#include <arb_msg_fwd.h>
#include "arb_msg_nospam.h"
#include <arb_string.h>
#include <arb_backtrace.h>
#include <smartptr.h>
#include <arb_handlers.h>
#include <arb_defs.h>
#include "arb_strbuf.h"

Include dependency graph for arb_msg.cxx:

Classes
class	GlobalStringBuffers

Macros
#define	GLOBAL_STRING_BUFFERS 4

#define	GBS_GLOBAL_STRING_SIZE 64000

#define	PRINT2BUFFER(buffer, bufsize, templat, parg) vsprintf(buffer, templat, parg)

#define	PRINT2BUFFER_CHECKED(printed, buffer, bufsize, templat, parg)

#define	BUFSIZE 1000

Functions
GlobalStringBuffers *	GBS_store_global_buffers ()

void	GBS_restore_global_buffers (GlobalStringBuffers *saved)

const char *	GBS_vglobal_string (const char *templat, va_list parg)

char *	GBS_vglobal_string_copy (const char *templat, va_list parg)

const char *	GBS_global_string_to_buffer (char buffer, size_t bufsize, const char templat,...)

char *	GBS_global_string_copy (const char *templat,...)

const char *	GBS_global_string (const char *templat,...)

const char *	GBS_static_string (const char *str)

GB_ERROR	GBK_assert_msg (const char assertion, const char file, int linenr)

GB_ERROR	GB_export_error (const char *error)

GB_ERROR	GB_export_errorf (const char *templat,...)

GB_ERROR	GB_IO_error (const char action, const char filename)

GB_ERROR	GB_export_IO_error (const char action, const char filename)

GB_ERROR	GB_print_error ()

GB_ERROR	GB_get_error ()

bool	GB_have_error ()

GB_ERROR	GB_await_error ()

void	GB_clear_error ()

GB_ERROR	GB_failedTo_error (const char do_something, const char special, GB_ERROR error)

GB_ERROR	GB_append_exportedError (GB_ERROR error)

class BackTraceInfo *	GBK_get_backtrace (size_t skipFramesAtBottom)

void	GBK_dump_former_backtrace (class BackTraceInfo trace, FILE out, const char *message)

void	GBK_free_backtrace (class BackTraceInfo *trace)

void	GBK_dump_backtrace (FILE out, const char message)

void	GB_internal_error (const char *message)

void	GB_internal_errorf (const char *templat,...)

void	GBK_terminate (const char *error)

void	GBK_terminatef (const char *templat,...)

void	GB_warning (const char *message)

void	GB_warningf (const char *templat,...)

void	GB_warning_if (const char *message)

void	GB_information (const char *message)

void	GB_informationf (const char *templat,...)

void	GBS_reuse_buffer (const char *global_buffer)

GB_ERROR	GBK_system (const char *system_command)

char *	GBK_singlequote (const char *arg)

char *	GBK_doublequote (const char *arg)

Variables
static size_t	last_global_string_size = 0

static GlobalStringBuffers	globBuf

static char *	GB_error_buffer = NULp

Macro Definition Documentation

#define GLOBAL_STRING_BUFFERS 4

Definition at line 41 of file arb_msg.cxx.

Referenced by GlobalStringBuffers::GlobalStringBuffers().

#define GBS_GLOBAL_STRING_SIZE 64000

Definition at line 44 of file arb_msg.cxx.

Referenced by GB_export_errorf().

#define PRINT2BUFFER	(	buffer,
		bufsize,
		templat,
		parg
	)	vsprintf(buffer, templat, parg)

Definition at line 55 of file arb_msg.cxx.

#define PRINT2BUFFER_CHECKED	(	printed,
		buffer,
		bufsize,
		templat,
		parg
	)

Value:

(printed) = PRINT2BUFFER(buffer, bufsize, templat, parg);           \
    if ((printed) < 0 || (size_t)(printed) >= (bufsize)) {              \
        GBK_terminatef("Internal buffer overflow (size=%zu, used=%i)\n", \
                       (bufsize), (printed));                           \
    }

Definition at line 58 of file arb_msg.cxx.

Referenced by GBS_global_string_to_buffer().

#define BUFSIZE 1000

Referenced by GBK_assert_msg().

Function Documentation

GlobalStringBuffers* GBS_store_global_buffers ( void )

Definition at line 156 of file arb_msg.cxx.

References GlobalStringBuffers::GlobalStringBuffers(), and globBuf.

void GBS_restore_global_buffers ( GlobalStringBuffers * saved )

Definition at line 162 of file arb_msg.cxx.

References globBuf.

const char* GBS_vglobal_string	(	const char *	templat,
		va_list	parg
	)

Definition at line 167 of file arb_msg.cxx.

References globBuf.

char* GBS_vglobal_string_copy	(	const char *	templat,
		va_list	parg
	)

Definition at line 172 of file arb_msg.cxx.

References ARB_strduplen(), and globBuf.

Referenced by GBS_global_string_copy().

const char* GBS_global_string_to_buffer	(	char *	buffer,
		size_t	bufsize,
		const char *	templat,
			...
	)

Definition at line 178 of file arb_msg.cxx.

References arb_assert, GlobalStringBuffers::parg, PRINT2BUFFER_CHECKED, va_end(), and va_start().

Referenced by aw_help_show_external_format(), GB_append_suffix(), GB_concat_path(), GBK_assert_msg(), group_species(), and AW_window::window_local_awarname().

char* GBS_global_string_copy	(	const char *	templat,
			...
	)

Definition at line 194 of file arb_msg.cxx.

References GBS_vglobal_string_copy(), GlobalStringBuffers::parg, result, va_end(), and va_start().

Referenced by TreeReader::add_warning(), ALI_translate_marked(), appendNameAndUsedBasePositions(), SEQIO::appendTo(), apply_ACI(), apply_auto_numeric_binop(), apply_double_binop(), apply_numeric_binop(), ARB_main(), arb_start_server(), ARB_textfiles_have_difflines(), arb_trace_argv(), ARB_zfopen(), AW_advice(), AW_edit(), AW_get_selected_fullname(), aw_help_back(), aw_help_helpfile_changed_cb(), aw_help_search(), aw_help_show_external_format(), aw_insert_message_in_tmp_message_delayed(), aw_install_xkeys(), AW_label_in_awar_list(), aw_message_save_cb(), AW_openURL(), aw_question(), aw_ref_to_title(), aw_root_init_font(), awar_matrix_cell(), awar_translate(), aws_init_localized(), awt_add_sequences_to_list(), awt_aps_go(), awt_create_input_mask(), awt_create_load_box(), AWT_create_mask_submenu(), awt_create_PTSERVER_selection_button(), awt_create_select_filter_win(), AWT_get_combined_filter_name(), awtc_move_hits(), awtc_remove_arb_acc(), binop_compare(), binop_contains(), binop_equals(), build_taxonomy_rek(), buildAllowedValuesString(), change_constraints(), check_and_correct_current_field(), colstat_2_gnuplot_cb(), CommandOutput::CommandOutput(), compress_sequence_tree(), concatenateAlignments(), concatenateFieldsCreateNewSpecies(), copy_field_into_partial_alignments(), AW_window::create_button(), create_calltexe_window(), create_color_button(), create_colorize_window(), create_colorset_representation(), create_config_manager_window(), create_font_button(), AW_window::create_input_field(), create_load_box_for_selection_lists(), create_loadsave_colored_window(), create_mark_menu_entry(), create_mark_menu_id(), create_modify_fields_window(), QUERY::create_query_box(), create_save_box_for_selection_lists(), create_split_gene(), create_tree_name(), createCallOnSocketHost(), createMergeSimilarSpeciesWindow(), Data::Data(), dated_info(), QUERY::DbQuery_update_list(), detect_sina_version(), ArbImporter::detectAvailableFields(), dump_internal(), dumpStreams(), ED4_get_NDS_text(), ed_submit_parse_event(), enter_stage_1_build_tree(), EXP_get_experiment_id(), expandSetVariables(), export_format_single(), export_to_DB(), export_tree_node_print(), export_tree_node_print_xml(), File_selection::fill(), EDB_root_bact::fill_species(), filter_posvar_SAI_for_ali(), SpecSetRegistry::find_best_matches_info(), find_macro_in(), format(), GB_find_all_files(), GB_find_executable(), GB_follow_unix_link(), gb_full_path(), GB_get_arb_revision_tag(), GB_get_callback_info(), GB_get_db_path(), GB_getenvARB_XCMD(), GB_install_pid(), GB_internal_error(), GB_read_as_string(), GB_symlink(), GB_TYPES_2_name(), GB_unique_filename(), GBP_add_callback(), gbp_create_callback_hashkey(), GBS_nameserver_tag(), GBS_ptserver_id_to_choice(), GBS_read_arb_tcp(), GBS_read_dir(), GBT_add_alignment_changekeys(), GBT_commit_rename_session(), GBT_create_alignment(), GBT_get_configuration_names(), GBT_macro_execute(), gbt_nonexisting_alignment(), gcman_specific_awarname(), gde_filter_weights(), GDE_makeawarname_in(), GDE_menuitem_cb(), GDE_startaction_cb(), gen_display(), gen_extract_gene_2_pseudoSpecies(), gen_get_gene_id(), GEN_global_gene_identifier(), GEN_root::GEN_root(), RefEntries::generate_item_error(), ED4_root::generate_window(), get_alitype_eval(), get_design_hinfo(), DisplayFormat::get_format(), get_full_qualified_help_file_name(), TypedDatabaseCallback::get_info(), get_local_help_url(), get_overlay_files(), RefEntries::RefSelector::get_refs(), DistanceCounter::get_report(), get_SAI_description(), export_sequence_data::get_seq_data(), get_shared_sellist_awar_base(), get_shared_sellist_awar_name(), get_short(), GroupFoldedKey::get_target_data(), GroupAIDkey::get_target_data(), GroupSizeKey::get_target_data(), GroupKeeledKey::get_target_data(), GroupZombiesKey::get_target_data(), GroupMarkedKey::get_target_data(), NestingLevelKey::get_target_data(), get_taxonomy_string(), ConsensusTreeBuilder::get_tree_remark(), getenv_autodirectory(), getenv_executable(), getenv_existing_directory(), GEN_map_window::init(), DBUI::init_info_window(), init_itemType_specific_window(), BI_helix::initFromData(), insert_genes_of_organism(), insert_section_header(), load_cb(), AW_window::local_id(), lookfont(), main(), make_async_call(), test_runtool::make_checked_piped_command(), make_limit_string(), makeTitle(), maxCompressionSteps(), mg_check_field_cb(), MG_exit(), MG_save_cb(), MG_update_example(), MP_Comment(), MP_new_sequence(), NameInformation::NameInformation(), NDS_create_window(), nds_restore_config(), ArbImporter::next_file(), GBT_config_parser::nextItem(), nt_create_config_after_import(), NT_create_sai_from_pfold(), NT_create_syncScroll_window(), nt_disconnect_from_db(), NT_fix_dict_compress(), NT_format_all_alignments(), nt_intro_start_merge(), NT_jump_cb(), NT_move_boot_branch(), NT_save_as_cb(), NT_start(), NTREE_move_tree_info(), pars_start_cb(), parse_helix_list(), pd_export_pt_server(), AWT_configuration::popup_edit_window(), popup_new_main_window(), predef_prg(), printFile(), ProbeMatchParser::ProbeMatchParser(), PT_dump_POS_TREE_recursive(), PT_prepare_data(), PV_SaveData(), PV_WriteTranslatedSequenceToDB(), query_rel_menu_entry(), quoted_if_containing_separator(), ArbImporter::read_data(), read_import_format(), readableItemname(), readXmlTree(), RecordingMacro::RecordingMacro(), remove_redundant_translation(), run_command(), save_cb(), save_search_paras_to_file(), ExportFieldScanner::scanFields(), QUERY::search_duplicated_field_content(), selectMnemonic(), TreeNode::set_bootstrap(), set_empty_addids(), BasicStatus::set_subtitle(), ACI_Labeler::speciesLabel(), split_alignment(), standard_list2file(), start_macro_cb(), start_pt_server(), string2enum_or_die(), FunInfo::switch_to(), target_ali_name(), trackAlignmentChanges(), AliAdmin::window_init(), NodeTextBuilder::work(), SpecSetRegistry::write_node_information(), and writeHistory().

const char* GBS_global_string	(	const char *	templat,
			...
	)

Definition at line 203 of file arb_msg.cxx.

const char* GBS_static_string ( const char * str )

GB_ERROR GBK_assert_msg	(	const char *	assertion,
		const char *	file,
		int	linenr
	)

Definition at line 216 of file arb_msg.cxx.

References ARB_alloc(), BUFSIZE, GBS_global_string_to_buffer(), last_global_string_size, NULp, and result.

GB_ERROR GB_export_error ( const char * error )

Definition at line 257 of file arb_msg.cxx.

References arb_assert, and GB_export_errorf().

Referenced by colorize_marked_cb(), colorize_queried_cb(), compress_sequence_tree(), create_gene_species(), ED4_pfold_calculate_secstruct_match(), ED4_show_protein_match_on_device(), EXP_get_first_experiment_data(), expandSetVariables(), find_sub_sub_by_quark(), findOrCreate_configuration(), gb_build_uncompress_tree(), GB_canonical_path(), gb_check_huffmann_tree(), GB_clone(), gb_clone_explicit(), GB_command_interpreter_in_env(), gb_copy_explicit(), GB_create(), GB_create_container(), GB_export_IO_error(), GB_fopen_tempfile(), GB_get_dictionary(), gb_is_valid_mapfile(), gb_load_dictionary_data(), GB_login(), GB_map_FILE(), gb_read_bin(), gb_read_bin_rek_V2(), GB_read_file(), GB_read_old_size(), GB_read_old_value(), gb_recover_corrupt_file(), gb_resort_system_folder_to_top(), gb_save_dictionary_data(), gb_search(), GB_searchOrCreate_float(), GB_searchOrCreate_int(), GB_searchOrCreate_string(), GB_size_of_FILE(), gb_uncompress_by_dictionary(), gb_uncompress_data(), GB_undo_info(), GB_unlink(), gbcmc_close(), GBCMC_find(), gbcmc_key_alloc(), gbcmc_send_undo_info_commands(), gbl_read_seq_sai_or_species(), GBS_compile_matcher(), GBS_eval_env(), GBS_get_arb_tcp_entries(), GBS_modify_tagged_string_with_ACI(), GBS_read_arb_tcp(), GBS_string_eval_in_env(), GBT_add_data(), GBT_create(), GBT_create_sequence_data(), GBT_gen_accession_number(), GBT_get_alignment(), GBT_is_partial(), GBT_open(), GEN_create_nonexisting_gene_rel_gene_data(), GEN_find_or_create_gene_rel_gene_data(), GEN_get_first_gene_data(), GEN_read_position(), get_default_alignment(), get_local_help_url(), RefEntries::RefSelector::get_refs(), main(), FilterDefinition::make_filter(), MG_equal_alignments(), PG_initSpeciesMaps(), prepare_and_get_selected_itemfield(), DI_MATRIX::save(), ACI_Labeler::speciesLabel(), TREE_export_tree(), and undo_entry().

GB_ERROR GB_export_errorf	(	const char *	templat,
			...
	)

Definition at line 262 of file arb_msg.cxx.

References GB_error_buffer, GBS_GLOBAL_STRING_SIZE, GlobalStringBuffers::parg, and va_start().

Referenced by apply_ACI(), arb_shell_expand(), arb_start_server(), AWTC_generate_one_name(), AWTC_makeUniqueShortName(), colstat_2_gnuplot_cb(), concatenateFieldsCreateNewSpecies(), count_bases(), createDataFromConsensus(), expect_entry(), experiment_copy_handler(), experiment_rename_handler(), export_structure_to_file(), find_or_create(), fullMacroname(), GB_canonical_path(), gb_clone_explicit(), gb_copy_explicit(), GB_create(), gb_expect_type(), GB_export_error(), GB_is_dictionary_compressed(), GB_map_FILE(), GB_map_file(), gb_read_bin_error(), gb_recover_corrupt_file(), GB_release(), gb_search(), GB_set_undo_mem(), gbcm_logout(), GBCMC_find(), gbcms_talking_begin_transaction(), gbcms_talking_find(), gbcms_talking_init_transaction(), GBS_read_dir(), GBT_create_alignment(), GBT_expect_item_rel_item_data(), GBT_find_or_create_item_rel_item_data(), GBT_get_alignment(), GBT_get_alignment_len(), GBT_get_alignment_type_string(), GBT_read_gene_sequence_and_length(), GBT_read_tree_and_size(), GBT_searchOrCreate_itemfield_according_to_changekey(), GBT_tree_info_string(), gen_extract_gene_2_pseudoSpecies(), GEN_organism_not_found(), GEN_species_add_entry(), get_default_alignment(), import_structure_from_file(), MG_equal_alignments(), MG_update_example(), nds_restore_config(), NTREE_move_tree_info(), SpeciesFlag::prepare_itemfield(), primer_design_event_init(), probe_design_event(), ArbImporter::read_data(), ED4_seq_colors::reload(), split_stat_filename(), GBL_IMPL::trace_params(), TranslateGeneToAminoAcidSequence(), TREE_load(), and TREE_write_XML().

GB_ERROR GB_IO_error	(	const char *	action,
		const char *	filename
	)

creates error message from current 'errno'

Parameters

action	may be NULp (otherwise it should contain sth like "writing" or "deleting")
filename	may be NULp (otherwise it should contain the filename, the IO-Error occurred for)

Returns: error message (in static buffer)

Definition at line 285 of file arb_msg.cxx.

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

Referenced by ARB_main(), ARB_zfclose(), ARB_zfopen(), TrackedFiles::check_changes(), detect_bitmap_size(), ed_save_var_to_file(), enter_stage_2_load_tree(), exit_remove_file(), export_format_single(), export_seq_data(), ArbDBWriter::finishSave(), GB_copy_file(), GB_create_directory(), GB_export_IO_error(), GB_fopen_tempfile(), gb_is_valid_mapfile(), GB_move_file(), GB_read_file(), gb_save_mapfile(), GB_set_mode_of_file(), GB_set_time_of_file(), GB_symlink(), GB_unlink(), GBK_system(), get_file_content_for_viewer(), StorableSelectionList::load(), FieldTransfer::RuleSet::loadFrom(), NTREE_move_tree_info(), PT_dump_POS_TREE_to_file(), PTD_write_chain_to_disk(), read_export_format(), read_import_format(), ReadGen(), RecordingMacro::RecordingMacro(), FileContent::save(), StorableSelectionList::save(), AWT_configuration::Save(), save_messagebox_content_to(), FieldTransfer::RuleSet::saveTo(), server_save(), start_pt_server(), and Mutex::~Mutex().

GB_ERROR GB_export_IO_error	(	const char *	action,
		const char *	filename
	)

Definition at line 318 of file arb_msg.cxx.

References GB_export_error(), and GB_IO_error().

Referenced by aw_help_search(), canvas_to_printer(), createCommentSkippingFileBuffer(), createFileBuffer(), and read_import_format().

GB_ERROR GB_print_error ( void )

Definition at line 324 of file arb_msg.cxx.

References fflush(), and GB_error_buffer.

Referenced by ALI_translate_marked(), ARB_main(), arb_prm_read(), gb_is_valid_mapfile(), GB_login(), gb_read_bin_error(), gb_unfold(), gbcms_talking_begin_transaction(), gbcms_talking_find(), gbcms_talking_init_transaction(), and ALI_ARBDB::open().

GB_ERROR GB_get_error ( void )

Definition at line 333 of file arb_msg.cxx.

References GB_error_buffer.

Referenced by GB_command_interpreter_in_env(), get_overlay_files(), SQ_evaluate(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass2(), and SQ_pass2_no_tree().

bool GB_have_error ( void )

Definition at line 338 of file arb_msg.cxx.

References GB_error_buffer.

Referenced by after_callback_guard(), alignment_vars_callback(), arb_look_and_start_server(), awt_create_PTSERVER_selection_button(), AWT_install_cb_guards(), before_callback_guard(), calc_and_update_alignment_errors_cb(), Candidate::Candidate(), check_for_remote_command(), CON_calc_max_freq(), NameServerConnection::connect(), copy_move_del_alignment(), copy_rename_handler(), WeightedFilter::create_aliview(), dump_internal(), edit_SAI_description(), SEQIO::export_by_format(), export_go_cb(), FastAligner_start(), File_selection::File_selection(), find_or_create(), find_SAI_candidates(), find_species_candidates(), fullMacroname(), GB_append_exportedError(), GB_clone(), gb_clone_explicit(), GB_command_interpreter_in_env(), GB_create(), GB_create_container(), GB_incur_error(), GB_incur_error_if(), GB_read_lossless_byte(), GB_read_lossless_float(), GB_read_lossless_int(), gb_search(), GB_searchOrCreate_float(), GB_searchOrCreate_int(), GB_searchOrCreate_string(), gbs_build_replace_string(), GBS_read_dir(), GBT_create(), GBT_expect_item_rel_item_data(), GBT_find_or_create(), GBT_get_alignment(), GBT_get_alignment_len(), GBT_get_alignment_type_string(), GBT_load_colorset(), GBT_log_to_tree_remark(), GBT_open(), GBT_searchOrCreate_itemfield_according_to_changekey(), gbt_write_tree_nodes(), GDE_startaction_cb(), gene_create_cb(), get_default_alignment(), FINAL_TYPE< SEQTYPE >::get_target_data(), GetDisplayInfo(), ArbImporter::import_data(), LoadMenus(), modsai_cb(), no_files_found_error(), pars_check_size(), prepare_and_get_selected_itemfield(), PV_WriteTranslatedSequenceToDB(), ArbImporter::read_data(), FieldTransfer::ReadRule::readFrom(), remote_command_handler(), ExportFieldScanner::scanFields(), SequenceHandler::SequenceHandler(), FieldTransfer::Rule::transferBy(), FieldTransfer::RuleSet::transferBy(), TranslateGeneToAminoAcidSequence(), update_RangeList(), and NodeTextBuilder::work().

GB_ERROR GB_await_error ( void )

Definition at line 342 of file arb_msg.cxx.

References arb_assert, GB_error_buffer, and NULp.

Referenced by PlugIn::activate(), ad_move_tree_info(), adaptCopiedAlignment(), FilteredExport::add_SAI_filter(), FINAL_TYPE< SEQTYPE >::addSequence(), after_callback_guard(), ALI_translate_marked(), alignCompactedTo(), announce_recording(), AP_calc_pos_var_pars(), SaiAciApplicator::apply(), TreeNode::apply_aci_to_remarks(), apply_filters(), apply_to_origin(), applyToItemFoundByKey(), arb_look_and_kill_server(), arb_look_and_start_ptserver(), arb_look_and_start_server(), ARB_main(), arb_start_server(), aw_help_browse(), aw_help_helpfile_changed_cb(), aw_help_search(), AW_select_nameserver(), awt_aps_go(), awt_open_ACI_URL_with_item(), AWT_show_file(), awtc_nn_search_all_listed(), AWTC_pars_names(), AWTC_recreate_name(), before_callback_guard(), build_consensus_tree(), calc_and_update_alignment_errors_cb(), calc_pvp(), ST_ML::calc_st_ml(), FieldReader::calc_value(), ColumnStat::calculate(), calculateEndPosition(), canvas_to_printer(), colstat_2_gnuplot_cb(), CommandOutput::CommandOutput(), compress_sequence_tree(), CON_calc_max_freq(), CON_calc_max_freq_cb(), CON_calculate(), concatenateAlignments(), concatenateFieldsCreateNewSpecies(), config_rename_handler(), NameServerConnection::connect(), copy_move_del_alignment(), copy_SAI_cb(), copy_SAI_to_species_cb(), copy_tree_container(), SequenceHandler::create(), create_ali_handler(), create_ali_intEntry(), create_ali_strEntry(), create_concatInfo_SAI(), create_consense_tree_cb(), create_data_entry(), create_gene_species(), create_genelike_entry(), create_macro_variables(), create_new_species(), create_split_gene(), createCommentSkippingFileBuffer(), createFileBuffer(), Data::Data(), DBerror::DBerror(), EntryRemover::del_unwanted_entries(), delete_macro_cb(), deleteRuleset_cb(), deleteSuperfluousQuicksaves(), di_calculate_compressed_matrix_cb(), DI_create_matrix_variables(), AP_sequence::do_lazy_load(), dot_missing_bases(), dot_sequence_by_consensus(), dump_internal(), ED4_get_NDS_text(), ed_submit_info_event(), ed_submit_parse_event(), edit_SAI_description(), ensure_trees_have_order(), enter_stage_1_build_tree(), MacroRecorder::execute(), experiment_copy_handler(), experiment_create_handler(), experiment_rename_handler(), export_format_single(), export_newick(), export_seq_data(), export_species_using_form(), export_to_DB(), extended_rename_handler(), DI_MATRIX::extract_from_tree(), FastAligner_start(), Itemfield_Selection::fill(), AWT_tree_selection::fill(), PT_selection::fill(), find_SAI_candidates(), find_species_candidates(), findAffectedKeys(), Structure3D::FindTypeOfRNA(), FINAL_TYPE< SEQTYPE >::finish(), flush_taxonomy_cb(), g_bs_convert_string_to_tagged_hash_with_rewrite(), GB_append_exportedError(), gb_clone_explicit(), GB_close(), gb_convert_compression(), gb_create_key(), GB_delete_database(), GB_get_macro_error(), GB_incur_error(), GB_install_pid(), gb_load_key_data_and_dictionaries(), GB_login(), gb_parse_ascii_rek(), gb_read_bin(), gb_recover_corrupt_file(), GB_searchOrCreate_float(), GB_searchOrCreate_int(), GB_searchOrCreate_string(), gb_uncompress_by_sequence(), gb_uncompress_data(), GB_unlink_or_warn(), GBC_await_error(), gbcm_open_socket(), gbcms_sighup(), gbl_ali_name(), gbl_apply_binary_operator(), gbl_command(), gbl_do(), gbl_eval(), gbl_exec(), gbl_read_seq_sai_or_species(), gbl_select(), gbl_sequence(), gbl_sequence_type(), gbl_srt(), gbs_build_replace_string(), GBT_add_new_changekey_to_keypath(), GBT_commit_rename_session(), GBT_compress_sequence_tree2(), GBT_config::GBT_config(), GBT_convert_changekey(), GBT_create_alignment(), GBT_find_or_create_item_rel_item_data(), GBT_load_colorset(), GBT_log_to_tree_remark(), GBT_macro_execute(), GBT_message(), GBT_read_gene_sequence_and_length(), gbt_read_tree_rek(), gbt_rename_alignment_of_item(), GBT_set_alignment_len(), GBT_set_startup_alignment(), 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_create_nonexisting_gene_rel_gene_data(), gen_extract_gene_2_pseudoSpecies(), GEN_is_genome_db(), GEN_make_node_text_nds(), GEN_root::GEN_root(), GEN_species_add_entry(), GEN_update_GENE_CONTENT(), GEN_write_position(), gene_copy_handler(), gene_create_cb(), gene_extract_handler(), gene_rename_handler(), get_cached_taxonomy(), get_DB_state(), FINAL_TYPE< SEQTYPE >::get_target_data(), GetDisplayInfo(), group_set_folded(), GS_calc_resulting_groupname(), FormatTester::handle_action_cb(), ArbImporter::import_data(), GBENTRY::index_check_out(), BI_helix::init(), BI_ecoli_ref::init(), probe_input_data::init(), ED4_root::init_alignment(), init_data(), init_tmp_branch(), insert_genes_of_organism(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), jobLabel(), AWT_configuration::Load(), load_and_add_tree(), load_and_startup_main_window(), ARB_seqtree_root::loadFromDB(), loadsave_colorset_cb(), main(), FilterDefinition::make_filter(), AW_awar::make_global(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), mark_action(), mark_gene_species_using_current_alignment(), mark_nontree_cb(), mark_tree_cb(), MERGE_sequences_simple(), mergeSimilarSpecies(), mg_check_field_cb(), MG_copy_and_check_alignments(), MG_create_db_dependent_rename_awars(), MG_create_field_content(), MG_merge_tagged_field_cb(), MG_transfer_extended(), MG_transfer_fields_info(), MG_transfer_one_species(), modify_fields_of_queried_cb(), modify_target_string(), modsai_cb(), move_species_to_extended(), SEC_structure_toggler::name(), nds_delete_database_entries(), nds_maintain_viewkeys(), ArbImporter::next_file(), no_files_found_error(), nt_add_partial(), nt_best_partial_match_rec(), NT_convert_gene_locations(), NT_count_different_chars(), NT_create_sai_from_pfold(), NT_createConcatenationAwars(), NT_del_mark_move_REF(), NT_import_sequences(), NT_importValidNames(), NT_mark_all_cb(), nt_species_join(), NT_suggestValidNames(), AP_main::open(), PH_root::open(), SelectedDatabase::open_db_for_merge(), parseCSV(), pd_export_pt_server(), pd_get_the_gene_names(), pd_get_the_names(), pd_kill_pt_server(), pd_query_pt_server(), PH_create_filter_variables(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), PosGene::PosGene(), preCreateTempfile(), predef_prg(), primer_design_event_go(), primer_design_event_init(), probe_design_event(), probe_match_event(), probe_read_data_base(), propertyName(), PT_prepare_data(), PT_prepare_species_sequence(), PTD_read_leafs_from_disk(), PV_WriteTranslatedSequenceToDB(), PVP_calculate(), react_to_command(), ArbImporter::read_data(), read_export_format(), read_tree_and_size_internal(), FieldTransfer::ReadRule::readFrom(), RecordingMacro::RecordingMacro(), RefEntries::refresh_result_cb(), CheckedConsistencies::register_as_performed(), resolve_IUPAC_target_string(), resort_data_base(), run_command(), run_server(), AP_pos_var::save_aliEntry_to_SAI(), GB_MAIN_TYPE::save_quick_as(), save_tree_as_newick(), GBT_config::saveAsOver(), scan_gene_positions(), ItemFieldShader::scan_value_range_cb(), SEC_structure_toggler::SEC_structure_toggler(), SequenceHandler::SequenceHandler(), AWT_configuration::set_config(), set_DB_state(), set_field_of_queried_cb(), set_intEntry_to(), BoundActionTracker::set_recording(), set_tree_idx(), setIntEntryToZero(), sina_start(), sort_tree_by_other_tree(), species_copy_cb(), species_create_handler(), ACI_Labeler::speciesLabel(), split_ali_cb(), split_alignment(), split_data_into_parts(), sq_calc_seq_quality_cb(), st_check_cb(), st_ml_add_quality_string_to_species(), start_remote_command_for_application(), StaticData::track_ali(), track_ali_change_cb(), trackAlignmentChanges(), transfer_field_of_listed_cb(), transfer_single_field(), transfer_tree(), translate_gene_sequence(), TranslateGeneToAminoAcidSequence(), translateSAItoColors(), TreeAdmin::tree_append_remark(), TREE_load_to_db(), tree_write_float(), TREE_write_Newick(), TREE_write_XML(), AW_awar::update(), GroupBuilder::update_group(), update_RangeList(), NodeTextBuilder::work(), FilteredExport::write_fasta(), SpecSetRegistry::write_node_information(), FieldTransfer::WriteRule::writeTo(), and writeToArb().

void GB_clear_error ( void )

Definition at line 354 of file arb_msg.cxx.

Referenced by ALI_translate_marked(), alignment_vars_callback(), AP_create_consensus_var(), aw_ref_to_title(), awt_create_select_filter_window_aw_cb(), awt_get_filter(), AWTI_import_set_ali_and_type(), ED4_terminal::changed_by_database(), check_socket_available(), colstat_2_gnuplot_cb(), colstat_ali_changed_cb(), compress_sequence_tree(), copy_move_del_alignment(), create_splitAlignment_awars(), di_autodetect_callback(), di_calculate_matrix(), export_seq_data(), FINAL_TYPE< SEQTYPE >::finish(), GB_login(), GB_searchOrCreate_string(), GBS_read_dir(), gbt_nonexisting_alignment(), GBT_searchOrCreate_itemfield_according_to_changekey(), GBT_set_startup_alignment(), gde_filter_weights(), GEN_species_add_entry(), gene_extract_handler(), MatrixOrder::MatrixOrder(), MG_copy_and_check_alignments(), NT_createConcatenationAwars(), pars_check_size(), pars_create_all_awars(), readable_pt_servername(), saiHasDataInAli(), split_alignment(), and valid_alignment_selected().

GB_ERROR GB_failedTo_error	(	const char *	do_something,
		const char *	special,
		GB_ERROR	error
	)

Definition at line 375 of file arb_msg.cxx.

References error(), and GBS_global_string().

Referenced by gb_add_reference(), GB_create_directory(), gb_create_reference(), GB_textprint(), perform_query_cb(), and read_export_format().

GB_ERROR GB_append_exportedError ( GB_ERROR error )

Definition at line 387 of file arb_msg.cxx.

References error(), GB_await_error(), GB_have_error(), and GBS_global_string().

Referenced by add_species_to_merge_list(), ALI_realign_marked(), ColumnStat::calculate(), CON_calc_max_freq(), CON_calculate(), do_sth_with_species(), resolve_IUPAC_target_string(), and Aligner::run().

class BackTraceInfo* GBK_get_backtrace ( size_t skipFramesAtBottom )

Definition at line 405 of file arb_msg.cxx.

References BackTraceInfo::BackTraceInfo().

void GBK_dump_former_backtrace	(	class BackTraceInfo *	trace,
		FILE *	out,
		const char *	message
	)

Definition at line 408 of file arb_msg.cxx.

References demangle_backtrace().

void GBK_free_backtrace ( class BackTraceInfo * trace )

Definition at line 412 of file arb_msg.cxx.

void GBK_dump_backtrace	(	FILE *	out,
		const char *	message
	)

Definition at line 416 of file arb_msg.cxx.

References BackTraceInfo::BackTraceInfo(), and demangle_backtrace().

Referenced by aw_question(), GB_internal_error(), gb_transactable_type(), GBK_terminate(), GBS_erase_hash(), nt_run(), sigsegv_handler(), and ED4_folding_line::warn_illegal_dimension().

void GB_internal_error ( const char * message )

void GB_internal_errorf	(	const char *	templat,
			...
	)

Definition at line 504 of file arb_msg.cxx.

References FORWARD_FORMATTED_NORETURN, and GB_internal_error().

Referenced by gb_build_uncompress_tree(), GB_create(), GB_create_container(), gb_find_by_nr(), gb_read_bin(), gbcm_read_two(), gbcmc_open(), gbcms_talking_find(), gbm_put_memblk(), imemerr(), and invalid_use_in_server().

void GBK_terminate ( const char * error )

Definition at line 509 of file arb_msg.cxx.

References ARB_CRASH_CODE, ARB_SIGSEGV, fflush(), fputs(), and GBK_dump_backtrace().

Referenced by AP_main::accept(), alloc_failure_panic(), AW_window::at_newline(), aw_initstatus(), AW_xfig::AW_xfig(), AWT_initTreeAwarRegistry(), VarUpdateInfo::change_from_widget(), TrackedFiles::check_changes(), die(), EdgeChain::EdgeChain(), GB_shell::ensure_inside(), enter_stage_1_build_tree(), GBDATA::expect_container(), GBDATA::expect_entry(), gb_create_key(), gb_find_or_create_quark(), GB_get_usable_memory(), gb_put_number(), GB_shell::GB_shell(), GB_test_transaction(), GBK_terminatef(), Sondentopf::gen_color_hash(), insert_species_into_tree(), MemBlock::MemBlock(), SelectedDatabase::open_db_for_merge(), NtreeCommandLine::parse(), PT_dump_POS_TREE_to_file(), PT_read_son< POS_TREE2 >(), PTD_write_node_to_disk(), AP_main::push_node(), Sondentopf::put_Sonde(), AP_main::revert(), TypedAliData< char >::slice_down(), LazyAliData::slice_down(), Sondentopf::Sondentopf(), startup_sequence_cb(), trf_commit(), and trf_create().

void GBK_terminatef	(	const char *	templat,
			...
	)

Definition at line 523 of file arb_msg.cxx.

References FORWARD_FORMATTED_NORETURN, and GBK_terminate().

Referenced by AW_gc_manager::add_gc_range(), AW_window::at(), aw_create_shell(), AW_scalar::AW_scalar(), AW_root::awar(), AW_ScalerTransformer::awar2scaler(), VarUpdateInfo::change_from_widget(), ed4_create_all_awars(), ensure_trees_have_order(), GB_atof(), gb_create_key(), GB_login(), GBK_terminate_on_error(), GBT_get_tree_names(), GEN_is_genome_db(), AW_awar::get_max(), AW_awar::get_min(), get_short(), initExtensions(), Mutex::Mutex(), nt_create_all_awars(), NTREE_move_tree_info(), Mutex::own_or_terminate(), propertyName(), AW_selection_list::refresh(), AW_window::refresh_toggle_field(), AW_awar::set_minmax(), BoundActionTracker::set_recording(), type_mismatch(), AW_awar::update(), write_scalervalue_to_awar(), AW_scalar::write_to(), and Mutex::~Mutex().

void GB_warning ( const char * message )

void GB_warningf	(	const char *	templat,
			...
	)

Definition at line 536 of file arb_msg.cxx.

References FORWARD_FORMATTED, and GB_warning().

Referenced by ALI_realign_marked(), ARB_warn_about_unwanted_chars(), AW_awar::AW_awar(), build_consensus_tree(), check_for_species_without_data(), compress_sequence_tree(), AP_sequence::do_lazy_load(), enter_stage_1_build_tree(), export_sequence_data::export_sequence_data(), Itemfield_Selection::fill(), ArbDBWriter::finishSave(), GB_close(), GB_existing_file(), GB_get_usable_memory(), GB_getenvPATH(), GB_resort_data_base(), GB_setenv(), gb_write_bin_rek(), GB_write_int(), gb_write_one_child(), GBS_erase_hash(), GBT_check_alignment(), GBT_check_data(), GBT_convert_changekey(), GBT_get_configuration_names(), gbt_rename_tree_rek(), GBT_tree_info_string(), GBT_write_group_name(), getenv_executable(), getenv_existing_directory(), ArbImporter::import_data(), openArb(), GB_MAIN_TYPE::save_quick_as(), saveArb(), Importer::show_warnings(), GBL_IMPL::trace_params(), and wait_for_dbentry().

void GB_warning_if ( const char * message )

this is the equivalent to aw_message_if() (from libraries which know nothing about GUI)

Definition at line 541 of file arb_msg.cxx.

References GB_warning().

Referenced by experiment_field_selection_list_rescan(), gene_field_selection_list_rescan(), and species_field_selection_list_rescan().

void GB_information ( const char * message )

Definition at line 548 of file arb_msg.cxx.

References active_arb_handlers, and arb_handlers::show_message.

Referenced by compress_sequence_tree(), and GB_informationf().

void GB_informationf	(	const char *	templat,
			...
	)

Definition at line 555 of file arb_msg.cxx.

References FORWARD_FORMATTED, and GB_information().

Referenced by export_format_single(), GB_find_executable(), GB_get_usable_memory(), GB_getenvPATH(), GB_login(), gb_read_bin(), and get_physical_memory().

void GBS_reuse_buffer ( const char * global_buffer )

Definition at line 563 of file arb_msg.cxx.

References globBuf.

Referenced by disexpectField(), GB_canonical_path(), and NT_convert_gene_locations().

GB_ERROR GBK_system ( const char * system_command )

char* GBK_singlequote ( const char * arg )

Enclose argument in single quotes (like 'arg') for POSIX shell commands.

Definition at line 599 of file arb_msg.cxx.

References ARB_strdup(), GBS_strstruct::cat_sQuoted(), GBS_strstruct::ncat(), GBS_strstruct::put(), and GBS_strstruct::release().

Referenced by ARB_main(), AW_edit(), aw_help_search(), awt_aps_go(), canvas_to_printer(), canvas_to_xfig_and_run_xfig(), createCallOnSocketHost(), GB_textprint(), GB_xcmd(), GBT_macro_execute(), test_runtool::make_checked_piped_command(), merge_from_to(), nt_start_editor_on_configuration(), run_command(), and start_pt_server().

char* GBK_doublequote ( const char * arg )

Enclose argument in single quotes (like "arg") for POSIX shell commands. Opposed to single quoted strings, shell will interpret double quoted strings.

Definition at line 624 of file arb_msg.cxx.

References GBS_strstruct::cat(), GBS_strstruct::ncat(), GBS_strstruct::put(), and GBS_strstruct::release().

Referenced by GB_xcmd().