AW_awar.cxx File Reference

#include "aw_nawar.hxx"
#include "aw_awar.hxx"
#include "aw_root.hxx"
#include "aw_msg.hxx"
#include "aw_window.hxx"
#include "aw_select.hxx"
#include <arb_str.h>
#include <arb_file.h>
#include <ad_cb.h>
#include <list>
#include <sys/stat.h>
#include <climits>
#include <cfloat>

Include dependency graph for AW_awar.cxx:

Go to the source code of this file.

Classes
struct	AW_widget_refresh_cb

Macros
#define	AWAR_EPS   0.00000001
#define	AWAR_CHANGE_DUMP(name, where, format)
#define	WRITE_BODY(self, format, func)
#define	WRITE_SKELETON(self, type, format, func)

Functions
static void	aw_cp_awar_2_widget_cb (AW_root *root, AW_widget_refresh_cb *widgetlist)
	WRITE_SKELETON (write_string, const char *,"%s", GB_write_string) WRITE_SKELETON(write_int
GB_write_int	WRITE_SKELETON (write_float, float,"%f", GB_write_float) WRITE_SKELETON(write_as_string
return	GB_read_as_string (gb_var)
static void	AW_var_gbdata_callback (GBDATA *, AW_awar *awar)
static void	AW_var_gbdata_callback_delete_intern (GBDATA *gbd, AW_awar *awar)
static void	AW_var_gbdata_callback_delete (GBDATA *gbd, AW_awar *awar)
bool	member_of_DB (GBDATA *gbd, GBDATA *gb_main)

Variables
static GB_ERROR	AW_MSG_UNMAPPED_AWAR
	long
	li
GB_write_int const char	s
GB_write_int const char GB_write_autoconv_string WRITE_SKELETON(write_pointer, GBDATA *,"%p", GB_write_pointer) char *AW_awa	if )(!gb_var) return strdup("")
GB_transaction	ta (gb_var)

Macro Definition Documentation

#define AWAR_EPS   0.00000001

Definition at line 30 of file AW_awar.cxx.

Referenced by AW_awar::update().

#define AWAR_CHANGE_DUMP	(		name,
			where,
			format
	)

Definition at line 35 of file AW_awar.cxx.

#define WRITE_BODY	(		self,
			format,
			func
	)

Value:

if (!gb_var) return AW_MSG_UNMAPPED_AWAR;           \
    aw_assert(!deny_write);                             \
    GB_transaction ta(gb_var);                          \
    AWAR_CHANGE_DUMP(awar_name, #self, format);         \
    GB_ERROR error = func(gb_var, para);                \
    if (!error) update_tmp_state_during_change()

Definition at line 132 of file AW_awar.cxx.

#define WRITE_SKELETON	(		self,
			type,
			format,
			func
	)

Value:

GB_ERROR AW_awar::self(type para) {                 \
        WRITE_BODY(self, format, func);                 \
        return error;                                   \
    }                                                   \
    GB_ERROR AW_awar::concatenate(re,self)(type para) { \
        WRITE_BODY(self, format, func);                 \
        GB_touch(gb_var);                               \
        return error;                                   \
    }

Definition at line 140 of file AW_awar.cxx.

Function Documentation

static void aw_cp_awar_2_widget_cb ( AW_root *  root, AW_widget_refresh_cb *  widgetlist  )

static

Definition at line 57 of file AW_awar.cxx.

References AW_widget_refresh_cb::aw, AW_WIDGET_CHOICE_MENU, AW_WIDGET_INPUT_FIELD, AW_WIDGET_LABEL_FIELD, AW_WIDGET_SCALER, AW_WIDGET_SELECTION_LIST, AW_WIDGET_TEXT_FIELD, AW_WIDGET_TOGGLE, AW_WIDGET_TOGGLE_FIELD, AW_widget_refresh_cb::awar, AW_widget_refresh_cb::cd, AW_root::changer_of_variable, NULp, AW_awar::read_as_string(), AW_window::refresh_option_menu(), AW_window::refresh_toggle_field(), AW_window::update_input_field(), AW_window::update_label(), AW_window::update_scaler(), AW_window::update_text_field(), AW_window::update_toggle(), AW_root::value_changed, AW_widget_refresh_cb::widget, and AW_widget_refresh_cb::widget_type.

Referenced by AW_widget_refresh_cb::AW_widget_refresh_cb(), and AW_widget_refresh_cb::~AW_widget_refresh_cb().

WRITE_SKELETON	(	write_string	,
		const char *	,
		"%s"	,
		GB_write_string
	)

GB_write_int WRITE_SKELETON	(	write_float	,
		float	,
		"%f"	,
		GB_write_float
	)

return GB_read_as_string

(

gb_var

)

static void AW_var_gbdata_callback ( GBDATA *  , AW_awar *  awar  )

static

Definition at line 268 of file AW_awar.cxx.

References AW_awar::update().

Referenced by AW_awar::map().

static void AW_var_gbdata_callback_delete_intern ( GBDATA *  gbd, AW_awar *  awar  )

static

Definition at line 273 of file AW_awar.cxx.

References aw_assert, AW_awar::gb_origin, AW_awar::gb_var, NULp, and AW_awar::update().

Referenced by AW_var_gbdata_callback_delete().

static void AW_var_gbdata_callback_delete ( GBDATA *  gbd, AW_awar *  awar  )

static

Definition at line 480 of file AW_awar.cxx.

References AW_var_gbdata_callback_delete_intern().

Referenced by AW_awar::map().

bool member_of_DB ( GBDATA *  gbd, GBDATA *  gb_main  )

inline

Definition at line 638 of file AW_awar.cxx.

References GB_get_root(), and gb_main.

Referenced by AW_awar::set_temp_if_is_default(), and AW_awar::unlink_from_DB().

Variable Documentation

GB_ERROR AW_MSG_UNMAPPED_AWAR

static

Initial value:

= "Error (unmapped AWAR):\n"
    "You cannot write to this field because it is either deleted or\n"
    "unmapped. Try to select a different item, reselect this and retry."

Definition at line 128 of file AW_awar.cxx.

long

Definition at line 152 of file AW_awar.cxx.

Referenced by aisc_broadcast(), aisc_get(), aisc_link(), aisc_talking(), aisc_talking_copy(), aisc_talking_create(), aisc_talking_find(), aisc_talking_get(), aisc_talking_init(), aisc_talking_sets(), alignToNextRelative(), SpecSetRegistry::allocate_bitstring(), an_get_prefix_hash(), ARB_main(), are_not_in_tree(), AW_awar::AW_awar(), aw_create_shell(), SpecSetRegistry::bitstring_longs(), cache_free_some_memory(), PH_filter::calculate_column_homology(), ED4_root::create_hierarchy(), ali_prealigner_mask::delete_expensive(), ED4_pfold_set_SAI(), Sondentopf::fill_Stat_Arrays(), find_gbdata_offset(), gb_read_bin_error(), gb_uncompress_bits(), gb_uncompress_huffmann(), gbcm_read_bin(), gbcm_write_bin(), gbcmc_unfold_list(), gbcms_talking_begin_transaction(), gbcms_talking_put_update(), gbcms_write_deleted(), gbcms_write_keys(), gbcms_write_updated(), gbs_numhash_index(), Sondentopf::gen_color_hash(), AW_awar::get(), get_cached_taxonomy(), PS_FileBuffer::get_long(), PS_FileBuffer::get_ulong(), getrel_GBDATA(), getSpeciesSortedByBadPositions(), getTrnsprob(), ALI_MAP::insert_marker(), ALI_PROFILE::is_in_helix(), ALI_PROFILE::is_outside_helix(), Structure3D::MapSaiToEcoliTemplate(), Structure3D::MapSearchStringsToEcoliTemplate(), GBS_strstruct::ncatPadded(), probe_design_event(), probe_design_send_data(), PH_display::resized(), sec2disp(), ALI_MAP::sequence(), sequence_is_partial(), ALI_MAP::sequence_without_inserts(), BasicStatus::set_gauge(), AW_selection_list::to_hash(), ED4_window::update_window_coords(), and ALI_PROFILE::w_binding().

li

Definition at line 152 of file AW_awar.cxx.

Referenced by Helpfile::extractInternalLinks(), and g_b_Consensus_add().

GB_write_int const char s

Definition at line 154 of file AW_awar.cxx.

Referenced by addSymParts(), ali_aligner_dellist_elem::ali_aligner_dellist_elem(), ALI_NORM_SEQUENCE::ALI_NORM_SEQUENCE(), Align(), AlignTwo(), AP_probe_design_event(), appendComment(), ARB_strlower(), ARB_strupper(), arb_trace_argv(), SimpleLocation::as_string(), aw_root_init_font(), awt_aps_text_changed(), awt_create_select_filter_window_aw_cb(), AWT_distance_meter::AWT_distance_meter(), balanc_(), balbak_(), bisect_(), bqr_(), ED4_SearchResults::buildColorString(), ST_Container::cache_Sonde(), cbabk2_(), cbal_(), cdiv_(), ChecksumCollector::checksum(), cinvit_(), colorDefChanged_callback(), GBL_streams::concatenated(), AP_STACK< AP_tree_nlen >::count_elements(), create_top_links(), createOriginRNS(), AW::crosspoint(), csroot_(), QUERY::DbQuery_update_list(), do_extract_words(), dumpSeqList(), ED4_CursorShape::ED4_CursorShape(), ED4_pfold_extend_nucleation_sites(), ED4_pfold_find_nucleation_sites(), ED4_pfold_resolve_overlaps(), encode_escaped_chars(), encodeEntities(), Helpfile::extractInternalLinks(), SEQIO::fgets_smartLF(), find_family(), firstChar(), freeBlock_(), g_b_Consensus_add(), g_b_Consensus_get_sequence(), gb_ascii_2_bin(), gb_bin_2_ascii(), gb_compress_bits(), gb_compress_huffmann(), GB_read_ints_pntr(), gb_recover_corrupt_file(), gb_uncompress_bits(), gb_uncompress_by_sequence(), gb_uncompress_huffmann(), GB_write_floats(), GB_write_ints(), gb_write_one_child(), GB_write_pntr(), gbl_and(), gbl_crop(), gbl_mid_streams(), gbl_not(), gbl_or(), gbs_compress_command(), GBS_string_matches(), GBT_splitNdestroy_string(), ED4_root::generate_window(), get_available_fontsizes(), get_design_hinfo(), TreeContainer::get_species_names(), getInt(), getSpeciesSortedByBadPositions(), getString(), getxnode(), TextRef::headTrimmed(), hqr2_(), hqr_(), htrib3_(), htribk_(), imtql1_(), imtql2_(), imtqlv_(), input_history_cb(), input_history_insert(), insert_species_into_tree(), invit_(), lookfont(), main(), AW_at_storage::make(), make_limit_string(), mark_action(), mark_referred_species(), mg_initialize_SAI_selectors(), mg_initialize_species_selectors(), minfit_(), MP_is_probe(), mutateRNS(), newIsland(), newMatrix(), newSpreading(), normalizeBaseFreqs(), normalizeRateParams(), nt_build_sai_string(), nt_species_join(), SQ_GroupData_Impl< 6 >::operator=(), parseCommandLine(), parsePosition(), pattern2str(), primer_design_event_go(), probe_design_event(), Sondentopf::put_Sonde(), pythag_(), qzhes_(), qzit_(), qzval_(), qzvec_(), ratqr_(), ArbImporter::read_data(), ArbImporter::read_line(), GBS_strstruct::release(), PartialSequence::release(), ED4_terminal::resolve_pointer_to_string_copy(), runtests(), save_search_paras_to_file(), ItemFieldShader::scan_value_range_cb(), QUERY::search_duplicated_field_content(), SearchTree::SearchTree(), searchWord(), shortenString(), SEC_root::split_loop(), SlaveCanvas_internal::store_positions_sorted(), str2pattern(), svd_(), swap_source_dest_cb(), TextRef::tailTrimmed(), tinvit_(), tql1_(), tql2_(), tqlrat_(), TranslateGeneToAminoAcidSequence(), trbak1_(), trbak3_(), tridib_(), trim(), tsturm_(), type2id(), SEC_root::unsplit_loop(), update_min_mutations(), updateScore(), updateTrnsprob(), uprootTree(), warnAboutDuplicate(), writeSeq(), Helpfile::writeXML(), and QUERY::DbQuery::~DbQuery().

GB_write_int const char GB_write_autoconv_string WRITE_SKELETON (write_pointer, GBDATA*, "%p", GB_write_pointer) char *AW_awa if)(!gb_var) return strdup("")

Definition at line 163 of file AW_awar.cxx.

Referenced by aisc_unlink(), AW_selection_list::delete_element_at(), AWT_graphic_tree::detect_group_state(), find_sub_by_quark(), find_sub_sub_by_quark(), gb_make_container(), gb_make_pre_defined_container(), gb_uncompress_huffmann(), gb_untouch_children(), gbcms_write_deleted(), ED4_manager::handle_move(), PS_print_and_evaluate_map(), AW_window::refresh_toggle_field(), List< Type >::remove_member_from_list(), AW_device::text_overlay(), GBL_IMPL::trace_params(), tree2newick(), ali_aligner_last_cell::update_left(), ali_aligner_last_cell::update_up(), and AWT_canvas::zoom().

GB_transaction ta(gb_var)

Referenced by ad_tree_set_security(), FINAL_TYPE< SEQTYPE >::addSequence(), adjustTreeRoot(), aed_start_naligning(), ali_checklen_cb(), ali_format_cb(), ALI_realign_marked(), alignment_vars_callback(), BranchWindow::analyseDistances(), announce_recording(), AP_create_consensus_var(), AP_create_pos_var_pars_window(), AP_tree_root::AP_tree_root(), ARB_main(), auto_select_pseudo_species(), AW_awar::AW_awar(), AW_DB_selection::AW_DB_selection(), AW_forget_all_window_geometry(), AW_reactivate_all_questions(), awar_updated_cb(), awt_create_CONFIG_selection_list(), awt_create_TREE_selection_list(), AWT_default_protein_type(), AWT_modify_managed_configs(), awtc_mark_hits(), awtc_nn_search(), AWTI_import_set_ali_and_type(), AP_sequence::bind_to_species(), BoundTreeAwarCallback::bind_tree_callback(), FieldSelDef::build_sel(), calc_and_update_alignment_errors_cb(), calc_pvp(), ST_ML::calc_st_ml(), ColumnStat::calculate(), calculate_clusters(), PH_filter::calculate_column_homology(), canvas_to_printer(), canvas_to_xfig(), FoundGroup::change_folding(), VarUpdateInfo::change_from_widget(), AWT_graphic_tree::check_for_DB_update(), AP_tree_root::check_update(), CheckedConsistencies::CheckedConsistencies(), ST_ML::clear_all(), clear_all_colors_cb(), clearMacroExecutionAuthorization(), clip_expose(), collectKeysRegisteredInDatabase(), colorize_marked_cb(), colorize_queried_cb(), colstat_2_gnuplot_cb(), COLSTAT_create_selection_window(), AP_tree::compute_tree(), CON_calc_max_freq(), CON_calculate_cb(), copy_move_del_alignment(), QUERY::copy_selection_list_2_query_box(), SEC_structure_toggler::copyTo(), ImportTestData::countSpeciesAndData(), create_consense_tree_cb(), ED4_root::create_hierarchy(), create_list_of_loaded_species(), create_loadsave_colored_window(), create_macro_variables(), create_mg_merge_tagged_fields_window(), create_primer_design_window(), create_probe_admin_window(), create_probe_design_window(), ColumnStat::create_sai_selection_list(), CreateRNA3DMainWindow(), createSaiProbeMatchWindow(), EXP_item_type_species_selector::current(), FINAL_TYPE< SEQTYPE >::current(), GEN_item_type_species_selector::current(), awt_string_handler::db_changed(), db_updated_cb(), delete_ali_cb(), GroupSearch::delete_found_groups(), FoundGroup::delete_from_DB(), delete_kept_ghostnodes(), TreeAdmin::delete_tree_cb(), ED4_manager::deleted_from_database(), di_calculate_compressed_matrix_cb(), di_calculate_matrix(), DI_create_matrix_variables(), di_mark_by_distance(), DI_timer(), PH_display::display(), AP_sequence::do_lazy_load(), dot_missing_bases(), ED4_text_terminal::draw(), ED4_compression_changed_cb(), ED4_create_consensus_awars(), ED4_create_NDS_awars(), ED4_CreateProteinViewer_window(), ED4_expose_cb(), ED4_get_and_jump_to_selected_SAI(), ED4_get_and_jump_to_species(), ED4_get_marked_from_menu(), ED4_helix_jump_opposite(), ED4_horizontal_change_cb(), ED4_input_cb(), ED4_jump_to_current_species(), ED4_mark_matching_species(), ED4_menu_highlight(), ED4_motion_cb(), ED4_pfold_select_SAI_and_update_option_menu(), ED4_pfold_set_SAI(), ED4_resize_cb(), ED4_restore_curpos(), ED4_scrollbar_change_cb(), ED4_set_protection(), ED4_store_curpos(), ED4_vertical_change_cb(), ed_submit_info_event(), edit_SAI_description(), AWT_configuration::erase_deleted_configs(), MacroRecorder::execute(), executeKeystroke(), expect_species_selected(), experiment_delete_cb(), export_go_cb(), export_nds_cb(), export_seq_data(), DI_MATRIX::extract_from_tree(), FastAligner_start(), field_convert_update_typesel_cb(), Itemfield_Selection::fill(), ALI_selection::fill(), AWT_tree_selection::fill(), SAI_selection::fill(), GroupBuilder::find_best_matching_subtree(), GroupSearch::fold_found_groups(), CheckedConsistencies::forgetDoneChecks(), GB_clear_macro_error(), GB_get_macro_error(), GB_set_macro_error(), GBT_compress_sequence_tree2(), GBT_config::GBT_config(), GBT_count_marked_species(), GBT_get_configuration_names(), GBT_open(), GDE_startaction_cb(), GEN_create_map(), GEN_gene_container_cb_installer(), GEN_root::GEN_root(), GEN_species_name_changed_cb(), GEN_update_GENE_CONTENT(), gene_delete_cb(), gene_extract_handler(), gene_rel_2_abs(), ArbParsimony::generate_tree(), probe_input_data::get_acc(), get_addid(), MutableBoundItemSel::get_any_item(), get_canvas_able_to_show(), probe_input_data::get_checksum(), AWT_configuration::get_config(), get_drawsize(), probe_input_data::get_fullname(), get_helix_string(), RegFieldSelection::get_keytype(), DbScanner::get_mapped_item_id(), ED4_base::get_name_of_species(), get_SAI_group(), get_SAI_groups(), InfoWindow::get_selected_item(), probe_input_data::get_shortname(), probe_input_data::get_start(), probe_input_data::get_stop(), GetDisplayInfo(), getKnownMacroClients(), group_and_refold_tree(), group_awar_changed_cb(), group_clusters(), AWT_graphic_tree::group_tree(), GS_calc_resulting_groupname(), GEN_graphic::handle_command(), AWT_graphic_tree::handle_command(), ED4_manager::handle_move(), ArbImporter::import_data(), GEN_map_window::init(), BI_helix::init(), BI_ecoli_ref::init(), ED4_root::init_alignment(), InsertDatainGDE(), AWT_canvas::instant_resize(), AP_tree_root::is_species_updated(), AP_tree_root::is_tree_updated(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), AP_tree::justify_branch_lenghs(), awt_input_handler::link_to(), DI_MATRIX::load(), load_and_add_tree(), PARSIMONY_testenv< SEQTYPE >::load_tree(), loadsave_colorset_cb(), main(), TreeAdmin::make_dest_treename_unique_cb(), AW_awar::make_global(), AW_awar::map(), DbScanner::Map(), map_extended(), map_SAI_to_scanner(), map_viewkeys(), mark_action(), mark_as_macro_executor(), mark_clusters(), 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_nontree_cb(), mark_organisms(), mark_organisms_with_marked_genes(), mark_referred_species(), GroupUIdata::mark_species(), mark_tree_cb(), BranchWindow::markDeepLeafs(), BranchWindow::markDegeneratedBranches(), BranchWindow::markLongBranches(), mg_get_selected_sai1(), mg_get_selected_sai2(), mg_get_selected_species1(), mg_get_selected_species2(), MG_map_species(), MG_transfer_tree(), MG_update_example(), modify_target_string(), modsai_cb(), MP_close_main(), MP_mark_probes_in_tree(), MP_normal_colors_in_tree(), MP_show_probes_in_tree(), NA_Alignment::NA_Alignment(), SEC_structure_toggler::name(), nds_create_vars(), nds_delete_database_entries(), nds_maintain_viewkeys(), nds_restore_config(), SEC_structure_toggler::next(), nt_add(), NT_alltree_remove_leafs(), NT_convert_gene_locations(), NT_create_alignment_vars(), NT_create_colstat_2_gnuplot_window(), NT_create_config_after_import(), nt_create_config_after_import(), nt_create_configuration(), NT_create_database_optimization_window(), NT_create_dna_2_pro_window(), NT_createConcatenationAwars(), NT_del_mark_move_REF(), nt_delete_configuration(), NT_delete_mark_all_cb(), NT_edit_bootstrap(), nt_extract_configuration(), NT_fix_dict_compress(), NT_fix_gene_data(), NT_format_all_alignments(), NT_import_sequences(), NT_jump_cb(), NT_justify_branch_lenghs(), NT_mark_all_cb(), NT_mark_duplicates(), NT_move_boot_branch(), NT_multifurcate_tree(), NT_pseudo_species_to_organism(), NT_remove_bootstrap(), NT_remove_leafs(), nt_rename_configuration(), NT_repair_DB(), NT_reset_branchlengths(), NT_reset_lzoom_cb(), NT_reset_pzoom_cb(), NT_resort_tree_cb(), NT_scale_tree(), NT_select_bottom_tree(), NT_undo_cb(), NT_with_displayed_tree_do(), pars_create_all_awars(), pars_generate_aliview(), pars_start_cb(), PARS_tree_init(), pd_export_pt_server(), CheckedConsistencies::perform_item_checks(), GroupSearch::perform_search(), PG_initSpeciesMaps(), PH_create_filter_variables(), PH_save_ml_cb(), PH_save_ml_multiline_cb(), popup_single_field_transfer_window(), predef_prg(), probe_input_data::preload_rel2abs(), primer_design_event_go(), primer_design_event_init(), probe_design_event(), propertyName(), PS_get_probe_for_path(), pt_init_main_struct(), PV_AddOrfTerminalsToLoadedSpecies(), PV_CreateAllTerminals(), PV_DisplayAminoAcidNames(), PV_ManageTerminals(), PV_SequenceUpdate_CB(), PVP_calculate(), query_count_items(), react_to_command(), AW_awar::read_char_pntr(), AW_awar::read_float(), AW_awar::read_int(), AW_awar::read_pointer(), AW_awar::read_string(), realign_event(), GroupUIdata::refill_result_list(), ImportTestData::refill_species_list(), ED4_root::refresh_all_windows(), RefEntries::refresh_result_cb(), ColumnStat::refresh_sai_selection_list(), CheckedConsistencies::register_as_performed(), RegFieldSelection::registrate(), GEN_graphic::reinit_gen_root(), AP_tree::relink(), AP_tree::relink_tree(), ImportTestData::remap_scanner(), SEC_structure_toggler::remove(), remove_from_consensus(), ED4_root::remove_from_highlighted(), AP_tree_root::remove_leafs(), FoundGroup::rename_by_ACI(), GroupSearch::rename_found_groups(), reorder_configs_cb(), reorder_trees_cb(), rerun_importTest_cb(), ED4_terminal::resolve_pointer_to_char_pntr(), RulerScaler::RulerScaler(), Aligner::run(), run_command(), run_server(), SaiCalculator::SaiCalculator(), saiChanged_callback(), DI_MATRIX::save(), AWT_graphic_tree::save_to_DB(), save_tree_as_newick(), ItemFieldShader::scan_value_range_cb(), ExportFieldScanner::scanFields(), SearchTree::SearchTree(), SEC_db_interface::SEC_db_interface(), SEC_structure_toggler::SEC_structure_toggler(), select_cluster_cb(), select_named_sequence_terminal(), select_representative(), server_main_loop(), AWT_configuration::set_config(), set_keep_ghostnodes(), BoundActionTracker::set_recording(), set_SAI_group(), AW_awar::set_temp_if_is_default(), ED4_cursor::set_to_terminal(), SEC_structure_toggler::setName(), ED4_cursor::show_cursor_at(), AWT_graphic_tree::show_ruler(), sort_tree_by_other_tree(), species_copy_cb(), species_delete_cb(), species_rename_cb(), species_rename_handler(), split_alignment(), sq_calc_seq_quality_cb(), SQ_remove_quality_entries(), st_check_cb(), st_remove_entries(), toggle_flag_cb(), toggle_helix_for_SAI(), toggle_mark_of_specData(), AW_awar::touch(), track_ali_change_cb(), trackAlignmentChanges(), TREE_load_to_db(), tree_vars_callback(), TREE_write_Newick(), TREE_write_XML(), AW_root::unlink_awars_from_DB(), update_colorset_selection_list(), update_default_treename_cb(), update_exportTest_result_cb(), GroupBuilder::update_group(), update_RangeList(), AP_tree_root::update_timers(), user_code_nr_changed_cb(), valid_alignment_selected(), RefEntries::ReferringEntriesHandler::with_all_referred_items(), AW_DB_selection::~AW_DB_selection(), and FieldTransfer::ItemClonedByRuleSet::~ItemClonedByRuleSet().