#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 "adperl.h"#include <arb_misc.h>#include <rpc/xdr.h>#include <set>
Go to the source code of this file.
Classes | |
| struct | gb_exitfun |
| class | 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 } |
Variables | |
| gb_local_data * | gb_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_shell * | inside_shell = NULp |
| static GB_test_shell_closed | shell_manager |
| static int | GB_info_deep = 15 |
Macro Definition Documentation
| #define INIT_TYPE_NAME | ( | t | ) | GB_TYPES_name[t] = #t |
Definition at line 35 of file arbdb.cxx.
Referenced by GB_TYPES_2_name().
| #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) |
Definition at line 161 of file arbdb.cxx.
Referenced by GB_read_bits_count(), GB_read_byte(), GB_read_bytes_count(), GB_read_float(), GB_read_floats_count(), GB_read_int(), GB_read_ints_count(), and GB_read_string_count().
| #define GB_TEST_READ_PTR | ( | gbd, | |
| type, | |||
| ignored | |||
| ) | EXPORT_ERROR_AND_RETURN_RES_IF_NOT_READABLE_AS_TYPE(gbd,NULp,type) |
Definition at line 162 of file arbdb.cxx.
Referenced by GB_read_bits_pntr(), GB_read_bytes_pntr(), GB_read_char_pntr(), GB_read_floats_pntr(), GB_read_ints_pntr(), GB_read_pointer(), and GB_read_string().
| #define GB_TEST_WRITE | ( | gbd, | |
| type, | |||
| ignored | |||
| ) | RETURN_ERROR_IF_NOT_WRITEABLE_AS_TYPE(gbd, type) |
Definition at line 163 of file arbdb.cxx.
Referenced by GB_write_bits(), GB_write_byte(), GB_write_bytes(), GB_write_float(), GB_write_floats(), GB_write_int(), GB_write_ints(), GB_write_pointer(), and GB_write_string().
| #define GB_TEST_NON_BUFFER | ( | x, | |
| gerror | |||
| ) |
Definition at line 165 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) |
Definition at line 1236 of file arbdb.cxx.
Referenced by GB_touch(), GB_write_bits(), GB_write_byte(), GB_write_flag(), GB_write_float(), GB_write_int(), GB_write_pntr(), GB_write_pointer(), GB_write_security_delete(), GB_write_security_levels(), GB_write_security_read(), and GB_write_security_write().
Enumeration Type Documentation
| enum CopyMode |
Function Documentation
Definition at line 37 of file arbdb.cxx.
References GB_BIT, GB_BITS, GB_BYTE, GB_BYTES, GB_DB, GB_FLOAT, GB_FLOATS, GB_INT, GB_INTS, GB_NONE, GB_OBSOLETE, GB_POINTER, GB_STRING, GB_STRING_SHRT, GB_TYPE_MAX, GBS_global_string_copy(), INIT_TYPE_NAME, initialized, NULp, and type.
Referenced by GB_get_type_name(), and gb_transactable_type().
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().
Definition at line 76 of file arbdb.cxx.
References ARB_strdup(), error(), GB_ARRAY_FLAGS(), gb_assert, GB_DELETED, GB_get_db_path(), GB_MAIN(), GB_OBSOLETE, GB_STRING, GB_TYPES_2_name(), GBK_dump_backtrace(), GBS_global_string(), NULp, and GBDATA::type().
Referenced by gb_type_readable_from(), and gb_type_writeable_to().
|
static |
Definition at line 103 of file arbdb.cxx.
References error(), GB_GET_SECURITY_WRITE, GB_MAIN(), GB_read_key_pntr(), GBS_global_string(), and GB_MAIN_TYPE::security_level.
Referenced by gb_type_writeable_to(), GB_write_security_delete(), GB_write_security_levels(), GB_write_security_read(), and GB_write_security_write().
Definition at line 116 of file arbdb.cxx.
References error(), GB_GET_SECURITY_WRITE, GB_MAIN(), gb_security_error(), and gb_transactable_type().
Definition at line 125 of file arbdb.cxx.
References gb_transactable_type().
Definition at line 129 of file arbdb.cxx.
References ARB_strdup(), error(), GB_get_db_path(), and GBS_global_string().
Definition at line 173 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 | ) |
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().
Definition at line 270 of file arbdb.cxx.
References gb_buffer::mem, NULp, and gb_buffer::size.
Referenced by gb_local_data::gb_local_data().
Definition at line 275 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().
Definition at line 284 of file arbdb.cxx.
References ARB_alloc(), ARB_calloc(), gb_buffer::mem, and gb_buffer::size.
Referenced by GB_increase_buffer(), and give_buffer().
Definition at line 294 of file arbdb.cxx.
References alloc_buffer(), gb_buffer::mem, and gb_buffer::size.
Referenced by GB_give_buffer(), and GB_give_buffer2().
|
static |
Definition at line 305 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().
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().
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().
Definition at line 330 of file arbdb.cxx.
References gb_local_data::buf1, and gb_buffer::size.
Referenced by gb_read_bin_rek_V2().
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().
|
static |
Definition at line 338 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 | ) |
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().
|
static |
Definition at line 415 of file arbdb.cxx.
References gb_exitfun::exitfun, and gb_exitfun::next.
Referenced by gb_local_data::~gb_local_data().
|
static |
Definition at line 423 of file arbdb.cxx.
References GB_shell::ensure_inside(), gbm_flush_mem(), gbm_free_mem(), NULp, and gb_local_data::~gb_local_data().
Referenced by gb_local_data::announce_db_close(), and GB_shell::~GB_shell().
| 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().
|
static |
Definition at line 581 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 | ||
| ) |
get data from server.
- Parameters
-
gbc container to unfold deep if != 0, then get subitems too. index_pos - >= 0, get indexed item from server
- <0, get all items
- Returns
- error on failure
Definition at line 586 of file arbdb.cxx.
References GBDATA::as_container(), GBDATA::as_entry(), GBCONTAINER::d, error(), flags, GBDATA::flags2, gb_flag_types2::folded_container, gb_create_header_array(), GB_DATA_LIST_HEADER(), GB_DELETED, GB_HEADER_LIST_GBD(), GB_internal_error(), GB_print_error(), gb_untouch_children(), gb_untouch_children_and_me(), gb_untouch_me(), gbcm_unfold_client(), GBCONTAINER_ELEM(), GBCONTAINER_MAIN(), GBDATA::is_container(), gb_data_list::nheader, and NULp.
Referenced by dump_internal(), find_sub_by_quark(), GB_clone(), gb_copy_explicit(), gb_find_by_nr(), GB_get_subfields(), gb_search_marked(), gbcmc_unfold_list(), and GB_MAIN_TYPE::login_remote().
|
static |
Definition at line 647 of file arbdb.cxx.
References gb_callback_list::call(), GB_MAIN_TYPE::close_callbacks, gb_assert, GB_CB_DELETE, gb_main, GB_MAIN_TYPE::gb_main(), and GB_MAIN().
Referenced by GB_close().
| 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().
| void gb_abort_and_close_all_DBs | ( | void | ) |
Definition at line 710 of file arbdb.cxx.
References GB_MAIN_TYPE::abort_transaction(), error(), GB_close(), gb_main, GB_MAIN(), gb_remembered_db(), and GB_MAIN_TYPE::get_transaction_level().
Referenced by GB_test_shell_closed::close_global_shell(), and GBP_prepare_to_die().
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().
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().
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().
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().
Definition at line 762 of file arbdb.cxx.
References GBDATA::as_entry(), and GBENTRY::memsize().
Referenced by compress_sequence_tree().
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().
Definition at line 900 of file arbdb.cxx.
References GBDATA::index.
Referenced by compress_sequence_tree().
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().
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().
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().
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().
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().
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().
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().
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().
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().
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().
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().
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().
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().
Definition at line 1048 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 1053 of file arbdb.cxx.
References GBDATA::as_entry(), GB_memdup(), GB_read_floats_pntr(), NULp, and GBENTRY::size().
reads basic db-field types and returns content as text.
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().
Definition at line 1086 of file arbdb.cxx.
References GB_read_key_pntr(), GB_read_type(), and GBS_global_string().
Referenced by GB_read_lossless_byte(), GB_read_lossless_float(), GB_read_lossless_int(), GB_write_lossless_byte(), GB_write_lossless_float(), and GB_write_lossless_int().
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().
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().
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().
Definition at line 1186 of file arbdb.cxx.
References GB_read_ints_count(), GB_read_ints_pntr(), and NULp.
Definition at line 1203 of file arbdb.cxx.
References GB_read_floats_count(), GB_read_floats_pntr(), and NULp.
|
static |
Definition at line 1223 of file arbdb.cxx.
References gb_callback_list::call(), gb_assert, GB_CB_CHANGED, GB_get_father(), GB_MAIN(), gb_remove_callbacks_marked_for_deletion(), and GBDATA::get_callbacks().
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().
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().
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().
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().
|
inline |
Definition at line 1300 of file arbdb.cxx.
References gb_save_extern_data_in_ts(), and gb_uncache().
Referenced by GB_write_bits(), gb_write_compressed_pntr(), and GB_write_pntr().
Definition at line 1317 of file arbdb.cxx.
References GBENTRY::cache_index, gb_flag_types::compressed_data, GBDATA::flags, gb_assert, GB_NORMAL_CHANGE, gb_save_extern_data_in_ts__and_uncache(), gb_touch_entry(), GBENTRY::insert_data(), and NULp.
Referenced by compress_sequence_tree().
| int gb_get_compression_mask | ( | GB_MAIN_TYPE * | Main, |
| GBQUARK | key, | ||
| int | gb_type | ||
| ) |
Definition at line 1329 of file arbdb.cxx.
References gb_Key::compression_mask, gb_Key::gb_key, gb_Key::gb_key_disabled, gb_load_single_key_data(), GB_MAIN_TYPE::gb_main(), and GB_MAIN_TYPE::keys.
Referenced by gb_create_dictionaries(), and GB_write_pntr().
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().
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().
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().
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().
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().
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().
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().
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().
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().
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().
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().
Definition at line 1576 of file arbdb.cxx.
References GB_GET_SECURITY_READ, and GB_test_transaction().
Definition at line 1580 of file arbdb.cxx.
References GB_GET_SECURITY_DELETE, and GB_test_transaction().
Referenced by ad_tree_set_security().
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().
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.
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.
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().
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().
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().
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_or_create_quark | ( | GB_MAIN_TYPE * | Main, |
| const char * | key | ||
| ) |
- Returns
- existing or newly created quark for 'key'
Definition at line 1668 of file arbdb.cxx.
References gb_create_key(), GBK_terminate(), and key2quark().
Referenced by compress_sequence_tree(), gb_find_or_create_NULL_quark(), GB_find_or_create_quark(), gb_fix_recursive(), gb_hierarchy_location::gb_hierarchy_location(), gb_load_key_data_and_dictionaries(), gb_make_entry(), and gb_save_dictionary_data().
| GBQUARK gb_find_or_create_NULL_quark | ( | GB_MAIN_TYPE * | Main, |
| const char * | key | ||
| ) |
Definition at line 1678 of file arbdb.cxx.
References gb_find_or_create_quark().
Referenced by gb_make_container().
- 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().
- 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().
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().
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().
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().
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().
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().
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().
| GBCONTAINER* gb_get_root | ( | GBENTRY * | gbe | ) |
Definition at line 1741 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 1742 of file arbdb.cxx.
References GB_MAIN(), and GB_MAIN_TYPE::root_container.
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().
| GBENTRY* gb_create | ( | GBCONTAINER * | father, |
| const char * | key, | ||
| GB_TYPES | type | ||
| ) |
Definition at line 1763 of file arbdb.cxx.
References GB_ARRAY_FLAGS(), gb_assert, GB_CREATED, GB_DELETED, GB_FATHER(), gb_make_entry(), gb_touch_entry(), and gb_touch_header().
Referenced by compress_sequence_tree(), find_or_create(), GB_create(), gb_load_single_key_data(), and gb_save_dictionary_data().
| GBCONTAINER* gb_create_container | ( | GBCONTAINER * | father, |
| const char * | key | ||
| ) |
Definition at line 1773 of file arbdb.cxx.
References GB_CREATED, GB_FATHER(), gb_make_container(), gb_touch_entry(), and gb_touch_header().
Referenced by compress_sequence_tree(), find_or_create(), GB_create_container(), gb_load_single_key_data(), and gb_save_dictionary_data().
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().
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().
Definition at line 1866 of file arbdb.cxx.
References error(), GB_BITS, GB_BYTES, GB_child(), GB_DB, GB_FLOATS, GB_INTS, GB_nextChild(), GB_read_string(), GB_STRING, GB_test_transaction(), GB_write_string(), NULp, and GBDATA::type().
Referenced by GB_delete().
| 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().
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().
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().
Definition at line 1945 of file arbdb.cxx.
References GB_DELETED, gb_touch_entry(), and NULp.
Referenced by gbcms_talking_put_update().
Definition at line 2012 of file arbdb.cxx.
References GBDATA::as_container(), GBDATA::as_entry(), CM_DROP_MARKS, CM_DROP_PROTECTION, CM_DROP_TEMPSTATE, CM_OVERWRITE_EXISTING, CM_SKIP_TEMP, gb_flag_types::compressed_data, GBENTRY::data(), error(), GBDATA::flags, GBDATA::flags2, GBCONTAINER::flags3, gb_flag_types2::folded_container, gb_assert, GB_BITS, GB_BYTE, GB_BYTES, GB_child(), GB_clear_temporary(), gb_clone_explicit(), GB_DB, GB_entry(), GB_export_error(), GB_export_errorf(), GB_FLOAT, GB_FLOATS, GB_incur_error_if(), GB_INT, GB_internal_error(), GB_INTS, GB_is_ancestor_of(), GB_is_temporary(), GB_KEY(), GB_KEY_QUARK(), GB_nextChild(), GB_nextEntry(), GB_NORMAL_CHANGE, GB_OBSOLETE, GB_read_byte(), GB_read_char_pntr(), GB_read_flag(), GB_read_float(), GB_read_int(), GB_read_key_pntr(), gb_save_extern_data_in_ts(), GB_set_temporary(), GB_STRING, GB_test_transaction(), gb_touch_entry(), gb_unfold(), GB_write_byte(), GB_write_flag(), GB_write_float(), GB_write_int(), GB_write_string(), implicated, GBENTRY::insert_data(), GBDATA::is_container(), GBENTRY::memsize(), NULp, gb_flag_types::security_delete, gb_flag_types::security_read, gb_flag_types::security_write, GBENTRY::size(), type, and GBDATA::type().
Referenced by gb_clone_explicit(), and gb_copy_checked().
|
static |
copy a clone of 'gb_source' into container 'gb_destCont' according to 'mode'.
- Returns
- pointer to copy on success or NULp (in which case an error may be exported).
Definition at line 1972 of file arbdb.cxx.
References GBDATA::as_container(), CM_OVERWRITE_EXISTING, CM_SKIP_TEMP, GBCONTAINER::d, error(), GBDATA::flags2, gb_flag_types2::folded_container, gb_assert, GB_await_error(), gb_copy_explicit(), GB_create(), GB_create_container(), gb_create_header_array(), GB_delete(), GB_export_error(), GB_export_errorf(), GB_have_error(), GB_is_ancestor_of(), GB_is_temporary(), GB_read_key_pntr(), GB_SYSTEM_FOLDER, GB_test_transaction(), IF_ASSERTION_USED, GBDATA::is_container(), NULp, gb_data_list::size, and GBDATA::type().
Referenced by GB_clone(), and gb_copy_explicit().
copies the content of 'source' into 'dest'. if 'dest' is a container, entries existing there will not be overwritten!
Definition at line 2142 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().
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().
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().
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().
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().
complete copy (does also copy temporary entries)
Definition at line 2190 of file arbdb.cxx.
References CM_COPY_FULL, and gb_copy_checked().
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.
Definition at line 2220 of file arbdb.cxx.
Referenced by GB_get_subfields().
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().
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().
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().
start a transaction if no transaction is running. (otherwise only trace nested transactions)
recommended transaction usage:
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().
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().
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().
Definition at line 2535 of file arbdb.cxx.
References GB_MAIN(), and GB_MAIN_TYPE::no_transaction().
Referenced by run_command().
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().
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().
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().
- 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().
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().
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().
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().
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().
| GB_ERROR gb_resort_system_folder_to_top | ( | GBCONTAINER * | gb_main | ) |
Definition at line 2705 of file arbdb.cxx.
References error(), GB_child(), GB_entry(), GB_export_error(), GB_nextChild(), GB_number_of_subentries(), GB_read_clients(), GB_resort_data_base(), GB_SYSTEM_FOLDER, and NULp.
Referenced by GB_login().
| STATIC_ASSERT_ANNOTATED | ( | ((GB_USERFLAG_ANY+1)&GB_USERFLAG_ANY) | = =0, |
| "not all bits set in GB_USERFLAG_ANY" | |||
| ) |
|
inline |
Definition at line 2741 of file arbdb.cxx.
References GB_USERFLAG_ANY.
Referenced by GB_clear_user_flag(), GB_raise_user_flag(), and GB_user_flag().
|
inline |
Definition at line 2746 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().
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().
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().
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().
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().
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().
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().
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().
Definition at line 2833 of file arbdb.cxx.
References GBCONTAINER::d, GB_MAIN_TYPE::dummy_father, gb_header_list::flags, GB_DATA_LIST_HEADER(), GB_DB, GB_FATHER(), GB_HEADER_LIST_GBD(), GB_MAIN(), GB_pop_transaction(), GB_push_transaction(), GB_read_as_string(), GB_read_key_pntr(), GB_type_2_char(), GBCONTAINER_MAIN(), gb_data_list::headermemsize, gb_header_flags::key_quark, gb_data_list::nheader, NULp, quark2key(), gb_data_list::size, type, and GBDATA::type().
Referenced by GB_info().
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().
Variable Documentation
| gb_local_data* gb_local = NULp |
Definition at line 33 of file arbdb.cxx.
Referenced by commit_or_abort_transaction(), gb_compress_bits(), GB_MAIN_TYPE::GB_MAIN_TYPE(), gb_read_bin(), gb_recover_corrupt_file(), gb_uncompress_bits(), gbcm_read_buffered(), gbcm_read_flush(), gbcm_write(), gbcm_write_flush(), gbcmc_open(), gbcms_talking_begin_transaction(), gbcms_talking_init_transaction(), and GB_MAIN_TYPE::~GB_MAIN_TYPE().
| const int gb_convert_type_2_compression_flags[] |
| int gb_convert_type_2_sizeof[] |
| int gb_convert_type_2_appendix_size[] |
Definition at line 244 of file arbdb.cxx.
Referenced by gb_read_pntr_ts().
|
static |
Definition at line 452 of file arbdb.cxx.
Referenced by GB_shell::in_shell().
|
static |
