ARB
Classes | Macros | Functions | Variables
adquery.cxx File Reference
#include "gb_aci.h"
#include "gb_comm.h"
#include "gb_index.h"
#include "gb_key.h"
#include "gb_localdata.h"
#include "gb_ta.h"
#include <algorithm>
#include <arb_strbuf.h>
#include <arb_match.h>
#include <cctype>
Include dependency graph for adquery.cxx:

Go to the source code of this file.

Classes

class  keychar_table
 

Macros

#define GB_PATH_MAX   1024
 
#define BUFFERSIZE   1024
 

Functions

static void build_GBDATA_path (GBDATA *gbd, char **buffer)
 
static const char * GB_get_GBDATA_path (GBDATA *gbd)
 
static bool gb_find_value_equal (GBDATA *gb, GB_TYPES type, const char *val, GB_CASE case_sens)
 
static GBDATA * find_sub_by_quark (GBCONTAINER *father, GBQUARK key_quark, GB_TYPES type, const char *val, GB_CASE case_sens, GBDATA *after, size_t skip_over)
 
GBDATA * GB_find_sub_by_quark (GBDATA *father, GBQUARK key_quark, GBDATA *after, size_t skip_over)
 
static GBDATA * GB_find_subcontent_by_quark (GBDATA *father, GBQUARK key_quark, GB_TYPES type, const char *val, GB_CASE case_sens, GBDATA *after, size_t skip_over)
 
static GBDATA * find_sub_sub_by_quark (GBCONTAINER *const father, const char *key, GBQUARK sub_key_quark, GB_TYPES type, const char *val, GB_CASE case_sens, GBDATA *after)
 
static GBDATA * gb_find_internal (GBDATA *gbd, const char *key, GB_TYPES type, const char *val, GB_CASE case_sens, GB_SEARCH_TYPE gbs)
 
GBDATA * GB_find (GBDATA *gbd, const char *key, GB_SEARCH_TYPE gbs)
 
GBDATA * GB_find_string (GBDATA *gbd, const char *key, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs)
 
NOT4PERL GBDATA * GB_find_int (GBDATA *gbd, const char *key, long val, GB_SEARCH_TYPE gbs)
 
GBDATA * GB_child (GBDATA *father)
 
GBDATA * GB_nextChild (GBDATA *child)
 
GBDATA * GB_entry (GBDATA *father, const char *key)
 
GBDATA * GB_nextEntry (GBDATA *entry)
 
GBDATA * GB_followingEntry (GBDATA *entry, size_t skip_over)
 
size_t GB_countEntries (GBDATA *father, const char *key)
 
GBDATA * GB_brother (GBDATA *entry, const char *key)
 
GBDATA * gb_find_by_nr (GBCONTAINER *father, int index)
 
const char * GB_first_non_key_char (const char *str)
 
GBDATA * find_or_create (GBCONTAINER *gb_parent, const char *key, GB_TYPES create, bool internflag)
 
GBDATA * gb_search (GBCONTAINER *gbc, const char *key, GB_TYPES create, int internflag)
 
GBDATA * GB_search (GBDATA *gbd, const char *fieldpath, GB_TYPES create)
 
static GBDATA * gb_expect_type (GBDATA *gbd, GB_TYPES expected_type, const char *fieldname)
 
GBDATA * GB_searchOrCreate_string (GBDATA *gb_container, const char *fieldpath, const char *default_value)
 
GBDATA * GB_searchOrCreate_int (GBDATA *gb_container, const char *fieldpath, long default_value)
 
GBDATA * GB_searchOrCreate_float (GBDATA *gb_container, const char *fieldpath, float default_value)
 
static GBDATA * gb_search_marked (GBCONTAINER *gbc, GBQUARK key_quark, int firstindex, size_t skip_over)
 
long GB_number_of_marked_subentries (GBDATA *gbd)
 
GBDATA * GB_first_marked (GBDATA *gbd, const char *keystring)
 
GBDATA * GB_following_marked (GBDATA *gbd, const char *keystring, size_t skip_over)
 
GBDATA * GB_next_marked (GBDATA *gbd, const char *keystring)
 

Variables

static keychar_table keychars
 

Macro Definition Documentation

#define GB_PATH_MAX   1024

Definition at line 24 of file adquery.cxx.

#define BUFFERSIZE   1024

Definition at line 42 of file adquery.cxx.

Referenced by GB_get_GBDATA_path().

Function Documentation

static void build_GBDATA_path ( GBDATA *  gbd,
char **  buffer 
)
static

Definition at line 26 of file adquery.cxx.

References buffer, GB_FATHER(), and GB_KEY().

Referenced by GB_get_GBDATA_path().

static const char* GB_get_GBDATA_path ( GBDATA *  gbd)
static

Definition at line 44 of file adquery.cxx.

References ARB_alloc(), assert_or_exit, buffer, BUFFERSIZE, build_GBDATA_path(), and NULp.

Referenced by find_sub_by_quark().

static bool gb_find_value_equal ( GBDATA *  gb,
GB_TYPES  type,
const char *  val,
GB_CASE  case_sens 
)
static

Definition at line 60 of file adquery.cxx.

References gb_assert, GB_INT, GB_internal_error(), GB_read_char_pntr(), GB_read_int(), GB_STRING, GBS_global_string(), GBS_string_matches(), GBDATA::is_a_string(), type, and GBDATA::type().

Referenced by find_sub_by_quark().

static GBDATA* find_sub_by_quark ( GBCONTAINER *  father,
GBQUARK  key_quark,
GB_TYPES  type,
const char *  val,
GB_CASE  case_sens,
GBDATA *  after,
size_t  skip_over 
)
static

Definition at line 94 of file adquery.cxx.

References GBCONTAINER::d, flags, gb_assert, GB_DATA_LIST_HEADER(), GB_DELETED, gb_find_value_equal(), GB_get_GBDATA_path(), GB_HEADER_LIST_GBD(), GB_internal_error(), gb_unfold(), GBS_global_string(), if, GBDATA::index, gb_data_list::nheader, and NULp.

Referenced by GB_find_sub_by_quark(), and GB_find_subcontent_by_quark().

GBDATA* GB_find_sub_by_quark ( GBDATA *  father,
GBQUARK  key_quark,
GBDATA *  after,
size_t  skip_over 
)

Definition at line 174 of file adquery.cxx.

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

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

static GBDATA* GB_find_subcontent_by_quark ( GBDATA *  father,
GBQUARK  key_quark,
GB_TYPES  type,
const char *  val,
GB_CASE  case_sens,
GBDATA *  after,
size_t  skip_over 
)
static

Definition at line 178 of file adquery.cxx.

References after(), GBDATA::expect_container(), find_sub_by_quark(), and type.

Referenced by find_sub_sub_by_quark(), and gb_find_internal().

static GBDATA* find_sub_sub_by_quark ( GBCONTAINER *const  father,
const char *  key,
GBQUARK  sub_key_quark,
GB_TYPES  type,
const char *  val,
GB_CASE  case_sens,
GBDATA *  after 
)
static

Definition at line 182 of file adquery.cxx.

References gb_header_flags::changed, GBCONTAINER::d, error(), flags, GBDATA::flags2, gb_flag_types2::folded_container, GB_ARRAY_FLAGS(), GB_DATA_LIST_HEADER(), GB_DELETED, GB_export_error(), GB_find_subcontent_by_quark(), GB_HEADER_LIST_GBD(), GB_INDEX_FILES_NEXT(), gb_index_find(), GB_internal_error(), GB_MAX_LOCAL_SEARCH, GBCMC_find(), GBCONTAINER_IFS(), GBCONTAINER_MAIN(), if, GBDATA::index, GB_MAIN_TYPE::is_client(), GBDATA::is_container(), gb_index_files::key, gb_data_list::nheader, NULp, SEARCH_CHILD_OF_NEXT, SEARCH_GRANDCHILD, GB_MAIN_TYPE::send_update_to_server(), gb_data_list::size, and gb_flag_types2::update_in_server.

Referenced by gb_find_internal().

static GBDATA* gb_find_internal ( GBDATA *  gbd,
const char *  key,
GB_TYPES  type,
const char *  val,
GB_CASE  case_sens,
GB_SEARCH_TYPE  gbs 
)
static

Definition at line 250 of file adquery.cxx.

References after(), GBDATA::as_container(), FALLTHROUGH, find_sub_sub_by_quark(), gb_assert, GB_FATHER(), GB_find_existing_quark(), GB_find_subcontent_by_quark(), GBDATA::is_container(), NULp, result, SEARCH_BROTHER, SEARCH_CHILD, SEARCH_CHILD_OF_NEXT, SEARCH_GRANDCHILD, and SEARCH_NEXT_BROTHER.

Referenced by GB_find(), GB_find_int(), and GB_find_string().

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

Definition at line 295 of file adquery.cxx.

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

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

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

Definition at line 302 of file adquery.cxx.

References gb_find_internal(), and GB_STRING.

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

NOT4PERL GBDATA* GB_find_int ( GBDATA *  gbd,
const char *  key,
long  val,
GB_SEARCH_TYPE  gbs 
)

Definition at line 311 of file adquery.cxx.

References GB_CASE_UNDEFINED, gb_find_internal(), and GB_INT.

Referenced by gbcms_talking_find().

GBDATA* GB_child ( GBDATA *  father)

Definition at line 322 of file adquery.cxx.

References GB_find(), NULp, and SEARCH_CHILD.

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

GBDATA* GB_nextChild ( GBDATA *  child)

Definition at line 326 of file adquery.cxx.

References GB_find(), NULp, and SEARCH_NEXT_BROTHER.

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

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

Definition at line 334 of file adquery.cxx.

References GB_find(), and SEARCH_CHILD.

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

GBDATA* GB_nextEntry ( GBDATA *  entry)

Definition at line 339 of file adquery.cxx.

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

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

GBDATA* GB_followingEntry ( GBDATA *  entry,
size_t  skip_over 
)

Definition at line 344 of file adquery.cxx.

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

size_t GB_countEntries ( GBDATA *  father,
const char *  key 
)

Definition at line 351 of file adquery.cxx.

References GB_entry(), and GB_nextEntry().

GBDATA* GB_brother ( GBDATA *  entry,
const char *  key 
)

Definition at line 361 of file adquery.cxx.

References GB_find(), and SEARCH_BROTHER.

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

GBDATA* gb_find_by_nr ( GBCONTAINER *  father,
int  index 
)

Definition at line 367 of file adquery.cxx.

References GBCONTAINER::d, gb_header_list::flags, flags, GB_DATA_LIST_HEADER(), GB_DELETED, GB_HEADER_LIST_GBD(), GB_internal_error(), GB_internal_errorf(), gb_unfold(), gb_header_flags::key_quark, gb_data_list::nheader, and NULp.

Referenced by gb_uncompress_by_sequence().

const char* GB_first_non_key_char ( const char *  str)

Definition at line 416 of file adquery.cxx.

References keychar_table::first_non_key_character().

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

GBDATA* find_or_create ( GBCONTAINER *  gb_parent,
const char *  key,
GB_TYPES  create,
bool  internflag 
)
inline

Definition at line 420 of file adquery.cxx.

References keychar_table::first_non_key_character(), gb_assert, gb_create(), GB_CREATE_CONTAINER, GB_create_container(), gb_create_container(), GB_entry(), GB_export_errorf(), GB_have_error(), and NULp.

Referenced by gb_search().

GBDATA* gb_search ( GBCONTAINER *  gbc,
const char *  key,
GB_TYPES  create,
int  internflag 
)

Definition at line 445 of file adquery.cxx.

References GBDATA::as_container(), find_or_create(), keychar_table::first_non_key_character(), gb_assert, GB_CREATE_CONTAINER, GB_export_error(), GB_export_errorf(), GB_FIND, gb_get_root(), GB_have_error(), gb_search(), GB_test_transaction(), GBDATA::get_father(), GBDATA::is_container(), and NULp.

Referenced by compress_sequence_tree(), gb_load_key_data_and_dictionaries(), gb_save_dictionary_data(), gb_search(), and GB_search().

GBDATA* GB_search ( GBDATA *  gbd,
const char *  fieldpath,
GB_TYPES  create 
)

Definition at line 531 of file adquery.cxx.

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

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

static GBDATA* gb_expect_type ( GBDATA *  gbd,
GB_TYPES  expected_type,
const char *  fieldname 
)
static

Definition at line 535 of file adquery.cxx.

References gb_assert, GB_export_errorf(), GB_FIND, NULp, type, and GBDATA::type().

Referenced by GB_searchOrCreate_float(), GB_searchOrCreate_int(), and GB_searchOrCreate_string().

GBDATA* GB_searchOrCreate_string ( GBDATA *  gb_container,
const char *  fieldpath,
const char *  default_value 
)

Definition at line 546 of file adquery.cxx.

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

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

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

Definition at line 569 of file adquery.cxx.

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

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

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

Definition at line 591 of file adquery.cxx.

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

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

static GBDATA* gb_search_marked ( GBCONTAINER *  gbc,
GBQUARK  key_quark,
int  firstindex,
size_t  skip_over 
)
static

Definition at line 613 of file adquery.cxx.

References GBCONTAINER::d, flags, GB_DATA_LIST_HEADER(), GB_DELETED, GB_HEADER_LIST_GBD(), gb_unfold(), GBCONTAINER_MAIN(), gb_data_list::nheader, NULp, gb_user::userbit, and GB_MAIN_TYPE::users.

Referenced by GB_first_marked(), and GB_following_marked().

long GB_number_of_marked_subentries ( GBDATA *  gbd)

Definition at line 635 of file adquery.cxx.

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

Referenced by GBT_count_marked_species(), and GBT_mark_all().

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

Definition at line 655 of file adquery.cxx.

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

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

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

Definition at line 663 of file adquery.cxx.

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

Referenced by GB_next_marked().

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

Definition at line 670 of file adquery.cxx.

References GB_following_marked().

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

Variable Documentation

keychar_table keychars
static

Definition at line 414 of file adquery.cxx.

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