#include "gb_local.h"#include <ad_config.h>#include "TreeNode.h"#include <arb_progress.h>#include <arb_strarray.h>#include <arb_file.h>#include <arb_diff.h>#include <cctype>#include "ad_colorset.h"
Go to the source code of this file.
Classes | |
| struct | gbt_renamed |
Functions | |
| GB_ERROR | GBT_begin_rename_session (GBDATA *gb_main, int all_flag) |
| GB_ERROR | GBT_rename_species (const char *oldname, const char *newname, bool ignore_protection) |
| static void | gbt_free_rename_session_data () |
| GB_ERROR | GBT_abort_rename_session () |
| static GB_ERROR | gbt_rename_tree_rek (TreeNode *tree, int tree_index) |
| GB_ERROR | GBT_commit_rename_session () |
Variables | |
| struct { | |
| GB_HASH * renamed_hash | |
| GB_HASH * old_species_hash | |
| GBDATA * gb_main | |
| GBDATA * gb_species_data | |
| int all_flag | |
| } | NameSession |
| static const char * | currentTreeName = NULp |
Function Documentation
Definition at line 37 of file adname.cxx.
References all_flag, error(), gb_main, GB_MIND_CASE, GB_push_transaction(), GBS_create_dynaval_hash(), GBS_dynaval_free(), GBT_create_species_hash(), GBT_get_species_count(), GBT_get_species_data(), hash_size(), NameSession, and NULp.
Referenced by AWTC_pars_names(), and AWTC_recreate_name().
Definition at line 65 of file adname.cxx.
References gbt_renamed::data, error(), gb_assert, GB_entry(), GB_write_string(), GBS_global_string(), GBS_read_hash(), GBS_write_hash(), GBT_find_species_rel_species_data(), NameSession, and NULp.
Referenced by AWTC_pars_names(), and AWTC_recreate_name().
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static |
Definition at line 116 of file adname.cxx.
References GBS_free_hash(), NameSession, and NULp.
Referenced by GBT_abort_rename_session(), and GBT_commit_rename_session().
| GB_ERROR GBT_abort_rename_session | ( | void | ) |
Definition at line 127 of file adname.cxx.
References GB_abort_transaction(), gbt_free_rename_session_data(), and NameSession.
Referenced by AWTC_pars_names(), and AWTC_recreate_name().
Definition at line 134 of file adname.cxx.
References buffer, gbt_renamed::data, GB_warningf(), GBS_read_hash(), TreeNode::is_leaf(), TreeNode::name, NameSession, NULp, and gbt_renamed::used_by.
Referenced by GBT_commit_rename_session().
| GB_ERROR GBT_commit_rename_session | ( | void | ) |
Definition at line 166 of file adname.cxx.
References arb_progress::allow_title_reuse(), GBT_config_item::append_to_config_string(), CI_END_OF_CONFIG, CI_SPECIES, gbt_renamed::data, destroy(), CharPtrArray::empty(), error(), GB_await_error(), GB_end_transaction(), GB_entry(), GB_read_char_pntr(), GB_write_string(), GBS_global_string(), GBS_global_string_copy(), GBS_read_hash(), GBT_colorset_root(), GBT_find_colorset(), gbt_free_rename_session_data(), GBT_get_colorset_names(), GBT_get_configuration_names(), GBT_get_tree_names(), GBT_load_colorset(), GBT_message(), GBT_read_tree(), gbt_rename_tree_rek(), GBT_save_colorset(), GBT_write_tree(), GEN_first_pseudo_species(), GEN_is_genome_db(), GEN_next_pseudo_species(), arb_progress::inc_and_check_user_abort(), GBT_config::MIDDLE_AREA, GBT_config_item::name, NameSession, GBT_config_parser::nextItem(), NULp, GBS_strstruct::release_memfriendly(), CharPtrArray::remove(), ConstStrArray::replace(), GBT_config::save(), GBT_config::set_definition(), CharPtrArray::size(), GBT_config::TOP_AREA, and GBT_config_item::type.
Referenced by AWTC_pars_names(), and AWTC_recreate_name().
Variable Documentation
| GB_HASH* renamed_hash |
Definition at line 30 of file adname.cxx.
| GB_HASH* old_species_hash |
Definition at line 31 of file adname.cxx.
| GBDATA* gb_main |
Definition at line 32 of file adname.cxx.
Referenced by RefEntries::addRefsTo(), adjustTreeRoot(), ali_checklen_cb(), ALI_create_admin_window(), alignment_vars_callback(), alignToNextRelative(), AP_tree_root::AP_tree_root(), ARB_bind_global_awars(), ARB_main(), awt_create_select_filter(), awtc_mark_hits(), awtc_nn_search(), awtc_nn_search_all_listed(), AWTC_recreate_name(), BoundTreeAwarCallback::bind_tree_callback(), bindAdmin(), boundloc_changed_cb(), build_reverse_complement(), calc_pvp(), calculate_clusters(), ED4_terminal::changed_by_database(), check_for_remote_command(), AP_tree_root::check_update(), config_rename_handler(), copy_rename_handler(), QUERY::count_queried_items(), create_ali_handler(), create_colorset_representation(), create_consense_tree_cb(), create_macro_variables(), create_new_species(), create_pars_init_window(), QUERY::create_query_box(), DBUI::create_species_query_window(), CreateRNA3DMainWindow(), createValNameList(), EXP_item_type_species_selector::current(), FINAL_TYPE< SEQTYPE >::current(), delete_ali_cb(), TreeAdmin::delete_tree_cb(), di_calculate_compressed_matrix_cb(), di_calculate_matrix(), di_calculate_tree_cb(), di_mark_by_distance(), dot_missing_bases(), ED4_alignment_length_changed(), ed4_create_all_awars(), ed4_create_mainDB_awars(), ED4_create_search_awars(), ED4_CreateProteinViewer_window(), ED4_exit(), ED4_get_marked_from_menu(), ED4_getSaiColorString(), ED4_jump_to_current_species(), ED4_menu_highlight(), ED4_pfold_select_SAI_and_update_option_menu(), ED4_remove_faligner_entries(), ED4_start_plugin(), ED4_timer(), ED4_undo_redo(), ED4_with_whole_block(), ensure_trees_have_order(), MacroRecorder::execute(), executeKeystroke(), EXP_create_experiment_query_window(), EXP_open_mask_window(), export_newick(), export_seq_data(), export_to_DB(), FastAligner_start(), field_convert_commit_cb(), field_convert_update_typesel_cb(), field_delete_cb(), AWT_tree_selection::fill(), SAI_selection::fill(), EDB_root_bact::fill_data(), MO_Liste::fill_marked_bakts(), flush_taxonomy_cb(), gb_abort_and_close_all_DBs(), gb_create_dictionaries(), GB_delete(), gb_delete_dummy_father(), GB_get_gb_main_during_cb(), gb_load_key_data_and_dictionaries(), GBCMS_open(), gbcms_talking_begin_transaction(), gbcms_talking_init_transaction(), gbl_ali_name(), gbl_sequence_type(), GBT_begin_rename_session(), GBT_compress_sequence_tree2(), gbt_read_tree_rek(), GDE_init(), GEN_create_gene_query_window(), GEN_open_mask_window(), GEN_root::GEN_root(), RefEntries::generate_item_error(), ArbParsimony::generate_tree(), MO_Liste::get_all_species(), get_first_organism(), ColumnStat::get_gb_main(), GroupUIdata::get_gb_main(), export_sequence_data::get_gb_main(), LocationEditor::get_gb_main(), ED4_root::get_gb_main(), AWT_graphic_tree::get_gbmain(), RegFieldSelection::get_keytype(), InfoWindow::get_selected_item(), get_taxonomy(), group_species(), hide_field_cb(), insdel_event(), insdel_sai_event(), insert_new_species_terminal(), AWT_canvas::instant_resize(), DI_MATRIX::load(), PHDATA::load(), PARSIMONY_testenv< SEQTYPE >::load_tree(), ARB_seqtree_root::loadFromDB(), macro_terminated(), main(), TreeAdmin::make_dest_treename_unique_cb(), map_extended(), mark_action(), mark_clusters(), GroupUIdata::mark_species(), member_of_DB(), MG_config_delete_cb(), MG_map_species(), MO_Liste::MO_Liste(), modsai_cb(), NT_activate_configMarkers_display(), nt_add(), nt_add_partial(), nt_disconnect_from_db(), NT_fix_dict_compress(), NT_open_mask_window(), AP_main::open(), SelectedDatabase::open_db_for_merge(), SAI_graphic::paint(), pars_generate_aliview(), pars_start_cb(), PARS_tree_init(), ph_exit(), PH_save_ml_cb(), AWT_canvas::pop_transaction(), popup_gene_location_editor(), popupSaiProbeMatchWindow(), SpeciesFlag::prepare_itemfield(), probe_match_event(), probe_read_data_base(), AWT_canvas::push_transaction(), PV_AddOrfTerminalsToLoadedSpecies(), PV_ManageTerminals(), PV_PrintMissingDBentryInformation(), PV_WriteTranslatedSequenceToDB(), query_count_items(), read_tree_and_size_internal(), realign_event(), BoundActionTracker::reconfigure(), GroupUIdata::refill_result_list(), RefEntries::refresh_result_cb(), RegFieldSelection::registrate(), reorder_configs_cb(), reorder_keys(), reorder_up_down(), restore_colorset_representation(), reverseComplement(), RNA3D_Graphics::RNA3D_Graphics(), run_close_callbacks(), run_command(), run_server(), SAI_graphic::SAI_graphic(), saiChanged_callback(), DI_MATRIX::save(), KeySorter::save_changes(), EDB_root_bact::save_current_config(), save_tree_as_newick(), ARB_seqtree_root::saveToDB(), SEC_undo_cb(), ArbImporter::set_db_4_nameserver(), sina_start(), ACI_Labeler::speciesLabel(), SQ_create_seq_quality_window(), SQ_pass2_on_tree(), st_remove_entries_cb(), start_SECEDIT_plugin(), startup_sequence_cb(), TranslateGeneToAminoAcidSequence(), TreeAdmin::tree_copy_or_rename_cb(), unlink_awar_from_DB(), user_code_nr_changed_cb(), ED4_terminal::write_sequence(), and write_sequence_autoinc_alisize().
| GBDATA* gb_species_data |
Definition at line 33 of file adname.cxx.
Referenced by addSpeciesToConcatenateList(), ARB_main(), calc_and_update_alignment_errors_cb(), compress_sequence_tree(), concatenateFieldsCreateNewSpecies(), copy_move_del_alignment(), copy_SAI_to_species_cb(), create_new_species(), DI_create_matrix_variables(), experiment_field_selection_list_rescan(), export_to_DB(), GBT_check_alignment(), GBT_gen_species_array(), GBT_mark_all(), gene_extract_handler(), gene_field_selection_list_rescan(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), ArbImporter::import_data(), launch_MapViewer_cb(), mark_action(), NT_resort_data_base_by_tree(), popup_new_main_window(), probe_match_event(), PT_init_input_data(), PT_prepare_data(), ALI_ARBDB::put_sequence(), ALI_ARBDB::put_sequence_string(), ArbImporter::read_data(), ReadArbdb(), QUERY::search_duplicated_field_content(), species_copy_cb(), species_create_handler(), and species_field_selection_list_rescan().
| int all_flag |
Definition at line 34 of file adname.cxx.
Referenced by GBT_begin_rename_session().
| struct { ... } NameSession |
Definition at line 132 of file adname.cxx.
