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source: tags/old_import_filter/NTREE/NT_extern.cxx

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Last change on this file was 10117, checked in by westram, 11 years ago
fix include-chaos in NTREE all headers named .h (some had .hxx) as .cxx file removed obsolete header (NT_dbrepair.hxx, nt_join.hxx) removed some more definitions of nt_assert
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 80.7 KB

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1	// =============================================================== //
2	// //
3	// File : NT_extern.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "map_viewer.h"
12	#include "NT_local.h"
13	#include "ad_trees.h"
14	#include "NT_cb.h"
15
16	#include <seq_quality.h>
17	#include <multi_probe.hxx>
18	#include <st_window.hxx>
19	#include <GEN.hxx>
20	#include <EXP.hxx>
21
22	#include <TreeCallbacks.hxx>
23	#include <AW_rename.hxx>
24	#include <probe_design.hxx>
25	#include <primer_design.hxx>
26	#include <gde.hxx>
27	#include <awtc_submission.hxx>
28
29	#include <awti_export.hxx>
30
31	#include <awt.hxx>
32	#include <macros.hxx>
33	#include <awt_config_manager.hxx>
34	#include <awt_input_mask.hxx>
35	#include <awt_sel_boxes.hxx>
36	#include <awt_www.hxx>
37	#include <nds.h>
38
39	#include <db_query.h>
40	#include <dbui.h>
41
42	#include <aw_advice.hxx>
43	#include <aw_preset.hxx>
44	#include <aw_awars.hxx>
45	#include <aw_global_awars.hxx>
46	#include <aw_file.hxx>
47	#include <aw_msg.hxx>
48	#include <arb_progress.h>
49	#include <aw_root.hxx>
50	#include <aw_question.hxx>
51	#include <arb_strbuf.h>
52	#include <arb_strarray.h>
53	#include <arb_file.h>
54
55	#include <arb_version.h>
56	#include <refentries.h>
57
58	#define AWAR_EXPORT_NDS "tmp/export_nds"
59	#define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/separator"
60	#define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species"
61	#define AWAR_NTREE_TITLE_MODE "tmp/title_mode"
62
63	void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
64	void create_cprofile_var(AW_root *aw_root, AW_default aw_def);
65
66	void create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
67	AW_window create_insertDeleteColumn_window(AW_root root);
68	AW_window create_insertDeleteBySAI_window(AW_root root, AW_CL cl_gbmain);
69
70	AW_window create_tree_window(AW_root aw_root, AWT_graphic *awd);
71
72	static void nt_changesecurity(AW_root *aw_root) {
73	int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
74	GB_push_transaction(GLOBAL.gb_main);
75	GB_change_my_security(GLOBAL.gb_main, level);
76	GB_pop_transaction(GLOBAL.gb_main);
77	}
78
79	static void export_nds_cb(AW_window *aww, AW_CL print_flag) {
80	GB_transaction dummy(GLOBAL.gb_main);
81	GBDATA *gb_species;
82	const char *buf;
83	AW_root *aw_root = aww->get_root();
84	char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
85	FILE *out = fopen(name, "w");
86
87	if (!out) {
88	delete name;
89	aw_message("Error: Cannot open and write to file");
90	return;
91	}
92	make_node_text_init(GLOBAL.gb_main);
93	NDS_Type nds_type = (NDS_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
94	char *tree_name = aw_root->awar(AWAR_TREE)->read_string();
95
96	for (gb_species = GBT_first_marked_species(GLOBAL.gb_main);
97	gb_species;
98	gb_species = GBT_next_marked_species(gb_species))
99	{
100	buf = make_node_text_nds(GLOBAL.gb_main, gb_species, nds_type, 0, tree_name);
101	fprintf(out, "%s\n", buf);
102	}
103	AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
104	fclose(out);
105	if (print_flag) {
106	GB_ERROR error = GB_textprint(name);
107	if (error) aw_message(error);
108	}
109	free(tree_name);
110	free(name);
111	}
112
113	static AW_window create_nds_export_window(AW_root root) {
114	AW_window_simple *aws = new AW_window_simple;
115	aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
116	aws->load_xfig("sel_box_nds.fig");
117
118	aws->callback((AW_CB0)AW_POPDOWN);
119	aws->at("close");
120	aws->create_button("CLOSE", "CLOSE", "C");
121
122	aws->callback(AW_POPUP_HELP, (AW_CL)"arb_export_nds.hlp");
123	aws->at("help");
124	aws->create_button("HELP", "HELP", "H");
125
126	aws->callback((AW_CB0)AW_POPDOWN);
127	aws->at("cancel");
128	aws->create_button("CLOSE", "CANCEL", "C");
129
130	aws->at("save");
131	aws->callback(export_nds_cb, 0);
132	aws->create_button("SAVE", "SAVE", "S");
133
134	aws->at("print");
135	aws->callback(export_nds_cb, 1);
136	aws->create_button("PRINT", "PRINT", "P");
137
138	aws->at("toggle1");
139	aws->label("Column output");
140	aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR);
141	aws->insert_default_option("Space padded", "S", NDS_OUTPUT_SPACE_PADDED);
142	aws->insert_option ("TAB separated", "T", NDS_OUTPUT_TAB_SEPARATED);
143	aws->insert_option ("Comma separated", "C", NDS_OUTPUT_COMMA_SEPARATED);
144	aws->update_option_menu();
145
146	AW_create_fileselection(aws, AWAR_EXPORT_NDS);
147
148	return aws;
149	}
150
151	static void create_export_nds_awars(AW_root *awr, AW_default def)
152	{
153	AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds", def);
154	awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, NDS_OUTPUT_SPACE_PADDED, def);
155	}
156
157	static void AWAR_INFO_BUTTON_TEXT_change_cb(AW_root *awr) {
158	char *value = awr->awar(AWAR_SPECIES_NAME)->read_string();
159	awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
160	free(value);
161	}
162
163	static void expert_mode_changed_cb(AW_root *aw_root) {
164	aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
165	}
166
167	static void NT_toggle_expert_mode(AW_window *aww, AW_CL, AW_CL) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
168	static void NT_toggle_focus_policy(AW_window *aww, AW_CL, AW_CL) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
169
170	static void nt_create_all_awars(AW_root *awr, AW_default def) {
171	// creates awars for all modules reachable from ARB_NT main window
172
173	awr->awar_string(AWAR_FOOTER, "", def);
174	if (GB_read_clients(GLOBAL.gb_main)>=0) {
175	awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
176	}
177	else {
178	awr->awar_string(AWAR_TREE, "", def);
179	}
180
181	awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main);
182	awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main);
183	awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main);
184	awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown", GLOBAL.gb_main);
185	awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main);
186	awr->awar(AWAR_SPECIES_NAME)->add_callback(AWAR_INFO_BUTTON_TEXT_change_cb);
187	awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
188
189	awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
190
191	GEN_create_awars(awr, def, GLOBAL.gb_main);
192	EXP_create_awars(awr, def, GLOBAL.gb_main);
193	#if defined(DEBUG)
194	AWT_create_db_browser_awars(awr, def);
195	#endif // DEBUG
196
197	AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
198
199	awr->awar_int(AWAR_SECURITY_LEVEL, 0, def);
200	awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
201	#if defined(DEBUG) && 0
202	awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
203	#endif // DEBUG
204
205	create_insertDeleteColumn_variables(awr, def);
206	create_probe_design_variables(awr, def, GLOBAL.gb_main);
207	create_primer_design_variables(awr, def, GLOBAL.gb_main);
208	create_trees_var(awr, def);
209	DBUI::create_dbui_awars(awr, def);
210	AP_create_consensus_var(awr, def);
211	GDE_create_var(awr, def, GLOBAL.gb_main);
212	create_cprofile_var(awr, def);
213	NT_create_transpro_variables(awr, def);
214	NT_build_resort_awars(awr, def);
215	NT_create_trackAliChanges_Awars(awr, GLOBAL.gb_main);
216
217	NT_create_alignment_vars(awr, def);
218	create_nds_vars(awr, def, GLOBAL.gb_main);
219	create_export_nds_awars(awr, def);
220	awt_create_dtree_awars(awr, GLOBAL.gb_main);
221
222	awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
223	awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
224
225	AWTC_create_submission_variables(awr, GLOBAL.gb_main);
226	NT_createConcatenationAwars(awr, def);
227	NT_createValidNamesAwars(awr, def); // lothar
228	SQ_create_awars(awr, def);
229	RefEntries::create_refentries_awars(awr, def);
230
231	GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
232	if (!error) {
233	AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
234	awar_expert->add_callback(expert_mode_changed_cb);
235	awar_expert->touch();
236
237	awt_create_aww_vars(awr, def);
238	}
239
240	if (error) aw_message(error);
241	}
242
243	// --------------------------------------------------------------------------------
244
245	bool nt_disconnect_from_db(AW_root aw_root, GBDATA& gb_main_ref) {
246	// ask user if DB was not saved
247	// returns true if user allows to quit
248
249	// @@@ code here could as well be applied to both merge DBs
250	// - question about saving only with target DB!
251
252	if (gb_main_ref) {
253	if (GB_read_clients(gb_main_ref)>=0) {
254	if (GB_read_clock(gb_main_ref) > GB_last_saved_clock(gb_main_ref)) {
255	long secs;
256	secs = GB_last_saved_time(gb_main_ref);
257
258	#if defined(DEBUG)
259	secs = GB_time_of_day(); // simulate "just saved"
260	#endif // DEBUG
261
262	const char *quit_buttons = "Quit ARB,Do NOT quit";
263	if (secs) {
264	secs = GB_time_of_day() - secs;
265	if (secs>10) {
266	char *question = GBS_global_string_copy("You last saved your data %li:%li minutes ago\nSure to quit ?", secs/60, secs%60);
267	int dontQuit = aw_question("quit_arb", question, quit_buttons);
268	free(question);
269	if (dontQuit) {
270	return false;
271	}
272	}
273	}
274	else {
275	if (aw_question("quit_arb", "You never saved any data\nSure to quit ???", quit_buttons)) {
276	return false;
277	}
278	}
279	}
280	}
281
282	GBCMS_shutdown(gb_main_ref);
283
284	GBDATA *gb_main = gb_main_ref;
285	gb_main_ref = NULL; // avoid further usage
286
287	nt_assert(aw_root);
288	#if defined(WARN_TODO)
289	#warning instead of directly calling the following functions, try to add them as GB_atclose-callbacks
290	#endif
291	aw_root->unlink_awars_from_DB(gb_main);
292	AWT_destroy_input_masks();
293	#if defined(DEBUG)
294	AWT_browser_forget_db(gb_main);
295	#endif // DEBUG
296
297	GB_close(gb_main);
298	}
299	return true;
300	}
301
302	static void nt_run(const char *command) {
303	GB_ERROR error = GBK_system(command);
304	if (error) {
305	fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
306	#if defined(DEBUG)
307	GBK_dump_backtrace(stderr, "nt_run-error");
308	#endif
309	}
310	}
311
312	void nt_start(const char *arb_ntree_args, bool restart_with_new_ARB_PID) {
313	char *command = GBS_global_string_copy("(%s %s) &", restart_with_new_ARB_PID ? "arb" : "arb_ntree", arb_ntree_args);
314	nt_run(command);
315	free(command);
316	}
317
318	__ATTR__NORETURN static void really_exit(int exitcode, bool kill_my_clients) {
319	if (kill_my_clients) {
320	nt_run("(arb_clean >/dev/null 2>&1;echo ARB done) &"); // kills all clients
321	}
322	exit(exitcode);
323	}
324
325	void nt_exit(AW_window *aws, AW_CL exitcode) {
326	AW_root *aw_root = aws->get_root();
327	shutdown_macro_recording(aw_root);
328	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
329	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
330	really_exit(exitcode, is_server_and_has_clients);
331	}
332	}
333	void nt_restart(AW_root aw_root, const char arb_ntree_args, bool restart_with_new_ARB_PID) {
334	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
335	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
336	nt_start(arb_ntree_args, restart_with_new_ARB_PID);
337	really_exit(EXIT_SUCCESS, restart_with_new_ARB_PID && is_server_and_has_clients);
338	}
339	}
340
341	static void nt_start_2nd_arb(AW_window *aww, AW_CL cl_quit) {
342	// start 2nd arb with intro window
343	AW_root *aw_root = aww->get_root();
344	char *dir4intro;
345	GB_split_full_path(aw_root->awar(AWAR_DB_PATH)->read_char_pntr(), &dir4intro, NULL, NULL, NULL);
346
347	if (cl_quit) {
348	nt_restart(aw_root, dir4intro, true);
349	}
350	else {
351	nt_start(dir4intro, true);
352	}
353	free(dir4intro);
354	}
355
356	// --------------------------------------------------------------------------------
357
358	static void NT_save_quick_cb(AW_window *aww) {
359	AW_root *awr = aww->get_root();
360	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
361
362	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
363
364	GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
365	free( filename);
366	if (error) aw_message(error);
367	else AW_refresh_fileselection(awr, "tmp/nt/arbdb");
368	}
369
370
371	static void NT_save_quick_as_cb(AW_window *aww) {
372	AW_root *awr = aww->get_root();
373	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
374	GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename);
375	if (!error) AW_refresh_fileselection(awr, "tmp/nt/arbdb");
376	aww->hide_or_notify(error);
377
378	free(filename);
379	}
380	static void NT_save_as_cb(AW_window *aww) {
381	AW_root *awr = aww->get_root();
382	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
383	char *filetype = awr->awar(AWAR_DB_TYPE)->read_string();
384
385	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
386	GB_ERROR error = GB_save(GLOBAL.gb_main, filename, filetype);
387	if (!error) AW_refresh_fileselection(awr, "tmp/nt/arbdb");
388	aww->hide_or_notify(error);
389
390	free(filetype);
391	free(filename);
392	}
393
394	static AW_window NT_create_save_quick_as(AW_root aw_root, char *base_name)
395	{
396	static AW_window_simple *aws = 0;
397	if (aws) return (AW_window *)aws;
398
399	aws = new AW_window_simple;
400	aws->init(aw_root, "SAVE_CHANGES_TO", "SAVE CHANGES TO");
401	aws->load_xfig("save_as.fig");
402
403	aws->at("close"); aws->callback((AW_CB0)AW_POPDOWN);
404	aws->create_button("CLOSE", "CLOSE", "C");
405
406	aws->callback(AW_POPUP_HELP, (AW_CL)"save.hlp");
407	aws->at("help");
408	aws->create_button("HELP", "HELP", "H");
409
410	AW_create_fileselection(aws, base_name);
411
412	aws->at("comment");
413	aws->create_text_field(AWAR_DB_COMMENT);
414
415	aws->at("save"); aws->callback(NT_save_quick_as_cb);
416	aws->create_button("SAVE", "SAVE", "S");
417
418	return aws;
419	}
420
421	static void NT_database_optimization(AW_window *aww) {
422	arb_progress progress("Optimizing database", 2);
423
424	GB_push_my_security(GLOBAL.gb_main);
425	GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
426	if (!error) {
427	ConstStrArray ali_names;
428	GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
429
430	arb_progress ali_progress("Optimizing sequence data", ali_names.size());
431	ali_progress.allow_title_reuse();
432
433	error = GBT_check_data(GLOBAL.gb_main, 0);
434	error = GB_end_transaction(GLOBAL.gb_main, error);
435
436	if (!error) {
437	char *tree_name = aww->get_root()->awar("tmp/nt/arbdb/optimize_tree_name")->read_string();
438	for (int i = 0; ali_names[i]; ++i) {
439	error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
440	ali_progress.inc_and_check_user_abort(error);
441	}
442	free(tree_name);
443	}
444	}
445	progress.inc_and_check_user_abort(error);
446
447	if (!error) {
448	error = GB_optimize(GLOBAL.gb_main);
449	progress.inc_and_check_user_abort(error);
450	}
451
452	GB_pop_my_security(GLOBAL.gb_main);
453	aww->hide_or_notify(error);
454	}
455
456	static AW_window NT_create_database_optimization_window(AW_root aw_root) {
457	static AW_window_simple *aws = 0;
458	if (aws) return (AW_window *)aws;
459	GB_transaction dummy(GLOBAL.gb_main);
460
461	const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
462	aw_root->awar_string("tmp/nt/arbdb/optimize_tree_name", largest_tree);
463
464	aws = new AW_window_simple;
465	aws->init(aw_root, "OPTIMIZE_DATABASE", "OPTIMIZE DATABASE");
466	aws->load_xfig("optimize.fig");
467
468	aws->at("trees");
469	awt_create_selection_list_on_trees(GLOBAL.gb_main, (AW_window *)aws, "tmp/nt/arbdb/optimize_tree_name");
470
471	aws->at("close"); aws->callback((AW_CB0)AW_POPDOWN);
472	aws->create_button("CLOSE", "CLOSE", "C");
473
474	aws->callback(AW_POPUP_HELP, (AW_CL)"optimize.hlp");
475	aws->at("help");
476	aws->create_button("HELP", "HELP", "H");
477
478	aws->at("go");
479	aws->callback(NT_database_optimization);
480	aws->create_button("GO", "GO");
481	return aws;
482	}
483
484	static AW_window NT_create_save_as(AW_root aw_root, const char *base_name)
485	{
486	static AW_window_simple *aws = 0;
487	if (aws) return (AW_window *)aws;
488
489	aws = new AW_window_simple;
490	aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
491	aws->load_xfig("save_as.fig");
492
493	aws->at("close"); aws->callback((AW_CB0)AW_POPDOWN);
494	aws->create_button("CLOSE", "CLOSE", "C");
495
496	aws->callback(AW_POPUP_HELP, (AW_CL)"save.hlp");
497	aws->at("help");
498	aws->create_button("HELP", "HELP", "H");
499
500	AW_create_fileselection(aws, base_name);
501
502	aws->at("type");
503	aws->label("Type ");
504	aws->create_option_menu(AWAR_DB_TYPE);
505	aws->insert_option("Binary", "B", "b");
506	aws->insert_option("Bin (with FastLoad File)", "f", "bm");
507	aws->insert_default_option("Ascii", "A", "a");
508	aws->update_option_menu();
509
510	aws->at("optimize");
511	aws->callback(AW_POPUP, (AW_CL)NT_create_database_optimization_window, 0);
512	aws->help_text("optimize.hlp");
513	aws->create_button("OPTIMIZE", "OPTIMIZE");
514
515	aws->at("save"); aws->callback(NT_save_as_cb);
516	aws->create_button("SAVE", "SAVE", "S");
517
518	aws->at("comment");
519	aws->create_text_field(AWAR_DB_COMMENT);
520
521	return aws;
522	}
523
524	static void NT_undo_cb(AW_window *, AW_CL undo_type, AW_CL ntw) {
525	GB_ERROR error = GB_undo(GLOBAL.gb_main, (GB_UNDO_TYPE)undo_type);
526	if (error) aw_message(error);
527	else {
528	GB_transaction dummy(GLOBAL.gb_main);
529	((AWT_canvas *)ntw)->refresh();
530	}
531	}
532
533	static AWT_config_mapping_def tree_setting_config_mapping[] = {
534	{ AWAR_DTREE_BASELINEWIDTH, "line_width" },
535	{ AWAR_DTREE_VERICAL_DIST, "vert_dist" },
536	{ AWAR_DTREE_AUTO_JUMP, "auto_jump" },
537	{ AWAR_DTREE_SHOW_CIRCLE, "show_circle" },
538	{ AWAR_DTREE_SHOW_BRACKETS, "show_brackets" },
539	{ AWAR_DTREE_USE_ELLIPSE, "use_ellipse" },
540	{ AWAR_DTREE_CIRCLE_ZOOM, "circle_zoom" },
541	{ AWAR_DTREE_CIRCLE_MAX_SIZE, "circle_max_size" },
542	{ AWAR_DTREE_GREY_LEVEL, "grey_level" },
543	{ AWAR_DTREE_DENDRO_ZOOM_TEXT, "dendro_zoomtext" },
544	{ AWAR_DTREE_DENDRO_XPAD, "dendro_xpadding" },
545	{ AWAR_DTREE_RADIAL_ZOOM_TEXT, "radial_zoomtext" },
546	{ AWAR_DTREE_RADIAL_XPAD, "radial_xpadding" },
547	{ 0, 0 }
548	};
549
550	static char tree_setting_store_config(AW_window aww, AW_CL, AW_CL) {
551	AWT_config_definition cdef(aww->get_root(), tree_setting_config_mapping);
552	return cdef.read();
553	}
554	static void tree_setting_restore_config(AW_window aww, const char stored_string, AW_CL, AW_CL) {
555	AWT_config_definition cdef(aww->get_root(), tree_setting_config_mapping);
556	cdef.write(stored_string);
557	}
558
559	static AW_window NT_create_tree_setting(AW_root aw_root)
560	{
561	static AW_window_simple *aws = 0;
562	if (aws) return (AW_window *)aws;
563
564	aws = new AW_window_simple;
565	aws->init(aw_root, "TREE_PROPS", "TREE SETTINGS");
566	aws->load_xfig("awt/tree_settings.fig");
567
568	aws->at("close");
569	aws->callback((AW_CB0)AW_POPDOWN);
570	aws->create_button("CLOSE", "CLOSE", "C");
571
572	aws->at("help");
573	aws->callback(AW_POPUP_HELP, (AW_CL)"nt_tree_settings.hlp");
574	aws->create_button("HELP", "HELP", "H");
575
576	aws->at("button");
577	aws->auto_space(10, 10);
578	aws->label_length(30);
579
580	aws->label("Base line width");
581	aws->create_input_field(AWAR_DTREE_BASELINEWIDTH, 4);
582	aws->at_newline();
583
584	aws->label("Relative vertical distance");
585	aws->create_input_field(AWAR_DTREE_VERICAL_DIST, 4);
586	aws->at_newline();
587
588	aws->label("Auto jump");
589	aws->create_toggle(AWAR_DTREE_AUTO_JUMP);
590	aws->at_newline();
591
592	aws->label("Show group brackets");
593	aws->create_toggle(AWAR_DTREE_SHOW_BRACKETS);
594	aws->at_newline();
595
596	aws->label("Show bootstrap circles");
597	aws->create_toggle(AWAR_DTREE_SHOW_CIRCLE);
598	aws->at_newline();
599
600	aws->label("Use ellipses");
601	aws->create_toggle(AWAR_DTREE_USE_ELLIPSE);
602	aws->at_newline();
603
604	aws->label("Bootstrap circle zoom factor");
605	aws->create_input_field(AWAR_DTREE_CIRCLE_ZOOM, 4);
606	aws->at_newline();
607
608	aws->label("Boostrap radius limit");
609	aws->create_input_field(AWAR_DTREE_CIRCLE_MAX_SIZE, 4);
610	aws->at_newline();
611
612	aws->label("Grey Level of Groups%");
613	aws->create_input_field(AWAR_DTREE_GREY_LEVEL, 4);
614	aws->at_newline();
615
616	aws->label("Text zoom/pad (dendro)");
617	aws->create_toggle(AWAR_DTREE_DENDRO_ZOOM_TEXT);
618	aws->create_input_field(AWAR_DTREE_DENDRO_XPAD, 4);
619	aws->at_newline();
620
621	aws->label("Text zoom/pad (radial)");
622	aws->create_toggle(AWAR_DTREE_RADIAL_ZOOM_TEXT);
623	aws->create_input_field(AWAR_DTREE_RADIAL_XPAD, 4);
624	aws->at_newline();
625
626	aws->at("config");
627	AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "tree_settings", tree_setting_store_config, tree_setting_restore_config, 0, 0);
628
629	return (AW_window *)aws;
630
631	}
632
633	enum streamSource { FROM_PIPE, FROM_FILE };
634	static char stream2str(streamSource source, const char commandOrFile) {
635	char *output = 0;
636	FILE *in = 0;
637
638	switch (source) {
639	case FROM_PIPE: in = popen(commandOrFile, "r"); break;
640	case FROM_FILE: in = fopen(commandOrFile, "rt"); break;
641	}
642
643	if (in) {
644	GBS_strstruct *out = GBS_stropen(2000);
645	int c;
646
647	while (EOF != (c = fgetc(in))) GBS_chrcat(out, c);
648
649	switch (source) {
650	case FROM_PIPE: pclose(in); break;
651	case FROM_FILE: fclose(in); break;
652	}
653
654	// skip trailing linefeeds
655	long offset = GBS_memoffset(out);
656	while (offset>0 && GBS_mempntr(out)[offset-1] == '\n') {
657	GBS_str_cut_tail(out, 1);
658	offset--;
659	}
660
661	output = GBS_strclose(out);
662	}
663	return output;
664	}
665
666	inline void removeTrailingNewlines(char *str) {
667	char *eos = strchr(str, 0)-1;
668	while (eos >= str && eos[0] == '\n') *eos-- = 0;
669	}
670
671	inline void append_named_value(GBS_strstruct out, const char prefix, const char *value) {
672	GBS_strcat(out, GBS_global_string("%-*s: %s\n", 12, prefix, value));
673	}
674	inline void append_command_output(GBS_strstruct out, const char prefix, const char *command) {
675	char *output = stream2str(FROM_PIPE, command);
676	if (output) {
677	removeTrailingNewlines(output);
678	if (strcmp(output, "unknown") != 0) append_named_value(out, prefix, output);
679	free(output);
680	}
681	}
682
683	static void append_existing_file(GBS_strstruct out, const char file) {
684	char *content = stream2str(FROM_FILE, file);
685	if (content) {
686	GBS_strcat(out, file);
687	GBS_strcat(out, ":");
688	GBS_chrcat(out, strchr(content, '\n') ? '\n' : ' ');
689	GBS_strcat(out, content);
690	GBS_chrcat(out, '\n');
691	free(content);
692	}
693	}
694
695	static char *get_system_info(bool extended) {
696	GBS_strstruct *info = GBS_stropen(2000);
697
698	GBS_strcat(info,
699	"\n\n"
700	"----------------------------------------\n"
701	"Information about your system:\n"
702	"----------------------------------------\n"
703	);
704	append_named_value(info, "ARB version", ARB_VERSION);
705	#if defined(SHOW_WHERE_BUILD)
706	append_named_value(info, "build by", ARB_BUILD_USER "@" ARB_BUILD_HOST);
707	#endif // SHOW_WHERE_BUILD
708	append_named_value(info, "ARBHOME", GB_getenvARBHOME());
709
710	GBS_chrcat(info, '\n');
711	append_command_output(info, "Kernel", "uname -srv");
712	append_command_output(info, "Machine", "uname -m");
713	append_command_output(info, "CPU", "uname -p");
714	append_command_output(info, "Platform", "uname -i");
715	append_command_output(info, "OS", "uname -o");
716
717	GBS_chrcat(info, '\n');
718	append_existing_file(info, "/proc/version");
719	append_existing_file(info, "/proc/version_signature");
720	if (extended) {
721	append_existing_file(info, "/proc/cpuinfo");
722	append_existing_file(info, "/proc/meminfo");
723	}
724
725	return GBS_strclose(info);
726	}
727
728	static void NT_submit_mail(AW_window *aww, AW_CL cl_awar_base) {
729	char *mail_file;
730	char *mail_name = GB_unique_filename("arb_bugreport", "txt");
731	FILE *mail = GB_fopen_tempfile(mail_name, "wt", &mail_file);
732	GB_ERROR error = 0;
733
734	if (!mail) error = GB_await_error();
735	else {
736	char awar_base = (char )cl_awar_base;
737	char *address = aww->get_root()->awar(GBS_global_string("%s/address", awar_base))->read_string();
738	char *text = aww->get_root()->awar(GBS_global_string("%s/text", awar_base))->read_string();
739	char *plainaddress = GBS_string_eval(address, "\"=:'=\\=", 0); // Remove all dangerous symbols
740
741	fprintf(mail, "%s\n", text);
742	fclose(mail);
743
744	const char *command = GBS_global_string("mail '%s' <%s", plainaddress, mail_file);
745
746	nt_assert(GB_is_privatefile(mail_file, false));
747
748	error = GBK_system(command);
749	GB_unlink_or_warn(mail_file, &error);
750
751	free(plainaddress);
752	free(text);
753	free(address);
754	}
755
756	aww->hide_or_notify(error);
757
758	free(mail_file);
759	free(mail_name);
760	}
761
762
763	static AW_window NT_submit_bug(AW_root aw_root, int bug_report) {
764	static AW_window_simple *awss[2] = { 0, 0 };
765	if (awss[bug_report]) return (AW_window *)awss[bug_report];
766
767	AW_window_simple *aws = new AW_window_simple;
768	if (bug_report) {
769	aws->init(aw_root, "SUBMIT_BUG", "Submit a bug");
770	}
771	else {
772	aws->init(aw_root, "SUBMIT_REG", "Submit registration");
773	}
774	aws->load_xfig("bug_report.fig");
775
776	aws->at("close");
777	aws->callback((AW_CB0)AW_POPDOWN);
778	aws->create_button("CLOSE", "CLOSE", "C");
779
780	aws->at("help");
781	aws->callback(AW_POPUP_HELP, (AW_CL)"registration.hlp");
782	aws->create_button("HELP", "HELP", "H");
783
784	aws->at("what");
785	aws->create_autosize_button(NULL, (bug_report ? "Bug report" : "ARB Registration"));
786
787	char *awar_name_start = GBS_global_string_copy("/tmp/nt/feedback/%s", bug_report ? "bugreport" : "registration");
788
789	{
790	const char *awar_name_address = GBS_global_string("%s/address", awar_name_start);
791	aw_root->awar_string(awar_name_address, "arb@arb-home.de");
792
793	aws->at("mail");
794	aws->create_input_field(awar_name_address);
795	}
796
797	{
798	char *system_info = get_system_info(bug_report);
799	char *custom_text = 0;
800
801	if (bug_report) {
802	custom_text = strdup("Bug occurred in:\n"
803	" [which part of ARB?]\n"
804	"\n"
805	"The bug [ ] is reproducible\n"
806	" [ ] occurs randomly\n"
807	" [ ] occurs with specific data\n"
808	"\n"
809	"Detailed description:\n"
810	"[put your bug description here]\n"
811	"\n"
812	"\n"
813	"\n"
814	"Note: If the bug only occurs with a specific database,\n"
815	" please provide a way how we can download your database.\n"
816	" (e.g. upload it to a filesharing site and provide the URL here)\n"
817	"\n"
818	);
819	}
820	else {
821	custom_text = GBS_global_string_copy("***** Registration *****\n"
822	"\n"
823	"Name : %s\n"
824	"Department : \n"
825	"How many users : \n"
826	"\n"
827	"Why do you want to use arb ?\n"
828	"\n",
829	GB_getenvUSER());
830	}
831
832	const char *awar_name_text = GBS_global_string("%s/text", awar_name_start);
833	aw_root->awar_string(awar_name_text, GBS_global_string("%s\n%s", custom_text, system_info));
834	aws->at("box");
835	aws->create_text_field(awar_name_text);
836
837	free(custom_text);
838	free(system_info);
839	}
840
841	aws->at("go");
842	aws->callback(NT_submit_mail, (AW_CL)awar_name_start); // do not free awar_name_start
843	aws->create_button("SEND", "SEND");
844
845	awss[bug_report] = aws; // store for further use
846
847	char *haveMail = GB_executable("mail");
848	if (haveMail) free(haveMail);
849	else aw_message("Won't be able to send your mail (no mail program found)\nCopy&paste the text to your favorite mail software");
850
851	return aws;
852	}
853
854	static void NT_modify_cb(AW_window *aww, AW_CL cd1, AW_CL cd2)
855	{
856	AWT_canvas canvas = (AWT_canvas)cd1;
857	AW_window *aws = DBUI::create_species_info_window(aww->get_root(), (AW_CL)canvas->gb_main);
858	aws->activate();
859	nt_mode_event(aww, canvas, (AWT_COMMAND_MODE)cd2);
860	}
861
862	static void NT_primer_cb() {
863	GB_ERROR error = GB_xcmd("arb_primer", true, false);
864	if (error) aw_message(error);
865	}
866
867	static void NT_mark_duplicates(AW_window *aww, AW_CL ntwcl) {
868	AWT_canvas ntw = (AWT_canvas )ntwcl;
869	GB_transaction dummy(ntw->gb_main);
870	NT_mark_all_cb(aww, (AW_CL)ntw, (AW_CL)0);
871	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
872	tree_root->mark_duplicates();
873	tree_root->compute_tree(ntw->gb_main);
874	ntw->refresh();
875	}
876
877	static void NT_justify_branch_lenghs(AW_window *, AW_CL cl_ntw, AW_CL) {
878	AWT_canvas ntw = (AWT_canvas )cl_ntw;
879	GB_transaction dummy(ntw->gb_main);
880	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
881
882	if (tree_root) {
883	tree_root->justify_branch_lenghs(ntw->gb_main);
884	tree_root->compute_tree(ntw->gb_main);
885	GB_ERROR error = AWT_TREE(ntw)->save(ntw->gb_main, 0, 0, 0);
886	if (error) aw_message(error);
887	ntw->refresh();
888	}
889	}
890
891	#if defined(DEBUG)
892	static void NT_fix_database(AW_window *) {
893	GB_ERROR err = 0;
894	err = GB_fix_database(GLOBAL.gb_main);
895	if (err) aw_message(err);
896	}
897	#endif
898
899	static void relink_pseudo_species_to_organisms(GBDATA &ref_gb_node, char &ref_name, GB_HASH *organism_hash) {
900	if (ref_gb_node) {
901	if (GEN_is_pseudo_gene_species(ref_gb_node)) {
902	GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
903
904	if (gb_organism) {
905	char *name = GBT_read_string(gb_organism, "name");
906
907	if (name) {
908	freeset(ref_name, name);
909	ref_gb_node = gb_organism;
910	}
911	}
912	}
913	}
914	}
915
916	static void NT_pseudo_species_to_organism(AW_window *, AW_CL ntwcl) {
917	AWT_canvas ntw = (AWT_canvas )ntwcl;
918	GB_transaction dummy(ntw->gb_main);
919	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
920
921	if (tree_root) {
922	GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
923	tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
924	tree_root->compute_tree(ntw->gb_main);
925	GB_ERROR error = AWT_TREE(ntw)->save(ntw->gb_main, 0, 0, 0);
926	if (error) aw_message(error);
927	ntw->refresh();
928	GBS_free_hash(organism_hash);
929	}
930	}
931
932
933	// #########################################
934	// #########################################
935	// ### ###
936	// ## user mask section ##
937	// ### ###
938	// #########################################
939	// #########################################
940
941	class nt_item_type_species_selector : public awt_item_type_selector {
942	public:
943	nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
944	virtual ~nt_item_type_species_selector() OVERRIDE {}
945
946	virtual const char *get_self_awar() const OVERRIDE {
947	return AWAR_SPECIES_NAME;
948	}
949	virtual size_t get_self_awar_content_length() const OVERRIDE {
950	return 12; // should be enough for "nnaammee.999"
951	}
952	virtual void add_awar_callbacks(AW_root root, void (f)(AW_root*, AW_CL), AW_CL cl_mask) const OVERRIDE { // add callbacks to awars
953	root->awar(get_self_awar())->add_callback(f, cl_mask);
954	}
955	virtual void remove_awar_callbacks(AW_root root, void (f)(AW_root*, AW_CL), AW_CL cl_mask) const OVERRIDE { // remove callbacks to awars
956	root->awar(get_self_awar())->remove_callback(f, cl_mask);
957	}
958	virtual GBDATA current(AW_root root, GBDATA *gb_main) const OVERRIDE { // give the current item
959	char *species_name = root->awar(get_self_awar())->read_string();
960	GBDATA *gb_species = 0;
961
962	if (species_name[0]) {
963	GB_transaction dummy(gb_main);
964	gb_species = GBT_find_species(gb_main, species_name);
965	}
966
967	free(species_name);
968	return gb_species;
969	}
970	virtual const char *getKeyPath() const OVERRIDE { // give the keypath for items
971	return CHANGE_KEY_PATH;
972	}
973	};
974
975	static nt_item_type_species_selector item_type_species;
976
977	static void NT_open_mask_window(AW_window *aww, AW_CL cl_id, AW_CL) {
978	int id = int(cl_id);
979	const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
980	nt_assert(descriptor);
981	if (descriptor) AWT_initialize_input_mask(aww->get_root(), GLOBAL.gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
982	}
983
984	static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
985	AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, 0);
986	}
987	static AW_window create_colorize_species_window(AW_root aw_root) {
988	return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
989	}
990
991	/**
992	* Updates marked counter and issues redraw on tree if #marked changes.
993	* Called on any change of species_information container.
994	*/
995	static void NT_update_marked_counter(GBDATA* /species_info/, int* cl_aww, GB_CB_TYPE /cbt/) {
996	AW_window* aww = (AW_window*) cl_aww;
997	long count = GBT_count_marked_species(GLOBAL.gb_main);
998	const char *buffer = count ? GBS_global_string("%li marked", count) : "";
999	AW_awar *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
1000	char *oldval = counter->read_string();
1001	if (strcmp(oldval, buffer)) {
1002	counter->write_string(buffer);
1003	aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
1004	}
1005	free(oldval);
1006	}
1007
1008	static void NT_popup_species_window(AW_window *aww, AW_CL cl_gb_main, AW_CL) {
1009	// used to avoid that the species info window is stored in a menu (or with a button)
1010	DBUI::create_species_info_window(aww->get_root(), cl_gb_main)->activate();
1011	}
1012
1013	// --------------------------------------------------------------------------------------------------
1014
1015	static void NT_alltree_remove_leafs(AW_window *, AW_CL cl_mode, AW_CL cl_gb_main) { // @@@ test and activate for public
1016	GBDATA gb_main = (GBDATA)cl_gb_main;
1017	GBT_TREE_REMOVE_TYPE mode = (GBT_TREE_REMOVE_TYPE)cl_mode;
1018
1019	GB_ERROR error = 0;
1020	GB_transaction ta(gb_main);
1021
1022	ConstStrArray tree_names;
1023	GBT_get_tree_names(tree_names, gb_main, false);
1024
1025	if (!tree_names.empty()) {
1026	int treeCount = tree_names.size();
1027	arb_progress progress("Deleting from trees", treeCount);
1028	GB_HASH *species_hash = GBT_create_species_hash(gb_main);
1029
1030	for (int t = 0; t<treeCount && !error; t++) {
1031	progress.subtitle(tree_names[t]);
1032	GBT_TREE *tree = GBT_read_tree(gb_main, tree_names[t], -sizeof(GBT_TREE));
1033	if (!tree) {
1034	aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
1035	}
1036	else {
1037	int removed = 0;
1038	int groups_removed = 0;
1039
1040	tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
1041
1042	nt_assert(removed >= groups_removed);
1043
1044	if (!tree) {
1045	aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
1046	}
1047	else {
1048	if (removed>0) {
1049	error = GBT_write_tree(gb_main, 0, tree_names[t], tree);
1050	if (groups_removed>0) {
1051	aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
1052	}
1053	else {
1054	aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
1055	}
1056	}
1057	GBT_delete_tree(tree);
1058	}
1059	}
1060	progress.inc_and_check_user_abort(error);
1061	}
1062
1063	GBS_free_hash(species_hash);
1064	}
1065
1066	aw_message_if(ta.close(error));
1067	}
1068
1069	GBT_TREE nt_get_tree_root_of_canvas(AWT_canvas ntw) {
1070	AWT_graphic_tree *tree = AWT_TREE(ntw);
1071	if (tree) {
1072	AP_tree *root = tree->get_root_node();
1073	if (root) return root->get_gbt_tree();
1074	}
1075	return NULL;
1076	}
1077
1078	// --------------------------------------------------------------------------------------------------
1079
1080	static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
1081	GB_transaction ta(gb_main);
1082	GBT_mark_all(gb_main, 0);
1083
1084	DBItemSetIter end = referred.end();
1085	for (DBItemSetIter s = referred.begin(); s != end; ++s) {
1086	GB_write_flag(*s, 1);
1087	}
1088	return ARB_ERROR();
1089	}
1090
1091	static AW_window create_mark_by_refentries_window(AW_root awr, AW_CL cl_gbmain) {
1092	static AW_window *aws = NULL;
1093	if (!aws) {
1094	static RefEntries::ReferringEntriesHandler reh((GBDATA*)cl_gbmain, SPECIES_get_selector());
1095	aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULL, "Mark referenced", mark_referred_species);
1096	}
1097	return aws;
1098	}
1099
1100	// --------------------------------------------------------------------------------------------------
1101
1102	static void merge_from_to(AW_root awr, const char db_awar_name, bool merge_to) {
1103	const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
1104
1105	char *cmd = GBS_global_string_copy(
1106	merge_to
1107	? "arb_ntree : %s &"
1108	: "arb_ntree %s : &",
1109	db_name);
1110
1111	aw_message_if(GBK_system(cmd));
1112	free(cmd);
1113	}
1114
1115	static void merge_from_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, false); }
1116	static void merge_into_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, true); }
1117
1118	static AW_window NT_create_merge_from_window(AW_root awr, AW_CL) {
1119	static char *awar_name = NULL; // do not free, bound to callback
1120
1121	AW_window *aw_from =
1122	awt_create_load_box(awr, "Merge data from", "other ARB database",
1123	".", ".arb", &awar_name,
1124	merge_from_cb, NULL, NULL, NULL, AW_CL(&awar_name));
1125	return aw_from;
1126	}
1127	static AW_window NT_create_merge_to_window(AW_root awr, AW_CL) {
1128	static char *awar_name = NULL; // do not free, bound to callback
1129
1130	AW_window *aw_to =
1131	awt_create_load_box(awr, "Merge data to", "other ARB database",
1132	".", ".arb", &awar_name,
1133	merge_into_cb, NULL, NULL, NULL, AW_CL(&awar_name));
1134	return aw_to;
1135	}
1136
1137	// --------------------------------------------------------------------------------------------------
1138
1139	int NT_get_canvas_id(AWT_canvas *ntw) {
1140	// return number of canvas [0..MAX_NT_WINDOWS-1]
1141
1142	const char *tree_awar_name = ntw->user_awar;
1143
1144	const unsigned LEN = 15;
1145	#if defined(ASSERTION_USED)
1146	const char *EXPECT = "focus/tree_name";
1147	#endif
1148
1149	nt_assert(strlen(EXPECT) == LEN);
1150	nt_assert(memcmp(tree_awar_name, EXPECT, LEN) == 0);
1151
1152	int id;
1153	switch (tree_awar_name[LEN]) {
1154	default :
1155	nt_assert(0);
1156	// NDEBUG: fallback to 0
1157	case 0:
1158	id = 0;
1159	break;
1160
1161	case '_':
1162	id = atoi(tree_awar_name+LEN+1);
1163	nt_assert(id >= 1);
1164	break;
1165	}
1166	return id;
1167	}
1168
1169	// ##########################################
1170	// ##########################################
1171	// ### ###
1172	// ## create main window ##
1173	// ### ###
1174	// ##########################################
1175	// ##########################################
1176
1177	static AW_window popup_new_main_window(AW_root awr, AW_CL clone) {
1178	GB_push_transaction(GLOBAL.gb_main);
1179
1180	char window_title[256];
1181	char * const awar_tree = (char *)GB_calloc(sizeof(char), strlen(AWAR_TREE) + 10); // do not free this
1182
1183	if (clone) {
1184	sprintf(awar_tree, AWAR_TREE "_%li", clone);
1185	sprintf(window_title, "ARB_NT_%li", clone);
1186	}
1187	else {
1188	sprintf(awar_tree, AWAR_TREE);
1189	sprintf(window_title, "ARB_NT");
1190	}
1191	AW_window_menu_modes *awm = new AW_window_menu_modes;
1192	awm->init(awr, window_title, window_title, 0, 0);
1193
1194	awm->button_length(5);
1195
1196	if (!clone) AW_init_color_group_defaults("arb_ntree");
1197
1198	AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1199
1200	AWT_canvas *ntw;
1201	{
1202	AP_tree_sort old_sort_type = tree->tree_sort;
1203	tree->set_tree_type(AP_LIST_SIMPLE, NULL); // avoid NDS warnings during startup
1204
1205	ntw = new AWT_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, awar_tree);
1206	tree->set_tree_type(old_sort_type, ntw);
1207	ntw->set_mode(AWT_MODE_SELECT);
1208	}
1209
1210	{
1211	AW_awar *tree_awar = awr->awar_string(awar_tree);
1212	const char *tree_name = tree_awar->read_char_pntr();
1213	const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1214
1215	if (existing_tree_name) {
1216	tree_awar->write_string(existing_tree_name);
1217	NT_reload_tree_event(awr, ntw, 1); // load first tree
1218	}
1219	else {
1220	AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE\|AW_ADVICE_HELP, 0, "no_tree.hlp");
1221	tree->set_tree_type(AP_LIST_NDS, ntw); // no tree -> show NDS list
1222	}
1223
1224	tree_awar->add_callback((AW_RCB)NT_reload_tree_event, (AW_CL)ntw, 1);
1225	}
1226
1227	awr->awar(AWAR_SPECIES_NAME)->add_callback((AW_RCB)NT_jump_cb_auto, (AW_CL)ntw, 0);
1228	awr->awar(AWAR_DTREE_VERICAL_DIST)->add_callback((AW_RCB)AWT_resize_cb, (AW_CL)ntw, 0);
1229	awr->awar(AWAR_DTREE_BASELINEWIDTH)->add_callback((AW_RCB)AWT_expose_cb, (AW_CL)ntw, 0);
1230	awr->awar(AWAR_DTREE_SHOW_CIRCLE)->add_callback((AW_RCB)AWT_expose_cb, (AW_CL)ntw, 0);
1231	awr->awar(AWAR_DTREE_SHOW_BRACKETS)->add_callback((AW_RCB)AWT_expose_cb, (AW_CL)ntw, 0);
1232	awr->awar(AWAR_DTREE_CIRCLE_ZOOM)->add_callback((AW_RCB)AWT_expose_cb, (AW_CL)ntw, 0);
1233	awr->awar(AWAR_DTREE_CIRCLE_MAX_SIZE)->add_callback((AW_RCB)AWT_expose_cb, (AW_CL)ntw, 0);
1234	awr->awar(AWAR_DTREE_USE_ELLIPSE)->add_callback((AW_RCB)AWT_expose_cb, (AW_CL)ntw, 0);
1235
1236	awr->awar(AWAR_DTREE_RADIAL_ZOOM_TEXT)->add_callback((AW_RCB)NT_reinit_treetype, (AW_CL)ntw, 0);
1237	awr->awar(AWAR_DTREE_RADIAL_XPAD)->add_callback((AW_RCB)NT_reinit_treetype, (AW_CL)ntw, 0);
1238	awr->awar(AWAR_DTREE_DENDRO_ZOOM_TEXT)->add_callback((AW_RCB)NT_reinit_treetype, (AW_CL)ntw, 0);
1239	awr->awar(AWAR_DTREE_DENDRO_XPAD)->add_callback((AW_RCB)NT_reinit_treetype, (AW_CL)ntw, 0);
1240
1241	awr->awar(AWAR_TREE_REFRESH)->add_callback((AW_RCB)AWT_expose_cb, (AW_CL)ntw, 0);
1242	awr->awar(AWAR_COLOR_GROUPS_USE)->add_callback((AW_RCB)NT_recompute_cb, (AW_CL)ntw, 0);
1243
1244	GBDATA *gb_arb_presets = GB_search(GLOBAL.gb_main, "arb_presets", GB_CREATE_CONTAINER);
1245	GB_add_callback(gb_arb_presets, GB_CB_CHANGED, (GB_CB)AWT_expose_cb, (int *)ntw);
1246
1247	bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1248
1249	// --------------
1250	// File
1251
1252	#if defined(DEBUG)
1253	AWT_create_debug_menu(awm);
1254	#endif // DEBUG
1255
1256	bool allow_new_window = (NT_get_canvas_id(ntw)+1) < MAX_NT_WINDOWS;
1257
1258	if (clone) {
1259	awm->create_menu("File", "F", AWM_ALL);
1260	if (allow_new_window) {
1261	awm->insert_menu_topic(awm->local_id("new_window"), "New window (same database)", "N", "newwindow.hlp", AWM_ALL, AW_POPUP, (AW_CL)popup_new_main_window, clone+1);
1262	}
1263	awm->insert_menu_topic("close", "Close", "C", 0, AWM_ALL, (AW_CB)AW_POPDOWN, 0, 0);
1264	}
1265	else {
1266	#if defined(DEBUG)
1267	// add more to debug-menu
1268	awm->sep______________();
1269	awm->insert_menu_topic("fix_db", "Fix database", "F", 0, AWM_ALL, (AW_CB)NT_fix_database, 0, 0);
1270	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);
1271	awm->insert_menu_topic("test_compr", "Test compression", "T", 0, AWM_ALL, (AW_CB)GBT_compression_test, (AW_CL) GLOBAL.gb_main, 0);
1272	awm->sep______________();
1273	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);
1274	#endif // DEBUG
1275
1276	awm->create_menu("File", "F", AWM_ALL);
1277	{
1278	awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, (AW_CB)NT_save_quick_cb, 0, 0);
1279	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");
1280	if (allow_new_window) {
1281	awm->sep______________();
1282	awm->insert_menu_topic("new_window", "New window (same database)", "N", "newwindow.hlp", AWM_ALL, AW_POPUP, (AW_CL)popup_new_main_window, clone+1);
1283	}
1284	awm->sep______________();
1285	awm->insert_menu_topic("optimize_db", "Optimize database", "O", "optimize.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_database_optimization_window, 0);
1286	awm->sep______________();
1287
1288	awm->insert_sub_menu("Import", "I");
1289	{
1290	awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_merge_from_window, 0);
1291	awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, NT_import_sequences, 0, 0);
1292	GDE_load_menu(awm, AWM_EXP, "Import");
1293	}
1294	awm->close_sub_menu();
1295
1296	awm->insert_sub_menu("Export", "E");
1297	{
1298	awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_merge_to_window, 0);
1299	awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, AW_POPUP, (AW_CL)open_AWTC_export_window, (AW_CL)GLOBAL.gb_main);
1300	GDE_load_menu(awm, AWM_ALL, "Export");
1301	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);
1302	}
1303	awm->close_sub_menu();
1304	awm->sep______________();
1305
1306	insert_macro_menu_entry(awm, false);
1307
1308	awm->insert_sub_menu("Registration/Bug report/Version info", "R");
1309	{
1310	awm->insert_menu_topic("registration", "Registration", "R", "registration.hlp", AWM_ALL, (AW_CB)AW_POPUP, (AW_CL)NT_submit_bug, 0);
1311	awm->insert_menu_topic("bug_report", "Bug report", "B", "registration.hlp", AWM_ALL, (AW_CB)AW_POPUP, (AW_CL)NT_submit_bug, 1);
1312	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);
1313	}
1314	awm->close_sub_menu();
1315	#if 0
1316	awm->sep______________();
1317	awm->insert_menu_topic("undo", "Undo", "U", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_cb, (AW_CL)GB_UNDO_UNDO, (AW_CL)ntw);
1318	awm->insert_menu_topic("redo", "Redo", "d", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_cb, (AW_CL)GB_UNDO_REDO, (AW_CL)ntw);
1319	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);
1320	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);
1321	#endif
1322
1323	awm->sep______________();
1324
1325	awm->insert_menu_topic("new_arb", "Start second database", "o", "quit.hlp", AWM_ALL, nt_start_2nd_arb, 0);
1326	awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, nt_start_2nd_arb, 1);
1327	awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, nt_exit, EXIT_SUCCESS);
1328	}
1329
1330	// -----------------
1331	// Species
1332
1333	awm->create_menu("Species", "c", AWM_ALL);
1334	{
1335	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);
1336	awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, NT_popup_species_window, (AW_CL)GLOBAL.gb_main, 0);
1337
1338	awm->sep______________();
1339
1340	NT_insert_mark_submenus(awm, ntw, 1);
1341	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);
1342	awm->insert_menu_topic("species_colors", "Set Colors", "l", "mark_colors.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_colorize_species_window, 0);
1343	awm->insert_menu_topic("selection_admin", "Configurations", "o", "configuration.hlp", AWM_ALL, NT_popup_configuration_admin, (AW_CL)ntw, 0);
1344
1345	awm->sep______________();
1346
1347	awm->insert_sub_menu("Database fields admin", "f");
1348	DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1349	awm->close_sub_menu();
1350	NT_create_mask_submenu(awm);
1351
1352	awm->sep______________();
1353
1354	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);
1355
1356	awm->insert_sub_menu("Sort Species", "r");
1357	{
1358	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);
1359	awm->insert_menu_topic("sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, NT_resort_data_by_phylogeny, (AW_CL)ntw, 0);
1360	}
1361	awm->close_sub_menu();
1362
1363	awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1364	{
1365	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);
1366	awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "join_species.hlp", AWM_EXP, AW_POPUP, (AW_CL)NT_create_species_join_window, 0);
1367	}
1368	awm->close_sub_menu();
1369
1370	awm->sep______________();
1371
1372	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);
1373
1374	awm->sep______________();
1375
1376	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);
1377
1378	awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1379	{
1380	awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames, 0, 0);
1381	awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames, 0, 0);
1382	awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames, 0, 0);
1383	awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, AW_POPUP, (AW_CL)NT_searchManuallyNames, 0);
1384	}
1385	awm->close_sub_menu();
1386	}
1387
1388	// ----------------------------
1389	// Genes + Experiment
1390
1391	if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1392
1393	// ------------------
1394	// Sequence
1395
1396	awm->create_menu("Sequence", "S", AWM_ALL);
1397	{
1398	awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_alignment_window, 0);
1399	awm->insert_sub_menu("Insert/delete", "I");
1400	{
1401	awm->insert_menu_topic("ins_del_col", ".. column", "I", "insdel.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_insertDeleteColumn_window, 0);
1402	awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_insertDeleteBySAI_window, (AW_CL)GLOBAL.gb_main);
1403	}
1404	awm->close_sub_menu();
1405	awm->sep______________();
1406
1407	awm->insert_sub_menu("Edit Sequences", "E");
1408	{
1409	awm->insert_menu_topic("new_arb_edit4", "Using marked species and tree", "m", "arb_edit4.hlp", AWM_ALL, NT_start_editor_on_tree, 0, (AW_CL)ntw);
1410	awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, NT_start_editor_on_tree, -1, (AW_CL)ntw);
1411	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);
1412	}
1413	awm->close_sub_menu();
1414
1415	awm->sep______________();
1416
1417	awm->insert_sub_menu("Align Sequences", "S");
1418	{
1419	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);
1420	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);
1421	GDE_load_menu(awm, AWM_ALL, "Align");
1422	}
1423	awm->close_sub_menu();
1424	awm->insert_menu_topic("seq_concat", "Concatenate Sequences/Alignments", "C", "concatenate_align.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_createConcatenationWindow, 0);
1425	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);
1426	awm->sep______________();
1427
1428	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);
1429	awm->insert_menu_topic("arb_dist", "Distance matrix", "D", "dist.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_dist &", 0);
1430	awm->sep______________();
1431
1432	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);
1433	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);
1434
1435	awm->sep______________();
1436
1437	GDE_load_menu(awm, AWM_ALL, "Print");
1438	}
1439
1440	// -------------
1441	// SAI
1442
1443	awm->create_menu("SAI", "A", AWM_ALL);
1444	{
1445	awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_extendeds_window, 0);
1446	awm->insert_sub_menu("Create SAI using ...", "C");
1447	{
1448	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);
1449	awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AW_POPUP, (AW_CL)AP_open_con_expert_window, 0);
1450	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);
1451	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);
1452	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);
1453
1454	GDE_load_menu(awm, AWM_EXP, "SAI");
1455	}
1456	awm->close_sub_menu();
1457
1458	awm->insert_sub_menu("Other functions", "O");
1459	{
1460	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);
1461	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);
1462	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);
1463	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);
1464	}
1465	awm->close_sub_menu();
1466	}
1467
1468	// ----------------
1469	// Probes
1470
1471	awm->create_menu("Probes", "P", AWM_ALL);
1472	{
1473	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);
1474	awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, AW_POPUP, (AW_CL)create_multiprobe_window, (AW_CL)ntw);
1475	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);
1476	awm->sep______________();
1477	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);
1478	awm->insert_menu_topic("primer_design", "Design Sequencing Primers", "S", "primer.hlp", AWM_EXP, (AW_CB)NT_primer_cb, 0, 0);
1479	awm->sep______________();
1480	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);
1481	}
1482
1483	}
1484
1485	// --------------
1486	// Tree
1487
1488	awm->create_menu("Tree", "T", AWM_ALL);
1489	{
1490	if (!clone) {
1491	awm->insert_sub_menu("Add Species to Existing Tree", "A");
1492	{
1493	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);
1494	awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_pars &", 0);
1495	GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1496	}
1497	awm->close_sub_menu();
1498	}
1499
1500	awm->insert_sub_menu("Remove Species from Tree", "R");
1501	{
1502	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);
1503	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);
1504	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);
1505	#if defined(DEVEL_RALF)
1506	#if defined(WARN_TODO)
1507	#warning add "remove duplicates from tree"
1508	#endif
1509	awm->sep______________();
1510	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);
1511	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);
1512	#endif // DEVEL_RALF
1513	}
1514	awm->close_sub_menu();
1515
1516	if (!clone) {
1517	awm->insert_sub_menu("Build tree from sequence data", "B");
1518	{
1519	awm->insert_sub_menu("Distance matrix methods", "D");
1520	awm->insert_menu_topic("arb_dist", "ARB Neighbour Joining", "J", "dist.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_dist &", 0);
1521	GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1522	awm->close_sub_menu();
1523
1524	awm->insert_sub_menu("Maximum Parsimony methods", "P");
1525	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1526	awm->close_sub_menu();
1527
1528	awm->insert_sub_menu("Maximum Likelihood methods", "L");
1529	GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelyhood EXP");
1530	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelyhood");
1531	awm->close_sub_menu();
1532
1533	awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1534	GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1535	awm->close_sub_menu();
1536	}
1537	awm->close_sub_menu();
1538	}
1539
1540	awm->insert_menu_topic("consense_tree", "Build consense tree", "c", "consense_tree.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_create_consense_window, 0);
1541	awm->sep______________();
1542
1543	awm->insert_sub_menu("Reset zoom", "z");
1544	{
1545	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);
1546	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);
1547	}
1548	awm->close_sub_menu();
1549	awm->insert_sub_menu("Collapse/Expand tree", "C");
1550	{
1551	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);
1552	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);
1553	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);
1554	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);
1555	awm->sep______________();
1556	NT_insert_color_collapse_submenu(awm, ntw);
1557	}
1558	awm->close_sub_menu();
1559	awm->insert_sub_menu("Beautify tree", "e");
1560	{
1561	awm->insert_menu_topic(awm->local_id("beautifyt_tree"), "#beautifyt.xpm", "", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 0);
1562	awm->insert_menu_topic(awm->local_id("beautifyc_tree"), "#beautifyc.xpm", "", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 1);
1563	awm->insert_menu_topic(awm->local_id("beautifyb_tree"), "#beautifyb.xpm", "", "resorttree.hlp", AWM_ALL, (AW_CB)NT_resort_tree_cb, (AW_CL)ntw, 2);
1564	}
1565	awm->close_sub_menu();
1566	awm->insert_sub_menu("Modify branches", "M");
1567	{
1568	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);
1569	awm->sep______________();
1570	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);
1571	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);
1572	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);
1573	awm->sep______________();
1574	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);
1575	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);
1576
1577	}
1578	awm->close_sub_menu();
1579
1580	awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "B", "branch_analysis.hlp", AWM_ALL, AW_POPUP, (AW_CL)NT_open_branch_analysis_window, (AW_CL)ntw);
1581	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);
1582
1583	awm->sep______________();
1584
1585	awm->insert_menu_topic(awm->local_id("tree_select"), "Select Tree", "T", 0, AWM_ALL, AW_POPUP, (AW_CL)NT_create_select_tree_window, (AW_CL)awar_tree);
1586	awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", 0, AWM_ALL, (AW_CB)NT_select_bottom_tree, (AW_CL)awar_tree, 0);
1587
1588	awm->sep______________();
1589
1590	if (!clone) {
1591	awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1592	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);
1593	}
1594	awm->sep______________();
1595
1596	awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, (AW_CB)AW_POPUP_HELP, (AW_CL)"trans_anal.hlp", 0);
1597
1598	awm->sep______________();
1599
1600	if (!clone) {
1601	awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, AWT_popup_print_window, (AW_CL)ntw, 0);
1602	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);
1603	awm->sep______________();
1604	}
1605
1606	if (is_genome_db) {
1607	awm->insert_sub_menu("Other..", "O", AWM_EXP);
1608	{
1609	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);
1610	}
1611	awm->close_sub_menu();
1612	}
1613	}
1614
1615	if (!clone) {
1616	// ---------------
1617	// Tools
1618
1619	awm->create_menu("Tools", "o", AWM_ALL);
1620	{
1621	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);
1622	awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1623	{
1624	awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, NT_rerepair_DB, (AW_CL)GLOBAL.gb_main, 0);
1625	}
1626	awm->close_sub_menu();
1627	awm->insert_sub_menu("Network", "N", AWM_EXP);
1628	{
1629	GDE_load_menu(awm, AWM_EXP, "User");
1630	}
1631	awm->close_sub_menu();
1632	awm->sep______________();
1633
1634	awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1635	{
1636	GDE_load_menu(awm, AWM_EXP, 0, 0);
1637	}
1638	awm->close_sub_menu();
1639
1640	awm->insert_sub_menu("WL specials", "W", AWM_EXP);
1641	{
1642	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);
1643	}
1644	awm->close_sub_menu();
1645
1646	awm->sep______________();
1647	awm->insert_menu_topic("xterm", "Start XTERM", "X", 0, AWM_ALL, (AW_CB)GB_xterm, 0, 0);
1648	}
1649	// --------------------
1650	// Properties
1651
1652	awm->create_menu("Properties", "r", AWM_ALL);
1653	{
1654	awm->insert_menu_topic("props_menu", "Frame settings", "F", "props_frame.hlp", AWM_ALL, AW_POPUP, (AW_CL)AW_preset_window, 0);
1655	awm->insert_sub_menu("Tree settings", "T");
1656	{
1657	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);
1658	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)ntw->gc_manager);
1659	}
1660	awm->close_sub_menu();
1661	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);
1662	awm->sep______________();
1663	awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", 0, AWM_ALL, NT_toggle_expert_mode, 0, 0);
1664	awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "f", 0, AWM_ALL, NT_toggle_focus_policy, 0, 0);
1665	awm->sep______________();
1666	AW_insert_common_property_menu_entries(awm);
1667	awm->sep______________();
1668	awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, (AW_CB) AW_save_properties, 0, 0);
1669	}
1670	}
1671
1672	awm->insert_help_topic("ARB_NT help", "N", "arb_ntree.hlp", AWM_ALL, (AW_CB)AW_POPUP_HELP, (AW_CL)"arb_ntree.hlp", 0);
1673
1674	awm->create_mode("select.xpm", "mode_select.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_SELECT);
1675	awm->create_mode("mark.xpm", "mode_mark.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_MARK);
1676	awm->create_mode("group.xpm", "mode_group.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_GROUP);
1677	awm->create_mode("pzoom.xpm", "mode_pzoom.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_ZOOM);
1678	awm->create_mode("lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_LZOOM);
1679	awm->create_mode("modify.xpm", "mode_info.hlp", AWM_ALL, (AW_CB)NT_modify_cb, (AW_CL)ntw, (AW_CL)AWT_MODE_EDIT);
1680	awm->create_mode("www_mode.xpm", "mode_www.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_WWW);
1681
1682	awm->create_mode("line.xpm", "mode_width.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_LINE);
1683	awm->create_mode("rot.xpm", "mode_rotate.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_ROT);
1684	awm->create_mode("spread.xpm", "mode_angle.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_SPREAD);
1685	awm->create_mode("swap.xpm", "mode_swap.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_SWAP);
1686	awm->create_mode("length.xpm", "mode_length.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_LENGTH);
1687	awm->create_mode("move.xpm", "mode_move.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_MOVE);
1688	awm->create_mode("setroot.xpm", "mode_set_root.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_SETROOT);
1689	awm->create_mode("reset.xpm", "mode_reset.hlp", AWM_ALL, (AW_CB)nt_mode_event, (AW_CL)ntw, (AW_CL)AWT_MODE_RESET);
1690
1691	awm->set_info_area_height(250);
1692	awm->at(5, 2);
1693	awm->auto_space(-2, -2);
1694	awm->shadow_width(1);
1695
1696	// -------------------------
1697	// create top area
1698
1699	int first_liney;
1700	int leftx;
1701	awm->get_at_position(&leftx, &first_liney);
1702
1703	// ---------------------
1704	// quit + help
1705
1706	awm->button_length(0);
1707
1708	if (clone) {
1709	awm->callback(AW_POPDOWN);
1710	awm->create_button("CLOSE", "#close.xpm");
1711	}
1712	else {
1713	awm->callback(nt_exit, EXIT_SUCCESS);
1714	awm->help_text("quit.hlp");
1715	awm->create_button("QUIT", "#quit.xpm");
1716	}
1717
1718	int db_pathx = awm->get_at_xposition();
1719
1720	// now fetch the yposition for the 2nd button line
1721	awm->at_newline();
1722	int second_liney = awm->get_at_yposition();
1723
1724	awm->callback(AW_help_entry_pressed);
1725	awm->help_text("arb_ntree.hlp");
1726	awm->create_button("?", "#help.xpm");
1727
1728	// --------------------------
1729	// save + undo/redo
1730
1731	awm->callback(NT_save_quick_cb);
1732	awm->help_text("save.hlp");
1733	awm->create_button("SAVE", "#save.xpm");
1734
1735	awm->callback(AW_POPUP, (AW_CL)NT_create_save_as, (AW_CL)"tmp/nt/arbdb");
1736	awm->help_text("saveas.hlp");
1737	awm->create_button("SAVE_AS", "#saveAs.xpm");
1738
1739	// undo/redo:
1740	awm->callback(NT_undo_cb, (AW_CL)GB_UNDO_UNDO, (AW_CL)ntw);
1741	awm->help_text("undo.hlp");
1742	awm->create_button("UNDO", "#undo.xpm");
1743
1744	awm->callback(NT_undo_cb, (AW_CL)GB_UNDO_REDO, (AW_CL)ntw);
1745	awm->help_text("undo.hlp");
1746	awm->create_button("REDO", "#redo.xpm");
1747
1748	int db_pathx2 = awm->get_at_xposition();
1749
1750	// fetch position for mode help-line:
1751	awm->at_newline();
1752	int third_liney = awm->get_at_yposition();
1753
1754	awm->at(db_pathx, first_liney);
1755	// size of DB-name button is determined by buttons below:
1756	awm->at_set_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1757	awm->callback(AW_POPUP, (AW_CL)NT_create_save_quick_as, (AW_CL)"tmp/nt/arbdb"); // do sth else
1758	awm->help_text("saveas.hlp");
1759	awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1760
1761	// -----------------------------
1762	// tree + tree display
1763
1764	#define TREE_BUTTON_OVERSIZE 6
1765
1766	int db_treex = awm->get_at_xposition();
1767	int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1768
1769	awm->at(db_treex, second_uppery);
1770	awm->button_length(0);
1771
1772	awm->callback((AW_CB)NT_set_tree_style, (AW_CL)ntw, (AW_CL)AP_TREE_RADIAL);
1773	awm->help_text("tr_type_radial.hlp");
1774	awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1775
1776	awm->callback((AW_CB)NT_set_tree_style, (AW_CL)ntw, (AW_CL)AP_TREE_NORMAL);
1777	awm->help_text("tr_type_list.hlp");
1778	awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1779
1780	awm->callback((AW_CB)NT_set_tree_style, (AW_CL)ntw, (AW_CL)AP_TREE_IRS);
1781	awm->help_text("tr_type_irs.hlp");
1782	awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1783
1784	awm->callback((AW_CB)NT_set_tree_style, (AW_CL)ntw, (AW_CL)AP_LIST_NDS);
1785	awm->help_text("tr_type_nds.hlp");
1786	awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1787
1788	int db_treex2 = awm->get_at_xposition();
1789
1790	awm->at(db_treex, first_liney);
1791	// size of tree-name button is determined by buttons below:
1792	awm->at_set_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1793	awm->callback((AW_CB2)AW_POPUP, (AW_CL)NT_create_select_tree_window, (AW_CL)awar_tree);
1794	awm->help_text("nt_tree_select.hlp");
1795	awm->create_button("SELECT_A_TREE", awar_tree);
1796
1797	// ---------------------------------------------------------------
1798	// protection, alignment + editor (and maybe Genome Map)
1799
1800	int db_alignx = awm->get_at_xposition();
1801
1802	// editor and genemap buttons have to be 44x24 sized
1803	#define EDIT_XSIZE 50
1804	#define EDIT_YSIZE 30 // same as 'save as' buttons
1805
1806	// first draw protection:
1807	int protectx = db_alignx + 2*EDIT_XSIZE;
1808
1809	awm->at(protectx+2, first_liney+1);
1810	awm->button_length(0);
1811	awm->create_button(NULL, "#protect.xpm");
1812
1813	awm->at(protectx, second_liney+2);
1814	awm->create_option_menu(AWAR_SECURITY_LEVEL);
1815	awm->insert_option("0", 0, 0);
1816	awm->insert_option("1", 0, 1);
1817	awm->insert_option("2", 0, 2);
1818	awm->insert_option("3", 0, 3);
1819	awm->insert_option("4", 0, 4);
1820	awm->insert_option("5", 0, 5);
1821	awm->insert_default_option("6", 0, 6);
1822	awm->update_option_menu();
1823
1824	int db_searchx = awm->get_at_xposition() - 7;
1825
1826	// draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1827	awm->at(db_alignx, second_liney);
1828
1829	awm->at_set_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1830	awm->callback(NT_start_editor_on_tree, 0, (AW_CL)ntw);
1831	awm->help_text("arb_edit4.hlp");
1832	awm->create_button("EDIT_SEQUENCES", "#edit.xpm");
1833
1834	if (is_genome_db) {
1835	awm->at_set_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1836	awm->callback((AW_CB)AW_POPUP, (AW_CL)GEN_create_first_map, (AW_CL)GLOBAL.gb_main); // initial gene map
1837	awm->help_text("gene_map.hlp");
1838	awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1839	}
1840
1841	int db_alignx2 = awm->get_at_xposition();
1842
1843	awm->at(db_alignx, first_liney);
1844	awm->at_set_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1845	awm->callback(AW_POPUP, (AW_CL)NT_open_select_alignment_window, 0);
1846	awm->help_text("nt_align_select.hlp");
1847	awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1848
1849	// -------------------------------
1850	// create mode-help line
1851
1852	awm->at(leftx, third_liney);
1853	awm->button_length(AWAR_FOOTER_MAX_LEN);
1854	awm->create_button(0, AWAR_FOOTER);
1855
1856	awm->at_newline();
1857	int bottomy = awm->get_at_yposition();
1858
1859	// ---------------------------------------
1860	// Info / marked / Search / Jump
1861
1862	awm->button_length(7);
1863
1864	awm->at(db_searchx, first_liney);
1865	awm->callback(AW_POPUP, (AW_CL)DBUI::create_species_query_window, (AW_CL)GLOBAL.gb_main);
1866	awm->help_text("sp_search.hlp");
1867	awm->create_button("SEARCH", "Search");
1868
1869	awm->at(db_searchx, second_uppery);
1870	awm->callback((AW_CB)NT_jump_cb, (AW_CL)ntw, 1);
1871	awm->help_text("tr_jump.hlp");
1872	awm->create_button("JUMP", "Jump");
1873
1874	int db_infox = awm->get_at_xposition();
1875
1876	awm->at(db_infox, first_liney);
1877	awm->button_length(13);
1878	awm->callback(NT_popup_species_window, (AW_CL)GLOBAL.gb_main, 0);
1879	awm->help_text("sp_search.hlp");
1880	awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1881
1882	awm->at(db_infox, second_uppery);
1883	awm->button_length(13);
1884	awm->help_text("marked_species.hlp");
1885	awm->callback(NT_popup_configuration_admin, (AW_CL)ntw, 0);
1886	awm->create_button("selection_admin", AWAR_MARKED_SPECIES_COUNTER);
1887	{
1888	GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1889	GB_add_callback(gb_species_data, GB_CB_CHANGED, NT_update_marked_counter, (int*)awm);
1890	NT_update_marked_counter(NULL, (int*)awm, GB_CB_NONE);
1891	}
1892
1893	// set height of top area:
1894	awm->set_info_area_height(bottomy+2);
1895	awm->set_bottom_area_height(0);
1896
1897	// ------------------------------------
1898	// Autostarts for development
1899
1900	#if defined(DEVEL_RALF)
1901	// if (is_genome_db) GEN_map_first(awr)->show();
1902	#endif // DEVEL_RALF
1903
1904	GB_pop_transaction(GLOBAL.gb_main);
1905
1906	return awm;
1907	}
1908
1909	void nt_create_main_window(AW_root *aw_root) {
1910	GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1911	if (error) aw_message(error);
1912
1913	nt_create_all_awars(aw_root, AW_ROOT_DEFAULT);
1914
1915	AW_window *aww = popup_new_main_window(aw_root, 0);
1916	aww->show();
1917
1918	error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1919	if (error) aw_message(error);
1920	}

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