#include <cstddef>#include <cstdlib>#include <cassert>#include <unistd.h>#include <cstdio>#include <cctype>#include <cstring>#include <cstdarg>#include <arb_early_check.h>#include <attributes.h>#include <arb_simple_assert.h>#include <arbtools.h>
Go to the source code of this file.
Classes | |
| struct | SymPart |
| struct | Word |
| class | LinePart |
| class | PartQueue |
| class | AttributeParser |
| struct | promotion |
Macros | |
| #define | mp_assert(cond) arb_assert(cond) |
| #define | DEBUG_PRINT(s) |
| #define | DEBUG_PRINT_STRING(name, str) |
| #define | PRINT(s) fputs((s), stdout) |
| #define | IS_CSYM(x) ((x) > 0 && (isalnum(x) || (x) == '_')) |
| #define | ABORTED ((Word *) -1) |
| #define | MAXPARAM 20 |
| #define | NEWBUFSIZ (20480*sizeof(char)) |
| #define | MAX_COMMENT_SIZE 10000 |
| #define | IS_PARM_NAME(w) |
| #define | DUMMY_COUNTER_POS 6 |
Functions | |
| static void | Version () |
| static void | errorAt (long line, const char *msg) |
| static void | error (const char *msg) |
| static void | errorf (const char *format,...) __attribute__((format(__printf__ |
| static SymPart * | makeSymPart (char *token) |
| static void | addSymParts (SymPart *&symParts, const char *parts) |
| static bool | matchesSymPart (const SymPart *symParts, const char *name) |
| static void | freeSymParts (SymPart *&symParts) |
| void | addRequiredSymParts (const char *parts) |
| void | addExcludedSymParts (const char *parts) |
| void | freeRequiredSymParts () |
| void | freeExcludedSymParts () |
| bool | hasRequiredSymPart (const char *name) |
| bool | hasExcludedSymPart (const char *name) |
| bool | wantPrototypeFor (const char *name) |
| static Word * | word_alloc (const char *s) |
| static void | word_free (Word *&word) |
| static int | List_len (Word *w) |
| static Word * | word_append (Word *w1, Word *w2) |
| static int | foundin (Word *w1, Word *w2) |
| static void | addword (Word *w, const char *s) |
| static void | typefixhack (Word *w) |
| static int | ngetc (FILE *f) |
| static void | clear_found_attribute () |
| static const char * | nextNonSpace (const char *ptr) |
| static const char * | nextNonWord (const char *ptr) |
| const char * | matchingParen (const char *from) |
| static void | search_comment_for_attribute () |
| static void | add_promotion (char *to_promote) |
| static void | print_promotions () |
| static void | search_comment_for_promotion () |
| static int | fnextch (FILE *f) |
| static int | nextch (FILE *f) |
| static int | getsym (char *buf, FILE *f) |
| static int | skipit (char *buf, FILE *f) |
| static int | is_type_word (char *s) |
| static Word * | typelist (Word *p) |
| static Word * | getparamlist (FILE *f) |
| Word * | getLastPtrRef (Word *w) |
| static void | emit (Word *wlist, Word *plist, long startline) |
| static void | getdecl (FILE *f, const char *header) |
| static __ATTR__NORETURN void | Usage (const char *msg=NULp) |
| static int | string_comparator (const void *v0, const void *v1) |
| static __ATTR__NORETURN void | MissingArgumentFor (char option) |
| static __ATTR__NORETURN void | UnknownOption (char option) |
| int | ARB_main (int argc, char *argv[]) |
Variables | |
| static int | donum = 0 |
| static int | define_macro = 0 |
| static int | use_macro = 0 |
| static int | use_main = 0 |
| static int | no_parm_names = 0 |
| static int | print_extern = 0 |
| static int | dont_promote = 0 |
| static int | promote_lines = 0 |
| static int | aisc = 0 |
| static int | cansibycplus = 0 |
| static int | promote_extern_c = 0 |
| static int | extern_c_seen = 0 |
| static int | search__ATTR__ = 0 |
| static const char * | include_wrapper = NULp |
| static int | inquote = 0 |
| static int | newline_seen = 1 |
| static int | glastc = ' ' |
| static char * | current_file = NULp |
| static char * | current_dir = NULp |
| static const char * | header_comment = NULp |
| static long | linenum = 1L |
| static char const * | macro_name = "P_" |
| static char const * | ourname |
| static SymPart * | requiredSymParts = NULp |
| static SymPart * | excludedSymParts = NULp |
| static char | last_comment [MAX_COMMENT_SIZE] |
| static int | lc_size = 0 |
| static char * | found__ATTR__ = NULp |
| static promotion * | promotions = NULp |
| static const char * | promotion_tag = "AISC_MKPT_PROMOTE:" |
| static int | promotion_tag_len = 18 |
Macro Definition Documentation
| #define mp_assert | ( | cond | ) | arb_assert(cond) |
Definition at line 32 of file mkptypes.cxx.
Referenced by PartQueue::append(), LinePart::behind(), LinePart::copyTo(), LinePart::error(), fnextch(), Sonde::gen_Hitliste(), MO_Liste::get_all_species(), Sonde::get_matching_species(), get_random(), getparamlist(), LinePart::LinePart(), MO_Liste::MO_Liste(), mp_file2list(), MP_get_comment(), MP_Window::MP_Window(), search_comment_for_promotion(), Sonde::Sonde(), PartQueue::to_string(), and track_ali_change_cb().
| #define DEBUG_PRINT | ( | s | ) |
Definition at line 44 of file mkptypes.cxx.
Referenced by addword(), ARB_main(), emit(), fnextch(), getdecl(), getparamlist(), getsym(), nextch(), search_comment_for_promotion(), and skipit().
| #define DEBUG_PRINT_STRING | ( | name, | |
| str | |||
| ) |
Definition at line 45 of file mkptypes.cxx.
Referenced by emit().
Definition at line 48 of file mkptypes.cxx.
Referenced by emit().
| #define IS_CSYM | ( | x | ) | ((x) > 0 && (isalnum(x) || (x) == '_')) |
Definition at line 50 of file mkptypes.cxx.
Referenced by emit(), getsym(), and typelist().
| #define ABORTED ((Word *) -1) |
Definition at line 51 of file mkptypes.cxx.
Referenced by getdecl(), and getparamlist().
| #define MAXPARAM 20 |
Definition at line 52 of file mkptypes.cxx.
Referenced by getparamlist().
| #define NEWBUFSIZ (20480*sizeof(char)) |
Definition at line 53 of file mkptypes.cxx.
Referenced by ARB_main().
| #define MAX_COMMENT_SIZE 10000 |
Definition at line 345 of file mkptypes.cxx.
Referenced by fnextch().
| #define IS_PARM_NAME | ( | w | ) |
Definition at line 922 of file mkptypes.cxx.
Referenced by emit().
| #define DUMMY_COUNTER_POS 6 |
Referenced by getparamlist().
Function Documentation
|
static |
Definition at line 1762 of file mkptypes.cxx.
Referenced by ARB_main().
|
static |
Definition at line 96 of file mkptypes.cxx.
References errorAt(), and linenum.
Referenced by GB_MAIN_TYPE::abort_transaction(), PlugIn::activate(), ad_move_tree_info(), ad_tree_set_security(), adaptCopiedAlignment(), awt_linked_to_item::add_db_callbacks(), AW_gc_manager::add_gc_range(), add_probe_to_collection_event(), add_rule_cb(), add_species_to_list_cb(), add_species_to_merge_list(), addid_changed_cb(), RefEntries::addRefsTo(), FINAL_TYPE< SEQTYPE >::addSequence(), adjustTreeRoot(), aed_start_naligning(), ali_checklen_cb(), ali_format_cb(), ALI_realign_marked(), ALI_translate_marked(), SEC_region::align_helix_strands(), alignCompactedTo(), alignTo(), alignToGroupConsensus(), alignToNextRelative(), arb_mem::alloc_aligned(), AP_calc_pos_var_pars(), SaiAciApplicator::apply(), EditedTerminal::apply(), apply_ACI(), TreeNode::apply_aci_to_remarks(), apply_command_to_alignment(), apply_filters(), AliApplicable::apply_to_alignment(), apply_to_origin(), applyToItemFoundByKey(), ARB_bind_global_awars(), ARB_delete_columns_using_SAI(), ARB_insdel_columns(), ARB_insert_columns_using_SAI(), arb_look_and_kill_server(), arb_look_and_start_server(), ARB_main(), arb_open_socket(), arb_open_tcp_socket(), arb_open_unix_socket(), arb_prm_menu(), arb_shell_expand(), arb_start_server(), ARB_textfiles_have_difflines(), arb_wait_for_server(), ARB_zfclose(), FINAL_TYPE< SEQTYPE >::ArbWriter(), askCopyMoveRuleset_cb(), AW_awar::AW_awar(), AW_create_fileselection_awars(), AW_edit(), AW_forget_all_window_geometry(), AW_get_font_specification(), aw_help_show_external_format(), aw_initstatus(), AW_openURL(), aw_question(), AW_save_specific_properties(), AW_select_nameserver(), AW_xfig::AW_xfig(), awt_aps_go(), awt_create_input_mask(), AWT_initialize_input_mask(), awt_open_ACI_URL_with_item(), awt_openDefaultURL_on_selected_species(), awt_openDefaultURL_with_item(), awt_rename_cb(), AWT_trigger_remote_action(), awtc_delete_names_file(), awtc_nn_search(), awtc_nn_search_all_listed(), AWTC_recreate_name(), AP_sequence::bind_to_species(), MostLikelySeq::bind_to_species(), boolchain_gui_changed_cb(), boundloc_changed_cb(), build_reverse_complement(), calc_and_update_alignment_errors_cb(), calc_pvp(), ST_ML::calc_st_ml(), ColumnStat::calculate(), DI_MATRIX::calculate(), calculate_and_check_ranges(), calculate_clusters(), PH_filter::calculate_column_homology(), call_edit(), cannot_fast_align(), AP_tree::cantMoveNextTo(), canvas_to_printer(), canvas_to_xfig(), canvas_to_xfig_and_run_xfig(), change_constraints(), FoundGroup::change_folding(), VarUpdateInfo::change_from_widget(), AliCompositeCommand::check_applicable_to(), check_argument_for_mode(), TrackedFiles::check_changes(), check_for_remote_command(), FieldTransfer::WriteRule::check_hkey(), check_valid_target_fts(), checkAndMergeFields(), cleanup_ptserver_database(), clear_all_colors(), clear_all_colors_cb(), clear_temp_flags(), clearMacroExecutionAuthorization(), GB_transaction::close(), BufferedPipeReader::close(), ClustalV_align(), colorize_marked_cb(), colorize_queried_cb(), colstat_2_gnuplot_cb(), GB_MAIN_TYPE::commit_transaction(), DI_MATRIX::compress(), compress_sequence_tree(), CON_calc_max_freq(), CON_calc_max_freq_cb(), CON_calculate(), CON_calculate_cb(), concatenateAlignments(), concatenateFieldsCreateNewSpecies(), config_comment_changed_cb(), config_rename_handler(), configure_macro_recording(), NameServerConnection::connect(), FieldTransfer::convertAndWrite(), copy_field_into_partial_alignments(), copy_move_del_alignment(), copy_rename_handler(), copy_SAI_cb(), copy_SAI_to_species_cb(), QUERY::copy_selection_list_2_query_box(), copyMoveRuleset_cb(), 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_list_of_loaded_species(), create_macro_variables(), create_modify_fields_window(), create_new_species(), create_split_gene(), createCopy_table_handler(), createDataFromConsensus(), createRuleset_cb(), RootSynchronizer::deconstruct_all_trees(), DeconstructedTree::deconstruct_weighted(), ScrollSynchronizer::define_dependency(), del_rule_cb(), EntryRemover::del_unwanted_entries(), delete_ali_cb(), GroupSearch::delete_found_groups(), FoundGroup::delete_from_DB(), delete_kept_ghostnodes(), delete_queried_species_cb(), delete_SAI_cb(), TreeAdmin::delete_tree_cb(), deleteDataOfKey(), deleteRuleset_cb(), deleteSuperfluousQuicksaves(), ArbImporter::detect_format(), di_autodetect_callback(), di_calculate_compressed_matrix_cb(), di_calculate_full_matrix_cb(), di_calculate_matrix(), di_calculate_tree_cb(), di_mark_by_distance(), di_save_matrix_cb(), di_view_matrix_cb(), distribute_xdata(), AP_sequence::do_lazy_load(), do_sth_with_species(), dot_missing_bases(), dot_sequence_by_consensus(), ed4_create_all_awars(), ED4_create_modsai_window(), ED4_jump_to_cursor_position(), ED4_load_new_config(), ED4_pfold_calculate_secstruct_match(), ED4_pfold_predict_structure(), ED4_pfold_set_SAI(), ED4_remove_faligner_entries(), ED4_set_protection(), ED4_show_protein_match_on_device(), ED4_start_editor_on_configuration(), ED4_start_plugin(), ED4_toggle_detailed_column_stats(), ED4_undo_redo(), ED4_with_whole_block(), edit_SAI_description(), editRuleset_cb(), ensure_trees_have_order(), enter_stage_1_build_tree(), enter_stage_2_load_tree(), AWT_configuration::erase_deleted_configs(), error_with_dbentry(), errorf(), exec_macro_cb(), MacroRecorder::execute(), execute_macro(), executeKeystroke(), EXP_get_first_experiment_data(), expandSetVariables(), expectContent(), BaseCounter::expectEqual(), expectToken(), experiment_copy_handler(), experiment_create_handler(), experiment_delete_cb(), experiment_rename_handler(), SEQIO::export_by_format(), export_format_multiple(), export_format_single(), export_go_cb(), export_nds_cb(), export_newick(), export_seq_data(), export_species_using_form(), export_structure_to_file(), export_to_DB(), export_tree_label(), export_tree_node_print(), export_tree_node_print_xml(), export_write_species(), extended_rename_handler(), DI_MATRIX::extract_from_tree(), FastSearchSequence::fast_align(), FastAligner_delete_temp_entries(), FastAligner_start(), field_convert_commit_cb(), field_create_cb(), field_delete_cb(), Itemfield_Selection::fill(), find_sub_sub_by_quark(), findAffectedKeys(), findOrCreate_configuration(), Structure3D::FindTypeOfRNA(), FINAL_TYPE< SEQTYPE >::finish(), firstCharOfAwarOrDefault(), flush_taxonomy_cb(), fnextch(), GroupSearch::fold_found_groups(), CheckedConsistencies::forgetDoneChecks(), format(), g_b_check_undo_size(), g_b_undo(), g_bs_convert_string_to_tagged_hash_with_rewrite(), gb_abort_and_close_all_DBs(), gb_add_reference(), GB_append_exportedError(), gb_build_uncompress_tree(), GB_clear_macro_error(), GB_clone(), gb_clone_explicit(), GB_close(), gb_commit_transaction_local_rek(), gb_convert_compression(), gb_convert_V2_to_V3(), gb_copy_explicit(), GB_copy_file(), gb_create_dictionaries(), GB_create_directory(), GB_create_index(), GB_create_parent_directory(), gb_create_reference(), GB_delete(), GB_delete_database(), gb_delete_reference(), GB_end_transaction(), GB_failedTo_error(), GB_finish_stream_save(), GB_fopen_tempfile(), GB_get_dictionary(), GB_get_macro_error(), GB_install_pid(), GB_IO_error(), GB_is_dictionary_compressed(), gb_is_valid_mapfile(), gb_load_dictionary_data(), gb_load_key_data_and_dictionaries(), GB_login(), GB_move_file(), GB_optimize(), gb_parse_ascii(), gb_parse_ascii_rek(), gb_read_ascii_beyond_header(), gb_read_bin(), GB_release(), gb_remove_all_but_main(), gb_remove_quick_saved(), GB_request_undo_type(), gb_resort_system_folder_to_top(), GB_safe_atof(), GB_safe_copy_file(), GB_safe_rename_file(), gb_save_dictionary_data(), GB_save_in_arbprop(), gb_save_mapfile(), gb_scan_directory(), gb_search_system_folder(), GB_searchOrCreate_float(), GB_searchOrCreate_int(), GB_searchOrCreate_string(), gb_security_error(), gb_set_compression(), GB_set_dictionary(), GB_set_macro_error(), GB_set_temporary(), gb_set_undo_sync(), GB_stream_save_part(), GB_symlink(), GB_textprint(), gb_transactable_type(), gb_type_writeable_to(), gb_uncompress_by_dictionary(), gb_uncompress_data(), GB_undo(), gb_unfold(), GB_write_autoconv_string(), GB_write_string(), gbcm_unfold_client(), gbcm_write_bin(), gbcmc_begin_transaction(), GBCMC_find(), gbcmc_init_transaction(), gbcmc_key_alloc(), gbcmc_send_undo_commands(), gbcmc_unfold_list(), GBCMS_accept_calls(), GBCMS_open(), gbcms_sighup(), gbcms_talking(), gbcms_talking_unfold(), gbcms_write_updated(), GBK_system(), GBK_test_address(), gbl_ali_name(), gbl_apply_binary_operator(), gbl_change_gc(), gbl_command(), gbl_do(), gbl_drop(), gbl_eval(), gbl_exec(), gbl_export_sequence(), gbl_filter(), gbl_findgene(), gbl_read_seq_sai_or_species(), gbl_select(), gbl_sequence(), gbl_sequence_type(), gbl_srt(), gbl_taxonomy(), GBP_add_callback(), GBP_remove_callback(), 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_alignment_changekeys(), GBT_add_data(), GBT_add_new_changekey_to_keypath(), GBT_begin_rename_session(), GBT_check_alignment(), GBT_check_alignment_name(), GBT_check_arb_file(), GBT_check_data(), GBT_check_tree_name(), GBT_commit_rename_session(), GBT_compress_sequence_tree2(), GBT_convert_changekey(), GBT_copy_tree(), GBT_create(), GBT_create_alignment(), GBT_create_sequence_data(), GBT_find_or_create_item_rel_item_data(), GBT_gen_accession_number(), GBT_get_configuration_names(), GBT_get_tree_names(), gbt_is_invalid(), GBT_is_partial(), GBT_link_tree(), gbt_link_tree_to_hash_rek(), GBT_link_tree_using_species_hash(), GBT_load_colorset(), GBT_log_to_tree_remark(), GBT_macro_execute(), GBT_message(), GBT_move_tree(), GBT_open(), GBT_read_gene_sequence_and_length(), GBT_read_tree_and_size(), GBT_remote_action_with_timeout(), GBT_remote_awar(), GBT_remote_read_awar(), gbt_rename_alignment_of_item(), GBT_rename_species(), GBT_rename_tree(), GBT_set_alignment_len(), GBT_set_startup_alignment(), gbt_set_type_of_changekey(), GBT_tree_2_newick(), gbt_wait_for_remote_action(), GBT_with_stored_species(), GBT_write_byte(), GBT_write_float(), GBT_write_group_name(), GBT_write_int(), GBT_write_string(), gbt_write_tree(), gbt_write_tree_nodes(), GBT_write_tree_with_remark(), GDE_startaction_cb(), GEN_create_nds_vars(), GEN_create_nonexisting_gene_rel_gene_data(), gen_extract_gene_2_pseudoSpecies(), GEN_find_or_create_gene_rel_gene_data(), GEN_get_first_gene_data(), Sonde::gen_Hitliste(), GEN_is_genome_db(), GEN_mark_organism_or_corresponding_organism(), GEN_perform_command(), GEN_read_position(), GEN_species_add_entry(), GEN_testAndRemoveTranslations(), GEN_undo_cb(), GEN_write_position(), gene_changed_cb(), gene_copy_handler(), gene_create_cb(), gene_delete_cb(), gene_extract_handler(), gene_rename_handler(), RefEntries::generate_item_error(), ConsensusTreeBuilder::get(), MO_Liste::get_all_species(), RootSynchronizer::get_DeconstructedTree(), Deletable::get_delete_error(), FINAL_TYPE< SEQTYPE >::get_error(), CLI::get_error(), TrackedFiles::get_error(), export_sequence_data::get_export_sequence(), SEQIO::get_exportFormat_information(), FINAL_TYPE< SEQTYPE >::get_marker_name(), FINAL_TYPE< SEQTYPE >::get_target_data(), AWT_configuration_selection::getConfigInfo(), GetDisplayInfo(), getenv_autodirectory(), SequenceHandler::getError(), getsym(), GI_importGenomeFile(), GLE_update_from_detailFields(), GLE_update_from_location(), grl_aid(), grl_groupsize(), grl_hitcount(), grl_hitidx(), grl_markedingroup(), grl_nesting(), group_clusters(), group_set_folded(), group_species(), MacroRecorder::handle_tracked_client_action(), hide_field_cb(), ArbImporter::import_data(), import_structure_from_file(), GBENTRY::index_check_out(), probe_input_data::init(), init(), init_data(), init_myers(), init_show_pair(), init_tmp_branch(), BI_helix::initFromData(), insdel_event(), insdel_sai_event(), insert_genes_of_organism(), insert_interruption_to_macro_cb(), InsertDatainGDE(), FieldTransfer::ItemClonedByRuleSet::ItemClonedByRuleSet(), launch_MapViewer_cb(), awt_input_handler::link_to(), link_to_tree(), ARB_seqtree_root::linkToDB(), StorableSelectionList::load(), AWT_configuration::Load(), DI_MATRIX::load(), load_and_add_tree(), load_and_startup_main_window(), load_cb(), AWT_graphic_tree::load_from_DB(), load_list_cb(), load_search_paras_from_file(), PARSIMONY_testenv< SEQTYPE >::load_tree(), LoadData(), LoadFile(), FieldTransfer::RuleSet::loadFrom(), ARB_seqtree_root::loadFromDB(), AP_tree_root::loadFromDB(), LoadMenus(), loadsave_colorset_cb(), GB_MAIN_TYPE::login_remote(), macro_terminated(), main(), SaiBoolRule::make(), SaiBoolchainOperator::make(), FilterDefinition::make_filter(), AW_awar::make_global(), di_protdist::makedists(), FieldTransfer::Rule::makeFromConfig(), AW_awar::map(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), mark_action(), mark_as_macro_executor(), mark_nontree_cb(), GroupUIdata::mark_species(), mark_tree_cb(), ED4_container::members_ok(), MERGE_create_main_window(), MERGE_sequences_simple(), mergeSimilarSpecies(), MG_adaptAllCopiedAlignments(), mg_check_field_cb(), MG_config_delete_cb(), MG_copy_and_check_alignments(), MG_create_db_dependent_rename_awars(), MG_create_merge_configs_window(), MG_create_merge_species_window(), MG_create_merge_trees_window(), MG_equal_alignments(), MG_expect_renamed(), MG_export_fields(), MG_extended_delete_cb(), MG_merge_tagged_field_cb(), MG_save_cb(), MG_save_quick_result_cb(), MG_transfer_config(), MG_transfer_extended(), MG_transfer_fields_info(), mg_transfer_listed_species(), MG_transfer_one_species(), mg_transfer_selected_species(), MG_transfer_tree(), MG_update_example(), mg_xfer_via_fts(), modify_fields_of_queried_cb(), modify_probe_event(), modify_target_string(), modsai_cb(), AP_tree::move_group_to(), move_species_to_extended(), mp_file2list(), mp_list2file(), multiroot_sync_subsetTrees(), nds_create_vars(), nds_delete_database_entries(), nds_maintain_viewkeys(), NDS_popup_select_srtaci_window(), nds_restore_config(), ArbImporter::next_file(), nextch(), no_files_found_error(), nt_add(), nt_add_partial(), NT_alltree_remove_leafs(), nt_best_partial_match_rec(), NT_convert_gene_locations(), NT_count_different_chars(), nt_create_all_awars(), nt_create_config_after_import(), nt_create_configuration(), NT_create_main_window(), NT_create_sai_from_pfold(), NT_database_optimization(), NT_del_mark_move_REF(), nt_delete_configuration(), nt_delete_database(), NT_delete_mark_all_cb(), NT_deleteValidNames(), NT_edit_bootstrap(), nt_extract_configuration(), NT_fix_gene_data(), NT_importValidNames(), nt_intro_start_existing(), NT_mark_all_cb(), NT_reload_tree_event(), NT_resort_data_by_phylogeny(), nt_run(), NT_save_as_cb(), NT_save_quick_as_cb(), NT_save_quick_cb(), nt_seq_load_cb(), nt_species_join(), NT_start_editor_on_tree(), NT_undo_cb(), NT_with_displayed_tree_do(), NTREE_move_tree_info(), ok_pressed(), AP_main::open(), PH_root::open(), SelectedDatabase::open_db_for_merge(), openMaskWindowByType(), revcomp_op::operate(), SpecificAliData< char >::operate_on_mem(), overwriteSelectedRule(), SAI_graphic::paint(), SEC_root::paint(), GB_MAIN_TYPE::panic_save(), pars_check_size(), pars_create_all_awars(), pars_generate_aliview(), pars_start_cb(), NtreeCommandLine::parse(), parseCSV(), parseFontString(), parsePositions(), parsesize(), pd_export_pt_server(), pd_get_the_gene_names(), pd_get_the_names(), pd_kill_pt_server(), pd_query_pt_server(), pd_start_pt_server(), perform_block_operation_on_part_of_sequence(), perform_block_operation_on_whole_sequence(), CheckedConsistencies::perform_item_checks(), perform_query_cb(), RefEntries::perform_refentries(), GroupSearch::perform_search(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), PH_save_ml_multiline_cb(), prepare_and_get_selected_itemfield(), SpeciesFlag::prepare_itemfield(), primer_design_event_go(), primer_design_event_init(), probe_design_event(), probe_match_all_event(), probe_match_event(), probe_match_event_using_awars(), probe_match_with_specificity_event(), probe_read_data_base(), protect_corruption_error(), PT_forwhole_chain(), PT_init_input_data(), pt_init_main_struct(), PT_init_map(), PT_prepare_data(), PT_prepare_species_sequence(), PT_start_design(), PTD_read_leafs_from_disk(), PTD_write_leafs_to_disk(), ptserver(), ptserver_gene(), PV_ComplementarySequence(), PV_WriteTranslatedSequenceToDB(), PVP_calculate(), react_to_command(), SEC_region::read(), ArbImporter::read_data(), SEC_root::read_data(), read_export_format(), ArbImporter::read_format(), read_import_format(), read_tree_and_size_internal(), readAndWrite(), ReadArbdb2(), readCompactedSequence(), ReadGen(), readLine(), realign_event(), db_interrupt_data::reconfigure(), RecordingMacro::RecordingMacro(), CheckedConsistencies::register_as_performed(), MacroRecorder::release(), AP_tree::relink(), remote_command_handler(), remove_dup_colors(), awt_mask_item::remove_name(), rename_both_databases(), FoundGroup::rename_by_ACI(), GroupSearch::rename_found_groups(), rename_SAI_cb(), renameDB(), renameQuicksaves(), reorder_configs_cb(), reorder_trees_cb(), request_sequence_refresh(), rerun_importTest_cb(), reserve_tree_idx(), AW_awar::reset_to_default(), resolve_IUPAC_target_string(), resort_data_base(), AWT_configuration::Restore(), restore_cb(), restore_colorset_representation(), AP_pos_var::retrieve(), revcomp_op::revcomp_op(), reverseComplement(), rootsync_subsetTrees_vs_selected(), ED4_manager::route_down_hierarchy(), rule_stack_cb(), ruleset_awar_changed_cb(), Aligner::run(), run_command(), run_rnacma(), run_server(), FileContent::save(), StorableSelectionList::save(), AWT_configuration::Save(), DI_MATRIX::save(), AP_pos_var::save_aliEntry_to_SAI(), GB_MAIN_TYPE::save_as(), save_cb(), EDB_root_bact::save_current_config(), save_list_cb(), save_messagebox_content_to(), AW_root::save_properties(), save_search_paras_to_file(), AWT_graphic_tree::save_to_DB(), save_tree_as_newick(), saveArb(), GBT_config::saveAsOver(), saveChangedRuleset(), FieldTransfer::RuleSet::saveTo(), ARB_seqtree_root::saveToDB(), AP_tree_root::saveToDB(), parameters::scan(), scan_gene_positions(), ItemFieldShader::scan_value_range_cb(), ExportFieldScanner::scanFields(), QUERY::search_duplicated_field_content(), PT_FamilyFinder::searchFamily(), SEC_delete_structure(), sec_expect_constraints(), sec_expect_keyword_and_doubles(), sec_expect_keyword_and_ints(), SEC_new_structure(), sec_scan_doubles(), sec_scan_ints(), SEC_toggle_cb(), SEC_undo_cb(), SEC_xstring_to_foldedHelixList(), GB_MAIN_TYPE::send_update_to_server(), server_load(), server_main_loop(), set_addid(), set_all_modules_to(), AWT_configuration::set_config(), set_DB_state(), Writer::set_error(), AliData::set_error(), set_field_of_queried_cb(), GroupSearch::set_marks_in_found_groups(), GroupSearch::set_marks_in_group(), awt_mask_item::set_name(), set_parents_with_only_temp_childs_temp(), set_protection_level(), set_protection_of_queried_cb(), BoundActionTracker::set_recording(), set_SAI_group(), set_tree_idx(), sort_dtree_by_other_tree_cb(), sort_tree_by_other_tree(), sort_tree_by_other_tree_cb(), species_copy_cb(), species_create_handler(), species_delete_cb(), species_rename_handler(), species_rename_join(), split_ali_cb(), split_alignment(), split_data_into_parts(), SEC_root::split_loop(), SQ_add_changekeys(), sq_calc_seq_quality_cb(), SQ_evaluate(), SQ_mark_species(), SQ_pass1(), SQ_pass1_no_tree(), SQ_pass1_on_tree(), SQ_pass2(), SQ_pass2_no_tree(), SQ_pass2_on_tree(), SQ_remove_quality_entries(), sq_remove_quality_entries_cb(), st_check_cb(), ST_Container::ST_Container(), st_ml_add_quality_string_to_species(), st_ml_check_sequence_quality(), st_ok_cb(), st_remove_entries(), standard_list2file(), start_macro_cb(), start_pt_server(), MacroRecorder::start_recording(), start_remote_command_for_application(), startup_dbserver(), startup_mainwindow_and_dbserver(), startup_sequence_cb(), RecordingMacro::stop(), MacroRecorder::stop_recording(), store_cb(), swap_configs(), FunInfo::switch_to(), sync_changed_cb(), throw_IO_error(), toggle_cursor_group_folding(), toggle_helix_for_SAI(), AW_awar::toggle_toggle(), GBL_IMPL::trace_params(), RecordingMacro::track_action(), RecordingMacro::track_awar_change(), trackAlignmentChanges(), transfer_field_of_listed_cb(), transfer_field_of_selected_cb(), transfer_single_field(), transfer_tree(), ScopedTransporter::transferAllIn(), FieldTransfer::Rule::transferBy(), FieldTransfer::RuleSet::transferBy(), ViaFtsTransporter::transferOne(), transform_gbd_to_leaf(), translate_getInfo(), translate_removeInfo(), translate_saveInfo(), TranslateGeneToAminoAcidSequence(), translateSAItoColors(), transpro_event(), TreeAdmin::tree_append_remark(), TreeAdmin::tree_copy_or_rename_cb(), TREE_load(), tree_load_cb(), TREE_load_to_db(), tree_renamed_cb(), tree_save_cb(), tree_size_ok(), tree_write_byte(), tree_write_float(), TREE_write_Newick(), AP_tree::tree_write_tree_rek(), TREE_write_XML(), FieldTransfer::unconvertedWrite(), undo_entry(), SEC_root::unsplit_loop(), ArbTcpDat::update(), update_example(), ScrollSynchronizer::update_explicit(), update_exportTest_result_cb(), update_format_description_and_suffix(), update_location_from_GEN_position(), update_RangeList(), use_editor_range_cb(), test_runtool::valgrinded_system(), RefEntries::ReferringEntriesHandler::with_all_referred_items(), NodeTextBuilder::work(), FilteredExport::write_fasta(), write_float_converted(), write_int_converted(), SpecSetRegistry::write_node_information(), write_sequence_autoinc_alisize(), AW_scalar::write_to(), writeHistory(), writeStringToAlignment(), FieldTransfer::WriteRule::writeTo(), writeToArb(), XML_recursive(), GB_transaction::~GB_transaction(), and Mutex::~Mutex().
|
static |
Definition at line 101 of file mkptypes.cxx.
References buffer, BUFFERSIZE, error(), EXIT_FAILURE, fputs(), va_end(), and va_start().
Referenced by LinePart::error(), and readSimCfg().
Definition at line 128 of file mkptypes.cxx.
References SymPart::And, SymPart::atStart, SymPart::len, SymPart::next, NULp, and SymPart::part.
Referenced by addSymParts().
Definition at line 150 of file mkptypes.cxx.
References makeSymPart(), SymPart::next, NULp, and s.
Referenced by addExcludedSymParts(), and addRequiredSymParts().
Definition at line 165 of file mkptypes.cxx.
References SymPart::And, SymPart::atStart, SymPart::len, SymPart::next, and SymPart::part.
Referenced by hasExcludedSymPart(), and hasRequiredSymPart().
|
static |
Definition at line 183 of file mkptypes.cxx.
References SymPart::And, SymPart::next, NULp, and SymPart::part.
Referenced by freeExcludedSymParts(), and freeRequiredSymParts().
|
inline |
|
inline |
|
inline |
|
inline |
|
inline |
Definition at line 209 of file mkptypes.cxx.
References matchesSymPart().
Referenced by wantPrototypeFor().
|
inline |
Definition at line 210 of file mkptypes.cxx.
References matchesSymPart().
Referenced by wantPrototypeFor().
|
inline |
Definition at line 212 of file mkptypes.cxx.
References hasExcludedSymPart(), and hasRequiredSymPart().
Referenced by getdecl().
Definition at line 225 of file mkptypes.cxx.
References Word::next, NULp, and Word::string.
Referenced by addword(), getdecl(), getparamlist(), typelist(), and word_append().
|
static |
Definition at line 238 of file mkptypes.cxx.
References Word::next, and NULp.
Referenced by getdecl(), and getparamlist().
Definition at line 248 of file mkptypes.cxx.
References Word::next, and Word::string.
Referenced by typefixhack().
Definition at line 260 of file mkptypes.cxx.
References Word::next, Word::string, and word_alloc().
Referenced by getparamlist().
Definition at line 281 of file mkptypes.cxx.
References Word::next, and Word::string.
Referenced by getparamlist().
Definition at line 295 of file mkptypes.cxx.
References DEBUG_PRINT, Word::next, and word_alloc().
Referenced by getdecl(), and getparamlist().
|
static |
Definition at line 306 of file mkptypes.cxx.
References List_len(), Word::next, NULp, and Word::string.
Referenced by getparamlist().
|
static |
|
static |
Definition at line 356 of file mkptypes.cxx.
Definition at line 360 of file mkptypes.cxx.
Definition at line 365 of file mkptypes.cxx.
References NULp.
|
static |
Definition at line 547 of file mkptypes.cxx.
References lc_size, and AttributeParser::parse().
Referenced by fnextch().
|
static |
Definition at line 565 of file mkptypes.cxx.
References promotion::next, NULp, promotions, and promotion::to_promote.
Referenced by search_comment_for_promotion().
|
static |
Definition at line 581 of file mkptypes.cxx.
References fputc(), promotion::next, NULp, promotions, and promotion::to_promote.
Referenced by emit().
|
static |
Definition at line 603 of file mkptypes.cxx.
References add_promotion(), DEBUG_PRINT, eol, lc_size, mp_assert, NULp, and promotion_tag_len.
Referenced by fnextch().
|
static |
Definition at line 647 of file mkptypes.cxx.
References DEBUG_PRINT, error(), errorAt(), linenum, MAX_COMMENT_SIZE, mp_assert, ngetc(), search_comment_for_attribute(), and search_comment_for_promotion().
Referenced by nextch().
|
static |
Definition at line 715 of file mkptypes.cxx.
References buffer, DEBUG_PRINT, error(), errorAt(), fnextch(), and linenum.
Referenced by getsym().
Definition at line 802 of file mkptypes.cxx.
References DEBUG_PRINT, error(), errorAt(), glastc, IS_CSYM, linenum, and nextch().
Referenced by getdecl(), getparamlist(), and skipit().
Definition at line 879 of file mkptypes.cxx.
References DEBUG_PRINT, and getsym().
Referenced by getdecl().
Definition at line 898 of file mkptypes.cxx.
References NULp.
Definition at line 928 of file mkptypes.cxx.
References IS_CSYM, Word::next, Word::string, and word_alloc().
Referenced by getparamlist().
|
static |
Definition at line 949 of file mkptypes.cxx.
References ABORTED, addword(), cleanup(), DEBUG_PRINT, DUMMY_COUNTER_POS, foundin(), getsym(), MAXPARAM, mp_assert, Word::next, NULp, result, Word::string, typefixhack(), typelist(), word_alloc(), word_append(), and word_free().
Referenced by getdecl().
Definition at line 1164 of file mkptypes.cxx.
References Word::next, NULp, and Word::string.
Referenced by emit().
Definition at line 1174 of file mkptypes.cxx.
References DEBUG_PRINT, DEBUG_PRINT_STRING, fputs(), getLastPtrRef(), IS_CSYM, IS_PARM_NAME, Word::next, PRINT, print_promotions(), and Word::string.
Referenced by getdecl().
|
static |
Definition at line 1345 of file mkptypes.cxx.
References ABORTED, addword(), clear_found_attribute(), DEBUG_PRINT, emit(), getparamlist(), getsym(), linenum, Word::next, NULp, skipit(), Word::string, wantPrototypeFor(), word_alloc(), and word_free().
Referenced by ARB_main().
|
static |
Definition at line 1489 of file mkptypes.cxx.
References EXIT_FAILURE, fputc(), and fputs().
Referenced by ARB_main(), MissingArgumentFor(), and UnknownOption().
|
static |
Definition at line 1530 of file mkptypes.cxx.
Referenced by ARB_main().
|
static |
Definition at line 1534 of file mkptypes.cxx.
References buffer, and Usage().
Referenced by ARB_main().
|
static |
Definition at line 1539 of file mkptypes.cxx.
References buffer, and Usage().
Referenced by ARB_main().
Definition at line 1545 of file mkptypes.cxx.
Variable Documentation
|
static |
Definition at line 56 of file mkptypes.cxx.
|
static |
Definition at line 57 of file mkptypes.cxx.
|
static |
Definition at line 58 of file mkptypes.cxx.
|
static |
Definition at line 59 of file mkptypes.cxx.
|
static |
Definition at line 60 of file mkptypes.cxx.
|
static |
Definition at line 61 of file mkptypes.cxx.
|
static |
Definition at line 62 of file mkptypes.cxx.
|
static |
Definition at line 63 of file mkptypes.cxx.
|
static |
Definition at line 64 of file mkptypes.cxx.
|
static |
Definition at line 65 of file mkptypes.cxx.
|
static |
Definition at line 66 of file mkptypes.cxx.
|
static |
Definition at line 67 of file mkptypes.cxx.
|
static |
Definition at line 68 of file mkptypes.cxx.
Definition at line 70 of file mkptypes.cxx.
|
static |
Definition at line 72 of file mkptypes.cxx.
Referenced by treeFinishCom().
|
static |
Definition at line 73 of file mkptypes.cxx.
|
static |
Definition at line 74 of file mkptypes.cxx.
Referenced by getsym().
Definition at line 76 of file mkptypes.cxx.
Definition at line 77 of file mkptypes.cxx.
Definition at line 78 of file mkptypes.cxx.
|
static |
Definition at line 79 of file mkptypes.cxx.
Referenced by ARB_main(), error(), fnextch(), getdecl(), getsym(), nextch(), and ngetc().
|
static |
Definition at line 81 of file mkptypes.cxx.
Referenced by NtreeCommandLine::autorun_macro(), create_colorize_window(), create_modify_fields_window(), GBT_relativeMacroname(), and ED4_root::generate_window().
|
static |
Definition at line 82 of file mkptypes.cxx.
Definition at line 200 of file mkptypes.cxx.
Definition at line 201 of file mkptypes.cxx.
|
static |
Definition at line 347 of file mkptypes.cxx.
|
static |
Definition at line 348 of file mkptypes.cxx.
Referenced by search_comment_for_attribute(), and search_comment_for_promotion().
Definition at line 349 of file mkptypes.cxx.
Definition at line 563 of file mkptypes.cxx.
Referenced by add_promotion(), and print_promotions().
|
static |
Definition at line 600 of file mkptypes.cxx.
|
static |
Definition at line 601 of file mkptypes.cxx.
Referenced by search_comment_for_promotion().
