ARB
Classes | Macros | Enumerations | Functions | Variables
arbdb.cxx File Reference
#include "gb_key.h"
#include "gb_comm.h"
#include "gb_compress.h"
#include "gb_localdata.h"
#include "gb_ta.h"
#include "gb_ts.h"
#include "gb_index.h"
#include <arb_misc.h>
#include <rpc/types.h>
#include <rpc/xdr.h>
#include <set>
Include dependency graph for arbdb.cxx:

Go to the source code of this file.

Classes

struct  gb_exitfun
 
struct  GB_test_shell_closed
 

Macros

#define INIT_TYPE_NAME(t)   GB_TYPES_name[t] = #t
 
#define RETURN_ERROR_IF_NOT_WRITEABLE_AS_TYPE(gbd, type)
 
#define EXPORT_ERROR_AND_RETURN_RES_IF_NOT_READABLE_AS_TYPE(gbd, res, type)
 
#define GB_TEST_READ_NUM(gbd, type, ignored)   EXPORT_ERROR_AND_RETURN_RES_IF_NOT_READABLE_AS_TYPE(gbd,0,type)
 
#define GB_TEST_READ_PTR(gbd, type, ignored)   EXPORT_ERROR_AND_RETURN_RES_IF_NOT_READABLE_AS_TYPE(gbd,NULp,type)
 
#define GB_TEST_WRITE(gbd, type, ignored)   RETURN_ERROR_IF_NOT_WRITEABLE_AS_TYPE(gbd, type)
 
#define GB_TEST_NON_BUFFER(x, gerror)
 
#define GB_DO_CALLBACKS(gbd)   do { if (GB_MAIN(gbd)->get_transaction_level() < 0) gb_do_callbacks(gbd); } while (0)
 

Enumerations

enum  CopyMode {
  CM_DROP_PROTECTION = 1, CM_DROP_MARKS = 2, CM_SKIP_TEMP = 4, CM_DROP_TEMPSTATE = 8,
  CM_OVERWRITE_EXISTING = 16, CM_COPY_TRADITIONAL = CM_DROP_PROTECTION|CM_DROP_MARKS|CM_DROP_TEMPSTATE, CM_COPY_WITHPROTECT = CM_COPY_TRADITIONAL & ~CM_DROP_PROTECTION, CM_COPY_STANDARD = CM_SKIP_TEMP,
  CM_COPY_FULL = 0
}
 

Functions

static const charGB_TYPES_2_name (GB_TYPES type)
 
const charGB_get_type_name (GBDATA *gbd)
 
GB_ERROR gb_transactable_type (GB_TYPES type, GBDATA *gbd)
 
static __ATTR__USERESULT GB_ERROR gb_security_error (GBDATA *gbd)
 
GB_ERROR gb_type_writeable_to (GB_TYPES type, GBDATA *gbd)
 
GB_ERROR gb_type_readable_from (GB_TYPES type, GBDATA *gbd)
 
GB_ERROR error_with_dbentry (const char *action, GBDATA *gbd, GB_ERROR error)
 
static GB_ERROR GB_safe_atof (const char *str, float *res)
 
float GB_atof (const char *str)
 
static void init_buffer (gb_buffer *buf, size_t initial_size)
 
static charcheck_out_buffer (gb_buffer *buf)
 
static void alloc_buffer (gb_buffer *buf, size_t size)
 
static GB_BUFFER give_buffer (gb_buffer *buf, size_t size)
 
static int is_in_buffer (gb_buffer *buf, GB_CBUFFER ptr)
 
GB_BUFFER GB_give_buffer (size_t size)
 
GB_BUFFER GB_increase_buffer (size_t size)
 
NOT4PERL int GB_give_buffer_size ()
 
GB_BUFFER GB_give_buffer2 (long size)
 
static int GB_is_in_buffer (GB_CBUFFER ptr)
 
charGB_check_out_buffer (GB_CBUFFER buffer)
 
GB_BUFFER GB_give_other_buffer (GB_CBUFFER buffer, long size)
 
void GB_atexit (void(*exitfun)())
 
static void run_and_destroy_exit_functions (gb_exitfun *fun)
 
static void GB_exit_gb ()
 
void GB_init_gb ()
 
int GB_open_DBs ()
 
static GBDATAgb_remembered_db ()
 
GB_ERROR gb_unfold (GBCONTAINER *gbc, long deep, int index_pos)
 
static void run_close_callbacks (GBDATA *gb_main)
 
void GB_close (GBDATA *gbd)
 
void gb_abort_and_close_all_DBs ()
 
long GB_read_int (GBDATA *gbd)
 
int GB_read_byte (GBDATA *gbd)
 
GBDATAGB_read_pointer (GBDATA *gbd)
 
float GB_read_float (GBDATA *gbd)
 
long GB_read_count (GBDATA *gbd)
 
long GB_read_memuse (GBDATA *gbd)
 
GB_CSTR GB_read_pntr (GBDATA *gbd)
 
int gb_read_nr (GBDATA *gbd)
 
GB_CSTR GB_read_char_pntr (GBDATA *gbd)
 
charGB_read_string (GBDATA *gbd)
 
size_t GB_read_string_count (GBDATA *gbd)
 
long GB_read_bits_count (GBDATA *gbd)
 
GB_CSTR GB_read_bits_pntr (GBDATA *gbd, char c_0, char c_1)
 
charGB_read_bits (GBDATA *gbd, char c_0, char c_1)
 
GB_CSTR GB_read_bytes_pntr (GBDATA *gbd)
 
long GB_read_bytes_count (GBDATA *gbd)
 
charGB_read_bytes (GBDATA *gbd)
 
GB_CUINT4GB_read_ints_pntr (GBDATA *gbd)
 
long GB_read_ints_count (GBDATA *gbd)
 
GB_UINT4GB_read_ints (GBDATA *gbd)
 
GB_CFLOATGB_read_floats_pntr (GBDATA *gbd)
 
static long GB_read_floats_count (GBDATA *gbd)
 
float * GB_read_floats (GBDATA *gbd)
 
charGB_read_as_string (GBDATA *gbd)
 
bool GB_readable_as_string (GBDATA *gbd)
 
GB_ERROR cannot_use_fun4entry (const char *fun, GBDATA *gb_entry)
 
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)
 
static void gb_do_callbacks (GBDATA *gbd)
 
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)
 
void gb_save_extern_data_in_ts__and_uncache (GBENTRY *gbe)
 
GB_ERROR gb_write_compressed_pntr (GBENTRY *gbe, const char *s, long memsize, long stored_size)
 
int gb_get_compression_mask (GB_MAIN_TYPE *Main, GBQUARK key, int gb_type)
 
GB_ERROR GB_write_pntr (GBDATA *gbd, const char *s, size_t bytes_size, size_t stored_size)
 
GB_ERROR GB_write_string (GBDATA *gbd, const char *s)
 
GB_ERROR GB_write_bits (GBDATA *gbd, const char *bits, long size, const char *c_0)
 
GB_ERROR GB_write_bytes (GBDATA *gbd, const char *s, long size)
 
GB_ERROR GB_write_ints (GBDATA *gbd, const GB_UINT4 *i, long size)
 
GB_ERROR GB_write_floats (GBDATA *gbd, const float *f, long size)
 
GB_ERROR GB_write_autoconv_string (GBDATA *gbd, const char *val)
 
GB_ERROR GB_write_lossless_byte (GBDATA *gbd, uint8_t byte)
 
GB_ERROR GB_write_lossless_int (GBDATA *gbd, int32_t i)
 
GB_ERROR GB_write_lossless_float (GBDATA *gbd, float f)
 
int GB_read_security_write (GBDATA *gbd)
 
int GB_read_security_read (GBDATA *gbd)
 
int GB_read_security_delete (GBDATA *gbd)
 
GB_ERROR GB_write_security_write (GBDATA *gbd, unsigned long level)
 
GB_ERROR GB_write_security_read (GBDATA *gbd, unsigned long level)
 
GB_ERROR GB_write_security_delete (GBDATA *gbd, unsigned long level)
 
GB_ERROR GB_write_security_levels (GBDATA *gbd, unsigned long readlevel, unsigned long writelevel, unsigned long deletelevel)
 
void GB_change_my_security (GBDATA *gbd, int level)
 
GB_TYPES GB_read_type (GBDATA *gbd)
 
bool GB_is_container (GBDATA *gbd)
 
charGB_read_key (GBDATA *gbd)
 
GB_CSTR GB_read_key_pntr (GBDATA *gbd)
 
GB_CSTR gb_read_key_pntr (GBDATA *gbd)
 
GBQUARK gb_find_or_create_quark (GB_MAIN_TYPE *Main, const char *key)
 
GBQUARK gb_find_or_create_NULL_quark (GB_MAIN_TYPE *Main, const char *key)
 
GBQUARK GB_find_existing_quark (GBDATA *gbd, const char *key)
 
GBQUARK GB_find_or_create_quark (GBDATA *gbd, const char *key)
 
GBQUARK GB_get_quark (GBDATA *gbd)
 
bool GB_has_key (GBDATA *gbd, const char *key)
 
long GB_read_clock (GBDATA *gbd)
 
GBDATAGB_get_father (GBDATA *gbd)
 
GBDATAGB_get_grandfather (GBDATA *gbd)
 
GBDATAGB_get_root (GBDATA *gbd)
 
GBCONTAINERgb_get_root (GBENTRY *gbe)
 
GBCONTAINERgb_get_root (GBCONTAINER *gbc)
 
bool GB_is_ancestor_of (GBDATA *gb_ancestor, GBDATA *gb_descendant)
 
GBENTRYgb_create (GBCONTAINER *father, const char *key, GB_TYPES type)
 
GBCONTAINERgb_create_container (GBCONTAINER *father, const char *key)
 
GBDATAGB_create (GBDATA *father, const char *key, GB_TYPES type)
 
GBDATAGB_create_container (GBDATA *father, const char *key)
 
static GB_ERROR gb_set_compression (GBDATA *source)
 
bool GB_allow_compression (GBDATA *gb_main, bool allow_compression)
 
GB_ERROR GB_delete (GBDATA *&source)
 
GB_ERROR gb_delete_force (GBDATA *source)
 
static GB_ERROR gb_copy_explicit (GBDATA *dest, GBDATA *source, CopyMode mode)
 
static GBDATAgb_clone_explicit (GBCONTAINER *gb_destCont, GBDATA *gb_source, CopyMode mode)
 
GB_ERROR gb_copy_checked (GBDATA *dest, GBDATA *source, CopyMode mode)
 
GB_ERROR GB_copy_dropProtectMarksAndTempstate (GBDATA *dest, GBDATA *source)
 
GB_ERROR GB_copy_dropMarksAndTempstate (GBDATA *dest, GBDATA *source)
 
GB_ERROR GB_copy_std (GBDATA *dest, GBDATA *source)
 
GB_ERROR GB_copy_overlay (GBDATA *dest, GBDATA *source)
 
GB_ERROR GB_copy_full (GBDATA *dest, GBDATA *source)
 
GBDATAGB_clone (GBDATA *gb_destCont, GBDATA *gb_source)
 
static chargb_stpcpy (char *dest, const char *source)
 
charGB_get_subfields (GBDATA *gbd)
 
GB_ERROR GB_set_temporary (GBDATA *gbd)
 
GB_ERROR GB_clear_temporary (GBDATA *gbd)
 
bool GB_is_temporary (GBDATA *gbd)
 
bool GB_in_temporary_branch (GBDATA *gbd)
 
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)
 
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)
 
GB_ERROR gb_resort_system_folder_to_top (GBCONTAINER *gb_main)
 
 STATIC_ASSERT_ANNOTATED (((GB_USERFLAG_ANY+1)&GB_USERFLAG_ANY)==0,"not all bits set in GB_USERFLAG_ANY")
 
bool legal_user_bitmask (unsigned char bitmask)
 
gb_flag_types2get_user_flags (GBDATA *gbd)
 
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)
 
static int gb_info (GBDATA *gbd, int deep)
 
int GB_info (GBDATA *gbd)
 
long GB_number_of_subentries (GBDATA *gbd)
 

Variables

gb_local_datagb_local = NULp
 
const int gb_convert_type_2_compression_flags []
 
int gb_convert_type_2_sizeof []
 
int gb_convert_type_2_appendix_size []
 
static unsigned char GB_BIT_compress_data []
 
static GB_shellinside_shell = NULp
 
static GB_test_shell_closed test
 
static int GB_info_deep = 15
 

Macro Definition Documentation

#define INIT_TYPE_NAME (   t)    GB_TYPES_name[t] = #t

Definition at line 28 of file arbdb.cxx.

Referenced by GB_TYPES_2_name().

#define RETURN_ERROR_IF_NOT_WRITEABLE_AS_TYPE (   gbd,
  type 
)
Value:
do { \
if (error) { \
return error_with_dbentry("write", gbd, error); \
} \
} while(0)
const char * GB_ERROR
Definition: arb_core.h:25
GB_TYPES type
GB_ERROR error_with_dbentry(const char *action, GBDATA *gbd, GB_ERROR error)
Definition: arbdb.cxx:122
static void error(const char *msg)
Definition: mkptypes.cxx:96
GB_write_int const char GB_write_autoconv_string WRITE_SKELETON(write_pointer, GBDATA *,"%p", GB_write_pointer) char *AW_awa if)(!gb_var) return strdup("")
Definition: AW_awar.cxx:166
GB_ERROR gb_type_writeable_to(GB_TYPES type, GBDATA *gbd)
Definition: arbdb.cxx:109

Definition at line 133 of file arbdb.cxx.

#define EXPORT_ERROR_AND_RETURN_RES_IF_NOT_READABLE_AS_TYPE (   gbd,
  res,
  type 
)
Value:
do { \
if (error) { \
error = error_with_dbentry("read", gbd, error); \
return res; \
} \
} while(0) \
const char * GB_ERROR
Definition: arb_core.h:25
GB_TYPES type
GB_ERROR GB_export_error(const char *error)
Definition: arb_msg.cxx:259
GB_ERROR error_with_dbentry(const char *action, GBDATA *gbd, GB_ERROR error)
Definition: arbdb.cxx:122
static void error(const char *msg)
Definition: mkptypes.cxx:96
GB_write_int const char GB_write_autoconv_string WRITE_SKELETON(write_pointer, GBDATA *,"%p", GB_write_pointer) char *AW_awa if)(!gb_var) return strdup("")
Definition: AW_awar.cxx:166
GB_ERROR gb_type_readable_from(GB_TYPES type, GBDATA *gbd)
Definition: arbdb.cxx:118

Definition at line 141 of file arbdb.cxx.

#define GB_TEST_READ_NUM (   gbd,
  type,
  ignored 
)    EXPORT_ERROR_AND_RETURN_RES_IF_NOT_READABLE_AS_TYPE(gbd,0,type)
#define GB_TEST_READ_PTR (   gbd,
  type,
  ignored 
)    EXPORT_ERROR_AND_RETURN_RES_IF_NOT_READABLE_AS_TYPE(gbd,NULp,type)
#define GB_TEST_WRITE (   gbd,
  type,
  ignored 
)    RETURN_ERROR_IF_NOT_WRITEABLE_AS_TYPE(gbd, type)
#define GB_TEST_NON_BUFFER (   x,
  gerror 
)
Value:
do { \
GBK_terminatef("%s: you are not allowed to write any data, which you get by pntr", gerror); \
} \
} while (0)
static int GB_is_in_buffer(GB_CBUFFER ptr)
Definition: arbdb.cxx:331
void GBK_terminatef(const char *templat,...)
Definition: arb_msg.cxx:477
GB_write_int const char GB_write_autoconv_string WRITE_SKELETON(write_pointer, GBDATA *,"%p", GB_write_pointer) char *AW_awa if)(!gb_var) return strdup("")
Definition: AW_awar.cxx:166

Definition at line 158 of file arbdb.cxx.

Referenced by GB_write_bits(), GB_write_floats(), GB_write_ints(), and GB_write_string().

#define GB_DO_CALLBACKS (   gbd)    do { if (GB_MAIN(gbd)->get_transaction_level() < 0) gb_do_callbacks(gbd); } while (0)

Enumeration Type Documentation

enum CopyMode
Enumerator
CM_DROP_PROTECTION 
CM_DROP_MARKS 
CM_SKIP_TEMP 
CM_DROP_TEMPSTATE 
CM_OVERWRITE_EXISTING 
CM_COPY_TRADITIONAL 
CM_COPY_WITHPROTECT 
CM_COPY_STANDARD 
CM_COPY_FULL 

Definition at line 1923 of file arbdb.cxx.

Function Documentation

static const char* GB_TYPES_2_name ( GB_TYPES  type)
static
const char* GB_get_type_name ( GBDATA gbd)

Definition at line 65 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().

GB_ERROR gb_transactable_type ( GB_TYPES  type,
GBDATA gbd 
)
inline
static __ATTR__USERESULT GB_ERROR gb_security_error ( GBDATA gbd)
static
GB_ERROR gb_type_writeable_to ( GB_TYPES  type,
GBDATA gbd 
)
inline
GB_ERROR gb_type_readable_from ( GB_TYPES  type,
GBDATA gbd 
)
inline

Definition at line 118 of file arbdb.cxx.

References gb_transactable_type().

GB_ERROR error_with_dbentry ( const char action,
GBDATA gbd,
GB_ERROR  error 
)
inline

Definition at line 122 of file arbdb.cxx.

References ARB_strdup(), error(), GB_get_db_path(), and GBS_global_string().

static GB_ERROR GB_safe_atof ( const char str,
float *  res 
)
static

Definition at line 166 of file arbdb.cxx.

References error(), GBS_global_string(), and NULp.

Referenced by GB_atof(), and GB_write_autoconv_string().

float GB_atof ( const char str)
static void init_buffer ( gb_buffer buf,
size_t  initial_size 
)
static

Definition at line 263 of file arbdb.cxx.

References gb_buffer::mem, NULp, and gb_buffer::size.

Referenced by gb_local_data::gb_local_data().

static char* check_out_buffer ( gb_buffer buf)
static

Definition at line 268 of file arbdb.cxx.

References gb_buffer::mem, NULp, and gb_buffer::size.

Referenced by GB_check_out_buffer(), and gb_local_data::~gb_local_data().

static void alloc_buffer ( gb_buffer buf,
size_t  size 
)
static

Definition at line 277 of file arbdb.cxx.

References ARB_alloc(), ARB_calloc(), gb_buffer::mem, and gb_buffer::size.

Referenced by GB_increase_buffer(), and give_buffer().

static GB_BUFFER give_buffer ( gb_buffer buf,
size_t  size 
)
static

Definition at line 287 of file arbdb.cxx.

References alloc_buffer(), gb_buffer::mem, and gb_buffer::size.

Referenced by GB_give_buffer(), and GB_give_buffer2().

static int is_in_buffer ( gb_buffer buf,
GB_CBUFFER  ptr 
)
static

Definition at line 298 of file arbdb.cxx.

References gb_buffer::mem, and gb_buffer::size.

Referenced by GB_check_out_buffer(), GB_give_other_buffer(), and GB_is_in_buffer().

GB_BUFFER GB_give_buffer ( size_t  size)
GB_BUFFER GB_increase_buffer ( size_t  size)

Definition at line 309 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 323 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 327 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().

static int GB_is_in_buffer ( GB_CBUFFER  ptr)
static

Definition at line 331 of file arbdb.cxx.

References gb_local_data::buf1, gb_local_data::buf2, buffer, and is_in_buffer().

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

Definition at line 395 of file arbdb.cxx.

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

Referenced by GB_remove_on_exit().

static void run_and_destroy_exit_functions ( gb_exitfun fun)
static

Definition at line 408 of file arbdb.cxx.

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

Referenced by gb_local_data::~gb_local_data().

static void GB_exit_gb ( )
static
void GB_init_gb ( void  )

Definition at line 482 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 492 of file arbdb.cxx.

References gb_local_data::open_dbs().

Referenced by aw_initstatus().

static GBDATA* gb_remembered_db ( )
static

Definition at line 551 of file arbdb.cxx.

References GB_MAIN_TYPE::gb_main(), gb_local_data::get_any_open_db(), and NULp.

Referenced by gb_abort_and_close_all_DBs().

GB_ERROR gb_unfold ( GBCONTAINER gbc,
long  deep,
int  index_pos 
)
static void run_close_callbacks ( GBDATA gb_main)
static
void GB_close ( GBDATA gbd)
void gb_abort_and_close_all_DBs ( void  )
long GB_read_int ( GBDATA gbd)

Definition at line 699 of file arbdb.cxx.

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

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

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

Definition at line 732 of file arbdb.cxx.

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

Referenced by compress_sequence_tree().

GB_CSTR GB_read_pntr ( GBDATA gbd)
int gb_read_nr ( GBDATA gbd)

Definition at line 870 of file arbdb.cxx.

References GBDATA::index.

Referenced by compress_sequence_tree().

GB_CSTR GB_read_char_pntr ( GBDATA gbd)

Definition at line 874 of file arbdb.cxx.

References GB_read_pntr(), GB_STRING, and GB_TEST_READ_PTR.

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

char* GB_read_string ( GBDATA gbd)

Definition at line 879 of file arbdb.cxx.

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

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

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

Definition at line 944 of file arbdb.cxx.

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

Referenced by gb_read_dict_data().

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

Definition at line 978 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 983 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)
static long GB_read_floats_count ( GBDATA gbd)
static

Definition at line 1018 of file arbdb.cxx.

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

Referenced by GB_read_from_floats().

float* GB_read_floats ( GBDATA gbd)

Definition at line 1023 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)
bool GB_readable_as_string ( GBDATA gbd)
GB_ERROR cannot_use_fun4entry ( const char fun,
GBDATA gb_entry 
)
inline
NOT4PERL uint8_t GB_read_lossless_byte ( GBDATA gbd,
GB_ERROR error 
)

Reads an uint8_t previously written with GB_write_lossless_byte()

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

Definition at line 1063 of file arbdb.cxx.

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

NOT4PERL int32_t GB_read_lossless_int ( GBDATA gbd,
GB_ERROR error 
)

Reads an int32_t previously written with GB_write_lossless_int()

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

Definition at line 1098 of file arbdb.cxx.

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

NOT4PERL float GB_read_lossless_float ( GBDATA gbd,
GB_ERROR error 
)

Reads a float previously written with GB_write_lossless_float()

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

Definition at line 1125 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 1156 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 1173 of file arbdb.cxx.

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

static void gb_do_callbacks ( GBDATA gbd)
static
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 
)
void gb_save_extern_data_in_ts__and_uncache ( GBENTRY gbe)
inline

Definition at line 1274 of file arbdb.cxx.

References gb_save_extern_data_in_ts(), and gb_uncache().

Referenced by gb_write_compressed_pntr(), and GB_write_pntr().

GB_ERROR gb_write_compressed_pntr ( GBENTRY gbe,
const char s,
long  memsize,
long  stored_size 
)
int gb_get_compression_mask ( GB_MAIN_TYPE Main,
GBQUARK  key,
int  gb_type 
)
GB_ERROR GB_write_pntr ( GBDATA gbd,
const char s,
size_t  bytes_size,
size_t  stored_size 
)
GB_ERROR GB_write_string ( GBDATA gbd,
const char s 
)

Definition at line 1361 of file arbdb.cxx.

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

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

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

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

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

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

@@ refer to GBT_write_int_converted / GBT_write_float_converted

Definition at line 1453 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(), and set_field_of_queried_cb().

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 1478 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 1497 of file arbdb.cxx.

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

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

GB_ERROR GB_write_lossless_float ( GBDATA gbd,
float  f 
)

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

Returns
error otherwise The corresponding field filter is FIELD_FILTER_FLOAT_WRITEABLE.

Definition at line 1520 of file arbdb.cxx.

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

Referenced by FieldTransfer::convertAndWrite().

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

Definition at line 1550 of file arbdb.cxx.

References GB_GET_SECURITY_READ, and GB_test_transaction().

int GB_read_security_delete ( GBDATA gbd)

Definition at line 1554 of file arbdb.cxx.

References GB_GET_SECURITY_DELETE, and GB_test_transaction().

Referenced by ad_tree_set_security().

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

Definition at line 1622 of file arbdb.cxx.

References GBDATA::is_container().

Referenced by gbs_build_replace_string(), and XML_recursive().

char* GB_read_key ( GBDATA gbd)
GB_CSTR GB_read_key_pntr ( GBDATA gbd)
GB_CSTR gb_read_key_pntr ( GBDATA gbd)

Definition at line 1638 of file arbdb.cxx.

References GB_KEY().

Referenced by g_b_undo_info().

GBQUARK gb_find_or_create_quark ( GB_MAIN_TYPE Main,
const char key 
)
GBQUARK gb_find_or_create_NULL_quark ( GB_MAIN_TYPE Main,
const char key 
)

Definition at line 1652 of file arbdb.cxx.

References gb_find_or_create_quark().

Referenced by gb_make_container().

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 1664 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 1669 of file arbdb.cxx.

References gb_find_or_create_quark(), and GB_MAIN().

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

GBQUARK GB_get_quark ( GBDATA gbd)
bool GB_has_key ( GBDATA gbd,
const char key 
)
long GB_read_clock ( GBDATA gbd)
GBDATA* GB_get_father ( GBDATA gbd)
GBDATA* GB_get_grandfather ( GBDATA gbd)
GBDATA* GB_get_root ( GBDATA gbd)
GBCONTAINER* gb_get_root ( GBENTRY gbe)

Definition at line 1715 of file arbdb.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::root_container.

Referenced by gb_search().

GBCONTAINER* gb_get_root ( GBCONTAINER gbc)

Definition at line 1716 of file arbdb.cxx.

References GB_MAIN(), and GB_MAIN_TYPE::root_container.

bool GB_is_ancestor_of ( GBDATA gb_ancestor,
GBDATA gb_descendant 
)
GBENTRY* gb_create ( GBCONTAINER father,
const char key,
GB_TYPES  type 
)
GBCONTAINER* gb_create_container ( GBCONTAINER father,
const char key 
)
GBDATA* GB_create ( GBDATA father,
const char key,
GB_TYPES  type 
)
GBDATA* GB_create_container ( GBDATA father,
const char key 
)

Create a new DB container

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

Definition at line 1803 of file arbdb.cxx.

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

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

static GB_ERROR gb_set_compression ( GBDATA source)
static
bool GB_allow_compression ( GBDATA gb_main,
bool  allow_compression 
)

Definition at line 1871 of file arbdb.cxx.

References GB_MAIN_TYPE::compression_mask, and GB_MAIN().

Referenced by GB_delete(), and gbt_write_tree().

GB_ERROR GB_delete ( GBDATA *&  source)

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

Definition at line 1880 of file arbdb.cxx.

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

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

GB_ERROR gb_delete_force ( GBDATA source)

Definition at line 1913 of file arbdb.cxx.

References GB_DELETED, gb_touch_entry(), and NULp.

Referenced by gbcms_talking_put_update().

static GB_ERROR gb_copy_explicit ( GBDATA dest,
GBDATA source,
CopyMode  mode 
)
static
static GBDATA* gb_clone_explicit ( GBCONTAINER gb_destCont,
GBDATA gb_source,
CopyMode  mode 
)
static
GB_ERROR gb_copy_checked ( GBDATA dest,
GBDATA source,
CopyMode  mode 
)
inline

copies the content of 'source' into 'dest'. if 'dest' is a container, entries existing there will not be overwritten!

Definition at line 2110 of file arbdb.cxx.

References gb_copy_explicit(), and GB_is_ancestor_of().

Referenced by GB_copy_dropMarksAndTempstate(), GB_copy_dropProtectMarksAndTempstate(), GB_copy_full(), GB_copy_overlay(), and GB_copy_std().

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

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

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

Will become obsolete!

Definition at line 2131 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 2142 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 2150 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 2158 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 2164 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.

static char* gb_stpcpy ( char dest,
const char source 
)
static

Definition at line 2188 of file arbdb.cxx.

Referenced by GB_get_subfields().

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 2193 of file arbdb.cxx.

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

Referenced by checkAndMergeFields(), and create_new_species().

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

Definition at line 2283 of file arbdb.cxx.

References GB_get_father(), and GB_is_temporary().

Referenced by GB_create().

GB_ERROR GB_push_transaction ( GBDATA gbd)

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

recommended transaction usage:

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

Definition at line 2458 of file arbdb.cxx.

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

Referenced by alignCompactedTo(), AP_create_max_freq_window(), ARB_main(), awt_string_handler::awar_changed(), awt_create_2_filter_window(), awt_create_select_filter(), awt_create_select_filter_win(), awt_create_select_filter_window_aw_cb(), awt_create_select_filter_window_gb_cb(), awt_get_filter(), boundloc_changed_cb(), build_reverse_complement(), calculateEndPosition(), check_for_remote_command(), CON_calculate(), concatenateAlignments(), concatenateFieldsCreateNewSpecies(), count_mark_all_cb(), DbScanner::create(), create_gene_species(), ED4_root::create_hierarchy(), create_nds_vars(), QUERY::create_query_box(), QUERY::DbQuery_update_list(), ED4_manager::deleted_from_database(), di_autodetect_callback(), DI_create_matrix_variables(), DI_create_matrix_window(), dump_internal(), ED4_getSaiColorString(), ED4_horizontal_change_cb(), ED4_scrollbar_change_cb(), ED4_vertical_change_cb(), 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(), ED4_manager::handle_move(), 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(), ED4_terminal::resolve_pointer_to_char_pntr(), Aligner::run(), AW_root::save_properties(), GBT_config::saveAsOver(), ARB_seqtree_root::saveToDB(), AP_tree_root::saveToDB(), set_addid(), set_DB_state(), species_field_selection_list_rescan(), sq_calc_seq_quality_cb(), SQ_evaluate(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), SQ_remove_quality_entries(), st_ok_cb(), translateSAItoColors(), QUERY::unquery_all(), and ED4_terminal::write_sequence().

GB_ERROR GB_pop_transaction ( GBDATA gbd)

commit a transaction started with GB_push_transaction()

Definition at line 2488 of file arbdb.cxx.

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

Referenced by alignCompactedTo(), AP_create_max_freq_window(), ARB_main(), awt_string_handler::awar_changed(), awt_create_2_filter_window(), awt_create_select_filter(), awt_create_select_filter_win(), awt_create_select_filter_window_aw_cb(), awt_create_select_filter_window_gb_cb(), awt_get_filter(), calculateEndPosition(), check_for_remote_command(), count_mark_all_cb(), DbScanner::create(), ED4_root::create_hierarchy(), create_nds_vars(), QUERY::create_query_box(), QUERY::DbQuery_update_list(), ED4_manager::deleted_from_database(), di_autodetect_callback(), DI_create_matrix_variables(), DI_create_matrix_window(), dump_internal(), ED4_getSaiColorString(), ED4_horizontal_change_cb(), ED4_scrollbar_change_cb(), ED4_vertical_change_cb(), experiment_field_selection_list_rescan(), field_create_cb(), MO_Liste::fill_marked_bakts(), Structure3D::FindTypeOfRNA(), GB_end_transaction(), gb_info(), GB_print_debug_information(), GBT_get_item_count(), GBT_install_message_handler(), GBT_mark_all(), GBT_mark_all_that(), GBT_read_as_string(), GBT_read_char_pntr(), GBT_read_float(), GBT_read_int(), GBT_read_string(), GBT_readOrCreate_char_pntr(), GBT_readOrCreate_float(), GBT_readOrCreate_int(), GBT_readOrCreate_string(), gene_field_selection_list_rescan(), MO_Liste::get_all_species(), ED4_manager::handle_move(), PHDATA::load(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), mark_queried_cb(), MP_mark_probes_in_tree(), new_gbt_message_created_cb(), nt_changesecurity(), NT_reload_tree_event(), perform_query_cb(), AWT_canvas::pop_transaction(), popup_new_main_window(), probe_match_event(), ED4_terminal::resolve_pointer_to_char_pntr(), AW_root::save_properties(), species_field_selection_list_rescan(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), SQ_pass2_no_tree(), SQ_remove_quality_entries(), translateSAItoColors(), QUERY::unquery_all(), and ED4_terminal::write_sequence().

GB_ERROR GB_begin_transaction ( GBDATA gbd)

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

See also
GB_commit_transaction() and GB_abort_transaction()

Definition at line 2492 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 2499 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 2503 of file arbdb.cxx.

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

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

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

abort or commit transaction

@ param error

  • if NULp commit transaction
  • else abort transaction

always commits in no-transaction-mode

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

Definition at line 2525 of file arbdb.cxx.

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

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

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

Definition at line 2554 of file arbdb.cxx.

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

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

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

return number of child entries

@@ does this work in clients ?

Definition at line 2600 of file arbdb.cxx.

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

Referenced by resort_data_base().

void GB_disable_quicksave ( GBDATA gbd,
const char reason 
)

Disable quicksaving database

Parameters
gbdany DB node
reasonwhy quicksaving is not allowed

Definition at line 2611 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 
)
GB_ERROR gb_resort_system_folder_to_top ( GBCONTAINER gb_main)
STATIC_ASSERT_ANNOTATED ( ((GB_USERFLAG_ANY+1)&GB_USERFLAG_ANY = =0,
"not all bits set in GB_USERFLAG_ANY  
)
bool legal_user_bitmask ( unsigned char  bitmask)
inline

Definition at line 2705 of file arbdb.cxx.

References GB_USERFLAG_ANY.

Referenced by GB_clear_user_flag(), GB_raise_user_flag(), and GB_user_flag().

gb_flag_types2& get_user_flags ( GBDATA gbd)
inline

Definition at line 2710 of file arbdb.cxx.

References GBDATA::expect_container(), and GBDATA::flags2.

Referenced by GB_clear_user_flag(), GB_raise_user_flag(), and GB_user_flag().

bool GB_user_flag ( GBDATA gbd,
unsigned char  user_bit 
)
void GB_raise_user_flag ( GBDATA gbd,
unsigned char  user_bit 
)
void GB_clear_user_flag ( GBDATA gbd,
unsigned char  user_bit 
)
void GB_write_user_flag ( GBDATA gbd,
unsigned char  user_bit,
bool  state 
)

Definition at line 2729 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 2737 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)
void GB_touch ( GBDATA gbd)
char GB_type_2_char ( GB_TYPES  type)

Definition at line 2773 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 
)
static int gb_info ( GBDATA gbd,
int  deep 
)
static
int GB_info ( GBDATA gbd)

Definition at line 2852 of file arbdb.cxx.

References gb_info().

long GB_number_of_subentries ( GBDATA gbd)

Variable Documentation

gb_local_data* gb_local = NULp
const int gb_convert_type_2_compression_flags[]
int gb_convert_type_2_sizeof[]
Initial value:
= {
0,
0,
sizeof(char),
sizeof(int),
sizeof(float),
0,
0,
0,
sizeof(char),
sizeof(int),
sizeof(float),
sizeof(char),
sizeof(char),
sizeof(char),
0,
0,
}

Definition at line 216 of file arbdb.cxx.

Referenced by gb_read_pntr_ts().

int gb_convert_type_2_appendix_size[]
Initial value:
= {
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
1,
1,
0,
0,
}

Definition at line 237 of file arbdb.cxx.

Referenced by gb_read_pntr_ts().

unsigned char GB_BIT_compress_data[]
static
Initial value:
= {
0x1d, GB_CS_OK, 0, 0,
0x04, GB_CS_OK, 0, 1,
0x0a, GB_CS_OK, 0, 2,
0x0b, GB_CS_OK, 0, 3,
0x0c, GB_CS_OK, 0, 4,
0x1a, GB_CS_OK, 0, 5,
0x1b, GB_CS_OK, 0, 6,
0x1c, GB_CS_OK, 0, 7,
0xf0, GB_CS_OK, 0, 8,
0xf1, GB_CS_OK, 0, 9,
0xf2, GB_CS_OK, 0, 10,
0xf3, GB_CS_OK, 0, 11,
0xf4, GB_CS_OK, 0, 12,
0xf5, GB_CS_OK, 0, 13,
0xf6, GB_CS_OK, 0, 14,
0xf7, GB_CS_OK, 0, 15,
0xf8, GB_CS_SUB, 0, 16,
0xf9, GB_CS_SUB, 0, 32,
0xfa, GB_CS_SUB, 0, 48,
0xfb, GB_CS_SUB, 0, 64,
0xfc, GB_CS_SUB, 0, 128,
0xfd, GB_CS_SUB, 1, 0,
0xfe, GB_CS_SUB, 2, 0,
0xff, GB_CS_SUB, 4, 0,
0
}

Definition at line 362 of file arbdb.cxx.

GB_shell* inside_shell = NULp
static

Definition at line 445 of file arbdb.cxx.

Referenced by GB_shell::in_shell().

GB_test_shell_closed test
static
int GB_info_deep = 15
static

Definition at line 2794 of file arbdb.cxx.