strngi,
		FILE *	out
	)

Definition at line 807 of file adstring.cxx.

Referenced by gb_write_one_child().

char* GBS_fconvert_string

(

char *

buffer

)

Definition at line 880 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 923 of file adstring.cxx.

References GBS_strstruct::put(), and GBS_strstruct::release_memfriendly().

Referenced by awt_aps_go(), and awt_aps_text_changed().

char* GBS_trim

(

const char *

str

)

Definition at line 947 of file adstring.cxx.

References ARB_strpartdup().

Referenced by TreeNode::apply_aci_to_remarks(), GS_calc_resulting_groupname(), write_float_converted(), and write_int_converted().

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

comment	may be NULp (=> result is 'action')
action	may NOT be NULp
stamp	true -> prefix current timestamp in front of 'action'

Returns

heap copy of concatenation

Definition at line 976 of file adstring.cxx.

References GBS_strstruct::cat(), dated_info(), GBS_strstruct::put(), and GBS_strstruct::release_memfriendly().

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 1007 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
	)

Definition at line 279 of file adsystem.cxx.

References DictData::data, error(), GB_export_error(), GB_free_dictionary(), gb_load_dictionary_data(), NULp, and DictData::size.

Referenced by findAffectedKeys().

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

Definition at line 295 of file adsystem.cxx.

References DictData::data, error(), gb_save_dictionary_data(), NULp, and DictData::size.

Referenced by Dict::assignToKey(), and Dict::unassignFromKey().

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
	)

Definition at line 275 of file adtcp.cxx.

References NULp, and result.

Referenced by arb_look_and_start_server(), AW_select_nameserver(), GBS_ptserver_id_to_choice(), and pd_export_pt_server().

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

)

Definition at line 312 of file adtcp.cxx.

References ASSERT_RESULT_PREDICATE, and gb_assert.

Referenced by arb_look_and_start_ptserver(), GBS_ptserver_id_to_choice(), pd_export_pt_server(), pd_kill_pt_server(), pd_query_pt_server(), pd_start_pt_server(), PT_FamilyFinder::searchFamily(), and test_ptserver_activate().

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 arb_look_and_kill_server(), arb_look_and_start_ptserver(), arb_look_and_start_server(), ARB_main(), arb_start_server(), AW_select_nameserver(), NameServerConnection::connect(), gbcm_open_socket(), GBS_ptserver_id_to_choice(), pd_export_pt_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 390 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

)

Definition at line 425 of file adtcp.cxx.

References GB_path_in_ARBLIB(), and RETURN_ONETIME_ALLOC.

Referenced by GBS_add_ptserver_logentry(), pd_edit_ptserver_log(), and PT_selection::PT_selection().

void GBS_add_ptserver_logentry

(

const char *

entry

)

Definition at line 429 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
	)

Definition at line 447 of file adtcp.cxx.

References ARB_strdup(), GBS_global_string_copy(), GBS_ptserver_tag(), GBS_read_arb_tcp(), GBS_scan_arb_tcp_param(), NULp, and result.

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

const char* GB_get_type_name

(

GBDATA *

gbd

)

Definition at line 72 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

)

Definition at line 190 of file arbdb.cxx.

References GB_safe_atof(), and GBK_terminatef().

Referenced by gb_parse_ascii_rek(), GB_read_lossless_float(), gbt_read_tree_rek(), and write_entry().

GB_BUFFER GB_give_buffer

(

size_t

size

)

Definition at line 311 of file arbdb.cxx.

References gb_local_data::buf1, and give_buffer().

Referenced by ED4_show_helix_on_device(), ED4_show_protein_match_on_device(), gb_bin_2_ascii(), GB_give_other_buffer(), gb_read_bin(), gb_read_bin_rek_V2(), gbcmc_begin_transaction(), gbcmc_sendupdate_create(), gbcmc_sendupdate_update(), gbcms_talking_begin_transaction(), gbcms_talking_put_update(), gbcms_talking_unfold(), ED4_root::generate_window(), get_design_hinfo(), get_design_info(), and pattern2str().

GB_BUFFER GB_increase_buffer

(

size_t

size

)

Definition at line 316 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 330 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 334 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

)

Definition at line 350 of file arbdb.cxx.

References gb_local_data::buf1, gb_local_data::buf2, check_out_buffer(), is_in_buffer(), and NULp.

Referenced by gb_uncompress_by_sequence().

GB_BUFFER GB_give_other_buffer	(	GB_CBUFFER	buffer,
		long	size
	)

Definition at line 363 of file arbdb.cxx.

References gb_local_data::buf1, GB_give_buffer(), GB_give_buffer2(), and is_in_buffer().

Referenced by g_b_uncompress_single_sequence_by_master(), gb_compress_bits(), gb_compress_by_dictionary(), gb_compress_equal_bytes(), gb_compress_huffmann(), gb_compress_longs(), gb_compress_seq_by_master(), GB_read_floats_pntr(), GB_read_ints_pntr(), gb_uncompress_bits(), gb_uncompress_by_dictionary_internal(), gb_uncompress_equal_bytes(), gb_uncompress_huffmann(), gb_uncompress_longs(), gb_uncompress_longs_old(), GB_write_floats(), GB_write_ints(), and GBT_tree_info_string().

void GB_atexit

(

void(*)()

exitfun

)

Definition at line 402 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 512 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 522 of file arbdb.cxx.

References gb_local_data::open_dbs().

Referenced by aw_initstatus().

void GB_close

(

GBDATA *

gbd

)

Definition at line 655 of file arbdb.cxx.

References GB_MAIN_TYPE::c_link, GB_MAIN_TYPE::cache, GB_MAIN_TYPE::call_pending_callbacks(), GB_MAIN_TYPE::close_callbacks, GB_MAIN_TYPE::dummy_father, gb_cache::entries, error(), GB_MAIN_TYPE::forget_hierarchy_cbs(), gb_assert, GB_await_error(), gb_delete_dummy_father(), GB_MAIN_TYPE::gb_main(), GB_MAIN(), GB_warningf(), gbcm_logout(), GBCM_SERVER_OK, gbcmc_close(), GBS_global_string(), GB_MAIN_TYPE::get_transaction_level(), GB_MAIN_TYPE::is_client(), GB_MAIN_TYPE::mapped, NULp, result, GB_MAIN_TYPE::root_container, and run_close_callbacks().

Referenced by ARB_main(), calc_pvp(), check_socket_available(), probe_struct_global::cleanup(), ALI_ARBDB::close(), SelectedDatabase::close_db(), closeArb(), di_exit(), ED4_exit(), export_newick(), export_seq_data(), ImportTestData::forgetLastImport(), gb_abort_and_close_all_DBs(), GBT_open(), main(), MG_exit(), nt_disconnect_from_db(), ph_exit(), run_command(), run_server(), save_tree_as_newick(), ALI_ARBDB::~ALI_ARBDB(), AP_main::~AP_main(), ArbImporter::~ArbImporter(), and ImportTestData::~ImportTestData().

long GB_read_int

(

GBDATA *

gbd

)

Definition at line 729 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(), 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(), nds_maintain_viewkeys(), 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

)

Definition at line 734 of file arbdb.cxx.

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

Referenced by do_hide_command_for_one_species(), do_mark_command_for_one_species(), dump_internal(), export_tree_node_print_xml(), gb_copy_explicit(), GB_read_as_string(), GB_read_lossless_byte(), gb_write_one_child(), GEN_make_node_text_nds(), GEN_root::GEN_root(), group_is_folded(), nt_build_conf_string_rek(), NT_convert_gene_locations(), tree_read_byte(), and NodeTextBuilder::work().

GBDATA* GB_read_pointer

(

GBDATA *

gbd

)

Definition at line 739 of file arbdb.cxx.

References GBDATA::as_entry(), GB_POINTER, GB_TEST_READ_PTR, GBENTRY::info, and gb_data_base_type_union::ptr.

Referenced by AW_awar::read_pointer().

float GB_read_float

(

GBDATA *

gbd

)

Definition at line 744 of file arbdb.cxx.

References GBDATA::as_entry(), GB_INTern::data, gb_assert, GB_FLOAT, GB_TEST_READ_NUM, gb_data_base_type_union::in, GBENTRY::info, and SIZOFINTERN.

Referenced by FieldReader::calc_value(), cmpByKey(), dump_internal(), gb_copy_explicit(), GB_read_as_string(), GB_read_lossless_byte(), GB_read_lossless_float(), GB_write_float(), gb_write_one_child(), GBT_read_float(), GBT_readOrCreate_float(), GEN_make_node_text_nds(), DB_scalable::read(), AW_awar::read_float(), ItemFieldShader::scan_value_range_cb(), SQ_pass2(), SQ_pass2_no_tree(), tree_read_float(), and NodeTextBuilder::work().

long GB_read_count

(

GBDATA *

gbd

)

Definition at line 758 of file arbdb.cxx.

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

Referenced by count_bases(), PH_display::display(), dump_internal(), GBT_check_alignment(), GBT_read_gene_sequence_and_length(), GEN_root::GEN_root(), GEN_write_position(), export_sequence_data::get_seq_data(), probe_input_data::init(), insert_genes_of_organism(), FilterDefinition::make_filter(), primer_design_event_go(), read_sequence_region(), and EDB_root_bact::search_sequence_data_rek().

long GB_read_memuse

(

GBDATA *

gbd

)

Definition at line 762 of file arbdb.cxx.

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

Referenced by compress_sequence_tree().

NOT4PERL long GB_calc_structure_size

(

GBDATA *

gbd

)

GB_CSTR GB_read_pntr

(

GBDATA *

gbd

)

Definition at line 877 of file arbdb.cxx.

References GBDATA::as_entry(), gb_flag_types::compressed_data, GBENTRY::data(), GBDATA::flags, gb_alloc_cache_index(), gb_read_cache(), gb_uncompress_data(), and GBENTRY::uncompressed_size().

Referenced by GB_read_bytes_pntr(), GB_read_char_pntr(), GB_read_floats_pntr(), GB_read_ints_pntr(), GB_read_string(), and GB_write_string().

GB_CSTR GB_read_char_pntr

(

GBDATA *

gbd

)

Definition at line 904 of file arbdb.cxx.

References GB_read_pntr(), GB_STRING, and GB_TEST_READ_PTR.

Referenced by ED4_root::add_to_highlighted(), 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(), copy_field_into_partial_alignments(), count_bases(), ImportTestData::countSpeciesAndData(), create_gene_species(), 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(), nds_maintain_viewkeys(), 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_highlighted(), 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 909 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

)

Definition at line 916 of file arbdb.cxx.

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

Referenced by ALI_translate_marked(), alignCompactedTo(), alignTo(), alignToNextRelative(), arb_prm_read(), PH_filter::calculate_column_homology(), compress_sequence_tree(), CON_insertSequences(), Data::Data(), dot_missing_bases(), dot_sequence_by_consensus(), ED4_get_marked_from_menu(), g_b_put_sequences_in_container(), gb_uncompress_by_sequence(), gbl_read_seq_sai_or_species(), GBT_check_alignment(), GEN_make_node_text_init(), NodeTextBuilder::init(), insert_new_species_terminal(), modsai_cb(), perform_block_operation_on_part_of_sequence(), perform_block_operation_on_whole_sequence(), probe_design_event(), PT_prepare_species_sequence(), PV_WriteTranslatedSequenceToDB(), readCompactedSequence(), ED4_terminal::resolve_pointer_to_char_pntr(), reverseComplement(), SEC_seq_data::SEC_seq_data(), MostLikelySeq::set_sequence(), st_ml_add_sequence_part_to_stat(), TranslateGeneToAminoAcidSequence(), and writeHistory().

long GB_read_bits_count

(

GBDATA *

gbd

)

Definition at line 921 of file arbdb.cxx.

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

Referenced by gbl_read_seq_sai_or_species(), and ED4_terminal::resolve_pointer_to_char_pntr().

GB_CSTR GB_read_bits_pntr	(	GBDATA *	gbd,
		char	c_0,
		char	c_1
	)

Definition at line 926 of file arbdb.cxx.

References GBDATA::as_entry(), GBENTRY::data(), gb_alloc_cache_index(), GB_BITS, GB_flush_cache(), gb_read_cache(), GB_TEST_READ_PTR, gb_uncompress_bits(), NULp, and GBENTRY::size().

Referenced by GB_read_bits(), gb_write_one_child(), and ED4_terminal::resolve_pointer_to_char_pntr().

char* GB_read_bits	(	GBDATA *	gbd,
		char	c_0,
		char	c_1
	)

Definition at line 958 of file arbdb.cxx.

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

Referenced by awt_create_select_filter_window_aw_cb(), GB_read_as_string(), and gbl_read_seq_sai_or_species().

GB_CSTR GB_read_bytes_pntr

(

GBDATA *

gbd

)

Definition at line 964 of file arbdb.cxx.

References GB_BYTES, GB_read_pntr(), and GB_TEST_READ_PTR.

Referenced by GB_read_bytes(), gb_read_dict_data(), get_data_n_size(), and ED4_terminal::resolve_pointer_to_char_pntr().

long GB_read_bytes_count

(

GBDATA *

gbd

)

Definition at line 969 of file arbdb.cxx.

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

Referenced by gb_read_dict_data(), and ED4_terminal::resolve_pointer_to_char_pntr().

char* GB_read_bytes

(

GBDATA *

gbd

)

Definition at line 974 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

)

Definition at line 979 of file arbdb.cxx.

References GBDATA::as_entry(), gb_flag_types::compressed_data, GBENTRY::data(), GBDATA::flags, GB_give_other_buffer(), GB_INTS, GB_read_pntr(), GB_TEST_READ_PTR, NULp, s, and GBENTRY::size().

Referenced by GB_read_from_ints(), GB_read_ints(), get_data_n_size(), and probe_input_data::preload_rel2abs().

long GB_read_ints_count

(

GBDATA *

gbd

)

Definition at line 1008 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 1013 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

)

Definition at line 1019 of file arbdb.cxx.

References GBDATA::as_entry(), gb_flag_types::compressed_data, GBENTRY::data(), GBDATA::flags, GB_FLOATS, GB_give_other_buffer(), GB_read_pntr(), GB_TEST_READ_PTR, NULp, and GBENTRY::size().

Referenced by GB_read_floats(), GB_read_from_floats(), and get_data_n_size().

float* GB_read_floats

(

GBDATA *

gbd

)

Definition at line 1053 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 1060 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 add_species_to_list_cb(), 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_SAI_id(), 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(), split_data_into_parts(), translateSAItoColors(), NodeTextBuilder::work(), and XML_recursive().

bool GB_readable_as_string

(

GBDATA *

gbd

)

See also

GB_TYPE_readable_as_string()

Definition at line 1080 of file arbdb.cxx.

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

Referenced by FINAL_TYPE< SEQTYPE >::get_target_data().

NOT4PERL uint8_t GB_read_lossless_byte	(	GBDATA *	gbd,
		GB_ERROR &	error
	)

Reads an uint8_t previously written with GB_write_lossless_byte()

Parameters

gbd	the DB field
error	result parameter (has to be NULp)

Returns

is undefined if error got set; contains read value otherwise

Definition at line 1093 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

gbd	the DB field
error	result parameter (has to be NULp)

Returns

is undefined if error got set; contains read value otherwise

Definition at line 1128 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

gbd	the DB field
error	result parameter (has to be NULp)

Returns

is undefined if error got set; contains read value otherwise

Definition at line 1155 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 1186 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 1203 of file arbdb.cxx.

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

GB_ERROR GB_write_byte	(	GBDATA *	gbd,
		int	i
	)

Definition at line 1238 of file arbdb.cxx.

References GBDATA::as_entry(), GB_BYTE, GB_DO_CALLBACKS, GB_NORMAL_CHANGE, gb_save_extern_data_in_ts(), GB_TEST_WRITE, gb_touch_entry(), gb_data_base_type_union::i, GBENTRY::info, and NULp.

Referenced by DB_create_byte_field(), do_hide_command_for_one_species(), gb_copy_explicit(), gb_parse_ascii_rek(), GB_write_autoconv_string(), GB_write_lossless_byte(), GBT_write_byte(), group_set_folded(), and tree_write_byte().

GB_ERROR GB_write_int	(	GBDATA *	gbd,
		long	i
	)

Definition at line 1250 of file arbdb.cxx.

References GBDATA::as_entry(), gb_assert, GB_DO_CALLBACKS, GB_get_db_path(), GB_INT, GB_NORMAL_CHANGE, gb_save_extern_data_in_ts(), GB_TEST_WRITE, gb_touch_entry(), GB_warningf(), gb_data_base_type_union::i, GBENTRY::info, and NULp.

Referenced by announce_recording(), apply_command_to_alignment(), AW_awar::AW_awar(), AW_reactivate_all_questions(), check_for_remote_command(), FieldTransfer::convertAndWrite(), create_ali_intEntry(), ensure_trees_have_order(), gb_copy_explicit(), gb_parse_ascii_rek(), GB_searchOrCreate_int(), GB_write_autoconv_string(), GB_write_lossless_byte(), GB_write_lossless_int(), GBT_check_alignment(), GBT_write_int(), gbt_write_tree_nodes(), GEN_is_genome_db(), GEN_write_position(), get_next_SAI_count(), mark_as_macro_executor(), nds_maintain_viewkeys(), NT_format_all_alignments(), PT_prepare_species_sequence(), set_DB_state(), set_intEntry_to(), BoundActionTracker::set_recording(), set_tree_idx(), setIntEntryToZero(), show_all_changekeys(), SQ_helix::SQ_calc_helix_layout(), SQ_physical_layout::SQ_calc_physical_layout(), SQ_ambiguities::SQ_count_ambiguities(), SQ_evaluate(), SQ_pass2(), SQ_pass2_no_tree(), start_remote_command_for_application(), toggle_helix_for_SAI(), FieldTransfer::unconvertedWrite(), DB_scalable::write(), write_entry(), and write_int_converted().

GB_ERROR GB_write_pointer	(	GBDATA *	gbd,
		GBDATA *	pointer
	)

Definition at line 1269 of file arbdb.cxx.

References GBDATA::as_entry(), GB_DO_CALLBACKS, GB_NORMAL_CHANGE, GB_POINTER, gb_save_extern_data_in_ts(), GB_TEST_WRITE, gb_touch_entry(), GBENTRY::info, NULp, and gb_data_base_type_union::ptr.

Referenced by AW_awar::AW_awar().

GB_ERROR GB_write_float	(	GBDATA *	gbd,
		float	f
	)

Definition at line 1281 of file arbdb.cxx.

References GBDATA::as_entry(), GB_INTern::data, gb_assert, GB_DO_CALLBACKS, GB_FLOAT, GB_NORMAL_CHANGE, GB_read_float(), gb_save_extern_data_in_ts(), GB_TEST_WRITE, gb_touch_entry(), gb_data_base_type_union::in, GBENTRY::info, NULp, and SIZOFINTERN.

Referenced by AW_awar::AW_awar(), FieldTransfer::convertAndWrite(), gb_copy_explicit(), gb_parse_ascii_rek(), GB_searchOrCreate_float(), GB_write_autoconv_string(), GB_write_lossless_byte(), GB_write_lossless_float(), GBT_write_float(), SQ_physical_layout::SQ_calc_physical_layout(), SQ_pass2(), SQ_pass2_no_tree(), FieldTransfer::unconvertedWrite(), DB_scalable::write(), write_entry(), and write_float_converted().

GB_ERROR GB_write_pntr	(	GBDATA *	gbd,
		const char *	s,
		size_t	bytes_size,
		size_t	stored_size
	)

Definition at line 1344 of file arbdb.cxx.

References GBDATA::as_entry(), GBENTRY::cache_index, gb_flag_types::compressed_data, GBDATA::flags, gb_assert, gb_compress_data(), GB_DO_CALLBACKS, gb_get_compression_mask(), GB_KEY_QUARK(), GB_MAIN(), GB_NORMAL_CHANGE, gb_save_extern_data_in_ts__and_uncache(), GB_STRING, gb_touch_entry(), implicated, GBENTRY::insert_data(), NULp, s, type, and GBDATA::type().

Referenced by createDataFromConsensus(), gb_convert_compression(), GB_write_bytes(), GB_write_floats(), GB_write_ints(), and GB_write_string().

GB_ERROR GB_write_string	(	GBDATA *	gbd,
		const char *	s
	)

Definition at line 1387 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(), copy_field_into_partial_alignments(), create_ali_strEntry(), create_concatInfo_SAI(), create_gene_species(), 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(), nds_maintain_viewkeys(), 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
	)

Definition at line 1418 of file arbdb.cxx.

References GBDATA::as_entry(), gb_flag_types::compressed_data, GBDATA::flags, GB_BITS, gb_compress_bits(), GB_DO_CALLBACKS, GB_NORMAL_CHANGE, gb_save_extern_data_in_ts__and_uncache(), GB_TEST_NON_BUFFER, GB_TEST_WRITE, gb_touch_entry(), GBENTRY::insert_data(), and NULp.

Referenced by EditedTerminal::apply(), gb_parse_ascii_rek(), GB_write_autoconv_string(), PH_save_ml_cb(), and ED4_terminal::write_sequence().

GB_ERROR GB_write_bytes	(	GBDATA *	gbd,
		const char *	s,
		long	size
	)

Definition at line 1434 of file arbdb.cxx.

References GB_BYTES, GB_TEST_WRITE, and GB_write_pntr().

Referenced by EditedTerminal::apply(), gb_convert_compression(), gb_save_dictionary_data(), PT_prepare_species_sequence(), and readAndWrite().

GB_ERROR GB_write_ints	(	GBDATA *	gbd,
		const GB_UINT4 *	i,
		long	size
	)

Definition at line 1439 of file arbdb.cxx.

References GB_give_other_buffer(), GB_INTS, GB_TEST_NON_BUFFER, GB_TEST_WRITE, GB_write_pntr(), and s.

Referenced by EditedTerminal::apply(), PT_prepare_species_sequence(), readAndWrite(), and AP_pos_var::save_aliEntry_to_SAI().

GB_ERROR GB_write_floats	(	GBDATA *	gbd,
		const float *	f,
		long	size
	)

Definition at line 1457 of file arbdb.cxx.

References GB_FLOATS, GB_give_other_buffer(), GB_TEST_NON_BUFFER, GB_TEST_WRITE, GB_write_pntr(), and s.

Referenced by EditedTerminal::apply(), readAndWrite(), and writeToArb().

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 1479 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(), split_data_into_parts(), 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 1504 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 1523 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 calc_and_update_alignment_errors_cb(), 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 1546 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

)

Definition at line 1572 of file arbdb.cxx.

References GB_GET_SECURITY_WRITE, and GB_test_transaction().

Referenced by copy_field_into_partial_alignments(), GBT_tree_info_string(), reverseComplement(), split_data_into_parts(), and tree_vars_callback().

int GB_read_security_read

(

GBDATA *

gbd

)

Definition at line 1576 of file arbdb.cxx.

References GB_GET_SECURITY_READ, and GB_test_transaction().

int GB_read_security_delete

(

GBDATA *

gbd

)

Definition at line 1580 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
	)

Definition at line 1584 of file arbdb.cxx.

References GB_DO_CALLBACKS, GB_GET_SECURITY_WRITE, GB_MAIN(), GB_NORMAL_CHANGE, GB_PUT_SECURITY_WRITE, gb_security_error(), GB_test_transaction(), gb_touch_entry(), NULp, and GB_MAIN_TYPE::security_level.

Referenced by ad_tree_set_security(), create_ali_intEntry(), create_ali_strEntry(), ED4_set_protection(), g_b_create_master(), gb_create_dict(), GBT_check_alignment(), GBT_create_sequence_data(), and set_protection_of_queried_cb().

GB_ERROR GB_write_security_read	(	GBDATA *	gbd,
		unsigned long	level
	)

Definition at line 1595 of file arbdb.cxx.

References GB_DO_CALLBACKS, GB_GET_SECURITY_READ, GB_GET_SECURITY_WRITE, GB_MAIN(), GB_NORMAL_CHANGE, GB_PUT_SECURITY_READ, gb_security_error(), GB_test_transaction(), gb_touch_entry(), NULp, and GB_MAIN_TYPE::security_level.

GB_ERROR GB_write_security_delete	(	GBDATA *	gbd,
		unsigned long	level
	)

Definition at line 1605 of file arbdb.cxx.

References GB_DO_CALLBACKS, GB_GET_SECURITY_DELETE, GB_GET_SECURITY_WRITE, GB_MAIN(), GB_NORMAL_CHANGE, GB_PUT_SECURITY_DELETE, gb_security_error(), GB_test_transaction(), gb_touch_entry(), NULp, and GB_MAIN_TYPE::security_level.

Referenced by ad_tree_set_security(), compress_sequence_tree(), create_ali_intEntry(), create_ali_strEntry(), GBT_check_alignment(), GBT_create(), GBT_create_alignment(), NT_deleteValidNames(), and set_protection_of_queried_cb().

GB_ERROR GB_write_security_levels	(	GBDATA *	gbd,
		unsigned long	readlevel,
		unsigned long	writelevel,
		unsigned long	deletelevel
	)

Definition at line 1615 of file arbdb.cxx.

References GB_DO_CALLBACKS, GB_GET_SECURITY_WRITE, GB_MAIN(), GB_NORMAL_CHANGE, GB_PUT_SECURITY_DELETE, GB_PUT_SECURITY_READ, GB_PUT_SECURITY_WRITE, gb_security_error(), GB_test_transaction(), gb_touch_entry(), NULp, and GB_MAIN_TYPE::security_level.

void GB_change_my_security	(	GBDATA *	gbd,
		int	level
	)

Definition at line 1627 of file arbdb.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::security_level.

Referenced by ed4_changesecurity(), MERGE_create_main_window(), and nt_changesecurity().

GB_TYPES GB_read_type

(

GBDATA *

gbd

)

Definition at line 1643 of file arbdb.cxx.

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

Referenced by ARB_is_alignment_relative_data(), AW_awar::AW_awar(), awt_string_handler::awar_changed(), awt_add_sequences_to_list(), awt_create_select_filter_window_aw_cb(), FieldReader::calc_value(), cannot_use_fun4entry(), ED4_terminal::changed_by_database(), checkAndMergeFields(), cmpByKey(), copy_field_into_partial_alignments(), count_bases(), create_new_species(), deleteDataOfKey(), ed_submit_info_event(), GB_command_interpreter_in_env(), gb_search_system_folder_rek(), gbl_read_seq_sai_or_species(), GBT_check_alignment(), gbt_scan_db_rek(), gbt_scan_db_start(), GEN_make_node_text_nds(), GEN_species_add_entry(), FINAL_TYPE< SEQTYPE >::get_first_field(), MG_create_remap(), NT_create_sai_from_pfold(), nt_species_join(), SequenceHandler::read_char_pntr(), readFirstCompressedDataOf(), FieldTransfer::ReadRule::readFrom(), ED4_terminal::resolve_pointer_to_char_pntr(), ItemFieldShader::scan_value_range_cb(), EDB_root_bact::search_sequence_data_rek(), SequenceHandler::SequenceHandler(), set_parents_with_only_temp_childs_temp(), split_data_into_parts(), testDictionaryCompression(), transfer_single_field(), NodeTextBuilder::work(), ED4_terminal::write_sequence(), and XML_recursive().

bool GB_is_container

(

GBDATA *

gbd

)

Definition at line 1648 of file arbdb.cxx.

References GBDATA::is_container().

Referenced by gbs_build_replace_string(), and XML_recursive().

char* GB_read_key

(

GBDATA *

gbd

)

Definition at line 1652 of file arbdb.cxx.

References ARB_strdup(), and GB_read_key_pntr().

Referenced by ColumnStat::calculate(), ed_submit_info_event(), get_canvas_able_to_show(), NT_create_sai_from_pfold(), and EDB_root_bact::search_sequence_data_rek().

GB_CSTR GB_read_key_pntr

(

GBDATA *

gbd

)

Definition at line 1656 of file arbdb.cxx.

References GB_KEY(), GB_KEY_QUARK(), GB_test_transaction(), and GBS_global_string().

Referenced by ARB_is_alignment_relative_data(), AW_forget_all_window_geometry(), awt_add_sequences_to_list(), cannot_use_fun4entry(), copy_field_into_partial_alignments(), AWT_configuration::erase_deleted_configs(), gb_clone_explicit(), gb_copy_explicit(), GB_create(), GB_get_subfields(), gb_info(), GB_is_dictionary_compressed(), GB_read_key(), GB_release(), gb_search_system_folder_rek(), gb_security_error(), GB_test_delete_possible(), gb_uncompress_data(), GB_write_autoconv_string(), gbcm_unfold_client(), gbl_findgene(), GBT_check_alignment(), GBT_expect_item_rel_item_data(), GBT_get_name_or_description(), GBT_get_tree_name(), GBT_get_tree_names(), gbt_scan_db_rek(), GBT_write_group_name(), gbt_write_tree_nodes(), FINAL_TYPE< SEQTYPE >::get_name(), FINAL_TYPE< SEQTYPE >::get_target_data(), FoundGroup::get_tree_name(), getKnownMacroClients(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), nds_delete_database_entries(), nt_species_join(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), read_tree_and_size_internal(), SequenceHandler::SequenceHandler(), AliEditor::shall_edit(), split_data_into_parts(), write_sequence_autoinc_alisize(), and XML_recursive().

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 1690 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 1695 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

)

Definition at line 1703 of file arbdb.cxx.

References GB_KEY_QUARK().

Referenced by FoundGroup::delete_from_DB(), deleteDataOfKey(), GB_followingEntry(), GB_has_key(), GB_nextEntry(), readFirstCompressedDataOf(), and testDictionaryCompression().

bool GB_has_key	(	GBDATA *	gbd,
		const char *	key
	)

Definition at line 1707 of file arbdb.cxx.

References GB_find_existing_quark(), and GB_get_quark().

Referenced by delete_unused_changekeys(), EXP_next_experiment(), GBT_next_marked_species(), GBT_next_SAI(), GBT_next_species(), GEN_create_nds_vars(), GEN_next_gene(), get_next_SAI(), is_tree(), PG_get_next_probe(), and PS_get_next_node().

long GB_read_clock

(

GBDATA *

gbd

)

Definition at line 1714 of file arbdb.cxx.

References GB_MAIN_TYPE::clock, GB_ARRAY_FLAGS(), GB_MAIN(), and GBDATA::update_date().

Referenced by ST_ML::calc_st_ml(), ED4_terminal::changed_by_database(), ST_ML::clear_all(), compress_sequence_tree(), ArbDBWriter::finishSave(), AP_tree_root::is_species_updated(), AP_tree_root::is_tree_updated(), nt_disconnect_from_db(), GB_MAIN_TYPE::save_quick(), SEC_structure_changed_cb(), AP_tree_root::update_timers(), and ED4_terminal::write_sequence().

GBDATA* GB_get_father

(

GBDATA *

gbd

)

Definition at line 1722 of file arbdb.cxx.

References GB_test_transaction(), and GBDATA::get_father().

Referenced by applyToItemFoundByKey(), ARB_is_alignment_relative_data(), awt_create_select_filter_window_aw_cb(), CON_export(), config_modified_cb(), copy_tree_container(), ensure_trees_have_order(), EXP_get_next_experiment_data(), gb_do_callbacks(), GB_in_temporary_branch(), gb_load_dictionary_data(), gbs_build_replace_string(), GBT_copy_tree(), GBT_expect_item_rel_item_data(), GBT_find_configuration(), GBT_find_item_rel_item_data(), GBT_get_alignment(), GBT_get_changekey(), GBT_move_tree(), GBT_tree_behind(), GBT_tree_infrontof(), GEN_find_or_create_gene_rel_gene_data(), GEN_find_origin_organism(), GEN_get_next_gene_data(), get_canvas_able_to_show(), FINAL_TYPE< SEQTYPE >::get_name(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), FoundGroup::get_tree_data(), FoundGroup::get_tree_order(), group_awar_changed_cb(), group_name_changed_cb(), identify_gb_item(), is_tree(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), launch_MapViewer_cb(), mg_check_field_cb(), MG_config_delete_cb(), MG_transfer_config(), species_copy_cb(), transfer_field_of_listed_cb(), tree_set_default_order(), write_sequence_autoinc_alisize(), and XML_recursive().

GBDATA* GB_get_grandfather

(

GBDATA *

gbd

)

Definition at line 1728 of file arbdb.cxx.

References GB_FATHER(), GB_test_transaction(), and NULp.

Referenced by copy_field_into_partial_alignments(), AP_sequence::do_lazy_load(), dot_sequence_by_consensus(), EXP_get_experiment_id(), gbl_findgene(), GBT_read_gene_sequence_and_length(), gen_get_gene_id(), GEN_global_gene_identifier(), GEN_write_position(), gene_requires(), EDB_root_bact::search_sequence_data_rek(), split_data_into_parts(), toggle_helix_for_SAI(), and toggle_mark_of_specData().

GBDATA* GB_get_root

(

GBDATA *

gbd

)

Definition at line 1740 of file arbdb.cxx.

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

Referenced by RefEntries::addRefsTo(), alignToNextRelative(), AWTC_recreate_name(), delete_kept_ghostnodes(), EG2PS_data::EG2PS_data(), ensure_trees_have_order(), EXP_get_next_experiment_data(), findAffectedKeys(), first_experiment_in_range(), first_gene_in_range(), GB_delete(), GBT_find_next_tree(), GBT_install_message_handler(), GBT_overwrite_tree(), gbt_read_tree_rek(), GBT_searchOrCreate_itemfield_according_to_changekey(), gde_filter_weights(), gen_extract_gene_2_pseudoSpecies(), GEN_get_next_gene_data(), GEN_is_organism(), GEN_NDS_changed(), RefEntries::generate_item_error(), get_first_organism(), get_first_SAI(), get_first_species(), AW_DB_selection::get_gb_main(), get_taxonomy(), macro_terminated(), member_of_DB(), read_tree_and_size_internal(), FieldTransfer::ReadRule::readFrom(), remove_dup_colors(), reverseComplement(), KeySorter::save_changes(), AW_root::unlink_awars_from_DB(), AP_tree_root::update_timers(), user_code_nr_changed_cb(), and write_sequence_autoinc_alisize().

bool GB_is_ancestor_of	(	GBDATA *	gb_ancestor,
		GBDATA *	gb_descendant
	)

Definition at line 1744 of file arbdb.cxx.

References GB_test_transaction(), GBDATA::get_father(), and GBDATA::is_container().

Referenced by GB_clone(), gb_clone_explicit(), gb_copy_checked(), gb_copy_explicit(), ScopedTransporter::markTarget(), and writeStringToAlignment().

GBDATA* GB_create	(	GBDATA *	father,
		const char *	key,
		GB_TYPES	type
	)

Create a DB entry

Parameters

father	container to create DB field in
key	name of field
type	field type

Returns

• created DB entry
• NULp on failure (error is exported then)

See also

GB_create_container()

Definition at line 1781 of file arbdb.cxx.

References GBDATA::expect_container(), gb_assert, GB_check_key(), gb_create(), GB_DB, GB_export_error(), GB_export_errorf(), GB_have_error(), GB_in_temporary_branch(), GB_internal_errorf(), GB_POINTER, GB_read_key_pntr(), GB_test_transaction(), GBDATA::is_entry(), NULp, type, and GBDATA::type().

Referenced by create_ali_intEntry(), create_ali_strEntry(), create_gene_species(), DB_create_byte_field(), DB_create_string_field(), do_hide_command_for_one_species(), gb_clone_explicit(), GBT_convert_changekey(), GBT_message(), GEN_is_genome_db(), GEN_species_add_entry(), group_set_folded(), MG_create_db_dependent_rename_awars(), nds_maintain_viewkeys(), NT_del_mark_move_REF(), nt_species_join(), PT_prepare_species_sequence(), CheckedConsistencies::register_as_performed(), set_tree_idx(), trackAlignmentChanges(), tree_write_byte(), and write_entry().

GBDATA* GB_create_container	(	GBDATA *	father,
		const char *	key
	)

Create a new DB container

Parameters

father	parent container
key	name of created container

Returns

• created container
• NULp on failure (error is exported then)

See also

GB_create()

Definition at line 1829 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_move_del_alignment(), copy_SAI_cb(), copy_SAI_to_species_cb(), copy_tree_container(), create_data_entry(), create_gene_species(), 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_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(), nds_delete_database_entries(), nds_maintain_viewkeys(), 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 1896 of file arbdb.cxx.

References GB_MAIN_TYPE::compression_mask, and GB_MAIN().

Referenced by GB_delete(), and gbt_write_tree().

GB_ERROR GB_test_delete_possible

(

GBDATA *

gb_obj

)

Definition at line 1904 of file arbdb.cxx.

References GB_GET_SECURITY_DELETE, GB_MAIN(), GB_read_key_pntr(), GB_test_transaction(), GBS_global_string(), NULp, and GB_MAIN_TYPE::security_level.

Referenced by GB_delete(), GB_set_temporary(), and GBT_rename_tree().

GB_ERROR GB_delete

(

GBDATA *&

source

)

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

Definition at line 1916 of file arbdb.cxx.

References GB_MAIN_TYPE::call_pending_callbacks(), gb_flag_types::compressed_data, error(), GBDATA::flags, GB_allow_compression(), gb_delete_entry(), GB_DELETED, GB_get_root(), gb_main, GB_MAIN(), gb_set_compression(), GB_test_delete_possible(), gb_touch_entry(), GB_MAIN_TYPE::get_transaction_level(), and RETURN_ERROR.

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(), copy_move_del_alignment(), 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_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(), nds_delete_database_entries(), nds_maintain_viewkeys(), 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
	)

traditional but NOT RECOMMENDED copy flavour.

resets protection (to current or to none?), clears all flags (including marks) and copies temporary entries, while clearing their temporary state (i.e. they may get saved to disk later)

Will become obsolete!

Definition at line 2152 of file arbdb.cxx.

References CM_COPY_TRADITIONAL, and gb_copy_checked().

Referenced by FINAL_TYPE< SEQTYPE >::addSequence(), concatenateFieldsCreateNewSpecies(), copy_move_del_alignment(), copy_SAI_cb(), copy_SAI_to_species_cb(), copy_tree_container(), create_new_species(), experiment_copy_handler(), gb_search_system_folder(), gbt_rename_alignment_of_item(), gene_copy_handler(), 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_species_join(), species_copy_cb(), transfer_single_field(), transfer_tree(), and SpecSetRegistry::write_node_information().

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 2163 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 2174 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 2182 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 2190 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 2196 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 2225 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

)

if the temporary flag is set, then that entry (including all subentries) will not be saved

See also

GB_clear_temporary() and GB_is_temporary()

Definition at line 2282 of file arbdb.cxx.

References error(), GBDATA::flags, GB_NORMAL_CHANGE, GB_test_delete_possible(), gb_touch_entry(), RETURN_ERROR, and gb_flag_types::temporary.

Referenced by AW_awar::AW_awar(), gb_convert_compression(), gb_copy_explicit(), init_tmp_branch(), set_keep_ghostnodes(), set_parents_with_only_temp_childs_temp(), st_ml_add_quality_string_to_species(), and writeStringToAlignment().

GB_ERROR GB_clear_temporary

(

GBDATA *

gbd

)

undo effect of GB_set_temporary()

Definition at line 2295 of file arbdb.cxx.

References GBDATA::flags, GB_NORMAL_CHANGE, GB_test_transaction(), gb_touch_entry(), NULp, and gb_flag_types::temporary.

Referenced by clear_temp_flags(), and gb_copy_explicit().

bool GB_is_temporary

(

GBDATA *

gbd

)

See also

GB_set_temporary() and GB_in_temporary_branch()

Definition at line 2304 of file arbdb.cxx.

References GBDATA::flags, GB_test_transaction(), and gb_flag_types::temporary.

Referenced by gb_clone_explicit(), gb_copy_explicit(), GB_in_temporary_branch(), and set_parents_with_only_temp_childs_temp().

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 2310 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:

GB_ERROR myFunc() {
    GB_ERROR error = GB_push_transaction(gbd);
    if (!error) {
        error = ...;
    }
    return GB_end_transaction(gbd, error);
}

void myFunc() {
    GB_ERROR error = GB_push_transaction(gbd);
    if (!error) {
        error = ...;
    }
    GB_end_transaction_show_error(gbd, error, aw_message);
}

See also

GB_pop_transaction(), GB_end_transaction(), GB_begin_transaction()

Definition at line 2494 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(), DbScanner::create(), create_gene_species(), ED4_root::create_hierarchy(), 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(), 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 2524 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(), check_for_remote_command(), DbScanner::create(), ED4_root::create_hierarchy(), 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(), 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(), 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(), 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 2528 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 2535 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 2539 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(), and nt_add_partial().

GB_ERROR GB_commit_transaction

(

GBDATA *

gbd

)

commit a transaction started with GB_begin_transaction()

commit changes made to DB.

in case of nested transactions, this is equal to GB_pop_transaction()

Definition at line 2551 of file arbdb.cxx.

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

Referenced by ARB_main(), FINAL_TYPE< SEQTYPE >::ArbWriter(), ALI_ARBDB::commit_transaction(), delete_queried_species_cb(), ED4_timer(), ED4_undo_redo(), enter_stage_1_build_tree(), gb_create_dictionaries(), GB_login(), gb_read_bin(), gbcms_talking_begin_transaction(), gbcms_talking_init_transaction(), GEN_undo_cb(), getArbFilter(), ArbImporter::import_data(), MG_save_cb(), MG_save_quick_result_cb(), nt_add_partial(), NT_deleteValidNames(), ALI_ARBDB::open(), pars_start_cb(), PT_init_input_data(), react_to_command(), reorder_keys(), reorder_up_down(), GB_MAIN_TYPE::save_quick(), SEC_undo_cb(), served(), sina_start(), and wait_for_dbentry().

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 2561 of file arbdb.cxx.

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

Referenced by ARB_main(), calculateEndPosition(), 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(), Structure3D::FindTypeOfRNA(), 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(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), mg_check_field_cb(), MG_copy_and_check_alignments(), 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(), pd_get_the_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(), st_ok_cb(), start_remote_command_for_application(), transfer_field_of_listed_cb(), transfer_field_of_selected_cb(), ScopedTransporter::transferAllIn(), translateSAItoColors(), TreeAdmin::tree_copy_or_rename_cb(), and writeToArb().

void GB_end_transaction_show_error	(	GBDATA *	gbd,
		GB_ERROR	error,
		void(*)(GB_ERROR)	error_handler
	)

like GB_end_transaction(), but show error using 'error_handler'

Definition at line 2584 of file arbdb.cxx.

References GB_end_transaction().

Referenced by awtc_nn_search_all_listed(), boundloc_changed_cb(), build_reverse_complement(), concatenateAlignments(), delete_SAI_cb(), ED4_remove_faligner_entries(), ED4_with_whole_block(), executeKeystroke(), export_to_DB(), field_convert_commit_cb(), field_delete_cb(), GEN_perform_command(), gene_create_cb(), group_species(), hide_field_cb(), insdel_event(), insdel_sai_event(), mergeSimilarSpecies(), MG_config_delete_cb(), MG_extended_delete_cb(), MG_merge_tagged_field_cb(), mg_transfer_listed_species(), MG_transfer_tree(), move_species_to_extended(), NT_count_different_chars(), NT_create_sai_from_pfold(), NT_suggestValidNames(), PV_WriteTranslatedSequenceToDB(), set_field_of_queried_cb(), set_protection_of_queried_cb(), species_rename_join(), and transpro_event().

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 2590 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

)

free cached data in client.

Warning: pointers into the freed region(s) will get invalid!

Definition at line 2600 of file arbdb.cxx.

References GB_MAIN_TYPE::call_pending_callbacks(), gb_header_flags::changed, GBCONTAINER::d, error(), GBDATA::flags2, gb_flag_types2::folded_container, GB_ARRAY_FLAGS(), GB_DB, gb_delete_entry(), GB_export_errorf(), GB_internal_error(), GB_MAIN(), GB_read_key_pntr(), GB_test_transaction(), GBCONTAINER_ELEM(), GB_MAIN_TYPE::is_server(), gb_data_list::nheader, NULp, GB_MAIN_TYPE::send_update_to_server(), GBDATA::type(), and gb_flag_types2::update_in_server.

Referenced by FINAL_TYPE< SEQTYPE >::addSequence(), main(), and MultiFastaWriter::readData().

int GB_nsons

(

GBDATA *

gbd

)

return number of child entries

@@ does this work in clients ?

Definition at line 2636 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

gbd	any DB node
reason	why quicksaving is not allowed

Definition at line 2647 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
	)

Definition at line 2655 of file arbdb.cxx.

References GBCONTAINER::d, father, GB_DATA_LIST_HEADER(), GB_disable_quicksave(), GB_FATHER(), GB_HEADER_LIST_GBD(), GB_inside_remote_action(), GB_NORMAL_CHANGE, GB_read_clients(), gb_touch_entry(), GB_warningf(), GBS_global_string(), GBDATA::index, NULp, and SET_GB_HEADER_LIST_GBD().

Referenced by gb_resort_system_folder_to_top(), resort_data_base(), and KeySorter::save_changes().

bool GB_user_flag	(	GBDATA *	gbd,
		unsigned char	user_bit
	)

Definition at line 2750 of file arbdb.cxx.

References gb_assert, get_user_flags(), legal_user_bitmask(), and gb_flag_types2::user_bits.

Referenced by gbt_write_tree(), QUERY::query_spec::is_queried(), QUERY::DbQuery::is_queried(), and NT_create_config_after_import().

void GB_raise_user_flag	(	GBDATA *	gbd,
		unsigned char	user_bit
	)

Definition at line 2755 of file arbdb.cxx.

References flags, gb_assert, get_user_flags(), legal_user_bitmask(), and gb_flag_types2::user_bits.

Referenced by GB_write_user_flag(), gbt_write_tree(), ScopedTransporter::markTarget(), MERGE_sequences_simple(), and SET_QUERIED().

void GB_clear_user_flag	(	GBDATA *	gbd,
		unsigned char	user_bit
	)

Definition at line 2760 of file arbdb.cxx.

References flags, gb_assert, GB_USERFLAG_ANY, get_user_flags(), legal_user_bitmask(), and gb_flag_types2::user_bits.

Referenced by CLEAR_QUERIED(), GB_write_user_flag(), gbt_write_tree_nodes(), and NT_create_config_after_import().

void GB_write_user_flag	(	GBDATA *	gbd,
		unsigned char	user_bit,
		bool	state
	)

Definition at line 2765 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
	)

Definition at line 2773 of file arbdb.cxx.

References GBDATA::expect_container(), gb_header_flags::flags, flags, GBDATA::flags, GB_ARRAY_FLAGS(), GB_DO_CALLBACKS, GB_FATHER(), GB_MAIN(), GB_NORMAL_CHANGE, GB_test_transaction(), gb_touch_entry(), gb_touch_header(), gb_flag_types::saved_flags, gb_user::userbit, and GB_MAIN_TYPE::users.

Referenced by FINAL_TYPE< SEQTYPE >::addSequence(), ALI_realign_marked(), ap_mark_duplicates_rek(), awtc_mark_hits(), command_on_GBDATA(), DB_create_container(), di_mark_by_distance(), do_mark_command_for_one_species(), ED4_mark_matching_species(), ED4_terminal::event_sent_by_parent(), gb_copy_explicit(), gb_parse_ascii_rek(), GBT_find_or_create_item_rel_item_data(), GBT_mark_all(), GBT_mark_all_that(), GBT_store_marked_species(), GEN_mark_organism_or_corresponding_organism(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), mark_action(), Cluster::mark_all_members(), mark_colored_cb(), mark_gene_species(), mark_gene_species_of_marked_genes(), mark_gene_species_using_current_alignment(), mark_genes_of_marked_gene_species(), mark_organisms(), mark_organisms_with_marked_genes(), mark_queried_cb(), mark_referred_species(), mark_species(), AWT_graphic_tree::mark_species_in_tree(), AWT_graphic_tree::mark_species_in_tree_that(), ARB_seqtree::mark_subtree(), ScopedTransporter::markTarget(), MERGE_sequences_simple(), mergeSimilarSpecies(), mg_check_field_cb(), MG_transfer_one_species(), MP_mark_probes_in_tree(), NT_create_config_after_import(), nt_extract_configuration(), DepthMarker::perform_marking(), probe_match_event(), restore_mark(), Aligner::run(), QUERY::search_duplicated_field_content(), ED4_multi_species_manager::selected_species_mark(), set_marks_of(), SQ_mark_species(), toggle_flag_cb(), toggle_mark_of_specData(), transfer_single_field(), and unmark_species().

int GB_read_flag

(

GBDATA *

gbd

)

Definition at line 2796 of file arbdb.cxx.

References flags, GB_ARRAY_FLAGS(), GB_MAIN(), and GB_test_transaction().

Referenced by brute_force_find_next_species(), ARB_seqtree::calcTreeInfo(), AP_tree::colorize(), colorize_marked_cb(), compare_hits(), ARB_seqtree::contains_marked_species(), QUERY::DbQuery_update_list(), AWT_graphic_tree::detect_group_state(), do_hide_command_for_one_species(), do_mark_command_for_one_species(), dot_sequence_by_consensus(), ED4_text_terminal::draw(), ED4_terminal::event_sent_by_parent(), gb_copy_explicit(), gb_write_one_child(), GBT_mark_all(), GBT_mark_all_that(), GBT_remove_leafs(), getDrawGcs(), AWT_graphic_tree::group_tree(), mark_action(), mark_colored_cb(), mark_gene_species(), mark_gene_species_of_marked_genes(), mark_genes_of_marked_gene_species(), mark_organisms(), mark_organisms_with_marked_genes(), mark_species(), AWT_graphic_tree::mark_species_in_tree(), AWT_graphic_tree::mark_species_in_tree_that(), ED4_multi_species_manager::marked_species_select(), nt_build_conf_string_rek(), NT_create_config_after_import(), nt_extract_configuration(), perform_query_cb(), probe_match_event(), AP_tree_root::remove_leafs(), set_marks_of(), SQ_mark_species(), toggle_flag_cb(), toggle_mark_of_specData(), AWT_graphic_tree::tree_has_marks(), unmark_species(), and AP_tree::update_subtree_information().

void GB_touch

(

GBDATA *

gbd

)

Definition at line 2802 of file arbdb.cxx.

References GB_DO_CALLBACKS, GB_NORMAL_CHANGE, GB_test_transaction(), and gb_touch_entry().

Referenced by flush_taxonomy_cb(), AP_tree::move_group_to(), ED4_root::refresh_all_windows(), AWT_graphic_tree::toggle_group(), and AW_awar::touch().

char GB_type_2_char

(

GB_TYPES

type

)

Definition at line 2809 of file arbdb.cxx.

References type.

Referenced by Itemfield_Selection::fill(), and gb_info().

void GB_print_debug_information	(	struct Unfixed_cb_parameter *	,
		GBDATA *	gb_main
	)

Definition at line 2814 of file arbdb.cxx.

References GB_MAIN(), GB_pop_transaction(), GB_push_transaction(), gbm_debug_mem(), gb_Key::key, GB_MAIN_TYPE::keycnt, GB_MAIN_TYPE::keys, gb_Key::next_free_key, and gb_Key::nref.

Referenced by popup_new_main_window().

int GB_info

(

GBDATA *

gbd

)

Definition at line 2888 of file arbdb.cxx.

References gb_info().

long GB_number_of_subentries

(

GBDATA *

gbd

)

Definition at line 2892 of file arbdb.cxx.

References GBCONTAINER::d, GBDATA::expect_container(), flags, GB_DATA_LIST_HEADER(), GB_DELETED, and gb_data_list::nheader.

Referenced by gb_resort_system_folder_to_top(), GBT_create_unique_item_identifier(), GBT_get_configuration_names(), GBT_get_item_count(), GBT_get_tree_names(), GBT_open(), MERGE_sequences_simple(), nt_build_sai_string(), PT_init_input_data(), PT_prepare_data(), QUERY::search_duplicated_field_content(), and UniqueNameDetector::UniqueNameDetector().

NOT4PERL char* GB_command_interpreter_in_env	(	const char *	str,
		const char *	commands,
		const GBL_call_env &	callEnv
	)

Definition at line 361 of file gb_aci.cxx.

References apply_ACI(), ARB_strdup(), ARB_strndup(), GBS_strstruct::cat(), gb_assert, GB_export_error(), GB_get_error(), GB_have_error(), GB_read_as_string(), GB_read_char_pntr(), GB_read_type(), GB_STRING, GBS_global_string(), GBS_regmatch(), GBS_regreplace(), GBS_string_eval_in_env(), GBS_strstruct::get_data(), GBL_call_env::get_item_ref(), GBS_strstruct::get_position(), GBL_IMPL::modify_trace_indent(), GBS_strstruct::nput(), NULp, GBL_IMPL::print_trace(), GBS_strstruct::put(), result, SmartMallocPtr, and GBL_IMPL::traceACI.

Referenced by SaiAciApplicator::apply(), TreeNode::apply_aci_to_remarks(), awt_open_ACI_URL_with_item(), FieldReader::calc_value(), ED4_get_NDS_text(), RefEntries::RefSelector::filter_refs(), g_bs_convert_string_to_tagged_hash_with_rewrite(), GB_command_interpreter(), gbs_build_replace_string(), GEN_make_node_text_nds(), GetDisplayInfo(), GS_calc_resulting_groupname(), GBL_call_env::interpret_subcommand(), MG_create_field_content(), modify_fields_of_queried_cb(), modsai_cb(), ArbImporter::read_data(), ItemFieldShader::scan_value_range_cb(), ACI_Labeler::speciesLabel(), NodeTextBuilder::work(), and SpecSetRegistry::write_node_information().

char* GB_command_interpreter	(	const char *	str,
		const char *	commands,
		GBDATA *	gb_main
	)

See also

GB_command_interpreter_in_env - this flavor runs in dummy environment

Definition at line 453 of file gb_aci.cxx.

References GB_command_interpreter_in_env(), and NULp.

Referenced by jobLabel().