Changeset 8360 for trunk

trunk/AWT/AWT_db_browser.cxx

r8309	r8360
1014	1014	awmm->insert_menu_topic("-db_browser", "Browse loaded database(s)", "B", "db_browser.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_db_browser, 0);
1015	1015
1016		awmm->~~insert_separator~~();
	1016	awmm->sep______________();
1017	1017	{
1018	1018	awmm->insert_sub_menu("Callbacks (dangerous! use at your own risk)", "C", AWM_ALL);
…	…
1023	1023	awmm->insert_menu_topic("!run_all_cbs_rnd", "Call all callbacks (random)", "r", "", AWM_ALL, callallcallbacks, 10, 0);
1024	1024	awmm->insert_menu_topic("!run_all_cbs_inf", "Call all callbacks (random repeated)", "p", "", AWM_ALL, callallcallbacks, 11, 0);
1025		awmm->~~insert_separator~~();
	1025	awmm->sep______________();
1026	1026	awmm->insert_menu_topic("!forget_called_cbs", "Forget called", "F", "", AWM_ALL, callallcallbacks, -1, 0);
1027	1027	awmm->insert_menu_topic("!mark_all_called", "Mark all called", "M", "", AWM_ALL, callallcallbacks, -2, 0);
1028	1028	awmm->close_sub_menu();
1029	1029	}
1030		awmm->~~insert_separator~~();
	1030	awmm->sep______________();
1031	1031
1032	1032	}

trunk/AWT/AWT_input_mask.cxx

r8359	r8360
2391	2391	}
2392	2392	}
2393		if (entries_made) awm->~~insert_separator~~();
	2393	if (entries_made) awm->sep______________();
2394	2394	}
2395	2395

trunk/DIST/DI_matr.cxx

r8358	r8360
1460	1460	aws->create_menu("Properties", "P", AWM_ALL);
1461	1461	aws->insert_menu_topic("frame_props", "Frame ...", "F", "props_frame.hlp", AWM_ALL, AW_POPUP,(AW_CL)AW_preset_window, 0);
1462		aws->~~insert_separator~~();
	1462	aws->sep______________();
1463	1463	AW_insert_common_property_menu_entries(aws);
1464		aws->~~insert_separator~~();
	1464	aws->sep______________();
1465	1465	aws->insert_menu_topic("save_props", "Save Properties (dist.arb)", "S", "savedef.hlp", AWM_ALL, (AW_CB)AW_save_properties, 0, 0);
1466	1466

trunk/EDIT4/ED4_root.cxx

r8358	r8360
1341	1341	if (!first_gc_manager) first_gc_manager = aw_gc_manager;
1342	1342
1343		~~#define SEP________________________SEP awmm->insert_separator()~~
1344
1345	1343	// ------------------------------
1346	1344	// File
…	…
1356	1354	awmm->insert_menu_topic("save_config", "Save Configuration", "S", 0, AWM_ALL, (AW_CB)ED4_save_configuration, (AW_CL) 0, (int)0);
1357	1355	awmm->insert_menu_topic("save_config_as", "Save Configuration As", "A", 0, AWM_ALL, AW_POPUP, (AW_CL) ED4_save_configuration_as_open_window, (int)0);
1358		~~SEP________________________SEP~~;
	1356	awmm->sep______________();
1359	1357	awmm->insert_menu_topic("load_config", "Load Configuration", "L", 0, AWM_ALL, AW_POPUP, (AW_CL)ED4_start_editor_on_old_configuration, 0);
1360	1358	awmm->insert_menu_topic("reload_config", "Reload Configuration", "R", 0, AWM_ALL, ED4_restart_editor, 0, 0);
1361		~~SEP________________________SEP~~;
	1359	awmm->sep______________();
1362	1360	GDE_load_menu(awmm, AWM_ALL, "Print");
1363		~~SEP________________________SEP~~;
	1361	awmm->sep______________();
1364	1362
1365	1363	if (clone) awmm->insert_menu_topic("close", "CLOSE", "C", 0, AWM_ALL, ED4_quit_editor, 0, 0);
…	…
1374	1372	awmm->insert_menu_topic("create_species_from_consensus", "Create new species from consensus", "u", 0, AWM_ALL, AW_POPUP, (AW_CL)ED4_create_new_seq_window, (int)1);
1375	1373	awmm->insert_menu_topic("copy_species", "Copy current species", "C", 0, AWM_ALL, AW_POPUP, (AW_CL)ED4_create_new_seq_window, (int)2);
1376		~~SEP________________________SEP~~;
	1374	awmm->sep______________();
1377	1375	awmm->insert_menu_topic("create_group", "Create new Group", "G", 0, AWM_ALL, group_species_cb, 0, 0);
1378	1376	awmm->insert_menu_topic("create_groups_by_field", "Create new groups using Field", "F", 0, AWM_ALL, group_species_cb, 1, 0);
…	…
1386	1384	awmm->insert_menu_topic("load_actual", "Load current species [GET]", "G", 0, AWM_ALL, ED4_get_and_jump_to_actual_from_menu, 0, 0);
1387	1385	awmm->insert_menu_topic("load_marked", "Load marked species", "m", 0, AWM_ALL, ED4_get_marked_from_menu, 0, 0);
1388		~~SEP________________________SEP~~;
	1386	awmm->sep______________();
1389	1387	awmm->insert_menu_topic("refresh_ecoli", "Reload Ecoli sequence", "E", "ecoliref.hlp", AWM_ALL, ED4_reload_ecoli_cb, 0, 0);
1390	1388	awmm->insert_menu_topic("refresh_helix", "Reload Helix", "H", "helix.hlp", AWM_ALL, ED4_reload_helix_cb, 0, 0);
1391	1389	awmm->insert_menu_topic("helix_jump_opposite", "Jump helix opposite [Ctrl-J]", "J", 0, AWM_ALL, ED4_helix_jump_opposite, 0, 0);
1392		~~SEP________________________SEP~~;
	1390	awmm->sep______________();
1393	1391
1394	1392	awmm->insert_sub_menu("Set protection of current ", "p");
…	…
1409	1407	#endif
1410	1408
1411		~~SEP________________________SEP~~;
	1409	awmm->sep______________();
1412	1410	awmm->insert_menu_topic("fast_aligner", INTEGRATED_ALIGNERS_TITLE " [Ctrl-A]", "I", "faligner.hlp", AWM_ALL, AW_POPUP, (AW_CL)ED4_create_faligner_window, (AW_CL)&dataAccess_4_aligner);
1413	1411	awmm->insert_menu_topic("fast_align_set_ref", "Set aligner reference [Ctrl-R]", "R", "faligner.hlp", AWM_ALL, (AW_CB)FastAligner_set_reference_species, (AW_CL)aw_root, 0);
…	…
1415	1413	awmm->insert_menu_topic("sina", "SINA (SILVA Incremental Aligner)", "S", "sina_main.hlp", sina_mask(aw_root), show_sina_window, (AW_CL)&dataAccess_4_aligner, 0);
1416	1414	awmm->insert_menu_topic("del_ali_tmp", "Remove all aligner Entries", "v", 0, AWM_ALL, ED4_remove_faligner_entries, 1, 0);
1417		~~SEP________________________SEP~~;
	1415	awmm->sep______________();
1418	1416	awmm->insert_menu_topic("missing_bases", "Dot potentially missing bases", "D", "missbase.hlp", AWM_EXP, ED4_popup_dot_missing_bases_window, 0, 0);
1419	1417
1420	1418	if (alignment_type == GB_AT_RNA) { // if the database contains valid alignment of rRNA sequences
1421		~~SEP________________________SEP~~;
	1419	awmm->sep______________();
1422	1420	awmm->insert_menu_topic("sec_edit", "Edit secondary structure", "c", "arb_secedit.hlp", AWM_ALL, ED4_start_plugin, (AW_CL)GLOBAL_gb_main, (AW_CL)"SECEDIT");
1423	1421	#if defined(ARB_OPENGL)
…	…
1466	1464	}
1467	1465	awmm->close_sub_menu();
1468		~~SEP________________________SEP~~;
	1466	awmm->sep______________();
1469	1467	awmm->insert_sub_menu("Cursor position ", "p");
1470	1468	awmm->insert_menu_topic("store_curpos", "Store cursor position", "S", 0, AWM_ALL, ED4_store_curpos, 0, 0);
…	…
1473	1471	awmm->close_sub_menu();
1474	1472
1475		~~SEP________________________SEP~~;
	1473	awmm->sep______________();
1476	1474	awmm->insert_menu_topic("change_cursor", "Change cursor type", "t", 0, AWM_ALL, ED4_change_cursor, 0, 0);
1477	1475	awmm->insert_menu_topic("show_all", "Show all bases ", "a", "set_reference.hlp", AWM_ALL, ED4_set_reference_species, 1, 0);
1478	1476	awmm->insert_menu_topic("show_diff", "Show only differences to selected", "d", "set_reference.hlp", AWM_ALL, ED4_set_reference_species, 0, 0);
1479		~~SEP________________________SEP~~;
	1477	awmm->sep______________();
1480	1478	awmm->insert_menu_topic("enable_col_stat", "Activate column statistics", "v", "st_ml.hlp", AWM_EXP, ED4_activate_col_stat, 0, 0);
1481	1479	awmm->insert_menu_topic("disable_col_stat", "Disable column statistics", "i", "st_ml.hlp", AWM_EXP, disable_col_stat, 0, 0);
1482	1480	awmm->insert_menu_topic("detail_col_stat", "Detailed column statistics", "c", "st_ml.hlp", AWM_EXP, ED4_show_detailed_column_stats, 0, 0);
1483	1481	awmm->insert_menu_topic("dcs_threshold", "Set threshold for D.c.s.", "f", "st_ml.hlp", AWM_EXP, ED4_set_col_stat_threshold, 1, 0);
1484		~~SEP________________________SEP~~;
	1482	awmm->sep______________();
1485	1483	awmm->insert_menu_topic("visualize_SAI", "Visualize SAIs", "z", "visualizeSAI.hlp", AWM_ALL, AW_POPUP, (AW_CL)ED4_createVisualizeSAI_window, 0);
1486	1484	// Enable ProteinViewer only for DNA sequence type
…	…
1499	1497	awmm->insert_menu_topic("select_all", "Select all species", "S", "e4_block.hlp", AWM_ALL, ED4_menu_select, AW_CL(ED4_MS_ALL), 0);
1500	1498	awmm->insert_menu_topic("deselect_all", "Deselect all species", "D", "e4_block.hlp", AWM_ALL, ED4_menu_select, AW_CL(ED4_MS_NONE), 0);
1501		~~SEP________________________SEP~~;
	1499	awmm->sep______________();
1502	1500	awmm->insert_menu_topic("mark_selected", "Mark selected species", "M", "e4_block.hlp", AWM_ALL, ED4_menu_select, AW_CL(ED4_MS_MARK_SELECTED), 0);
1503	1501	awmm->insert_menu_topic("unmark_selected", "Unmark selected species", "n", "e4_block.hlp", AWM_ALL, ED4_menu_select, AW_CL(ED4_MS_UNMARK_SELECTED), 0);
1504	1502	awmm->insert_menu_topic("unmark_all", "Unmark all species", "U", "e4_block.hlp", AWM_ALL, ED4_menu_select, AW_CL(ED4_MS_UNMARK_ALL), 0);
1505		~~SEP________________________SEP~~;
	1503	awmm->sep______________();
1506	1504	awmm->insert_menu_topic("invert_all", "Invert selected species", "I", "e4_block.hlp", AWM_ALL, ED4_menu_select, AW_CL(ED4_MS_INVERT), 0);
1507	1505	awmm->insert_menu_topic("invert_group", "Invert group", "g", "e4_block.hlp", AWM_ALL, ED4_menu_select, AW_CL(ED4_MS_INVERT_GROUP), 0);
1508		~~SEP________________________SEP~~;
	1506	awmm->sep______________();
1509	1507	awmm->insert_menu_topic("lowcase", "Change to lower case ", "w", "e4_block.hlp", AWM_ALL, ED4_menu_perform_block_operation, AW_CL(ED4_BO_LOWER_CASE), 0);
1510	1508	awmm->insert_menu_topic("upcase", "Change to upper case", "p", "e4_block.hlp", AWM_ALL, ED4_menu_perform_block_operation, AW_CL(ED4_BO_UPPER_CASE), 0);
1511		~~SEP________________________SEP~~;
	1509	awmm->sep______________();
1512	1510	awmm->insert_menu_topic("reverse", "Reverse selection ", "v", "e4_block.hlp", AWM_ALL, ED4_menu_perform_block_operation, AW_CL(ED4_BO_REVERSE), 0);
1513	1511	awmm->insert_menu_topic("complement", "Complement selection ", "o", "e4_block.hlp", AWM_ALL, ED4_menu_perform_block_operation, AW_CL(ED4_BO_COMPLEMENT), 0);
1514	1512	awmm->insert_menu_topic("reverse_complement", "Reverse complement", "t", "e4_block.hlp", AWM_ALL, ED4_menu_perform_block_operation, AW_CL(ED4_BO_REVERSE_COMPLEMENT), 0);
1515		~~SEP________________________SEP~~;
	1513	awmm->sep______________();
1516	1514	awmm->insert_menu_topic("unalignBlockLeft", "Unalign block", "a", "e4_block.hlp", AWM_ALL, ED4_menu_perform_block_operation, AW_CL(ED4_BO_UNALIGN), 0);
1517	1515	awmm->insert_menu_topic("unalignBlockRight", "Unalign block right", "b", "e4_block.hlp", AWM_ALL, ED4_menu_perform_block_operation, AW_CL(ED4_BO_UNALIGN_RIGHT), 0);
1518	1516	awmm->insert_menu_topic("replace", "Search & Replace ", "h", "e4_replace.hlp", AWM_ALL, AW_POPUP, (AW_CL) ED4_create_replace_window, 0);
1519		~~SEP________________________SEP~~;
	1517	awmm->sep______________();
1520	1518	awmm->insert_menu_topic("toggle_block_type", "Line block <-> Column block", "C", "e4_block.hlp", AWM_ALL, ED4_menu_select, AW_CL(ED4_MS_TOGGLE_BLOCKTYPE), 0);
1521	1519	awmm->insert_menu_topic("shift_left", "Shift block left ", "l", "e4_block.hlp", AWM_ALL, ED4_menu_perform_block_operation, AW_CL(ED4_BO_SHIFT_LEFT), 0);
…	…
1531	1529	awmm->insert_menu_topic("props_options", "Editor Options ", "O", "e4_options.hlp", AWM_ALL, AW_POPUP, (AW_CL)ED4_create_level_1_options_window, 0);
1532	1530	awmm->insert_menu_topic("props_consensus", "Consensus Definition ", "u", "e4_consensus.hlp", AWM_ALL, AW_POPUP, (AW_CL)ED4_create_consensus_definition_window, 0);
1533		~~SEP________________________SEP~~;
	1531	awmm->sep______________();
1534	1532
1535	1533	awmm->insert_menu_topic("props_data", "Change Colors & Fonts ", "C", 0, AWM_ALL, AW_POPUP, (AW_CL)ED4_create_gc_window, (AW_CL)first_gc_manager);
1536	1534	awmm->insert_menu_topic("props_seq_colors", "Set Sequence Colors ", "S", "no help", AWM_ALL, AW_POPUP, (AW_CL)create_seq_colors_window, (AW_CL)sequence_colors);
1537	1535
1538		~~SEP________________________SEP~~;
	1536	awmm->sep______________();
1539	1537
1540	1538	static AW_cb_struct *expose_cb = 0;
…	…
1546	1544	awmm->insert_menu_topic("props_key_map", "Key Mappings ", "K", "nekey_map.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_key_map_window, 0);
1547	1545	awmm->insert_menu_topic("props_nds", "Select visible info (NDS) ", "D", "ed4_nds.hlp", AWM_ALL, AW_POPUP, (AW_CL)ED4_create_nds_window, 0);
1548		~~SEP________________________SEP~~;
	1546	awmm->sep______________();
1549	1547	AW_insert_common_property_menu_entries(awmm);
1550		~~SEP________________________SEP~~;
	1548	awmm->sep______________();
1551	1549	awmm->insert_sub_menu("Save properties ...", "a");
1552	1550	{
…	…
1566	1564	const char *entry = GBS_global_string("Save loaded Properties (%s)", ED4_propertyName(default_mode));
1567	1565	awmm->insert_menu_topic("save_loaded_props", entry, "l", "e4_defaults.hlp", AWM_ALL, ED4_save_properties, (AW_CL)default_mode, 0);
1568		~~SEP________________________SEP~~;
	1566	awmm->sep______________();
1569	1567
1570	1568	for (int mode = 2; mode >= 0; --mode) {
…	…
1580	1578
1581	1579	// ----------------------------------------------------------------------------------------------------
1582
1583		~~#undef SEP________________________SEP~~
1584	1580
1585	1581	aw_root->awar_int(AWAR_EDIT_TITLE_MODE)->add_callback((AW_RCB1)title_mode_changed, (AW_CL)awmm);

trunk/GENOM/EXP_interface.cxx

r8359	r8360
470	470	aws->insert_menu_topic("exp_delete_field", "Delete/Hide Field ...", "D", "spaf_delete.hlp", AD_F_ALL, AW_POPUP, (AW_CL)DBUI::create_field_delete_window, (AW_CL)bis);
471	471	aws->insert_menu_topic("exp_create_field", "Create fields ...", "C", "spaf_create.hlp", AD_F_ALL, AW_POPUP, (AW_CL)DBUI::create_field_create_window, (AW_CL)bis);
472		aws->~~insert_separator~~();
	472	aws->sep______________();
473	473	aws->insert_menu_topic("exp_unhide_fields", "Show all hidden fields", "S", "scandb.hlp", AD_F_ALL, (AW_CB)experiment_field_selection_list_unhide_all_cb, (AW_CL)gb_main, FIELD_FILTER_NDS);
474		aws->~~insert_separator~~();
	474	aws->sep______________();
475	475	aws->insert_menu_topic("exp_scan_unknown_fields", "Scan unknown fields", "u", "scandb.hlp", AD_F_ALL, (AW_CB)experiment_field_selection_list_scan_unknown_cb, (AW_CL)gb_main, FIELD_FILTER_NDS);
476	476	aws->insert_menu_topic("exp_del_unused_fields", "Remove unused fields", "e", "scandb.hlp", AD_F_ALL, (AW_CB)experiment_field_selection_list_delete_unused_cb, (AW_CL)gb_main, FIELD_FILTER_NDS);
…	…
515	515	aws->insert_menu_topic("experiment_copy", "Copy ...", "y", "spa_copy.hlp", AD_F_ALL, AW_POPUP, (AW_CL)create_experiment_copy_window, (AW_CL)gb_main);
516	516	aws->insert_menu_topic("experiment_create", "Create ...", "C", "spa_create.hlp", AD_F_ALL, AW_POPUP, (AW_CL)create_experiment_create_window, (AW_CL)gb_main);
517		aws->~~insert_separator~~();
	517	aws->sep______________();
518	518
519	519	aws->create_menu("FIELDS", "F", AD_F_ALL);

trunk/GENOM/EXP_main.cxx

r8309	r8360
118	118	}
119	119
120		~~#define AWMIMT awm->insert_menu_topic~~
121
122	120	void EXP_create_experiments_submenu(AW_window_menu_modes awm, GBDATA gb_main, bool submenu) {
123	121	const char *title = "Experiment";
…	…
128	126
129	127	{
130		~~AWMIMT~~("experiment_info", "Experiment information", "i", "experiment_info.hlp", AWM_ALL, EXP_popup_experiment_window, (AW_CL)gb_main, 0);
131		~~AWMIMT~~("experiment_search", "Search and query", "q", "experiment_search.hlp", AWM_ALL, AW_POPUP, (AW_CL)EXP_create_experiment_query_window, (AW_CL)gb_main);
	128	awm->insert_menu_topic("experiment_info", "Experiment information", "i", "experiment_info.hlp", AWM_ALL, EXP_popup_experiment_window, (AW_CL)gb_main, 0);
	129	awm->insert_menu_topic("experiment_search", "Search and query", "q", "experiment_search.hlp", AWM_ALL, AW_POPUP, (AW_CL)EXP_create_experiment_query_window, (AW_CL)gb_main);
132	130
133	131	EXP_create_mask_submenu(awm, gb_main);
134	132
135		awm->~~insert_separator~~();
136		~~AWMIMT~~("experiment_colors", "Colors ...", "C", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_colorize_experiments_window, (AW_CL)gb_main);
	133	awm->sep______________();
	134	awm->insert_menu_topic("experiment_colors", "Colors ...", "C", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_colorize_experiments_window, (AW_CL)gb_main);
137	135
138		awm->~~insert_separator~~();
139		~~AWMIMT~~("pgt", "Proteom Genome Toolkit (PGT)", "P", "pgt.hlp", AWM_ALL, EXP_run_pgt, 0, 0);
	136	awm->sep______________();
	137	awm->insert_menu_topic("pgt", "Proteom Genome Toolkit (PGT)", "P", "pgt.hlp", AWM_ALL, EXP_run_pgt, 0, 0);
140	138	}
141	139	if (submenu) awm->close_sub_menu();

trunk/GENOM/GEN_interface.cxx

r8359	r8360
939	939	aws->insert_menu_topic("gen_delete_field", "Delete/Hide field ...", "D", "spaf_delete.hlp", AD_F_ALL, AW_POPUP, (AW_CL)DBUI::create_field_delete_window, (AW_CL)bis);
940	940	aws->insert_menu_topic("gen_create_field", "Create fields ...", "C", "spaf_create.hlp", AD_F_ALL, AW_POPUP, (AW_CL)DBUI::create_field_create_window, (AW_CL)bis);
941		aws->~~insert_separator~~();
	941	aws->sep______________();
942	942	aws->insert_menu_topic("gen_unhide_fields", "Show all hidden fields", "S", "scandb.hlp", AD_F_ALL, (AW_CB)gene_field_selection_list_unhide_all_cb, (AW_CL)gb_main, FIELD_FILTER_NDS);
943		aws->~~insert_separator~~();
	943	aws->sep______________();
944	944	aws->insert_menu_topic("gen_scan_unknown_fields", "Scan unknown fields", "u", "scandb.hlp", AD_F_ALL, (AW_CB)gene_field_selection_list_scan_unknown_cb, (AW_CL)gb_main, FIELD_FILTER_NDS);
945	945	aws->insert_menu_topic("gen_del_unused_fields", "Remove unused fields", "e", "scandb.hlp", AD_F_ALL, (AW_CB)gene_field_selection_list_delete_unused_cb, (AW_CL)gb_main, FIELD_FILTER_NDS);
946	946	aws->insert_menu_topic("gen_refresh_fields", "Refresh fields (both)", "f", "scandb.hlp", AD_F_ALL, (AW_CB)gene_field_selection_list_update_cb, (AW_CL)gb_main, FIELD_FILTER_NDS);
947		aws->~~insert_separator~~();
	947	aws->sep______________();
948	948	aws->insert_menu_topic("gen_edit_loc", "Edit gene location", "l", "gen_create.hlp", AD_F_ALL, popup_gene_location_editor, (AW_CL)gb_main, 0);
949	949	}
…	…
983	983	aws->insert_menu_topic("gene_copy", "Copy ...", "y", "spa_copy.hlp", AD_F_ALL, AW_POPUP, (AW_CL)create_gene_copy_window, (AW_CL)gb_main);
984	984	aws->insert_menu_topic("gene_create", "Create ...", "C", "gen_create.hlp", AD_F_ALL, AW_POPUP, (AW_CL)create_gene_create_window, (AW_CL)gb_main);
985		aws->~~insert_separator~~();
	985	aws->sep______________();
986	986
987	987	aws->create_menu("FIELDS", "F", AD_F_ALL);

trunk/GENOM/GEN_map.cxx

r8359	r8360
1299	1299	}
1300	1300
1301		~~#define AWMIMT awm->insert_menu_topic~~
1302
1303	1301	static void GEN_insert_extract_submenu(AW_window_menu_modes awm, GBDATA gb_main, const char macro_prefix, const char submenu_name, const char hot_key, const char help_file) {
1304	1302	awm->insert_sub_menu(submenu_name, hot_key);
…	…
1307	1305
1308	1306	sprintf(macro_name_buffer, "%s_of_current", macro_prefix);
1309		~~AWMIMT~~(macro_name_buffer, "of current species...", "c", help_file, AWM_ALL, AW_POPUP, (AW_CL)create_gene_extract_window, (AW_CL)GEN_extract_mode_param::get(gb_main, GEN_PERFORM_CURRENT_ORGANISM));
	1307	awm->insert_menu_topic(macro_name_buffer, "of current species...", "c", help_file, AWM_ALL, AW_POPUP, (AW_CL)create_gene_extract_window, (AW_CL)GEN_extract_mode_param::get(gb_main, GEN_PERFORM_CURRENT_ORGANISM));
1310	1308
1311	1309	sprintf(macro_name_buffer, "%s_of_marked", macro_prefix);
1312		~~AWMIMT~~(macro_name_buffer, "of marked species...", "m", help_file, AWM_ALL, AW_POPUP, (AW_CL)create_gene_extract_window, (AW_CL)GEN_extract_mode_param::get(gb_main, GEN_PERFORM_MARKED_ORGANISMS));
	1310	awm->insert_menu_topic(macro_name_buffer, "of marked species...", "m", help_file, AWM_ALL, AW_POPUP, (AW_CL)create_gene_extract_window, (AW_CL)GEN_extract_mode_param::get(gb_main, GEN_PERFORM_MARKED_ORGANISMS));
1313	1311
1314	1312	sprintf(macro_name_buffer, "%s_of_all", macro_prefix);
1315		~~AWMIMT~~(macro_name_buffer, "of all species...", "a", help_file, AWM_ALL, AW_POPUP, (AW_CL)create_gene_extract_window, (AW_CL)GEN_extract_mode_param::get(gb_main, GEN_PERFORM_ALL_ORGANISMS));
	1313	awm->insert_menu_topic(macro_name_buffer, "of all species...", "a", help_file, AWM_ALL, AW_POPUP, (AW_CL)create_gene_extract_window, (AW_CL)GEN_extract_mode_param::get(gb_main, GEN_PERFORM_ALL_ORGANISMS));
1316	1314
1317	1315	awm->close_sub_menu();
…	…
1326	1324
1327	1325	sprintf(macro_name_buffer, "%s_of_current", macro_prefix);
1328		~~AWMIMT~~(macro_name_buffer, "of current species", "c", help_file, AWM_ALL, command, GEN_PERFORM_CURRENT_ORGANISM, command_mode);
	1326	awm->insert_menu_topic(macro_name_buffer, "of current species", "c", help_file, AWM_ALL, command, GEN_PERFORM_CURRENT_ORGANISM, command_mode);
1329	1327
1330	1328	sprintf(macro_name_buffer, "%s_of_all_but_current", macro_prefix);
1331		~~AWMIMT~~(macro_name_buffer, "of all but current species", "b", help_file, AWM_ALL, command, GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM, command_mode);
	1329	awm->insert_menu_topic(macro_name_buffer, "of all but current species", "b", help_file, AWM_ALL, command, GEN_PERFORM_ALL_BUT_CURRENT_ORGANISM, command_mode);
1332	1330
1333	1331	sprintf(macro_name_buffer, "%s_of_marked", macro_prefix);
1334		~~AWMIMT~~(macro_name_buffer, "of marked species", "m", help_file, AWM_ALL, command, GEN_PERFORM_MARKED_ORGANISMS, command_mode);
	1332	awm->insert_menu_topic(macro_name_buffer, "of marked species", "m", help_file, AWM_ALL, command, GEN_PERFORM_MARKED_ORGANISMS, command_mode);
1335	1333
1336	1334	sprintf(macro_name_buffer, "%s_of_all", macro_prefix);
1337		~~AWMIMT~~(macro_name_buffer, "of all species", "a", help_file, AWM_ALL, command, GEN_PERFORM_ALL_ORGANISMS, command_mode);
	1335	awm->insert_menu_topic(macro_name_buffer, "of all species", "a", help_file, AWM_ALL, command, GEN_PERFORM_ALL_ORGANISMS, command_mode);
1338	1336
1339	1337	awm->close_sub_menu();
…	…
1456	1454
1457	1455	{
1458		~~AWMIMT~~("organism_info", "Organism information", "i", "organism_info.hlp", AWM_ALL, GEN_popup_organism_window, (AW_CL)gb_main, 0);
1459
1460		awm->~~insert_separator~~();
1461
1462		~~AWMIMT~~("mark_organisms", "Mark All organisms", "A", "organism_mark.hlp", AWM_ALL, mark_organisms, 1, (AW_CL)gb_main);
1463		~~AWMIMT~~("mark_organisms_unmark_rest", "Mark all organisms, unmark Rest", "R", "organism_mark.hlp", AWM_ALL, mark_organisms, 3, (AW_CL)gb_main);
1464		~~AWMIMT~~("unmark_organisms", "Unmark all organisms", "U", "organism_mark.hlp", AWM_ALL, mark_organisms, 0, (AW_CL)gb_main);
1465		~~AWMIMT~~("invmark_organisms", "Invert marks of all organisms", "v", "organism_mark.hlp", AWM_ALL, mark_organisms, 2, (AW_CL)gb_main);
1466		awm->~~insert_separator~~();
1467		~~AWMIMT~~("mark_organisms_with_marked_genes", "Mark organisms with marked Genes", "G", "organism_mark.hlp", AWM_ALL, mark_organisms_with_marked_genes, (AW_CL)gb_main, 0);
1468		awm->~~insert_separator~~();
1469		~~AWMIMT~~("organism_colors", "Colors ...", "C", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_colorize_organisms_window, (AW_CL)gb_main);
	1456	awm->insert_menu_topic("organism_info", "Organism information", "i", "organism_info.hlp", AWM_ALL, GEN_popup_organism_window, (AW_CL)gb_main, 0);
	1457
	1458	awm->sep______________();
	1459
	1460	awm->insert_menu_topic("mark_organisms", "Mark All organisms", "A", "organism_mark.hlp", AWM_ALL, mark_organisms, 1, (AW_CL)gb_main);
	1461	awm->insert_menu_topic("mark_organisms_unmark_rest", "Mark all organisms, unmark Rest", "R", "organism_mark.hlp", AWM_ALL, mark_organisms, 3, (AW_CL)gb_main);
	1462	awm->insert_menu_topic("unmark_organisms", "Unmark all organisms", "U", "organism_mark.hlp", AWM_ALL, mark_organisms, 0, (AW_CL)gb_main);
	1463	awm->insert_menu_topic("invmark_organisms", "Invert marks of all organisms", "v", "organism_mark.hlp", AWM_ALL, mark_organisms, 2, (AW_CL)gb_main);
	1464	awm->sep______________();
	1465	awm->insert_menu_topic("mark_organisms_with_marked_genes", "Mark organisms with marked Genes", "G", "organism_mark.hlp", AWM_ALL, mark_organisms_with_marked_genes, (AW_CL)gb_main, 0);
	1466	awm->sep______________();
	1467	awm->insert_menu_topic("organism_colors", "Colors ...", "C", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_colorize_organisms_window, (AW_CL)gb_main);
1470	1468	}
1471	1469	if (submenu) awm->close_sub_menu();
…	…
1480	1478
1481	1479	{
1482		~~AWMIMT~~("mark_gene_species", "Mark All gene-species", "A", "gene_species_mark.hlp", AWM_ALL, mark_gene_species, 1, (AW_CL)gb_main);
1483		~~AWMIMT~~("mark_gene_species_unmark_rest", "Mark all gene-species, unmark Rest", "R", "gene_species_mark.hlp", AWM_ALL, mark_gene_species, 3, (AW_CL)gb_main);
1484		~~AWMIMT~~("unmark_gene_species", "Unmark all gene-species", "U", "gene_species_mark.hlp", AWM_ALL, mark_gene_species, 0, (AW_CL)gb_main);
1485		~~AWMIMT~~("invmark_gene_species", "Invert marks of all gene-species", "I", "gene_species_mark.hlp", AWM_ALL, mark_gene_species, 2, (AW_CL)gb_main);
1486		awm->~~insert_separator~~();
1487		~~AWMIMT~~("mark_gene_species_of_marked_genes", "Mark gene-species of marked genes", "M", "gene_species_mark.hlp", AWM_ALL, mark_gene_species_of_marked_genes, (AW_CL)gb_main, 0);
1488		~~AWMIMT~~("mark_gene_species_curr_ali", "Mark all gene-species using Current alignment", "C", "gene_species_mark.hlp", AWM_ALL, mark_gene_species_using_current_alignment, (AW_CL)gb_main, 0);
	1480	awm->insert_menu_topic("mark_gene_species", "Mark All gene-species", "A", "gene_species_mark.hlp", AWM_ALL, mark_gene_species, 1, (AW_CL)gb_main);
	1481	awm->insert_menu_topic("mark_gene_species_unmark_rest", "Mark all gene-species, unmark Rest", "R", "gene_species_mark.hlp", AWM_ALL, mark_gene_species, 3, (AW_CL)gb_main);
	1482	awm->insert_menu_topic("unmark_gene_species", "Unmark all gene-species", "U", "gene_species_mark.hlp", AWM_ALL, mark_gene_species, 0, (AW_CL)gb_main);
	1483	awm->insert_menu_topic("invmark_gene_species", "Invert marks of all gene-species", "I", "gene_species_mark.hlp", AWM_ALL, mark_gene_species, 2, (AW_CL)gb_main);
	1484	awm->sep______________();
	1485	awm->insert_menu_topic("mark_gene_species_of_marked_genes", "Mark gene-species of marked genes", "M", "gene_species_mark.hlp", AWM_ALL, mark_gene_species_of_marked_genes, (AW_CL)gb_main, 0);
	1486	awm->insert_menu_topic("mark_gene_species_curr_ali", "Mark all gene-species using Current alignment", "C", "gene_species_mark.hlp", AWM_ALL, mark_gene_species_using_current_alignment, (AW_CL)gb_main, 0);
1489	1487	}
1490	1488
…	…
1501	1499	{
1502	1500	#if defined(DEBUG)
1503		~~AWMIMT~~("debug_awars", "[DEBUG] Show main AWARs", "", "no.hlp", AWM_ALL, AW_POPUP, (AW_CL)GEN_create_awar_debug_window, 0);
1504		awm->~~insert_separator~~();
	1501	awm->insert_menu_topic("debug_awars", "[DEBUG] Show main AWARs", "", "no.hlp", AWM_ALL, AW_POPUP, (AW_CL)GEN_create_awar_debug_window, 0);
	1502	awm->sep______________();
1505	1503	#endif // DEBUG
1506	1504
1507	1505	if (for_ARB_NTREE) {
1508		~~AWMIMT~~("gene_map", "Gene Map", "p", "gene_map.hlp", AWM_ALL, AW_POPUP, (AW_CL)GEN_create_first_map, (AW_CL)gb_main); // initial gene map
1509		awm->~~insert_separator~~();
	1506	awm->insert_menu_topic("gene_map", "Gene Map", "p", "gene_map.hlp", AWM_ALL, AW_POPUP, (AW_CL)GEN_create_first_map, (AW_CL)gb_main); // initial gene map
	1507	awm->sep______________();
1510	1508
1511	1509	GEN_create_gene_species_submenu(awm, gb_main, true); // Gene-species
1512	1510	GEN_create_organism_submenu (awm, gb_main, true); // Organisms
1513	1511	EXP_create_experiments_submenu (awm, gb_main, true); // Experiments
1514		awm->~~insert_separator~~();
1515		}
1516
1517		~~AWMIMT~~("gene_info", "Gene information", "i", "gene_info.hlp", AWM_ALL, AW_POPUP, (AW_CL)GEN_create_gene_window, (AW_CL)gb_main);
1518		~~AWMIMT~~("gene_search", "Search and Query", "Q", "gene_search.hlp", AWM_ALL, AW_POPUP, (AW_CL)GEN_create_gene_query_window, (AW_CL)gb_main);
	1512	awm->sep______________();
	1513	}
	1514
	1515	awm->insert_menu_topic("gene_info", "Gene information", "i", "gene_info.hlp", AWM_ALL, AW_POPUP, (AW_CL)GEN_create_gene_window, (AW_CL)gb_main);
	1516	awm->insert_menu_topic("gene_search", "Search and Query", "Q", "gene_search.hlp", AWM_ALL, AW_POPUP, (AW_CL)GEN_create_gene_query_window, (AW_CL)gb_main);
1519	1517
1520	1518	GEN_create_mask_submenu(awm, gb_main);
1521	1519
1522		awm->~~insert_separator~~();
	1520	awm->sep______________();
1523	1521
1524	1522	GEN_insert_mark_submenu(awm, gb_main, "gene_mark_all", "Mark all genes", "M", "gene_mark.hlp", GEN_MARK);
…	…
1527	1525	GEN_insert_mark_submenu(awm, gb_main, "gene_count_marked", "Count marked genes", "C", "gene_mark.hlp", GEN_COUNT_MARKED);
1528	1526
1529		~~AWMIMT~~("gene_colors", "Colors ...", "l", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_colorize_genes_window, (AW_CL)gb_main);
1530
1531		awm->~~insert_separator~~();
1532
1533		~~AWMIMT~~("mark_genes_of_marked_gene_species", "Mark genes of marked gene-species", "g", "gene_mark.hlp", AWM_ALL, mark_genes_of_marked_gene_species, (AW_CL)gb_main, 0);
1534
1535		awm->~~insert_separator~~();
	1527	awm->insert_menu_topic("gene_colors", "Colors ...", "l", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_colorize_genes_window, (AW_CL)gb_main);
	1528
	1529	awm->sep______________();
	1530
	1531	awm->insert_menu_topic("mark_genes_of_marked_gene_species", "Mark genes of marked gene-species", "g", "gene_mark.hlp", AWM_ALL, mark_genes_of_marked_gene_species, (AW_CL)gb_main, 0);
	1532
	1533	awm->sep______________();
1536	1534
1537	1535	GEN_insert_extract_submenu(awm, gb_main, "gene_extract_marked", "Extract marked genes", "E", "gene_extract.hlp");
1538	1536
1539	1537	if (!for_ARB_NTREE) { // only in ARB_GENE_MAP:
1540		awm->~~insert_separator~~();
	1538	awm->sep______________();
1541	1539	GEN_insert_mark_submenu(awm, gb_main, "gene_mark_hidden", "Mark hidden genes", "", "gene_hide.hlp", GEN_MARK_HIDDEN);
1542	1540	GEN_insert_mark_submenu(awm, gb_main, "gene_mark_visible", "Mark visible genes", "", "gene_hide.hlp", GEN_MARK_VISIBLE);
1543	1541
1544		awm->~~insert_separator~~();
	1542	awm->sep______________();
1545	1543	GEN_insert_mark_submenu(awm, gb_main, "gene_unmark_hidden", "Unmark hidden genes", "", "gene_hide.hlp", GEN_UNMARK_HIDDEN);
1546	1544	GEN_insert_mark_submenu(awm, gb_main, "gene_unmark_visible", "Unmark visible genes", "", "gene_hide.hlp", GEN_UNMARK_VISIBLE);
…	…
1549	1547	}
1550	1548
1551		#undef ~~AWMIMT~~
	1549	#undef awm->insert_menu_topic
1552	1550
1553	1551	static void GEN_create_hide_submenu(AW_window_menu_modes awm, GBDATA gb_main) {
…	…
1558	1556	GEN_insert_hide_submenu(awm, gb_main, "gene_invhide_marked", "Invert-hide marked genes", "v", "gene_hide.hlp", GEN_INVERT_HIDE_MARKED);
1559	1557
1560		awm->~~insert_separator~~();
	1558	awm->sep______________();
1561	1559	GEN_insert_hide_submenu(awm, gb_main, "gene_hide_all", "Hide all genes", "", "gene_hide.hlp", GEN_HIDE_ALL);
1562	1560	GEN_insert_hide_submenu(awm, gb_main, "gene_unhide_all", "Unhide all genes", "", "gene_hide.hlp", GEN_UNHIDE_ALL);
…	…
1659	1657	insert_menu_topic("gene_options", "Options", "O", "gene_options.hlp", AWM_ALL, AW_POPUP, (AW_CL)GEN_create_options_window, 0);
1660	1658	insert_menu_topic("gene_nds", "NDS ( Select Gene Information ) ...", "N", "props_nds.hlp", AWM_ALL, AW_POPUP, (AW_CL)GEN_open_nds_window, (AW_CL)gb_main);
1661		~~insert_separator~~();
	1659	sep______________();
1662	1660	AW_insert_common_property_menu_entries(this);
1663		~~insert_separator~~();
	1661	sep______________();
1664	1662	insert_menu_topic("gene_save_props", "Save Defaults (ntree.arb)", "D", "savedef.hlp", AWM_ALL, (AW_CB) AW_save_properties, 0, 0);
1665	1663

trunk/MERGE/MG_main.cxx

r8359	r8360
242	242	}
243	243
244		awm->~~insert_separator~~();
	244	awm->sep______________();
245	245	AW_insert_common_property_menu_entries(awm);
246		awm->~~insert_separator~~();
	246	awm->sep______________();
247	247	awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "p", "savedef.hlp", AWM_ALL, (AW_CB)AW_save_properties, 0, 0);
248	248

trunk/MERGE/MG_species.cxx

r8359	r8360
1035	1035	"mergetaggedfield.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_mg_merge_tagged_fields, 0);
1036	1036
1037		aws->~~insert_separator~~();
	1037	aws->sep______________();
1038	1038	aws->insert_menu_topic("def_gene_species_field_xfer", "Define field transfer for gene-species", "g", "gene_species_field_transfer.hlp",
1039	1039	AWM_ALL, AW_POPUP, (AW_CL)MG_gene_species_create_field_transfer_def_window, 0);

trunk/NTREE/NT_extern.cxx

r8359	r8360
1090	1090	// ##########################################
1091	1091
1092		~~#define AWMIMT awm->insert_menu_topic~~
1093		~~#define SEP________________________SEP() awm->insert_separator()~~
1094
1095	1092	static AW_window popup_new_main_window(AW_root awr, AW_CL clone) {
1096	1093	GB_push_transaction(GLOBAL_gb_main);
…	…
1177	1174	if (clone) {
1178	1175	awm->create_menu("File", "F", AWM_ALL);
1179		~~AWMIMT~~("new_window", "New window", "N", "newwindow.hlp", AWM_ALL, AW_POPUP, (AW_CL)popup_new_main_window, clone+1);
1180		~~AWMIMT~~("close", "Close", "C", 0, AWM_ALL, (AW_CB)AW_POPDOWN, 0, 0);
	1176	awm->insert_menu_topic("new_window", "New window", "N", "newwindow.hlp", AWM_ALL, AW_POPUP, (AW_CL)popup_new_main_window, clone+1);
	1177	awm->insert_menu_topic("close", "Close", "C", 0, AWM_ALL, (AW_CB)AW_POPDOWN, 0, 0);
1181	1178	}
1182	1179	else {
1183	1180	#if defined(DEBUG)
1184	1181	// add more to debug-menu
1185		~~SEP________________________SEP~~();
1186		~~AWMIMT~~("fix_db", "Fix database", "F", 0, AWM_ALL, (AW_CB)NT_fix_database, 0, 0);
1187		~~AWMIMT~~("debug_arbdb", "Print debug information", "d", 0, AWM_ALL, (AW_CB)GB_print_debug_information, (AW_CL) GLOBAL_gb_main, 0);
1188		~~AWMIMT~~("test_compr", "Test compression", "T", 0, AWM_ALL, (AW_CB)GBT_compression_test, (AW_CL) GLOBAL_gb_main, 0);
1189		~~SEP________________________SEP~~();
1190		~~AWMIMT~~("table_admin", "Table Admin (unfinished/unknown purpose)", "A", "tableadm.hlp", AWM_ALL, AW_POPUP, (AW_CL)AWT_create_tables_admin_window, (AW_CL)GLOBAL_gb_main);
	1182	awm->sep______________();
	1183	awm->insert_menu_topic("fix_db", "Fix database", "F", 0, AWM_ALL, (AW_CB)NT_fix_database, 0, 0);
	1184	awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", 0, AWM_ALL, (AW_CB)GB_print_debug_information, (AW_CL) GLOBAL_gb_main, 0);
	1185	awm->insert_menu_topic("test_compr", "Test compression", "T", 0, AWM_ALL, (AW_CB)GBT_compression_test, (AW_CL) GLOBAL_gb_main, 0);
	1186	awm->sep______________();
	1187	awm->insert_menu_topic("table_admin", "Table Admin (unfinished/unknown purpose)", "A", "tableadm.hlp", AWM_ALL, AW_POPUP, (AW_CL)AWT_create_tables_admin_window, (AW_CL)GLOBAL_gb_main);
1191	1188	#endif // DEBUG
1192	1189
1193	1190	awm->create_menu("File", "F", AWM_ALL);
1194	1191	{
1195		~~AWMIMT~~("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, (AW_CB)NT_save_quick_cb, 0, 0);
1196		~~AWMIMT~~("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_save_as, (AW_CL)"tmp/nt/arbdb");
1197		~~SEP________________________SEP~~();
1198		~~AWMIMT~~("new_window", "New window", "N", "newwindow.hlp", AWM_ALL, AW_POPUP, (AW_CL)popup_new_main_window, clone+1);
1199		~~SEP________________________SEP~~();
1200		~~AWMIMT~~("optimize_db", "Optimize database", "O", "optimize.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_database_optimization_window, 0);
1201		~~SEP________________________SEP~~();
	1192	awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, (AW_CB)NT_save_quick_cb, 0, 0);
	1193	awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_save_as, (AW_CL)"tmp/nt/arbdb");
	1194	awm->sep______________();
	1195	awm->insert_menu_topic("new_window", "New window", "N", "newwindow.hlp", AWM_ALL, AW_POPUP, (AW_CL)popup_new_main_window, clone+1);
	1196	awm->sep______________();
	1197	awm->insert_menu_topic("optimize_db", "Optimize database", "O", "optimize.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_database_optimization_window, 0);
	1198	awm->sep______________();
1202	1199
1203	1200	awm->insert_sub_menu("Import", "I");
1204	1201	{
1205		~~AWMIMT~~("import_seq", "Import sequences and fields", "I", "arb_import.hlp", AWM_ALL, NT_import_sequences, 0, 0);
	1202	awm->insert_menu_topic("import_seq", "Import sequences and fields", "I", "arb_import.hlp", AWM_ALL, NT_import_sequences, 0, 0);
1206	1203	GDE_load_menu(awm, AWM_EXP, "Import");
1207	1204	}
…	…
1210	1207	awm->insert_sub_menu("Export", "E");
1211	1208	{
1212		~~AWMIMT~~("export_to_ARB", "Export seq/tree/SAI's to new ARB database", "A", "arb_ntree.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_ntree -export &", 0);
1213		~~AWMIMT~~("export_seqs", "Export sequences to foreign format", "f", "arb_export.hlp", AWM_ALL, AW_POPUP, (AW_CL)open_AWTC_export_window, (AW_CL)GLOBAL_gb_main);
	1209	awm->insert_menu_topic("export_to_ARB", "Export seq/tree/SAI's to new ARB database", "A", "arb_ntree.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_ntree -export &", 0);
	1210	awm->insert_menu_topic("export_seqs", "Export sequences to foreign format", "f", "arb_export.hlp", AWM_ALL, AW_POPUP, (AW_CL)open_AWTC_export_window, (AW_CL)GLOBAL_gb_main);
1214	1211	GDE_load_menu(awm, AWM_ALL, "Export");
1215		~~AWMIMT~~("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_nds_export_window, 0);
	1212	awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_nds_export_window, 0);
1216	1213	}
1217	1214	awm->close_sub_menu();
1218		~~SEP________________________SEP~~();
1219
1220		~~AWMIMT~~("macros", "Macros ", "M", "macro.hlp", AWM_ALL, (AW_CB)AW_POPUP, (AW_CL)awt_open_macro_window, (AW_CL)"ARB_NT");
	1215	awm->sep______________();
	1216
	1217	awm->insert_menu_topic("macros", "Macros ", "M", "macro.hlp", AWM_ALL, (AW_CB)AW_POPUP, (AW_CL)awt_open_macro_window, (AW_CL)"ARB_NT");
1221	1218
1222	1219	awm->insert_sub_menu("Registration/Bug report/Version info", "R");
1223	1220	{
1224		~~AWMIMT~~("registration", "Registration", "R", "registration.hlp", AWM_ALL, (AW_CB)AW_POPUP, (AW_CL)NT_submit_bug, 0);
1225		~~AWMIMT~~("bug_report", "Bug report", "B", "registration.hlp", AWM_ALL, (AW_CB)AW_POPUP, (AW_CL)NT_submit_bug, 1);
1226		~~AWMIMT~~("version_info", "Version info (" ARB_VERSION ")", "V", "version.hlp", AWM_ALL, (AW_CB)AW_POPUP_HELP, (AW_CL)"version.hlp", 0);
	1221	awm->insert_menu_topic("registration", "Registration", "R", "registration.hlp", AWM_ALL, (AW_CB)AW_POPUP, (AW_CL)NT_submit_bug, 0);
	1222	awm->insert_menu_topic("bug_report", "Bug report", "B", "registration.hlp", AWM_ALL, (AW_CB)AW_POPUP, (AW_CL)NT_submit_bug, 1);
	1223	awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION ")", "V", "version.hlp", AWM_ALL, (AW_CB)AW_POPUP_HELP, (AW_CL)"version.hlp", 0);
1227	1224	}
1228	1225	awm->close_sub_menu();
1229	1226	#if 0
1230		~~SEP________________________SEP~~();
1231		~~AWMIMT~~("undo", "Undo", "U", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_cb, (AW_CL)GB_UNDO_UNDO, (AW_CL)ntw);
1232		~~AWMIMT~~("redo", "Redo", "d", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_cb, (AW_CL)GB_UNDO_REDO, (AW_CL)ntw);
1233		~~AWMIMT~~("undo_info", "Undo info", "f", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_info_cb, (AW_CL)GB_UNDO_UNDO, (AW_CL)0);
1234		~~AWMIMT~~("redo_info", "Redo info", "o", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_info_cb, (AW_CL)GB_UNDO_REDO, (AW_CL)0);
1235
1236		~~SEP________________________SEP~~();
	1227	awm->sep______________();
	1228	awm->insert_menu_topic("undo", "Undo", "U", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_cb, (AW_CL)GB_UNDO_UNDO, (AW_CL)ntw);
	1229	awm->insert_menu_topic("redo", "Redo", "d", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_cb, (AW_CL)GB_UNDO_REDO, (AW_CL)ntw);
	1230	awm->insert_menu_topic("undo_info", "Undo info", "f", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_info_cb, (AW_CL)GB_UNDO_UNDO, (AW_CL)0);
	1231	awm->insert_menu_topic("redo_info", "Redo info", "o", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_info_cb, (AW_CL)GB_UNDO_REDO, (AW_CL)0);
	1232
	1233	awm->sep______________();
1237	1234	#endif
1238	1235	if (!GLOBAL_NT.extern_quit_button) {
1239		~~AWMIMT~~("quit", "Quit", "Q", "quit.hlp", AWM_ALL, (AW_CB)nt_exit, 0, 0);
	1236	awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, (AW_CB)nt_exit, 0, 0);
1240	1237	}
1241	1238
…	…
1246	1243	awm->create_menu("Species", "c", AWM_ALL);
1247	1244	{
1248		~~AWMIMT~~("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, AW_POPUP, (AW_CL)DBUI::create_species_query_window, (AW_CL)GLOBAL_gb_main);
1249		~~AWMIMT~~("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, NT_popup_species_window, (AW_CL)GLOBAL_gb_main, 0);
1250
1251		~~SEP________________________SEP~~();
	1245	awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, AW_POPUP, (AW_CL)DBUI::create_species_query_window, (AW_CL)GLOBAL_gb_main);
	1246	awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, NT_popup_species_window, (AW_CL)GLOBAL_gb_main, 0);
	1247
	1248	awm->sep______________();
1252	1249
1253	1250	NT_insert_mark_submenus(awm, ntw, 1);
1254		~~AWMIMT~~("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, AW_POPUP, (AW_CL)create_mark_by_refentries_window, (AW_CL)GLOBAL_gb_main);
1255		~~AWMIMT~~("species_colors", "Set Colors", "l", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_colorize_species_window, 0);
1256		~~AWMIMT~~("selection_admin", "Configurations", "o", "configuration.hlp", AWM_ALL, NT_popup_configuration_admin, 0, 0);
1257
1258		~~SEP________________________SEP~~();
	1251	awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, AW_POPUP, (AW_CL)create_mark_by_refentries_window, (AW_CL)GLOBAL_gb_main);
	1252	awm->insert_menu_topic("species_colors", "Set Colors", "l", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_colorize_species_window, 0);
	1253	awm->insert_menu_topic("selection_admin", "Configurations", "o", "configuration.hlp", AWM_ALL, NT_popup_configuration_admin, 0, 0);
	1254
	1255	awm->sep______________();
1259	1256
1260	1257	awm->insert_sub_menu("Database fields admin", "f");
…	…
1263	1260	NT_create_mask_submenu(awm);
1264	1261
1265		~~SEP________________________SEP~~();
1266
1267		~~AWMIMT~~("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, (AW_CB)NT_delete_mark_all_cb, (AW_CL)ntw, 0);
	1262	awm->sep______________();
	1263
	1264	awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, (AW_CB)NT_delete_mark_all_cb, (AW_CL)ntw, 0);
1268	1265
1269	1266	awm->insert_sub_menu("Sort Species", "r");
1270	1267	{
1271		~~AWMIMT~~("sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_build_resort_window, 0);
1272		~~AWMIMT~~("sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, NT_resort_data_by_phylogeny, 0, 0);
	1268	awm->insert_menu_topic("sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_build_resort_window, 0);
	1269	awm->insert_menu_topic("sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, NT_resort_data_by_phylogeny, 0, 0);
1273	1270	}
1274	1271	awm->close_sub_menu();
…	…
1276	1273	awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1277	1274	{
1278		~~AWMIMT~~("merge_species", "Create merged species from similar species", "m", "sp_merge.hlp", AWM_EXP, AW_POPUP, (AW_CL)NT_createMergeSimilarSpeciesWindow, 0);
1279		~~AWMIMT~~("join_marked", "Join Marked Species", "J", "join_species.hlp", AWM_EXP, AW_POPUP, (AW_CL)create_species_join_window, 0);
	1275	awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "sp_merge.hlp", AWM_EXP, AW_POPUP, (AW_CL)NT_createMergeSimilarSpeciesWindow, 0);
	1276	awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "join_species.hlp", AWM_EXP, AW_POPUP, (AW_CL)create_species_join_window, 0);
1280	1277	}
1281	1278	awm->close_sub_menu();
1282	1279
1283		~~SEP________________________SEP~~();
1284
1285		~~AWMIMT~~("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, AW_POPUP, (AW_CL)AWTC_create_submission_window, (AW_CL)GLOBAL_gb_main);
1286
1287		~~SEP________________________SEP~~();
1288
1289		~~AWMIMT~~("new_names", "Generate New Names", "e", "sp_rename.hlp", AWM_ALL, AW_POPUP, (AW_CL)AWTC_create_rename_window, (AW_CL)GLOBAL_gb_main);
	1280	awm->sep______________();
	1281
	1282	awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, AW_POPUP, (AW_CL)AWTC_create_submission_window, (AW_CL)GLOBAL_gb_main);
	1283
	1284	awm->sep______________();
	1285
	1286	awm->insert_menu_topic("new_names", "Generate New Names", "e", "sp_rename.hlp", AWM_ALL, AW_POPUP, (AW_CL)AWTC_create_rename_window, (AW_CL)GLOBAL_gb_main);
1290	1287
1291	1288	awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1292	1289	{
1293		~~AWMIMT~~("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames, 0, 0);
1294		~~AWMIMT~~("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames, 0, 0);
1295		~~AWMIMT~~("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames, 0, 0);
1296		~~AWMIMT~~("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, AW_POPUP, (AW_CL)NT_searchManuallyNames, 0);
	1290	awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames, 0, 0);
	1291	awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames, 0, 0);
	1292	awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames, 0, 0);
	1293	awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, AW_POPUP, (AW_CL)NT_searchManuallyNames, 0);
1297	1294	}
1298	1295	awm->close_sub_menu();
…	…
1309	1306	awm->create_menu("Sequence", "S", AWM_ALL);
1310	1307	{
1311		~~AWMIMT~~("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_alignment_window, 0);
1312		~~AWMIMT~~("ins_del_col", "Insert/Delete Column", "I", "insdelchar.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_insertchar_window, 0);
1313		~~SEP________________________SEP~~();
	1308	awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_alignment_window, 0);
	1309	awm->insert_menu_topic("ins_del_col", "Insert/Delete Column", "I", "insdelchar.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_insertchar_window, 0);
	1310	awm->sep______________();
1314	1311
1315	1312	awm->insert_sub_menu("Edit Sequences", "E");
1316	1313	{
1317		~~AWMIMT~~("new_arb_edit4", "Using marked species and tree", "m", "arb_edit4.hlp", AWM_ALL, NT_start_editor_on_tree, 0, 0);
1318		~~AWMIMT~~("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, NT_start_editor_on_tree, -1, 0);
1319		~~AWMIMT~~("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_start_editor_on_old_configuration, 0);
	1314	awm->insert_menu_topic("new_arb_edit4", "Using marked species and tree", "m", "arb_edit4.hlp", AWM_ALL, NT_start_editor_on_tree, 0, 0);
	1315	awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, NT_start_editor_on_tree, -1, 0);
	1316	awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_start_editor_on_old_configuration, 0);
1320	1317	}
1321	1318	awm->close_sub_menu();
1322	1319
1323		~~SEP________________________SEP~~();
	1320	awm->sep______________();
1324	1321
1325	1322	awm->insert_sub_menu("Align Sequences", "S");
1326	1323	{
1327		~~AWMIMT~~("arb_align", "Align sequence into an existing alignment", "A", "align.hlp", AWM_EXP, (AW_CB) AW_POPUP_HELP, (AW_CL)"align.hlp", 0);
1328		~~AWMIMT~~("realign_dna", "Realign nucleic acid according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_realign_dna_window, 0);
	1324	awm->insert_menu_topic("arb_align", "Align sequence into an existing alignment", "A", "align.hlp", AWM_EXP, (AW_CB) AW_POPUP_HELP, (AW_CL)"align.hlp", 0);
	1325	awm->insert_menu_topic("realign_dna", "Realign nucleic acid according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_realign_dna_window, 0);
1329	1326	GDE_load_menu(awm, AWM_ALL, "Align");
1330	1327	}
1331	1328	awm->close_sub_menu();
1332		~~AWMIMT~~("seq_concat", "Concatenate Sequences/Alignments", "C", "concatenate_align.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_createConcatenationWindow, 0);
1333		~~AWMIMT~~("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, AW_POPUP, (AW_CL)NT_create_trackAliChanges_window, 0);
1334		~~SEP________________________SEP~~();
1335
1336		~~AWMIMT~~("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_dna_2_pro_window, 0);
1337		~~AWMIMT~~("arb_dist", "Distance matrix", "D", "dist.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_dist &", 0);
1338		~~SEP________________________SEP~~();
1339
1340		~~AWMIMT~~("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, AW_POPUP, (AW_CL)SQ_create_seq_quality_window, (AW_CL)GLOBAL_gb_main);
1341		~~AWMIMT~~("chimera_check", "Chimera Check", "m", "check_quality.hlp", AWM_EXP, AW_POPUP, (AW_CL)STAT_create_quality_check_window, (AW_CL)GLOBAL_gb_main);
1342
1343		~~SEP________________________SEP~~();
	1329	awm->insert_menu_topic("seq_concat", "Concatenate Sequences/Alignments", "C", "concatenate_align.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_createConcatenationWindow, 0);
	1330	awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, AW_POPUP, (AW_CL)NT_create_trackAliChanges_window, 0);
	1331	awm->sep______________();
	1332
	1333	awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_dna_2_pro_window, 0);
	1334	awm->insert_menu_topic("arb_dist", "Distance matrix", "D", "dist.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_dist &", 0);
	1335	awm->sep______________();
	1336
	1337	awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, AW_POPUP, (AW_CL)SQ_create_seq_quality_window, (AW_CL)GLOBAL_gb_main);
	1338	awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "check_quality.hlp", AWM_EXP, AW_POPUP, (AW_CL)STAT_create_quality_check_window, (AW_CL)GLOBAL_gb_main);
	1339
	1340	awm->sep______________();
1344	1341
1345	1342	GDE_load_menu(awm, AWM_ALL, "Print");
…	…
1350	1347	awm->create_menu("SAI", "A", AWM_ALL);
1351	1348	{
1352		~~AWMIMT~~("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_extendeds_window, 0);
	1349	awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_extendeds_window, 0);
1353	1350	awm->insert_sub_menu("Create SAI using ...", "C");
1354	1351	{
1355		~~AWMIMT~~("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AW_POPUP, (AW_CL)AP_open_max_freq_window, 0);
1356		~~AWMIMT~~("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AW_POPUP, (AW_CL)AP_open_con_expert_window, 0);
1357		~~AWMIMT~~("pos_var_pars", "Positional variability + Column statistic (parsimony method)", "a", "pos_var_pars.hlp", AWM_ALL, AW_POPUP, (AW_CL)AP_open_pos_var_pars_window, 0);
1358		~~AWMIMT~~("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_phylo &", 0);
1359		~~AWMIMT~~("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold, (AW_CL)ntw, 0);
	1352	awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AW_POPUP, (AW_CL)AP_open_max_freq_window, 0);
	1353	awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AW_POPUP, (AW_CL)AP_open_con_expert_window, 0);
	1354	awm->insert_menu_topic("pos_var_pars", "Positional variability + Column statistic (parsimony method)", "a", "pos_var_pars.hlp", AWM_ALL, AW_POPUP, (AW_CL)AP_open_pos_var_pars_window, 0);
	1355	awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_phylo &", 0);
	1356	awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold, (AW_CL)ntw, 0);
1360	1357
1361	1358	GDE_load_menu(awm, AWM_EXP, "SAI");
…	…
1365	1362	awm->insert_sub_menu("Other functions", "O");
1366	1363	{
1367		~~AWMIMT~~("pos_var_dist", "Positional variability (distance method)", "P", "pos_variability.ps", AWM_EXP, AW_POPUP, (AW_CL)AP_open_cprofile_window, 0);
1368		~~AWMIMT~~("count_different_chars", "Count different chars/column", "C", "count_chars.hlp", AWM_EXP, NT_count_different_chars, (AW_CL)GLOBAL_gb_main, 0);
1369		~~AWMIMT~~("corr_mutat_analysis", "Compute clusters of correlated positions", "m", "", AWM_ALL, NT_system_in_xterm_cb, (AW_CL)"arb_rnacma", 0);
1370		~~AWMIMT~~("export_pos_var", "Export Column Statistic (GNUPLOT format)", "E", "csp_2_gnuplot.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_colstat_2_gnuplot_window, 0);
	1364	awm->insert_menu_topic("pos_var_dist", "Positional variability (distance method)", "P", "pos_variability.ps", AWM_EXP, AW_POPUP, (AW_CL)AP_open_cprofile_window, 0);
	1365	awm->insert_menu_topic("count_different_chars", "Count different chars/column", "C", "count_chars.hlp", AWM_EXP, NT_count_different_chars, (AW_CL)GLOBAL_gb_main, 0);
	1366	awm->insert_menu_topic("corr_mutat_analysis", "Compute clusters of correlated positions", "m", "", AWM_ALL, NT_system_in_xterm_cb, (AW_CL)"arb_rnacma", 0);
	1367	awm->insert_menu_topic("export_pos_var", "Export Column Statistic (GNUPLOT format)", "E", "csp_2_gnuplot.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_colstat_2_gnuplot_window, 0);
1371	1368	}
1372	1369	awm->close_sub_menu();
…	…
1378	1375	awm->create_menu("Probes", "P", AWM_ALL);
1379	1376	{
1380		~~AWMIMT~~("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_probe_design_window, (AW_CL)GLOBAL_gb_main);
1381		~~AWMIMT~~("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_multiprobe_window, (AW_CL)ntw);
1382		~~AWMIMT~~("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_probe_match_window, (AW_CL)GLOBAL_gb_main);
1383		~~SEP________________________SEP~~();
1384		~~AWMIMT~~("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, AW_POPUP,(AW_CL)create_primer_design_window, (AW_CL)GLOBAL_gb_main);
1385		~~AWMIMT~~("primer_design", "Design Sequencing Primers", "S", "primer.hlp", AWM_EXP, (AW_CB)NT_primer_cb, 0, 0);
1386		~~SEP________________________SEP~~();
1387		~~AWMIMT~~("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_probe_admin_window, (AW_CL)GLOBAL_gb_main);
	1377	awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_probe_design_window, (AW_CL)GLOBAL_gb_main);
	1378	awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_multiprobe_window, (AW_CL)ntw);
	1379	awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_probe_match_window, (AW_CL)GLOBAL_gb_main);
	1380	awm->sep______________();
	1381	awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, AW_POPUP,(AW_CL)create_primer_design_window, (AW_CL)GLOBAL_gb_main);
	1382	awm->insert_menu_topic("primer_design", "Design Sequencing Primers", "S", "primer.hlp", AWM_EXP, (AW_CB)NT_primer_cb, 0, 0);
	1383	awm->sep______________();
	1384	awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_probe_admin_window, (AW_CL)GLOBAL_gb_main);
1388	1385	}
1389	1386
…	…
1398	1395	awm->insert_sub_menu("Add Species to Existing Tree", "A");
1399	1396	{
1400		~~AWMIMT~~("arb_pars_quick", "ARB Parsimony (Quick add marked)", "Q", "pars.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_pars -add_marked -quit &", 0);
1401		~~AWMIMT~~("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_pars &", 0);
	1397	awm->insert_menu_topic("arb_pars_quick", "ARB Parsimony (Quick add marked)", "Q", "pars.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_pars -add_marked -quit &", 0);
	1398	awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_pars &", 0);
1402	1399	GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1403	1400	}
…	…
1407	1404	awm->insert_sub_menu("Remove Species from Tree", "R");
1408	1405	{
1409		~~AWMIMT~~(awm->local_id("tree_remove_deleted"), "Remove zombies", "z", "trm_del.hlp", AWM_ALL, (AW_CB)NT_remove_leafs, (AW_CL)ntw, AWT_REMOVE_DELETED);
1410		~~AWMIMT~~(awm->local_id("tree_remove_marked"), "Remove marked", "m", "trm_mrkd.hlp", AWM_ALL, (AW_CB)NT_remove_leafs, (AW_CL)ntw, AWT_REMOVE_MARKED);
1411		~~AWMIMT~~(awm->local_id("tree_keep_marked"), "Keep marked", "K", "tkeep_mrkd.hlp", AWM_ALL, (AW_CB)NT_remove_leafs, (AW_CL)ntw, AWT_REMOVE_NOT_MARKED\|AWT_REMOVE_DELETED);
	1406	awm->insert_menu_topic(awm->local_id("tree_remove_deleted"), "Remove zombies", "z", "trm_del.hlp", AWM_ALL, (AW_CB)NT_remove_leafs, (AW_CL)ntw, AWT_REMOVE_DELETED);
	1407	awm->insert_menu_topic(awm->local_id("tree_remove_marked"), "Remove marked", "m", "trm_mrkd.hlp", AWM_ALL, (AW_CB)NT_remove_leafs, (AW_CL)ntw, AWT_REMOVE_MARKED);
	1408	awm->insert_menu_topic(awm->local_id("tree_keep_marked"), "Keep marked", "K", "tkeep_mrkd.hlp", AWM_ALL, (AW_CB)NT_remove_leafs, (AW_CL)ntw, AWT_REMOVE_NOT_MARKED\|AWT_REMOVE_DELETED);
1412	1409	#if defined(DEVEL_RALF)
1413	1410	#if defined(WARN_TODO)
1414	1411	#warning add "remove duplicates from tree"
1415	1412	#endif
1416		~~SEP________________________SEP~~();
1417		~~AWMIMT~~("all_tree_remove_deleted", "Remove zombies from all trees", "a", "trm_del.hlp", AWM_ALL, (AW_CB)NT_alltree_remove_leafs, AWT_REMOVE_DELETED, (AW_CL)GLOBAL_gb_main);
1418		~~AWMIMT~~("all_tree_remove_marked", "Remove marked from all trees", "l", "trm_del.hlp", AWM_ALL, (AW_CB)NT_alltree_remove_leafs, AWT_REMOVE_MARKED, (AW_CL)GLOBAL_gb_main);
	1413	awm->sep______________();
	1414	awm->insert_menu_topic("all_tree_remove_deleted", "Remove zombies from all trees", "a", "trm_del.hlp", AWM_ALL, (AW_CB)NT_alltree_remove_leafs, AWT_REMOVE_DELETED, (AW_CL)GLOBAL_gb_main);
	1415	awm->insert_menu_topic("all_tree_remove_marked", "Remove marked from all trees", "l", "trm_del.hlp", AWM_ALL, (AW_CB)NT_alltree_remove_leafs, AWT_REMOVE_MARKED, (AW_CL)GLOBAL_gb_main);
1419	1416	#endif // DEVEL_RALF
1420	1417	}
…	…
1425	1422	{
1426	1423	awm->insert_sub_menu("Distance matrix methods", "D");
1427		~~AWMIMT~~("arb_dist", "ARB Neighbour Joining", "J", "dist.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_dist &", 0);
	1424	awm->insert_menu_topic("arb_dist", "ARB Neighbour Joining", "J", "dist.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_dist &", 0);
1428	1425	GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1429	1426	awm->close_sub_menu();
…	…
1445	1442	}
1446	1443
1447		~~SEP________________________SEP~~();
	1444	awm->sep______________();
1448	1445
1449	1446	awm->insert_sub_menu("Reset zoom", "z");
1450	1447	{
1451		~~AWMIMT~~(awm->local_id("reset_logical_zoom"), "Logical zoom", "L", "rst_log_zoom.hlp", AWM_ALL, (AW_CB)NT_reset_lzoom_cb, (AW_CL)ntw, 0);
1452		~~AWMIMT~~(awm->local_id("reset_physical_zoom"), "Physical zoom", "P", "rst_phys_zoom.hlp", AWM_ALL, (AW_CB)NT_reset_pzoom_cb, (AW_CL)ntw, 0);
	1448	awm->insert_menu_topic(awm->local_id("reset_logical_zoom"), "Logical zoom", "L", "rst_log_zoom.hlp", AWM_ALL, (AW_CB)NT_reset_lzoom_cb, (AW_CL)ntw, 0);
	1449	awm->insert_menu_topic(awm->local_id("reset_physical_zoom"), "Physical zoom", "P", "rst_phys_zoom.hlp", AWM_ALL, (AW_CB)NT_reset_pzoom_cb, (AW_CL)ntw, 0);
1453	1450	}
1454	1451	awm->close_sub_menu();
1455	1452	awm->insert_sub_menu("Collapse/Expand tree", "C");
1456	1453	{
1457		~~AWMIMT~~(awm->local_id("tree_group_all"), "Group all", "a", "tgroupall.hlp", AWM_ALL, (AW_CB)NT_group_tree_cb, (AW_CL)ntw, 0);
1458		~~AWMIMT~~(awm->local_id("tree_group_not_marked"), "Group all except marked", "m", "tgroupnmrkd.hlp", AWM_ALL, (AW_CB)NT_group_not_marked_cb, (AW_CL)ntw, 0);
1459		~~AWMIMT~~(awm->local_id("tree_group_term_groups"), "Group terminal groups", "t", "tgroupterm.hlp", AWM_ALL, (AW_CB)NT_group_terminal_cb, (AW_CL)ntw, 0);
1460		~~AWMIMT~~(awm->local_id("tree_ungroup_all"), "Ungroup all", "U", "tungroupall.hlp", AWM_ALL, (AW_CB)NT_ungroup_all_cb, (AW_CL)ntw, 0);
1461		~~SEP________________________SEP~~();
	1454	awm->insert_menu_topic(awm->local_id("tree_group_all"), "Group all", "a", "tgroupall.hlp", AWM_ALL, (AW_CB)NT_group_tree_cb, (AW_CL)ntw, 0);
	1455	awm->insert_menu_topic(awm->local_id("tree_group_not_marked"), "Group all except marked", "m", "tgroupnmrkd.hlp", AWM_ALL, (AW_CB)NT_group_not_marked_cb, (AW_CL)ntw, 0);
	1456	awm->insert_menu_topic(awm->local_id("tree_group_term_groups"), "Group terminal groups", "t", "tgroupterm.hlp", AWM_ALL, (AW_CB)NT_group_terminal_cb, (AW_CL)ntw, 0);
	1457	awm->insert_menu_topic(awm->local_id("tree_ungroup_all"), "Ungroup all", "U", "tungroupall.hlp", AWM_ALL, (AW_CB)NT_ungroup_all_cb, (AW_CL)ntw, 0);
	1458	awm->sep______________();
1462	1459	NT_insert_color_collapse_submenu(awm, ntw);
1463	1460	}
…	…
1465	1462	awm->insert_sub_menu("Beautify tree", "e");
1466	1463	{
1467		~~AWMIMT~~(awm->local_id("beautifyt_tree"), "#beautifyt.bitmap", "", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 0);
1468		~~AWMIMT~~(awm->local_id("beautifyc_tree"), "#beautifyc.bitmap", "", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 1);
1469		~~AWMIMT~~(awm->local_id("beautifyb_tree"), "#beautifyb.bitmap", "", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 2);
	1464	awm->insert_menu_topic(awm->local_id("beautifyt_tree"), "#beautifyt.bitmap", "", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 0);
	1465	awm->insert_menu_topic(awm->local_id("beautifyc_tree"), "#beautifyc.bitmap", "", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 1);
	1466	awm->insert_menu_topic(awm->local_id("beautifyb_tree"), "#beautifyb.bitmap", "", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 2);
1470	1467	}
1471	1468	awm->close_sub_menu();
1472	1469	awm->insert_sub_menu("Modify branches", "M");
1473	1470	{
1474		~~AWMIMT~~(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, NT_remove_bootstrap, (AW_CL)ntw, 0);
1475		~~SEP________________________SEP~~();
1476		~~AWMIMT~~(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, NT_reset_branchlengths, (AW_CL)ntw, 0);
1477		~~AWMIMT~~(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, NT_justify_branch_lenghs, (AW_CL)ntw, 0);
1478		~~AWMIMT~~(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, NT_scale_tree, (AW_CL)ntw, 0);
1479		~~SEP________________________SEP~~();
1480		~~AWMIMT~~(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, NT_move_boot_branch, (AW_CL)ntw, 0);
1481		~~AWMIMT~~(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, NT_move_boot_branch, (AW_CL)ntw, 1);
	1471	awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, NT_remove_bootstrap, (AW_CL)ntw, 0);
	1472	awm->sep______________();
	1473	awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, NT_reset_branchlengths, (AW_CL)ntw, 0);
	1474	awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, NT_justify_branch_lenghs, (AW_CL)ntw, 0);
	1475	awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, NT_scale_tree, (AW_CL)ntw, 0);
	1476	awm->sep______________();
	1477	awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, NT_move_boot_branch, (AW_CL)ntw, 0);
	1478	awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, NT_move_boot_branch, (AW_CL)ntw, 1);
1482	1479
1483	1480	}
1484	1481	awm->close_sub_menu();
1485		~~AWMIMT~~(awm->local_id("mark_long_branches"), "Mark long branches", "k", "mark_long_branches.hlp", AWM_ALL, (AW_CB)NT_mark_long_branches, (AW_CL)ntw, 0);
1486		~~AWMIMT~~(awm->local_id("mark_deep_branches"), "Mark deep branches", "d", "mark_deep_branches.hlp", AWM_EXP, (AW_CB)NT_mark_deep_branches, (AW_CL)ntw, 0);
1487		~~AWMIMT~~(awm->local_id("mark_degen_branches"), "Mark degenerated branches", "g", "mark_degen_branches.hlp", AWM_EXP, (AW_CB)NT_mark_degenerated_branches, (AW_CL)ntw, 0);
1488		~~AWMIMT~~(awm->local_id("mark_duplicates"), "Mark duplicates", "u", "mark_duplicates.hlp", AWM_ALL, (AW_CB)NT_mark_duplicates, (AW_CL)ntw, 0);
1489
1490		~~SEP________________________SEP~~();
1491
1492		~~AWMIMT~~(awm->local_id("tree_select"), "Select Tree", "T", 0, AWM_ALL, AW_POPUP, (AW_CL)NT_open_select_tree_window, (AW_CL)awar_tree);
1493		~~AWMIMT~~(awm->local_id("tree_select_latest"), "Select Last Tree", "L", 0, AWM_ALL, (AW_CB)NT_select_last_tree, (AW_CL)awar_tree, 0);
1494
1495		~~SEP________________________SEP~~();
	1482	awm->insert_menu_topic(awm->local_id("mark_long_branches"), "Mark long branches", "k", "mark_long_branches.hlp", AWM_ALL, (AW_CB)NT_mark_long_branches, (AW_CL)ntw, 0);
	1483	awm->insert_menu_topic(awm->local_id("mark_deep_branches"), "Mark deep branches", "d", "mark_deep_branches.hlp", AWM_EXP, (AW_CB)NT_mark_deep_branches, (AW_CL)ntw, 0);
	1484	awm->insert_menu_topic(awm->local_id("mark_degen_branches"), "Mark degenerated branches", "g", "mark_degen_branches.hlp", AWM_EXP, (AW_CB)NT_mark_degenerated_branches, (AW_CL)ntw, 0);
	1485	awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "u", "mark_duplicates.hlp", AWM_ALL, (AW_CB)NT_mark_duplicates, (AW_CL)ntw, 0);
	1486
	1487	awm->sep______________();
	1488
	1489	awm->insert_menu_topic(awm->local_id("tree_select"), "Select Tree", "T", 0, AWM_ALL, AW_POPUP, (AW_CL)NT_open_select_tree_window, (AW_CL)awar_tree);
	1490	awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", 0, AWM_ALL, (AW_CB)NT_select_last_tree, (AW_CL)awar_tree, 0);
	1491
	1492	awm->sep______________();
1496	1493
1497	1494	if (!clone) {
1498		~~AWMIMT~~("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_trees_window, 0);
1499		~~AWMIMT~~("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, AW_POPUP, (AW_CL)AWT_create_nds_window, (AW_CL)GLOBAL_gb_main);
1500		}
1501		~~SEP________________________SEP~~();
1502
1503		~~AWMIMT~~("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, (AW_CB)AW_POPUP_HELP, (AW_CL)"trans_anal.hlp", 0);
1504
1505		~~SEP________________________SEP~~();
	1495	awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_trees_window, 0);
	1496	awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, AW_POPUP, (AW_CL)AWT_create_nds_window, (AW_CL)GLOBAL_gb_main);
	1497	}
	1498	awm->sep______________();
	1499
	1500	awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, (AW_CB)AW_POPUP_HELP, (AW_CL)"trans_anal.hlp", 0);
	1501
	1502	awm->sep______________();
1506	1503
1507	1504	if (!clone) {
1508		~~AWMIMT~~("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, AWT_popup_print_window, (AW_CL)ntw, 0);
1509		~~AWMIMT~~("tree_2_xfig", "Export tree to XFIG", "X", "tree2file.hlp", AWM_ALL, AWT_popup_tree_export_window, (AW_CL)ntw, 0);
1510		~~SEP________________________SEP~~();
	1505	awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, AWT_popup_print_window, (AW_CL)ntw, 0);
	1506	awm->insert_menu_topic("tree_2_xfig", "Export tree to XFIG", "X", "tree2file.hlp", AWM_ALL, AWT_popup_tree_export_window, (AW_CL)ntw, 0);
	1507	awm->sep______________();
1511	1508	}
1512	1509
…	…
1514	1511	awm->insert_sub_menu("Other..", "O", AWM_EXP);
1515	1512	{
1516		~~AWMIMT~~(awm->local_id("tree_pseudo_species_to_organism"), "Change pseudo species to organisms in tree", "p", "tree_pseudo.hlp", AWM_EXP, (AW_CB)NT_pseudo_species_to_organism, (AW_CL)ntw, 0);
	1513	awm->insert_menu_topic(awm->local_id("tree_pseudo_species_to_organism"), "Change pseudo species to organisms in tree", "p", "tree_pseudo.hlp", AWM_EXP, (AW_CB)NT_pseudo_species_to_organism, (AW_CL)ntw, 0);
1517	1514	}
1518	1515	awm->close_sub_menu();
…	…
1526	1523	awm->create_menu("Tools", "o", AWM_ALL);
1527	1524	{
1528		~~AWMIMT~~("names_admin", "Name server admin", "s", "namesadmin.hlp", AWM_ALL, AW_POPUP, (AW_CL)AW_create_namesadmin_window, (AW_CL)GLOBAL_gb_main);
	1525	awm->insert_menu_topic("names_admin", "Name server admin", "s", "namesadmin.hlp", AWM_ALL, AW_POPUP, (AW_CL)AW_create_namesadmin_window, (AW_CL)GLOBAL_gb_main);
1529	1526	awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1530	1527	{
1531		~~AWMIMT~~("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, NT_rerepair_DB, (AW_CL)GLOBAL_gb_main, 0);
	1528	awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, NT_rerepair_DB, (AW_CL)GLOBAL_gb_main, 0);
1532	1529	}
1533	1530	awm->close_sub_menu();
…	…
1537	1534	}
1538	1535	awm->close_sub_menu();
1539		~~SEP________________________SEP~~();
	1536	awm->sep______________();
1540	1537
1541	1538	awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
…	…
1547	1544	awm->insert_sub_menu("WL specials", "W", AWM_EXP);
1548	1545	{
1549		~~AWMIMT~~(awm->local_id("view_probe_group_result"), "View probe group result", "V", "", AWM_EXP, AW_POPUP, (AW_CL)create_probe_group_result_window, (AW_CL)ntw);
	1546	awm->insert_menu_topic(awm->local_id("view_probe_group_result"), "View probe group result", "V", "", AWM_EXP, AW_POPUP, (AW_CL)create_probe_group_result_window, (AW_CL)ntw);
1550	1547	}
1551	1548	awm->close_sub_menu();
1552	1549
1553		~~SEP________________________SEP~~();
1554		~~AWMIMT~~("xterm", "Start XTERM", "X", 0, AWM_ALL, (AW_CB)GB_xterm, 0, 0);
	1550	awm->sep______________();
	1551	awm->insert_menu_topic("xterm", "Start XTERM", "X", 0, AWM_ALL, (AW_CB)GB_xterm, 0, 0);
1555	1552	}
1556	1553	// -------------------
…	…
1559	1556	awm->create_menu("Properties", "r", AWM_ALL);
1560	1557	{
1561		~~AWMIMT~~("props_menu", "Frame settings", "F", "props_frame.hlp", AWM_ALL, AW_POPUP, (AW_CL)AW_preset_window, 0);
	1558	awm->insert_menu_topic("props_menu", "Frame settings", "F", "props_frame.hlp", AWM_ALL, AW_POPUP, (AW_CL)AW_preset_window, 0);
1562	1559	awm->insert_sub_menu("Tree settings", "T");
1563	1560	{
1564		~~AWMIMT~~(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_tree_setting, (AW_CL)ntw);
1565		~~AWMIMT~~("props_tree", "Tree colors & fonts", "c", "nt_props_data.hlp", AWM_ALL, AW_POPUP, (AW_CL)AW_create_gc_window, (AW_CL)aw_gc_manager);
	1561	awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_tree_setting, (AW_CL)ntw);
	1562	awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "nt_props_data.hlp", AWM_ALL, AW_POPUP, (AW_CL)AW_create_gc_window, (AW_CL)aw_gc_manager);
1566	1563	}
1567	1564	awm->close_sub_menu();
1568		~~AWMIMT~~("props_www", "Search world wide web (WWW)", "W", "props_www.hlp", AWM_ALL, AW_POPUP, (AW_CL)AWT_open_www_window, (AW_CL)GLOBAL_gb_main);
1569		~~SEP________________________SEP~~();
1570		~~AWMIMT~~("!toggle_expert", "Toggle expert mode", "x", 0, AWM_ALL, NT_toggle_expert_mode, 0, 0);
1571		~~AWMIMT~~("!toggle_focus", "Toggle focus follows mouse", "f", 0, AWM_ALL, NT_toggle_focus_policy, 0, 0);
1572		~~SEP________________________SEP~~();
	1565	awm->insert_menu_topic("props_www", "Search world wide web (WWW)", "W", "props_www.hlp", AWM_ALL, AW_POPUP, (AW_CL)AWT_open_www_window, (AW_CL)GLOBAL_gb_main);
	1566	awm->sep______________();
	1567	awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", 0, AWM_ALL, NT_toggle_expert_mode, 0, 0);
	1568	awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "f", 0, AWM_ALL, NT_toggle_focus_policy, 0, 0);
	1569	awm->sep______________();
1573	1570	AW_insert_common_property_menu_entries(awm);
1574		~~SEP________________________SEP~~();
1575		~~AWMIMT~~("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, (AW_CB) AW_save_properties, 0, 0);
	1571	awm->sep______________();
	1572	awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, (AW_CB) AW_save_properties, 0, 0);
1576	1573	}
1577	1574	}

trunk/PARSIMONY/PARS_main.cxx

r8359	r8360
1184	1184	awm->insert_menu_topic(0, "Sort tree by name", "o", "", AWM_ALL, (AW_CB)TESTMENU_sortTreeByName, (AW_CL)ntw, 0);
1185	1185	awm->insert_menu_topic(0, "Build & dump chain", "c", "", AWM_ALL, (AW_CB)TESTMENU_buildAndDumpChain, (AW_CL)ntw, 0);
1186		awm->~~insert_separator~~();
	1186	awm->sep______________();
1187	1187	awm->insert_menu_topic(0, "Add marked species", "A", "pa_quick.hlp", AWM_ALL, (AW_CB)TESTMENU_quick_add, (AW_CL)ntw, NT_ADD_MARKED);
1188	1188	awm->insert_menu_topic(0, "Add marked species + NNI", "N", "pa_add.hlp", AWM_ALL, (AW_CB)TESTMENU_add, (AW_CL)ntw, NT_ADD_MARKED);
1189	1189	awm->insert_menu_topic(0, "Remove & add marked species", "o", "pa_add.hlp", AWM_ALL, (AW_CB)TESTMENU_rquick_add_test, (AW_CL)ntw, NT_ADD_MARKED);
1190	1190	awm->insert_menu_topic(0, "Remove & add marked + NNI", "v", "pa_add.hlp", AWM_ALL, (AW_CB)TESTMENU_radd, (AW_CL)ntw, NT_ADD_MARKED);
1191		awm->~~insert_separator~~();
	1191	awm->sep______________();
1192	1192	awm->insert_menu_topic(0, "Add selected species", "l", "pa_quick_sel.hlp", AWM_ALL, (AW_CB)TESTMENU_quick_add, (AW_CL)ntw, NT_ADD_SELECTED);
1193	1193	awm->insert_menu_topic(0, "Add selected species + NNI", "I", "pa_add_sel.hlp", AWM_ALL, (AW_CB)TESTMENU_add, (AW_CL)ntw, NT_ADD_SELECTED);
…	…
1338	1338	awm->insert_menu_topic("nds", "NDS (Node Display Setup) ...", "N", "props_nds.hlp", AWM_ALL, AW_POPUP, (AW_CL)AWT_create_nds_window, (AW_CL)ntw->gb_main);
1339	1339
1340		awm->~~insert_separator~~();
	1340	awm->sep______________();
1341	1341	awm->insert_menu_topic("tree_2_xfig", "Export tree to XFIG ...", "E", "tree2file.hlp", AWM_ALL, AWT_popup_tree_export_window, (AW_CL)ntw, 0);
1342	1342	awm->insert_menu_topic("tree_print", "Print tree ...", "P", "tree2prt.hlp", AWM_ALL, AWT_popup_print_window, (AW_CL)ntw, 0);
1343		awm->~~insert_separator~~();
	1343	awm->sep______________();
1344	1344	awm->insert_sub_menu("Collapse/Expand Tree", "C");
1345	1345	{
…	…
1347	1347	awm->insert_menu_topic("tree_group_not_marked", "Group All Except Marked", "M", "tgroupnmrkd.hlp", AWM_ALL, (AW_CB)NT_group_not_marked_cb, (AW_CL)ntw, 0);
1348	1348	awm->insert_menu_topic("tree_ungroup_all", "Ungroup All", "U", "tungroupall.hlp", AWM_ALL, (AW_CB)NT_ungroup_all_cb, (AW_CL)ntw, 0);
1349		awm->~~insert_separator~~();
	1349	awm->sep______________();
1350	1350	NT_insert_color_collapse_submenu(awm, ntw);
1351	1351	}
1352	1352	awm->close_sub_menu();
1353		awm->~~insert_separator~~();
	1353	awm->sep______________();
1354	1354	awm->insert_sub_menu("Remove Species from Tree", "R");
1355	1355	{
…	…
1365	1365	awm->insert_menu_topic("rm_add_marked", "Remove & Add Marked Species", "R", "pa_add.hlp", AWM_ALL, (AW_CB)NT_rquick_add, (AW_CL)ntw, NT_ADD_MARKED);
1366	1366	awm->insert_menu_topic("rm_add_marked_nni\|", "Remove & Add Marked + Local Optimization (NNI)", "L", "pa_add.hlp", AWM_ALL, (AW_CB)NT_radd, (AW_CL)ntw, NT_ADD_MARKED);
1367		awm->~~insert_separator~~();
	1367	awm->sep______________();
1368	1368	awm->insert_menu_topic("add_marked_partial", "Add Marked Partial Species", "P", "pa_partial.hlp", AWM_ALL, NT_partial_add, (AW_CL)ntw, (AW_CL)0);
1369		awm->~~insert_separator~~();
	1369	awm->sep______________();
1370	1370	awm->insert_menu_topic("add_selected", "Add Selected Species", "S", "pa_quick_sel.hlp", AWM_ALL, (AW_CB)NT_quick_add, (AW_CL)ntw, NT_ADD_SELECTED);
1371	1371	awm->insert_menu_topic("add_selected_nni", "Add Selected Species + Local Optimization (NNI)", "O", "pa_add_sel.hlp", AWM_ALL, (AW_CB)NT_add, (AW_CL)ntw, NT_ADD_SELECTED);
1372	1372	}
1373	1373	awm->close_sub_menu();
1374		awm->~~insert_separator~~();
	1374	awm->sep______________();
1375	1375	awm->insert_sub_menu("Tree Optimization", "O");
1376	1376	{
…	…
1380	1380	awm->close_sub_menu();
1381	1381	awm->insert_menu_topic("reset", "Reset optimal parsimony", "s", "", AWM_ALL, (AW_CB)pars_reset_optimal_parsimony, (AW_CL)ntw, 0);
1382		awm->~~insert_separator~~();
	1382	awm->sep______________();
1383	1383	awm->insert_menu_topic("beautify_tree", "Beautify Tree", "B", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 0);
1384	1384	awm->insert_menu_topic("calc_branch_lengths", "Calculate Branch Lengths", "L", "pa_branchlengths.hlp", AWM_ALL, (AW_CB)NT_branch_lengths, (AW_CL)ntw, 0);
1385		awm->~~insert_separator~~();
	1385	awm->sep______________();
1386	1386	awm->insert_menu_topic("calc_upper_bootstrap_indep", "Calculate Upper Bootstrap Limit (dependent NNI)", "d", "pa_bootstrap.hlp", AWM_ALL, (AW_CB)NT_bootstrap, (AW_CL)ntw, 0);
1387	1387	awm->insert_menu_topic("calc_upper_bootstrap_dep", "Calculate Upper Bootstrap Limit (independent NNI)", "i", "pa_bootstrap.hlp", AWM_ALL, (AW_CB)NT_bootstrap, (AW_CL)ntw, 1);
…	…
1405	1405	awm->insert_menu_topic("props_tree2", "Tree: Settings ...", "T", "nt_tree_settings.hlp", AWM_ALL, AW_POPUP,(AW_CL)NT_create_tree_setting, (AW_CL)ntw);
1406	1406	awm->insert_menu_topic("props_kl", "KERN. LIN ...", "K", "kernlin.hlp", AWM_ALL, AW_POPUP,(AW_CL)create_kernighan_window, 0);
1407		awm->~~insert_separator~~();
	1407	awm->sep______________();
1408	1408	AW_insert_common_property_menu_entries(awm);
1409		awm->~~insert_separator~~();
	1409	awm->sep______________();
1410	1410	awm->insert_menu_topic("save_props", "Save Defaults (pars.arb)", "D", "savedef.hlp", AWM_ALL, (AW_CB)AW_save_properties, 0, 0);
1411	1411	}

trunk/PHYLO/PH_main.cxx

r8358	r8360
472	472	awm->insert_menu_topic("props_menu", "Menu: Colors and Fonts ...", "M", "props_frame.hlp", AWM_ALL, AW_POPUP,(AW_CL)AW_preset_window, 0);
473	473	awm->insert_menu_topic("props_data", "Data: Colors and Fonts ...", "D", "ph_props_data.hlp", AWM_ALL, AW_POPUP,(AW_CL)AW_create_gc_window, (AW_CL)gcmiddle);
474		awm->~~insert_separator~~();
	474	awm->sep______________();
475	475	AW_insert_common_property_menu_entries(awm);
476		awm->~~insert_separator~~();
	476	awm->sep______________();
477	477	awm->insert_menu_topic("save_props", "Save Properties (phylo.arb)", "S", "savedef.hlp", AWM_ALL, (AW_CB)AW_save_properties, 0, 0);
478	478

trunk/SECEDIT/SEC_main.cxx

r8359	r8360
741	741	awm->insert_menu_topic("secedit_rename", "Rename structure", "R", 0, AWM_ALL, SEC_rename_structure, (AW_CL)db, 0);
742	742	awm->insert_menu_topic("secedit_delete", "Delete structure", "D", 0, AWM_ALL, SEC_delete_structure, (AW_CL)db, 0);
743		awm->~~insert_separator~~();
	743	awm->sep______________();
744	744	awm->insert_menu_topic("secedit_import", "Load structure", "L", "secedit_imexport.hlp", AWM_ALL, AW_POPUP, (AW_CL)SEC_import, (AW_CL)db);
745	745	awm->insert_menu_topic("secedit_export", "Save structure", "S", "secedit_imexport.hlp", AWM_ALL, AW_POPUP, (AW_CL)SEC_export, (AW_CL)db);
746		awm->~~insert_separator~~();
	746	awm->sep______________();
747	747	awm->insert_menu_topic("secStruct2xfig", "Export Structure to XFIG", "X", "sec_layout.hlp", AWM_ALL, AWT_popup_sec_export_window, (AW_CL)ntw, 0);
748	748	awm->insert_menu_topic("print_secedit", "Print Structure", "P", "secedit2prt.hlp", AWM_ALL, AWT_popup_print_window, (AW_CL)ntw, 0);
749		awm->~~insert_separator~~();
	749	awm->sep______________();
750	750
751	751	awm->insert_menu_topic("close", "Close", "C", "quit.hlp", AWM_ALL, (AW_CB)AW_POPDOWN, 0, 0);
…	…
753	753	awm->create_menu("Properties", "P", AWM_ALL);
754	754	awm->insert_menu_topic("sec_display", "Display options", "D", "sec_display.hlp", AWM_ALL, AW_POPUP, (AW_CL)SEC_create_display_window, 0);
755		awm->~~insert_separator~~();
	755	awm->sep______________();
756	756	awm->insert_menu_topic("props_secedit", "Change Colors and Fonts", "C", "secedit_props_data.hlp", AWM_ALL, AW_POPUP, (AW_CL)AW_create_gc_window, (AW_CL)aw_gc_manager);
757		awm->~~insert_separator~~();
	757	awm->sep______________();
758	758	awm->insert_menu_topic("sync_search_colors", "Sync search colors with EDIT4", "s", "sync_colors.hlp", AWM_ALL, SEC_sync_colors, (AW_CL)1, 0);
759	759	awm->insert_menu_topic("sync_range_colors", "Sync range colors with EDIT4", "r", "sync_colors.hlp", AWM_ALL, SEC_sync_colors, (AW_CL)2, 0);
760	760	awm->insert_menu_topic("sync_other_colors", "Sync other colors with EDIT4", "o", "sync_colors.hlp", AWM_ALL, SEC_sync_colors, (AW_CL)4, 0);
761	761	awm->insert_menu_topic("sync_all_colors", "Sync all colors with EDIT4", "a", "sync_colors.hlp", AWM_ALL, SEC_sync_colors, (AW_CL)(1\|2\|4), 0);
762		awm->~~insert_separator~~();
	762	awm->sep______________();
763	763	awm->insert_menu_topic("sec_save_props", "How to save properties", "p", "savedef.hlp", AWM_ALL, (AW_CB) AW_POPUP_HELP, (AW_CL)"sec_props.hlp", 0);
764	764

trunk/SL/DB_QUERY/db_query.cxx

r8359	r8360
2837	2837	if (awtqs->use_menu) {
2838	2838	sprintf(buffer, "Set Protection of Fields of Listed %s", Items); query_rel_menu_entry(aws, "s_prot_of_listed", query_id, buffer, "P", "set_protection.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_set_protection_window, (AW_CL)query);
2839		aws->~~insert_separator~~();
	2839	aws->sep______________();
2840	2840	sprintf(buffer, "Mark Listed %s, don't Change Rest", Items); query_rel_menu_entry(aws, "mark_listed", query_id, buffer, "M", "mark.hlp", AWM_ALL, mark_queried_cb, (AW_CL)query, (AW_CL)1 \| 8);
2841	2841	sprintf(buffer, "Mark Listed %s, Unmark Rest", Items); query_rel_menu_entry(aws, "mark_listed_unmark_rest", query_id, buffer, "L", "mark.hlp", AWM_ALL, mark_queried_cb, (AW_CL)query, (AW_CL)1);
2842	2842	sprintf(buffer, "Unmark Listed %s, don't Change Rest", Items); query_rel_menu_entry(aws, "unmark_listed", query_id, buffer, "U", "mark.hlp", AWM_ALL, mark_queried_cb, (AW_CL)query, (AW_CL)0 \| 8);
2843	2843	sprintf(buffer, "Unmark Listed %s, Mark Rest", Items); query_rel_menu_entry(aws, "unmark_listed_mark_rest", query_id, buffer, "R", "mark.hlp", AWM_ALL, mark_queried_cb, (AW_CL)query, (AW_CL)0);
2844		aws->~~insert_separator~~();
	2844	aws->sep______________();
2845	2845
2846	2846
…	…
2849	2849	if (query->gb_ref) {
2850	2850	dbq_assert(query->selector.type == QUERY_ITEM_SPECIES); // stuff below works only for species
2851		aws->~~insert_separator~~();
	2851	aws->sep______________();
2852	2852	if (query->expect_hit_in_ref_list) {
2853	2853	aws->insert_menu_topic("search_equal_fields_and_listed_in_I", "Search entries existing in both DBs and listed in the DB I hitlist", "S",

trunk/SL/DB_UI/ui_species.cxx

r8359	r8360
915	915	aws->insert_menu_topic("spec_create_field", "Create fields ...", "C", "spaf_create.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_field_create_window, (AW_CL)bis);
916	916	aws->insert_menu_topic("spec_convert_field", "Convert fields ...", "t", "spaf_convert.hlp", AWM_EXP, AW_POPUP, (AW_CL)create_field_convert_window, (AW_CL)bis);
917		aws->~~insert_separator~~();
	917	aws->sep______________();
918	918	aws->insert_menu_topic("spec_unhide_fields", "Show all hidden fields", "S", "scandb.hlp", AWM_ALL, (AW_CB)species_field_selection_list_unhide_all_cb, (AW_CL)gb_main, FIELD_FILTER_NDS);
919		aws->~~insert_separator~~();
	919	aws->sep______________();
920	920	aws->insert_menu_topic("spec_scan_unknown_fields", "Scan unknown fields", "u", "scandb.hlp", AWM_ALL, (AW_CB)species_field_selection_list_scan_unknown_cb, (AW_CL)gb_main, FIELD_FILTER_NDS);
921	921	aws->insert_menu_topic("spec_del_unused_fields", "Forget unused fields", "e", "scandb.hlp", AWM_ALL, (AW_CB)species_field_selection_list_delete_unused_cb, (AW_CL)gb_main, FIELD_FILTER_NDS);
…	…
1359	1359	aws->insert_menu_topic("species_create", "Create", "C", "spa_create.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_species_create_window, (AW_CL)gb_main);
1360	1360	aws->insert_menu_topic("species_convert_2_sai", "Convert to SAI", "S", "sp_sp_2_ext.hlp", AWM_ALL, move_species_to_extended, (AW_CL)gb_main, 0);
1361		aws->~~insert_separator~~();
	1361	aws->sep______________();
1362	1362
1363	1363	aws->create_menu("FIELDS", "F", AWM_ALL);

trunk/SL/TREEDISP/TreeCallbacks.cxx

r8313	r8360
325	325	nt_insert_mark_topic(awm, mask, attrib, "unmark_all", "Unmark all %sSpecies%s", "U", "sp_umrk_all.hlp", (AW_CB)NT_mark_all_cb, (AW_CL)ntw, (AW_CL)(0+affect));
326	326	nt_insert_mark_topic(awm, mask, attrib, "swap_marked", "Invert marks of all %sSpecies%s", "I", "sp_invert_mrk.hlp", (AW_CB)NT_mark_all_cb, (AW_CL)ntw, (AW_CL)(2+affect));
327		awm->~~insert_separator~~();
	327	awm->sep______________();
328	328
329	329	char *label = create_mark_menu_entry(attrib, "%sSpecies%s in Tree");
…	…
353	353	{
354	354	awm->insert_menu_topic("count_marked", "Count Marked Species", "C", "sp_count_mrk.hlp", AWM_ALL, (AW_CB)NT_count_mark_all_cb, (AW_CL)ntw, 0);
355		awm->~~insert_separator~~();
	355	awm->sep______________();
356	356	nt_insert_mark_topics(awm, AWM_ALL, ntw, 0, 0);
357		awm->~~insert_separator~~();
	357	awm->sep______________();
358	358
359	359	awm->insert_sub_menu("Complete sequences", "o");

trunk/SOURCE_TOOLS/check_ressources.pl

r6191	r8360
354	354	(
355	355	# regexp for function, param numbers, expectInIndex, isRessource,
356		~~[ qr/\b(AWMIMT)\b/, [ 2 ], \%pixmap, \&isBitmapRef, ],~~
357		~~[ qr/\b(AWMIMT)\b/, [ 4 ], \%helpfile, \&isHelpRef, ],~~
358	356	[ qr/\b(AW_POPUP_HELP)\b/, [ 2 ], \%helpfile, \&isHelpRef, ],
359	357	[ qr/\b(PGT_LoadPixmap)\b/, [ 1 ], \%pixmap, \&isPGTres, ],

trunk/WINDOW/AW_window.cxx

r8359	r8360
2984	2984	}
2985	2985
2986		void AW_window::~~insert_separator~~() {
	2986	void AW_window::sep______________() {
2987	2987	// create one help-sub-menu-point
2988	2988	XtVaCreateManagedWidget("", xmSeparatorWidgetClass,
2989	2989	p_w->menu_bar[p_w->menu_deep],
2990		~~NULL);~~
2991		}
2992
2993		~~void AW_window::insert_separator_help() {~~
2994		~~// create one help-sub-menu-point~~
2995		~~XtVaCreateManagedWidget("", xmSeparatorWidgetClass,~~
2996		~~p_w->help_pull_down,~~
2997	2990	NULL);
2998	2991	}

trunk/WINDOW/aw_window.hxx

r8279	r8360
361	361	void insert_sub_menu(AW_label name, const char *mnemonic, AW_active mask = AWM_ALL);
362	362	void insert_menu_topic(const char id, AW_label name, const char mnemonic, const char help_text, AW_active mask, void (f)(AW_window*, AW_CL, AW_CL), AW_CL cd1, AW_CL cd2);
	363	void sep______________(); // insert a separator
363	364	void close_sub_menu();
364	365
365		~~void insert_separator();~~
366	366	void insert_help_topic(AW_label name, const char mnemonic, const char help_text, AW_active mask, void (f)(AW_window, AW_CL, AW_CL), AW_CL cd1, AW_CL cd2);
367		void insert_separator_help();
	367
368	368	// ************ Create modes on the left side ****************
369	369	int create_mode(const char pixmap, const char help_text, AW_active mask, void (f)(AW_window, AW_CL, AW_CL), AW_CL cd1, AW_CL cd2);

Context Navigation

Legend:

trunk/AWT/AWT_db_browser.cxx

trunk/AWT/AWT_input_mask.cxx

trunk/DIST/DI_matr.cxx

trunk/EDIT4/ED4_root.cxx

trunk/GENOM/EXP_interface.cxx

trunk/GENOM/EXP_main.cxx

trunk/GENOM/GEN_interface.cxx

trunk/GENOM/GEN_map.cxx

trunk/MERGE/MG_main.cxx

trunk/MERGE/MG_species.cxx

trunk/NTREE/NT_extern.cxx

trunk/PARSIMONY/PARS_main.cxx

trunk/PHYLO/PH_main.cxx

trunk/SECEDIT/SEC_main.cxx

trunk/SL/DB_QUERY/db_query.cxx

trunk/SL/DB_UI/ui_species.cxx

trunk/SL/TREEDISP/TreeCallbacks.cxx

trunk/SOURCE_TOOLS/check_ressources.pl

trunk/WINDOW/AW_window.cxx

trunk/WINDOW/aw_window.hxx

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