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source: tags/arb-6.0/NTREE/NT_extern.cxx

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Last change on this file was 12303, checked in by westram, 10 years ago
merge bugfixes since [12269] from 'trunk' into 'rc' adds: log:trunk@12271:12276,12278,12282:12297,12300:12302
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 75.2 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 <awt_TreeAwars.hxx>
38	#include <nds.h>
39
40	#include <db_query.h>
41	#include <dbui.h>
42
43	#include <aw_advice.hxx>
44	#include <aw_preset.hxx>
45	#include <aw_awars.hxx>
46	#include <aw_global_awars.hxx>
47	#include <aw_file.hxx>
48	#include <aw_msg.hxx>
49	#include <arb_progress.h>
50	#include <aw_root.hxx>
51	#include <aw_question.hxx>
52	#include <arb_strbuf.h>
53	#include <arb_strarray.h>
54	#include <arb_file.h>
55	#include <ad_cb.h>
56
57	#include <arb_version.h>
58	#include <refentries.h>
59	#include <rootAsWin.h>
60
61	#define AWAR_EXPORT_NDS "tmp/export_nds"
62	#define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/separator"
63	#define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species"
64	#define AWAR_NTREE_TITLE_MODE "tmp/title_mode"
65
66	void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
67
68	void create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
69	AW_window create_insertDeleteColumn_window(AW_root root);
70	AW_window create_insertDeleteBySAI_window(AW_root root, GBDATA *gb_main);
71
72	AW_window create_tree_window(AW_root aw_root, AWT_graphic *awd);
73
74	static void nt_changesecurity(AW_root *aw_root) {
75	int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
76	GB_push_transaction(GLOBAL.gb_main);
77	GB_change_my_security(GLOBAL.gb_main, level);
78	GB_pop_transaction(GLOBAL.gb_main);
79	}
80
81	static void export_nds_cb(AW_window *aww, AW_CL print_flag) {
82	AW_root *aw_root = aww->get_root();
83	char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
84	FILE *out = fopen(name, "w");
85
86	if (!out) {
87	aw_message("Error: Cannot open and write to file");
88	}
89	else {
90	GB_transaction ta(GLOBAL.gb_main);
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 (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
97	gb_species;
98	gb_species = GBT_next_marked_species(gb_species))
99	{
100	const char *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	}
111	free(name);
112	}
113
114	static AW_window create_nds_export_window(AW_root root) {
115	AW_window_simple *aws = new AW_window_simple;
116	aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
117	aws->load_xfig("sel_box_nds.fig");
118
119	aws->callback((AW_CB0)AW_POPDOWN);
120	aws->at("close");
121	aws->create_button("CLOSE", "CLOSE", "C");
122
123	aws->callback(makeHelpCallback("arb_export_nds.hlp"));
124	aws->at("help");
125	aws->create_button("HELP", "HELP", "H");
126
127	aws->callback((AW_CB0)AW_POPDOWN);
128	aws->at("cancel");
129	aws->create_button("CLOSE", "CANCEL", "C");
130
131	aws->at("save");
132	aws->callback(export_nds_cb, 0);
133	aws->create_button("SAVE", "SAVE", "S");
134
135	aws->at("print");
136	aws->callback(export_nds_cb, 1);
137	aws->create_button("PRINT", "PRINT", "P");
138
139	aws->at("toggle1");
140	aws->label("Column output");
141	aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR, true);
142	aws->insert_default_option("Space padded", "S", NDS_OUTPUT_SPACE_PADDED);
143	aws->insert_option ("TAB separated", "T", NDS_OUTPUT_TAB_SEPARATED);
144	aws->insert_option ("Comma separated", "C", NDS_OUTPUT_COMMA_SEPARATED);
145	aws->update_option_menu();
146
147	AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS);
148
149	return aws;
150	}
151
152	static void create_export_nds_awars(AW_root *awr, AW_default def)
153	{
154	AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds");
155	awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, NDS_OUTPUT_SPACE_PADDED, def);
156	}
157
158	static void AWAR_INFO_BUTTON_TEXT_change_cb(AW_root *awr) {
159	char *value = awr->awar(AWAR_SPECIES_NAME)->read_string();
160	awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
161	free(value);
162	}
163
164	static void expert_mode_changed_cb(AW_root *aw_root) {
165	aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
166	}
167
168	static void NT_toggle_expert_mode(AW_window *aww, AW_CL, AW_CL) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
169	static void NT_toggle_focus_policy(AW_window *aww, AW_CL, AW_CL) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
170
171	static void nt_create_all_awars(AW_root *awr, AW_default def) {
172	// creates awars for all modules reachable from ARB_NT main window
173
174	awr->awar_string(AWAR_FOOTER, "", def);
175	if (GB_read_clients(GLOBAL.gb_main)>=0) {
176	awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
177	}
178	else {
179	awr->awar_string(AWAR_TREE, "", def);
180	}
181
182	awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main);
183	awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main);
184	awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main);
185	awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown", GLOBAL.gb_main);
186	awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main);
187	awr->awar(AWAR_SPECIES_NAME)->add_callback(AWAR_INFO_BUTTON_TEXT_change_cb);
188	awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
189
190	awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
191
192	GEN_create_awars(awr, def, GLOBAL.gb_main);
193	EXP_create_awars(awr, def, GLOBAL.gb_main);
194	#if defined(DEBUG)
195	AWT_create_db_browser_awars(awr, def);
196	#endif // DEBUG
197
198	AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
199
200	awr->awar_int(AWAR_SECURITY_LEVEL, 0, def);
201	awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
202	#if defined(DEBUG) && 0
203	awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
204	#endif // DEBUG
205
206	create_insertDeleteColumn_variables(awr, def);
207	create_probe_design_variables(awr, def, GLOBAL.gb_main);
208	create_primer_design_variables(awr, def, GLOBAL.gb_main);
209	create_trees_var(awr, def);
210	DBUI::create_dbui_awars(awr, def);
211	AP_create_consensus_var(awr, def);
212	{
213	GB_ERROR gde_err = GDE_create_var(awr, def, GLOBAL.gb_main, 0, GDE_WINDOWTYPE_DEFAULT, 0);
214	if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
215	}
216	NT_create_transpro_variables(awr, def);
217	NT_create_resort_awars(awr, def);
218	NT_create_trackAliChanges_Awars(awr, GLOBAL.gb_main);
219
220	NT_create_alignment_vars(awr, def);
221	create_nds_vars(awr, def, GLOBAL.gb_main);
222	create_export_nds_awars(awr, def);
223	awt_create_dtree_awars(awr, GLOBAL.gb_main);
224
225	awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
226	awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
227
228	AWTC_create_submission_variables(awr, GLOBAL.gb_main);
229	NT_createConcatenationAwars(awr, def);
230	NT_createValidNamesAwars(awr, def); // lothar
231	SQ_create_awars(awr, def);
232	RefEntries::create_refentries_awars(awr, def);
233
234	NT_create_multifurcate_tree_awars(awr, def);
235
236	GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
237	if (!error) {
238	AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
239	awar_expert->add_callback(expert_mode_changed_cb);
240	awar_expert->touch();
241
242	awt_create_aww_vars(awr, def);
243	}
244
245	if (error) aw_message(error);
246	}
247
248	// --------------------------------------------------------------------------------
249
250	bool nt_disconnect_from_db(AW_root aw_root, GBDATA& gb_main_ref) {
251	// ask user if DB was not saved
252	// returns true if user allows to quit
253
254	// @@@ code here could as well be applied to both merge DBs
255	// - question about saving only with target DB!
256
257	if (gb_main_ref) {
258	if (GB_read_clients(gb_main_ref)>=0) {
259	if (GB_read_clock(gb_main_ref) > GB_last_saved_clock(gb_main_ref)) {
260	long secs;
261	secs = GB_last_saved_time(gb_main_ref);
262
263	#if defined(DEBUG)
264	secs = GB_time_of_day(); // simulate "just saved"
265	#endif // DEBUG
266
267	const char *quit_buttons = "Quit ARB,Do NOT quit";
268	if (secs) {
269	secs = GB_time_of_day() - secs;
270	if (secs>10) {
271	char *question = GBS_global_string_copy("You last saved your data %li:%li minutes ago\nSure to quit ?", secs/60, secs%60);
272	int dontQuit = aw_question("quit_arb", question, quit_buttons);
273	free(question);
274	if (dontQuit) {
275	return false;
276	}
277	}
278	}
279	else {
280	if (aw_question("quit_arb", "You never saved any data\nSure to quit ???", quit_buttons)) {
281	return false;
282	}
283	}
284	}
285	}
286
287	GBCMS_shutdown(gb_main_ref);
288
289	GBDATA *gb_main = gb_main_ref;
290	gb_main_ref = NULL; // avoid further usage
291
292	nt_assert(aw_root);
293	#if defined(WARN_TODO)
294	#warning instead of directly calling the following functions, try to add them as GB_atclose-callbacks
295	#endif
296	aw_root->unlink_awars_from_DB(gb_main);
297	AWT_destroy_input_masks();
298	#if defined(DEBUG)
299	AWT_browser_forget_db(gb_main);
300	#endif // DEBUG
301
302	GB_close(gb_main);
303	}
304	return true;
305	}
306
307	static void nt_run(const char *command) {
308	GB_ERROR error = GBK_system(command);
309	if (error) {
310	fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
311	#if defined(DEBUG)
312	GBK_dump_backtrace(stderr, "nt_run-error");
313	#endif
314	}
315	}
316
317	void nt_start(const char *arb_ntree_args, bool restart_with_new_ARB_PID) {
318	char *command = GBS_global_string_copy("arb_launcher --async %s %s", restart_with_new_ARB_PID ? "arb" : "arb_ntree", arb_ntree_args);
319	nt_run(command);
320	free(command);
321	}
322
323	__ATTR__NORETURN static void really_exit(int exitcode, bool kill_my_clients) {
324	if (kill_my_clients) {
325	nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
326	}
327	exit(exitcode);
328	}
329
330	void nt_exit(AW_window *aws, AW_CL exitcode) {
331	AW_root *aw_root = aws->get_root();
332	shutdown_macro_recording(aw_root);
333	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
334	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
335	really_exit(exitcode, is_server_and_has_clients);
336	}
337	}
338	void nt_restart(AW_root aw_root, const char arb_ntree_args) {
339	// restarts arb_ntree (with new ARB_PID)
340	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
341	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
342	nt_start(arb_ntree_args, true);
343	really_exit(EXIT_SUCCESS, is_server_and_has_clients);
344	}
345	}
346
347	static void nt_start_2nd_arb(AW_window *aww, AW_CL cl_quit) {
348	// start 2nd arb with intro window
349	AW_root *aw_root = aww->get_root();
350	char *dir4intro;
351	GB_split_full_path(aw_root->awar(AWAR_DB_PATH)->read_char_pntr(), &dir4intro, NULL, NULL, NULL);
352	if (!dir4intro) {
353	dir4intro = strdup(".");
354	}
355
356	if (cl_quit) {
357	nt_restart(aw_root, dir4intro);
358	}
359	else {
360	nt_start(dir4intro, true);
361	}
362	free(dir4intro);
363	}
364
365	// --------------------------------------------------------------------------------
366
367	static void NT_save_quick_cb(AW_window *aww) {
368	AW_root *awr = aww->get_root();
369	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
370
371	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
372
373	GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
374	free( filename);
375	if (error) aw_message(error);
376	else AW_refresh_fileselection(awr, "tmp/nt/arbdb");
377	}
378
379
380	static void NT_save_quick_as_cb(AW_window *aww) {
381	AW_root *awr = aww->get_root();
382	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
383	GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename);
384	if (!error) AW_refresh_fileselection(awr, "tmp/nt/arbdb");
385	aww->hide_or_notify(error);
386
387	free(filename);
388	}
389	static void NT_save_as_cb(AW_window *aww) {
390	AW_root *awr = aww->get_root();
391	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
392	char *filetype = awr->awar(AWAR_DB_TYPE)->read_string();
393
394	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
395	GB_ERROR error = GB_save(GLOBAL.gb_main, filename, filetype);
396	if (!error) AW_refresh_fileselection(awr, "tmp/nt/arbdb");
397	aww->hide_or_notify(error);
398
399	free(filetype);
400	free(filename);
401	}
402
403	static AW_window NT_create_save_quick_as_window(AW_root aw_root, const char *base_name) {
404	static AW_window_simple *aws = 0;
405	if (!aws) {
406	aws = new AW_window_simple;
407	aws->init(aw_root, "SAVE_CHANGES_TO", "SAVE CHANGES TO");
408	aws->load_xfig("save_as.fig");
409
410	aws->at("close"); aws->callback((AW_CB0)AW_POPDOWN);
411	aws->create_button("CLOSE", "CLOSE", "C");
412
413	aws->callback(makeHelpCallback("save.hlp"));
414	aws->at("help");
415	aws->create_button("HELP", "HELP", "H");
416
417	AW_create_standard_fileselection(aws, base_name);
418
419	aws->at("comment");
420	aws->create_text_field(AWAR_DB_COMMENT);
421
422	aws->at("save"); aws->callback(NT_save_quick_as_cb);
423	aws->create_button("SAVE", "SAVE", "S");
424	}
425	return aws;
426	}
427
428	static void NT_database_optimization(AW_window *aww) {
429	arb_progress progress("Optimizing database", 2);
430
431	GB_push_my_security(GLOBAL.gb_main);
432	GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
433	if (!error) {
434	ConstStrArray ali_names;
435	GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
436
437	arb_progress ali_progress("Optimizing sequence data", ali_names.size());
438	ali_progress.allow_title_reuse();
439
440	error = GBT_check_data(GLOBAL.gb_main, 0);
441	error = GB_end_transaction(GLOBAL.gb_main, error);
442
443	if (!error) {
444	char *tree_name = aww->get_root()->awar("tmp/nt/arbdb/optimize_tree_name")->read_string();
445	for (int i = 0; ali_names[i]; ++i) {
446	error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
447	ali_progress.inc_and_check_user_abort(error);
448	}
449	free(tree_name);
450	}
451	}
452	progress.inc_and_check_user_abort(error);
453
454	if (!error) {
455	error = GB_optimize(GLOBAL.gb_main);
456	progress.inc_and_check_user_abort(error);
457	}
458
459	GB_pop_my_security(GLOBAL.gb_main);
460	aww->hide_or_notify(error);
461	}
462
463	static AW_window NT_create_database_optimization_window(AW_root aw_root) {
464	static AW_window_simple *aws = 0;
465	if (aws) return (AW_window *)aws;
466	GB_transaction ta(GLOBAL.gb_main);
467
468	const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
469	aw_root->awar_string("tmp/nt/arbdb/optimize_tree_name", largest_tree);
470
471	aws = new AW_window_simple;
472	aws->init(aw_root, "OPTIMIZE_DATABASE", "OPTIMIZE DATABASE");
473	aws->load_xfig("optimize.fig");
474
475	aws->at("trees");
476	awt_create_selection_list_on_trees(GLOBAL.gb_main, aws, "tmp/nt/arbdb/optimize_tree_name", true);
477
478	aws->at("close"); aws->callback((AW_CB0)AW_POPDOWN);
479	aws->create_button("CLOSE", "CLOSE", "C");
480
481	aws->callback(makeHelpCallback("optimize.hlp"));
482	aws->at("help");
483	aws->create_button("HELP", "HELP", "H");
484
485	aws->at("go");
486	aws->callback(NT_database_optimization);
487	aws->create_button("GO", "GO");
488	return aws;
489	}
490
491	static AW_window NT_create_save_as(AW_root aw_root, const char *base_name)
492	{
493	static AW_window_simple *aws = 0;
494	if (aws) return (AW_window *)aws;
495
496	aws = new AW_window_simple;
497	aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
498	aws->load_xfig("save_as.fig");
499
500	aws->at("close"); aws->callback((AW_CB0)AW_POPDOWN);
501	aws->create_button("CLOSE", "CLOSE", "C");
502
503	aws->callback(makeHelpCallback("save.hlp"));
504	aws->at("help");
505	aws->create_button("HELP", "HELP", "H");
506
507	AW_create_standard_fileselection(aws, base_name);
508
509	aws->at("type");
510	aws->label("Type ");
511	aws->create_option_menu(AWAR_DB_TYPE, true);
512	aws->insert_option("Binary", "B", "b");
513	aws->insert_option("Bin (with FastLoad File)", "f", "bm");
514	aws->insert_default_option("Ascii", "A", "a");
515	aws->update_option_menu();
516
517	aws->at("optimize");
518	aws->callback(NT_create_database_optimization_window);
519	aws->help_text("optimize.hlp");
520	aws->create_button("OPTIMIZE", "OPTIMIZE");
521
522	aws->at("save"); aws->callback(NT_save_as_cb);
523	aws->create_button("SAVE", "SAVE", "S");
524
525	aws->at("comment");
526	aws->create_text_field(AWAR_DB_COMMENT);
527
528	return aws;
529	}
530
531	static void NT_undo_cb(AW_window *, AW_CL undo_type, AW_CL ntw) {
532	GB_ERROR error = GB_undo(GLOBAL.gb_main, (GB_UNDO_TYPE)undo_type);
533	if (error) aw_message(error);
534	else {
535	GB_transaction ta(GLOBAL.gb_main);
536	((AWT_canvas *)ntw)->refresh();
537	}
538	}
539
540	static AWT_config_mapping_def tree_setting_config_mapping[] = {
541	{ AWAR_DTREE_BASELINEWIDTH, "line_width" },
542	{ AWAR_DTREE_VERICAL_DIST, "vert_dist" },
543	{ AWAR_DTREE_AUTO_JUMP, "auto_jump" },
544	{ AWAR_DTREE_SHOW_CIRCLE, "show_circle" },
545	{ AWAR_DTREE_SHOW_BRACKETS, "show_brackets" },
546	{ AWAR_DTREE_USE_ELLIPSE, "use_ellipse" },
547	{ AWAR_DTREE_CIRCLE_ZOOM, "circle_zoom" },
548	{ AWAR_DTREE_CIRCLE_MAX_SIZE, "circle_max_size" },
549	{ AWAR_DTREE_GREY_LEVEL, "grey_level" },
550	{ AWAR_DTREE_DENDRO_ZOOM_TEXT, "dendro_zoomtext" },
551	{ AWAR_DTREE_DENDRO_XPAD, "dendro_xpadding" },
552	{ AWAR_DTREE_RADIAL_ZOOM_TEXT, "radial_zoomtext" },
553	{ AWAR_DTREE_RADIAL_XPAD, "radial_xpadding" },
554	{ 0, 0 }
555	};
556
557	static char tree_setting_store_config(AW_window aww, AW_CL, AW_CL) {
558	AWT_config_definition cdef(aww->get_root(), tree_setting_config_mapping);
559	return cdef.read();
560	}
561	static void tree_setting_restore_config(AW_window aww, const char stored_string, AW_CL, AW_CL) {
562	AWT_config_definition cdef(aww->get_root(), tree_setting_config_mapping);
563	cdef.write(stored_string);
564	}
565
566	static AW_window NT_create_tree_settings_window(AW_root aw_root) {
567	static AW_window_simple *aws = 0;
568	if (aws) return (AW_window *)aws;
569
570	aws = new AW_window_simple;
571	aws->init(aw_root, "TREE_PROPS", "TREE SETTINGS");
572	aws->load_xfig("awt/tree_settings.fig");
573
574	aws->at("close");
575	aws->callback((AW_CB0)AW_POPDOWN);
576	aws->create_button("CLOSE", "CLOSE", "C");
577
578	aws->at("help");
579	aws->callback(makeHelpCallback("nt_tree_settings.hlp"));
580	aws->create_button("HELP", "HELP", "H");
581
582	aws->at("button");
583	aws->auto_space(10, 10);
584	aws->label_length(30);
585
586	aws->label("Base line width");
587	aws->create_input_field(AWAR_DTREE_BASELINEWIDTH, 4);
588	aws->at_newline();
589
590	aws->label("Relative vertical distance");
591	aws->create_input_field(AWAR_DTREE_VERICAL_DIST, 4);
592	aws->at_newline();
593
594	aws->label("Auto jump");
595	aws->create_toggle(AWAR_DTREE_AUTO_JUMP);
596	aws->at_newline();
597
598	aws->label("Show group brackets");
599	aws->create_toggle(AWAR_DTREE_SHOW_BRACKETS);
600	aws->at_newline();
601
602	aws->label("Show bootstrap circles");
603	aws->create_toggle(AWAR_DTREE_SHOW_CIRCLE);
604	aws->at_newline();
605
606	aws->label("Use ellipses");
607	aws->create_toggle(AWAR_DTREE_USE_ELLIPSE);
608	aws->at_newline();
609
610	aws->label("Bootstrap circle zoom factor");
611	aws->create_input_field(AWAR_DTREE_CIRCLE_ZOOM, 4);
612	aws->at_newline();
613
614	aws->label("Boostrap radius limit");
615	aws->create_input_field(AWAR_DTREE_CIRCLE_MAX_SIZE, 4);
616	aws->at_newline();
617
618	aws->label("Grey Level of Groups%");
619	aws->create_input_field(AWAR_DTREE_GREY_LEVEL, 4);
620	aws->at_newline();
621
622	aws->label("Text zoom/pad (dendro)");
623	aws->create_toggle(AWAR_DTREE_DENDRO_ZOOM_TEXT);
624	aws->create_input_field(AWAR_DTREE_DENDRO_XPAD, 4);
625	aws->at_newline();
626
627	aws->label("Text zoom/pad (radial)");
628	aws->create_toggle(AWAR_DTREE_RADIAL_ZOOM_TEXT);
629	aws->create_input_field(AWAR_DTREE_RADIAL_XPAD, 4);
630	aws->at_newline();
631
632	aws->at("config");
633	AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "tree_settings", tree_setting_store_config, tree_setting_restore_config, 0, 0);
634
635	return (AW_window *)aws;
636
637	}
638
639	enum streamSource { FROM_PIPE, FROM_FILE };
640	static char stream2str(streamSource source, const char commandOrFile) {
641	char *output = 0;
642	FILE *in = 0;
643
644	switch (source) {
645	case FROM_PIPE: in = popen(commandOrFile, "r"); break;
646	case FROM_FILE: in = fopen(commandOrFile, "rt"); break;
647	}
648
649	if (in) {
650	GBS_strstruct *out = GBS_stropen(2000);
651	int c;
652
653	while (EOF != (c = fgetc(in))) GBS_chrcat(out, c);
654
655	switch (source) {
656	case FROM_PIPE: pclose(in); break;
657	case FROM_FILE: fclose(in); break;
658	}
659
660	// skip trailing linefeeds
661	long offset = GBS_memoffset(out);
662	while (offset>0 && GBS_mempntr(out)[offset-1] == '\n') {
663	GBS_str_cut_tail(out, 1);
664	offset--;
665	}
666
667	output = GBS_strclose(out);
668	}
669	return output;
670	}
671
672	inline void removeTrailingNewlines(char *str) {
673	char *eos = strchr(str, 0)-1;
674	while (eos >= str && eos[0] == '\n') *eos-- = 0;
675	}
676
677	inline void append_named_value(GBS_strstruct out, const char prefix, const char *value) {
678	GBS_strcat(out, GBS_global_string("%-*s: %s\n", 12, prefix, value));
679	}
680	inline void append_command_output(GBS_strstruct out, const char prefix, const char *command) {
681	char *output = stream2str(FROM_PIPE, command);
682	if (output) {
683	removeTrailingNewlines(output);
684	if (strcmp(output, "unknown") != 0) append_named_value(out, prefix, output);
685	free(output);
686	}
687	}
688
689	static void NT_modify_cb(UNFIXED, AWT_canvas *canvas, AWT_COMMAND_MODE mode) {
690	DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
691	nt_mode_event(NULL, canvas, mode);
692	}
693
694	static void NT_primer_cb() {
695	GB_ERROR error = GB_xcmd("arb_primer", true, false);
696	if (error) aw_message(error);
697	}
698
699	static void NT_mark_duplicates(UNFIXED, AWT_canvas *ntw) {
700	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
701	if (tree_root) {
702	GB_transaction ta(ntw->gb_main);
703	NT_mark_all_cb(NULL, ntw, 0);
704
705	tree_root->mark_duplicates();
706	tree_root->compute_tree();
707	ntw->refresh();
708	}
709	}
710
711	static void NT_justify_branch_lenghs(UNFIXED, AWT_canvas *ntw) {
712	GB_transaction ta(ntw->gb_main);
713	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
714
715	if (tree_root) {
716	tree_root->justify_branch_lenghs(ntw->gb_main);
717	tree_root->compute_tree();
718	GB_ERROR error = AWT_TREE(ntw)->save(ntw->gb_main, 0, 0, 0);
719	if (error) aw_message(error);
720	ntw->refresh();
721	}
722	}
723
724	#if defined(DEBUG)
725	static void NT_fix_database(AW_window *) {
726	GB_ERROR err = 0;
727	err = GB_fix_database(GLOBAL.gb_main);
728	if (err) aw_message(err);
729	}
730	#endif
731
732	static void relink_pseudo_species_to_organisms(GBDATA &ref_gb_node, char &ref_name, GB_HASH *organism_hash) {
733	if (ref_gb_node) {
734	if (GEN_is_pseudo_gene_species(ref_gb_node)) {
735	GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
736
737	if (gb_organism) {
738	char *name = GBT_read_string(gb_organism, "name");
739
740	if (name) {
741	freeset(ref_name, name);
742	ref_gb_node = gb_organism;
743	}
744	}
745	}
746	}
747	}
748
749	static void NT_pseudo_species_to_organism(AW_window *, AW_CL ntwcl) {
750	AWT_canvas ntw = (AWT_canvas )ntwcl;
751	GB_transaction ta(ntw->gb_main);
752	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
753
754	if (tree_root) {
755	GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
756	tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
757	tree_root->compute_tree();
758	GB_ERROR error = AWT_TREE(ntw)->save(ntw->gb_main, 0, 0, 0);
759	if (error) aw_message(error);
760	ntw->refresh();
761	GBS_free_hash(organism_hash);
762	}
763	}
764
765
766	// #########################################
767	// #########################################
768	// ### ###
769	// ## user mask section ##
770	// ### ###
771	// #########################################
772	// #########################################
773
774	struct nt_item_type_species_selector : public awt_item_type_selector {
775	nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
776	virtual ~nt_item_type_species_selector() OVERRIDE {}
777
778	virtual const char *get_self_awar() const OVERRIDE {
779	return AWAR_SPECIES_NAME;
780	}
781	virtual size_t get_self_awar_content_length() const OVERRIDE {
782	return 12; // should be enough for "nnaammee.999"
783	}
784	virtual GBDATA current(AW_root root, GBDATA *gb_main) const OVERRIDE { // give the current item
785	char *species_name = root->awar(get_self_awar())->read_string();
786	GBDATA *gb_species = 0;
787
788	if (species_name[0]) {
789	GB_transaction ta(gb_main);
790	gb_species = GBT_find_species(gb_main, species_name);
791	}
792
793	free(species_name);
794	return gb_species;
795	}
796	virtual const char *getKeyPath() const OVERRIDE { // give the keypath for items
797	return CHANGE_KEY_PATH;
798	}
799	};
800
801	static nt_item_type_species_selector item_type_species;
802
803	static void NT_open_mask_window(AW_window aww, int id, GBDATA gb_main) {
804	const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
805	nt_assert(descriptor);
806	if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
807	}
808
809	static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
810	AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
811	}
812	static AW_window create_colorize_species_window(AW_root aw_root) {
813	return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
814	}
815
816	static void NT_update_marked_counter(GBDATA, AW_window aww) {
817	/*! Updates marked counter and issues redraw on tree if number of marked species changes.
818	* Called on any change of species_information container.
819	*/
820	long count = GBT_count_marked_species(GLOBAL.gb_main);
821	const char *buffer = count ? GBS_global_string("%li marked", count) : "";
822	AW_awar *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
823	char *oldval = counter->read_string();
824	if (strcmp(oldval, buffer)) {
825	counter->write_string(buffer);
826	aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
827	}
828	free(oldval);
829	}
830
831	// --------------------------------------------------------------------------------------------------
832
833	static void NT_alltree_remove_leafs(AW_window , GBT_TreeRemoveType mode, GBDATA gb_main) {
834	GB_ERROR error = 0;
835	GB_transaction ta(gb_main);
836
837	ConstStrArray tree_names;
838	GBT_get_tree_names(tree_names, gb_main, false);
839
840	if (!tree_names.empty()) {
841	int treeCount = tree_names.size();
842
843	const char *whats_removed = NULL;
844	switch (mode) {
845	case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
846	case GBT_REMOVE_MARKED: whats_removed = "marked"; break;
847	default: nt_assert(0); break;
848	}
849
850	const char *task = GBS_global_string("Deleting %s from %i trees", whats_removed, treeCount);
851
852	arb_progress progress(task, treeCount);
853	GB_HASH *species_hash = GBT_create_species_hash(gb_main);
854
855	int modified = 0;
856
857	for (int t = 0; t<treeCount && !error; t++) {
858	progress.subtitle(tree_names[t]);
859	GBT_TREE *tree = GBT_read_tree(gb_main, tree_names[t], GBT_TREE_NodeFactory());
860	if (!tree) {
861	aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
862	}
863	else {
864	int removed = 0;
865	int groups_removed = 0;
866
867	tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
868
869	nt_assert(removed >= groups_removed);
870
871	if (!tree) {
872	aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
873	}
874	else {
875	if (removed>0) {
876	error = GBT_write_tree(gb_main, tree_names[t], tree);
877	if (error) {
878	aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
879	}
880	else {
881	if (groups_removed>0) {
882	aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
883	}
884	else {
885	aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
886	}
887	modified++;
888	}
889	}
890	delete tree;
891	}
892	}
893	progress.inc_and_check_user_abort(error);
894	}
895
896	if (modified) {
897	aw_message(GBS_global_string("Changed %i of %i trees.", modified, treeCount));
898	}
899	else {
900	aw_message("No tree modified");
901	}
902
903	GBS_free_hash(species_hash);
904	}
905
906	aw_message_if(ta.close(error));
907	}
908
909	GBT_TREE nt_get_tree_root_of_canvas(AWT_canvas ntw) {
910	AWT_graphic_tree *tree = AWT_TREE(ntw);
911	if (tree) {
912	AP_tree *root = tree->get_root_node();
913	if (root) return root;
914	}
915	return NULL;
916	}
917
918	// --------------------------------------------------------------------------------------------------
919
920	static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
921	GB_transaction ta(gb_main);
922	GBT_mark_all(gb_main, 0);
923
924	DBItemSetIter end = referred.end();
925	for (DBItemSetIter s = referred.begin(); s != end; ++s) {
926	GB_write_flag(*s, 1);
927	}
928	return ARB_ERROR();
929	}
930
931	static AW_window create_mark_by_refentries_window(AW_root awr, GBDATA *gbmain) {
932	static AW_window *aws = NULL;
933	if (!aws) {
934	static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
935	aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULL, "Mark referenced", mark_referred_species);
936	}
937	return aws;
938	}
939
940	// --------------------------------------------------------------------------------------------------
941
942	static void merge_from_to(AW_root awr, const char db_awar_name, bool merge_to) {
943	const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
944
945	char *cmd = GBS_global_string_copy(
946	merge_to
947	? "arb_ntree : %s &"
948	: "arb_ntree %s : &",
949	db_name);
950
951	aw_message_if(GBK_system(cmd));
952	free(cmd);
953	}
954
955	static void merge_from_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, false); }
956	static void merge_into_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, true); }
957
958	static AW_window NT_create_merge_from_window(AW_root awr) {
959	static char *awar_name = NULL; // do not free, bound to callback
960	AW_window *aw_from =
961	awt_create_load_box(awr, "Merge data from", "other ARB database",
962	".", ".arb", &awar_name,
963	makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
964	return aw_from;
965	}
966	static AW_window NT_create_merge_to_window(AW_root awr) {
967	static char *awar_name = NULL; // do not free, bound to callback
968	AW_window *aw_to =
969	awt_create_load_box(awr, "Merge data to", "other ARB database",
970	".", ".arb", &awar_name,
971	makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
972	makeWindowCallback(AW_POPDOWN), NULL);
973	return aw_to;
974	}
975
976	// --------------------------------------------------------------------------------------------------
977
978	int NT_get_canvas_id(AWT_canvas *ntw) {
979	// return number of canvas [0..MAX_NT_WINDOWS-1]
980
981	const char *tree_awar_name = ntw->user_awar;
982
983	const unsigned LEN = 15;
984	#if defined(ASSERTION_USED)
985	const char *EXPECT = "focus/tree_name";
986	#endif
987
988	nt_assert(strlen(EXPECT) == LEN);
989	nt_assert(memcmp(tree_awar_name, EXPECT, LEN) == 0);
990
991	int id;
992	switch (tree_awar_name[LEN]) {
993	default :
994	nt_assert(0);
995	// NDEBUG: fallback to 0
996	case 0:
997	id = 0;
998	break;
999
1000	case '_':
1001	id = atoi(tree_awar_name+LEN+1);
1002	nt_assert(id >= 1);
1003	break;
1004	}
1005	return id;
1006	}
1007
1008	static void update_main_window_title(AW_root* awr, AW_window_menu_modes* aww, int clone) {
1009	const char* filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
1010	if (clone) {
1011	aww->set_window_title(GBS_global_string("%s - ARB (%i)", filename, clone));
1012	}
1013	else {
1014	aww->set_window_title(GBS_global_string("%s - ARB", filename));
1015	}
1016	}
1017
1018	static void canvas_tree_awar_changed_cb(AW_awar , bool, AWT_canvas ntw) {
1019	NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
1020	}
1021
1022	// ##########################################
1023	// ##########################################
1024	// ### ###
1025	// ## create main window ##
1026	// ### ###
1027	// ##########################################
1028	// ##########################################
1029
1030	static AW_window popup_new_main_window(AW_root awr, int clone) {
1031	GB_push_transaction(GLOBAL.gb_main);
1032
1033	char window_title[256];
1034	char * const awar_tree = (char *)GB_calloc(sizeof(char), strlen(AWAR_TREE) + 10); // do not free this
1035
1036	if (clone) {
1037	sprintf(awar_tree, AWAR_TREE "_%i", clone);
1038	sprintf(window_title, "ARB_NT_%i", clone);
1039	}
1040	else {
1041	sprintf(awar_tree, AWAR_TREE);
1042	sprintf(window_title, "ARB_NT");
1043	}
1044	AW_window_menu_modes *awm = new AW_window_menu_modes;
1045	awm->init(awr, window_title, window_title, 0, 0);
1046
1047	awr->awar(AWAR_DB_NAME)
1048	->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1049	->update();
1050
1051	awm->button_length(5);
1052
1053	if (!clone) AW_init_color_group_defaults("arb_ntree");
1054
1055	AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1056
1057	AWT_canvas *ntw;
1058	{
1059	AP_tree_display_type old_sort_type = tree->tree_sort;
1060	tree->set_tree_type(AP_LIST_SIMPLE, NULL); // avoid NDS warnings during startup
1061
1062	ntw = new AWT_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, awar_tree);
1063	tree->set_tree_type(old_sort_type, ntw);
1064	ntw->set_mode(AWT_MODE_SELECT);
1065	}
1066
1067	{
1068	AW_awar *tree_awar = awr->awar_string(awar_tree);
1069	const char *tree_name = tree_awar->read_char_pntr();
1070	const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1071
1072	if (existing_tree_name) {
1073	tree_awar->write_string(existing_tree_name);
1074	NT_reload_tree_event(awr, ntw, true); // load first tree
1075	}
1076	else {
1077	AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, 0, "no_tree.hlp");
1078	tree->set_tree_type(AP_LIST_NDS, ntw); // no tree -> show NDS list
1079	}
1080
1081	AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1082	}
1083
1084	awr->awar(AWAR_SPECIES_NAME)->add_callback(makeRootCallback(TREE_auto_jump_cb, ntw));
1085
1086	awr->awar(AWAR_DTREE_VERICAL_DIST)->add_callback(makeRootCallback(AWT_resize_cb, ntw));
1087
1088	RootCallback expose_cb = makeRootCallback(AWT_expose_cb, ntw);
1089	awr->awar(AWAR_DTREE_BASELINEWIDTH) ->add_callback(expose_cb);
1090	awr->awar(AWAR_DTREE_SHOW_CIRCLE) ->add_callback(expose_cb);
1091	awr->awar(AWAR_DTREE_SHOW_BRACKETS) ->add_callback(expose_cb);
1092	awr->awar(AWAR_DTREE_CIRCLE_ZOOM) ->add_callback(expose_cb);
1093	awr->awar(AWAR_DTREE_CIRCLE_MAX_SIZE)->add_callback(expose_cb);
1094	awr->awar(AWAR_DTREE_USE_ELLIPSE) ->add_callback(expose_cb);
1095
1096	RootCallback reinit_treetype_cb = makeRootCallback(NT_reinit_treetype, ntw);
1097	awr->awar(AWAR_DTREE_RADIAL_ZOOM_TEXT)->add_callback(reinit_treetype_cb);
1098	awr->awar(AWAR_DTREE_RADIAL_XPAD) ->add_callback(reinit_treetype_cb);
1099	awr->awar(AWAR_DTREE_DENDRO_ZOOM_TEXT)->add_callback(reinit_treetype_cb);
1100	awr->awar(AWAR_DTREE_DENDRO_XPAD) ->add_callback(reinit_treetype_cb);
1101
1102	awr->awar(AWAR_TREE_REFRESH)->add_callback(expose_cb);
1103	awr->awar(AWAR_COLOR_GROUPS_USE)->add_callback(makeRootCallback(TREE_recompute_cb, ntw));
1104
1105	GBDATA *gb_arb_presets = GB_search(GLOBAL.gb_main, "arb_presets", GB_CREATE_CONTAINER);
1106	GB_add_callback(gb_arb_presets, GB_CB_CHANGED, makeDatabaseCallback(AWT_expose_cb, ntw));
1107
1108	bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1109
1110	WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1111
1112	// --------------
1113	// File
1114
1115	#if defined(DEBUG)
1116	AWT_create_debug_menu(awm);
1117	#endif // DEBUG
1118
1119	bool allow_new_window = (NT_get_canvas_id(ntw)+1) < MAX_NT_WINDOWS;
1120
1121	if (clone) {
1122	awm->create_menu("File", "F", AWM_ALL);
1123	if (allow_new_window) {
1124	awm->insert_menu_topic(awm->local_id("new_window"), "New window (same database)", "N", "newwindow.hlp", AWM_ALL, makeCreateWindowCallback(popup_new_main_window, clone+1));
1125	}
1126	awm->insert_menu_topic("close", "Close", "C", 0, AWM_ALL, (AW_CB)AW_POPDOWN, 0, 0);
1127	}
1128	else {
1129	#if defined(DEBUG)
1130	// add more to debug-menu
1131	awm->sep______________();
1132	awm->insert_menu_topic("fix_db", "Fix database", "F", 0, AWM_ALL, (AW_CB)NT_fix_database, 0, 0);
1133	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);
1134	awm->insert_menu_topic("test_compr", "Test compression", "T", 0, AWM_ALL, (AW_CB)GBT_compression_test, (AW_CL) GLOBAL.gb_main, 0);
1135	awm->sep______________();
1136	awm->insert_menu_topic("table_admin", "Table Admin (unfinished/unknown purpose)", "A", "tableadm.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_tables_admin_window, GLOBAL.gb_main));
1137	#endif // DEBUG
1138
1139	awm->create_menu("File", "F", AWM_ALL);
1140	{
1141	awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, (AW_CB)NT_save_quick_cb, 0, 0);
1142	awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, "tmp/nt/arbdb"));
1143	if (allow_new_window) {
1144	awm->sep______________();
1145	awm->insert_menu_topic("new_window", "New window (same database)", "N", "newwindow.hlp", AWM_ALL, makeCreateWindowCallback(popup_new_main_window, clone+1));
1146	}
1147	awm->sep______________();
1148	awm->insert_menu_topic("optimize_db", "Optimize database", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window);
1149	awm->sep______________();
1150
1151	awm->insert_sub_menu("Import", "I");
1152	{
1153	awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1154	awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, NT_import_sequences, 0, 0);
1155	GDE_load_menu(awm, AWM_EXP, "Import");
1156	}
1157	awm->close_sub_menu();
1158
1159	awm->insert_sub_menu("Export", "E");
1160	{
1161	awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1162	awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1163	GDE_load_menu(awm, AWM_ALL, "Export");
1164	awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window);
1165	}
1166	awm->close_sub_menu();
1167	awm->sep______________();
1168
1169	insert_macro_menu_entry(awm, false);
1170
1171	awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1172	{
1173	awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp"));
1174	awm->insert_menu_topic("bug_report", "Report bug", "b", NULL, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1175	awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULL, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1176	}
1177	awm->close_sub_menu();
1178	#if 0
1179	awm->sep______________();
1180	awm->insert_menu_topic("undo", "Undo", "U", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_cb, (AW_CL)GB_UNDO_UNDO, (AW_CL)ntw);
1181	awm->insert_menu_topic("redo", "Redo", "d", "undo.hlp", AWM_ALL, (AW_CB)NT_undo_cb, (AW_CL)GB_UNDO_REDO, (AW_CL)ntw);
1182	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);
1183	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);
1184	#endif
1185
1186	awm->sep______________();
1187
1188	awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, nt_start_2nd_arb, 0);
1189	awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, nt_start_2nd_arb, 1);
1190	awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, nt_exit, EXIT_SUCCESS);
1191	}
1192
1193	// -----------------
1194	// Species
1195
1196	awm->create_menu("Species", "c", AWM_ALL);
1197	{
1198	awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1199	awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb);
1200
1201	awm->sep______________();
1202
1203	NT_insert_mark_submenus(awm, ntw, 1);
1204	awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1205	awm->insert_menu_topic("species_colors", "Set Colors", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window);
1206	awm->insert_menu_topic("selection_admin", "Configurations", "o", "configuration.hlp", AWM_ALL, NT_popup_configuration_admin, (AW_CL)ntw, 0);
1207
1208	awm->sep______________();
1209
1210	awm->insert_sub_menu("Database fields admin", "f");
1211	DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1212	awm->close_sub_menu();
1213	NT_create_mask_submenu(awm);
1214
1215	awm->sep______________();
1216
1217	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);
1218
1219	awm->insert_sub_menu("Sort Species", "s");
1220	{
1221	awm->insert_menu_topic("sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window);
1222	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);
1223	}
1224	awm->close_sub_menu();
1225
1226	awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1227	{
1228	awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "sp_merge.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1229	awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "join_species.hlp", AWM_EXP, NT_create_species_join_window);
1230	}
1231	awm->close_sub_menu();
1232
1233	awm->sep______________();
1234
1235	awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1236
1237	awm->sep______________();
1238
1239	awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "sp_rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1240
1241	awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1242	{
1243	awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames, 0, 0);
1244	awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames, 0, 0);
1245	awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames, 0, 0);
1246	awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window);
1247	}
1248	awm->close_sub_menu();
1249	}
1250
1251	// ----------------------------
1252	// Genes + Experiment
1253
1254	if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1255
1256	// ------------------
1257	// Sequence
1258
1259	awm->create_menu("Sequence", "S", AWM_ALL);
1260	{
1261	awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_window, (AW_window*)0));
1262	awm->insert_sub_menu("Insert/delete", "I");
1263	{
1264	awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window);
1265	awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main));
1266	}
1267	awm->close_sub_menu();
1268	awm->sep______________();
1269
1270	awm->insert_sub_menu("Edit Sequences", "E");
1271	{
1272	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);
1273	awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, NT_start_editor_on_tree, -1, (AW_CL)ntw);
1274	awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1275	}
1276	awm->close_sub_menu();
1277
1278	awm->sep______________();
1279
1280	awm->insert_sub_menu("Align Sequences", "S");
1281	{
1282	awm->insert_menu_topic("realign_dna", "Realign nucleic acid according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1283	GDE_load_menu(awm, AWM_ALL, "Align");
1284	}
1285	awm->close_sub_menu();
1286	awm->insert_menu_topic("seq_concat", "Concatenate Sequences/Alignments", "C", "concatenate_align.hlp", AWM_ALL, NT_createConcatenationWindow);
1287	awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1288	awm->sep______________();
1289
1290	awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1291	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_dist &", 0);
1292	awm->sep______________();
1293
1294	awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1295	awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1296
1297	awm->sep______________();
1298
1299	GDE_load_menu(awm, AWM_ALL, "Print");
1300	}
1301
1302	// -------------
1303	// SAI
1304
1305	awm->create_menu("SAI", "A", AWM_ALL);
1306	{
1307	awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1308	awm->insert_sub_menu("Create SAI using ...", "C");
1309	{
1310	awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window);
1311	awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window);
1312	awm->insert_menu_topic("pos_var_pars", "Positional variability + Column statistic (parsimony method)", "a", "pos_var_pars.hlp", AWM_ALL, AP_create_pos_var_pars_window);
1313	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);
1314	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);
1315
1316	GDE_load_menu(awm, AWM_EXP, "SAI");
1317	}
1318	awm->close_sub_menu();
1319
1320	awm->insert_sub_menu("Other functions", "O");
1321	{
1322	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);
1323	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);
1324	awm->insert_menu_topic("export_pos_var", "Export Column Statistic (GNUPLOT format)", "E", "csp_2_gnuplot.hlp", AWM_ALL, NT_create_colstat_2_gnuplot_window);
1325	}
1326	awm->close_sub_menu();
1327	}
1328
1329	// ----------------
1330	// Probes
1331
1332	awm->create_menu("Probes", "P", AWM_ALL);
1333	{
1334	awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1335	awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1336	awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1337	awm->sep______________();
1338	awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1339	awm->insert_menu_topic("primer_design", "Design Sequencing Primers", "S", "primer.hlp", AWM_EXP, (AW_CB)NT_primer_cb, 0, 0);
1340	awm->sep______________();
1341	awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1342	}
1343
1344	}
1345
1346	// --------------
1347	// Tree
1348
1349	awm->create_menu("Tree", "T", AWM_ALL);
1350	{
1351	if (!clone) {
1352	awm->insert_sub_menu("Add Species to Existing Tree", "A");
1353	{
1354	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);
1355	awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_pars &", 0);
1356	GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1357	}
1358	awm->close_sub_menu();
1359	}
1360
1361	awm->insert_sub_menu("Remove Species from Tree", "R");
1362	{
1363	awm->insert_menu_topic(awm->local_id("tree_remove_deleted"), "Remove zombies", "z", "trm_del.hlp", AWM_ALL, makeWindowCallback(NT_remove_leafs, ntw, AWT_REMOVE_ZOMBIES));
1364	awm->insert_menu_topic(awm->local_id("tree_remove_marked"), "Remove marked", "m", "trm_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_remove_leafs, ntw, AWT_REMOVE_MARKED));
1365	awm->insert_menu_topic(awm->local_id("tree_keep_marked"), "Keep marked", "K", "tkeep_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_remove_leafs, ntw, AWT_KEEP_MARKED));
1366	awm->sep______________();
1367	awm->insert_menu_topic("all_tree_remove_deleted", "Remove zombies from ALL trees", "A", "trm_del.hlp", AWM_ALL, makeWindowCallback(NT_alltree_remove_leafs, GBT_REMOVE_ZOMBIES, GLOBAL.gb_main));
1368	awm->insert_menu_topic("all_tree_remove_marked", "Remove marked from ALL trees", "L", "trm_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_alltree_remove_leafs, GBT_REMOVE_MARKED, GLOBAL.gb_main));
1369	}
1370	awm->close_sub_menu();
1371
1372	if (!clone) {
1373	awm->insert_sub_menu("Build tree from sequence data", "B");
1374	{
1375	awm->insert_sub_menu("Distance matrix methods", "D");
1376	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, (AW_CB)NT_system_cb, (AW_CL)"arb_dist &", 0);
1377	GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1378	awm->close_sub_menu();
1379
1380	awm->insert_sub_menu("Maximum Parsimony methods", "P");
1381	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1382	awm->close_sub_menu();
1383
1384	awm->insert_sub_menu("Maximum Likelihood methods", "L");
1385	GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelyhood EXP");
1386	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelyhood");
1387	awm->close_sub_menu();
1388
1389	awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1390	GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1391	awm->close_sub_menu();
1392	}
1393	awm->close_sub_menu();
1394	}
1395
1396	awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1397	awm->sep______________();
1398
1399	awm->insert_sub_menu("Reset zoom", "z");
1400	{
1401	awm->insert_menu_topic(awm->local_id("reset_logical_zoom"), "Logical zoom", "L", "rst_log_zoom.hlp", AWM_ALL, makeWindowCallback(NT_reset_lzoom_cb, ntw));
1402	awm->insert_menu_topic(awm->local_id("reset_physical_zoom"), "Physical zoom", "P", "rst_phys_zoom.hlp", AWM_ALL, makeWindowCallback(NT_reset_pzoom_cb, ntw));
1403	}
1404	awm->close_sub_menu();
1405	awm->insert_sub_menu("Collapse/Expand tree", "d");
1406	{
1407	awm->insert_menu_topic(awm->local_id("tree_group_all"), "Group all", "a", "tgroupall.hlp", AWM_ALL, makeWindowCallback(NT_group_tree_cb, ntw));
1408	awm->insert_menu_topic(awm->local_id("tree_group_not_marked"), "Group all except marked", "m", "tgroupnmrkd.hlp", AWM_ALL, makeWindowCallback(NT_group_not_marked_cb, ntw));
1409	awm->insert_menu_topic(awm->local_id("tree_group_term_groups"), "Group terminal groups", "t", "tgroupterm.hlp", AWM_ALL, makeWindowCallback(NT_group_terminal_cb, ntw));
1410	awm->insert_menu_topic(awm->local_id("tree_ungroup_all"), "Ungroup all", "U", "tungroupall.hlp", AWM_ALL, makeWindowCallback(NT_ungroup_all_cb, ntw));
1411	awm->sep______________();
1412	NT_insert_color_collapse_submenu(awm, ntw);
1413	}
1414	awm->close_sub_menu();
1415	awm->insert_sub_menu("Beautify tree", "e");
1416	{
1417	awm->insert_menu_topic(awm->local_id("beautifyt_tree"), "#beautifyt.xpm", "", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_TOP));
1418	awm->insert_menu_topic(awm->local_id("beautifyc_tree"), "#beautifyc.xpm", "", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_EDGE));
1419	awm->insert_menu_topic(awm->local_id("beautifyb_tree"), "#beautifyb.xpm", "", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_BOTTOM));
1420	awm->insert_menu_topic(awm->local_id("beautifyr_tree"), "Radial tree (1)", "1", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_CENTER));
1421	awm->insert_menu_topic(awm->local_id("beautifyr2_tree"), "Radial tree (2)", "2", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_ALTERNATING));
1422	awm->sep______________();
1423	awm->insert_menu_topic(awm->local_id("sort_by_other"), "By other tree", "o", "resortbyother.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_sort_tree_by_other_tree_window, ntw));
1424	}
1425	awm->close_sub_menu();
1426	awm->insert_sub_menu("Modify branches", "M");
1427	{
1428	awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw));
1429	awm->insert_menu_topic(awm->local_id("tree_toggle_bootstraps"), "Toggle 100% bootstraps", "1", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_toggle_bootstrap100, ntw));
1430	awm->sep______________();
1431	awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw));
1432	awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1433	awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw));
1434	awm->sep______________();
1435	awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1436	awm->sep______________();
1437	awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1438	awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1439
1440	}
1441	awm->close_sub_menu();
1442
1443	awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "s", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1444	awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "u", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback(NT_mark_duplicates, ntw));
1445
1446	awm->sep______________();
1447
1448	awm->insert_menu_topic(awm->local_id("tree_select"), "Select Tree", "T", 0, AWM_ALL, makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1449	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);
1450
1451	awm->sep______________();
1452
1453	if (!clone) {
1454	awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1455	awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_nds_window, GLOBAL.gb_main));
1456	}
1457	awm->sep______________();
1458
1459	awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1460
1461	awm->sep______________();
1462
1463	if (!clone) {
1464	awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, ntw));
1465	awm->insert_menu_topic("tree_2_xfig", "Export tree to XFIG", "X", "tree2file.hlp", AWM_ALL, makeWindowCallback(AWT_popup_tree_export_window, ntw));
1466	awm->sep______________();
1467	}
1468
1469	if (is_genome_db) {
1470	awm->insert_sub_menu("Other..", "O", AWM_EXP);
1471	{
1472	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);
1473	}
1474	awm->close_sub_menu();
1475	}
1476	}
1477
1478	if (!clone) {
1479	// ---------------
1480	// Tools
1481
1482	awm->create_menu("Tools", "o", AWM_ALL);
1483	{
1484	awm->insert_menu_topic("names_admin", "Name server admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_namesadmin_window, GLOBAL.gb_main));
1485	awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1486	{
1487	awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, NT_rerepair_DB, (AW_CL)GLOBAL.gb_main, 0);
1488	}
1489	awm->close_sub_menu();
1490	awm->insert_sub_menu("Network", "N", AWM_EXP);
1491	{
1492	GDE_load_menu(awm, AWM_EXP, "User");
1493	}
1494	awm->close_sub_menu();
1495	awm->sep______________();
1496
1497	awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1498	{
1499	GDE_load_menu(awm, AWM_EXP, NULL);
1500	}
1501	awm->close_sub_menu();
1502
1503	awm->insert_sub_menu("WL specials", "W", AWM_EXP);
1504	{
1505	awm->insert_menu_topic(awm->local_id("view_probe_group_result"), "View probe group result", "V", "", AWM_EXP, makeCreateWindowCallback(create_probe_group_result_window, ntw));
1506	}
1507	awm->close_sub_menu();
1508
1509	awm->sep______________();
1510	awm->insert_menu_topic("xterm", "Start XTERM", "X", 0, AWM_ALL, (AW_CB)GB_xterm, 0, 0);
1511	}
1512	// --------------------
1513	// Properties
1514
1515	awm->create_menu("Properties", "r", AWM_ALL);
1516	{
1517	awm->insert_menu_topic("props_menu", "Frame settings", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1518	awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, NT_create_tree_settings_window);
1519	awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "nt_props_data.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1520	awm->insert_menu_topic("props_www", "Search world wide web (WWW)", "W", "props_www.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_www_window, GLOBAL.gb_main));
1521	awm->sep______________();
1522	awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", 0, AWM_ALL, NT_toggle_expert_mode, 0, 0);
1523	awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", 0, AWM_ALL, NT_toggle_focus_policy, 0, 0);
1524	awm->sep______________();
1525	AW_insert_common_property_menu_entries(awm);
1526	awm->sep______________();
1527	awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1528	}
1529	}
1530
1531	awm->insert_help_topic("ARB_NT help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1532
1533	// ----------------------
1534	// mode buttons
1535	//
1536	// keep them synchronized as far as possible with those in ARB_PARSIMONY
1537	// see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1538
1539	awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1540	awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1541	awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1542	awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1543	awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1544
1545
1546	awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_modify_cb, ntw, AWT_MODE_INFO));
1547	awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW));
1548
1549	// topology-modification-modes
1550	awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1551	awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1552	awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1553	awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1554	awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1555
1556	// layout-modes
1557	awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1558	awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1559	awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1560
1561	awm->set_info_area_height(250);
1562	awm->at(5, 2);
1563	awm->auto_space(-2, -2);
1564	awm->shadow_width(1);
1565
1566	// -------------------------
1567	// create top area
1568
1569	int first_liney;
1570	int leftx;
1571	awm->get_at_position(&leftx, &first_liney);
1572
1573	// ---------------------
1574	// quit + help
1575
1576	awm->button_length(0);
1577
1578	if (clone) {
1579	awm->callback(AW_POPDOWN);
1580	awm->create_button("CLOSE", "#close.xpm");
1581	}
1582	else {
1583	awm->callback(nt_exit, EXIT_SUCCESS);
1584	awm->help_text("quit.hlp");
1585	awm->create_button("QUIT", "#quit.xpm");
1586	}
1587
1588	int db_pathx = awm->get_at_xposition();
1589
1590	// now fetch the yposition for the 2nd button line
1591	awm->at_newline();
1592	int second_liney = awm->get_at_yposition();
1593
1594	awm->callback(AW_help_entry_pressed);
1595	awm->help_text("arb_ntree.hlp");
1596	awm->create_button("?", "#help.xpm");
1597
1598	// --------------------------
1599	// save + undo/redo
1600
1601	awm->callback(NT_save_quick_cb);
1602	awm->help_text("save.hlp");
1603	awm->create_button("SAVE", "#save.xpm");
1604
1605	awm->callback(makeCreateWindowCallback(NT_create_save_as, "tmp/nt/arbdb"));
1606	awm->help_text("saveas.hlp");
1607	awm->create_button("SAVE_AS", "#saveAs.xpm");
1608
1609	// undo/redo:
1610	awm->callback(NT_undo_cb, (AW_CL)GB_UNDO_UNDO, (AW_CL)ntw);
1611	awm->help_text("undo.hlp");
1612	awm->create_button("UNDO", "#undo.xpm");
1613
1614	awm->callback(NT_undo_cb, (AW_CL)GB_UNDO_REDO, (AW_CL)ntw);
1615	awm->help_text("undo.hlp");
1616	awm->create_button("REDO", "#redo.xpm");
1617
1618	int db_pathx2 = awm->get_at_xposition();
1619
1620	// fetch position for mode help-line:
1621	awm->at_newline();
1622	int third_liney = awm->get_at_yposition();
1623
1624	awm->at(db_pathx, first_liney);
1625	// size of DB-name button is determined by buttons below:
1626	awm->at_set_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1627	awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, "tmp/nt/arbdb"));
1628	awm->help_text("saveas.hlp");
1629	awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1630
1631	// -----------------------------
1632	// tree + tree display
1633
1634	#define TREE_BUTTON_OVERSIZE 6
1635
1636	int db_treex = awm->get_at_xposition();
1637	int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1638
1639	awm->at(db_treex, second_uppery);
1640	awm->button_length(0);
1641
1642	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1643	awm->help_text("tr_type_radial.hlp");
1644	awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1645
1646	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1647	awm->help_text("tr_type_list.hlp");
1648	awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1649
1650	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1651	awm->help_text("tr_type_irs.hlp");
1652	awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1653
1654	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1655	awm->help_text("tr_type_nds.hlp");
1656	awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1657
1658	int db_treex2 = awm->get_at_xposition();
1659
1660	awm->at(db_treex, first_liney);
1661	// size of tree-name button is determined by buttons below:
1662	awm->at_set_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1663	awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1664	awm->help_text("nt_tree_select.hlp");
1665	awm->create_button("SELECT_A_TREE", awar_tree);
1666
1667	// ---------------------------------------------------------------
1668	// protection, alignment + editor (and maybe Genome Map)
1669
1670	int db_alignx = awm->get_at_xposition();
1671
1672	// editor and genemap buttons have to be 44x24 sized
1673	#define EDIT_XSIZE 50
1674	#define EDIT_YSIZE 30 // same as 'save as' buttons
1675
1676	// first draw protection:
1677	int protectx = db_alignx + 2*EDIT_XSIZE;
1678
1679	awm->at(protectx+2, first_liney+1);
1680	awm->button_length(0);
1681	awm->create_button(NULL, "#protect.xpm");
1682
1683	awm->at(protectx, second_liney+2);
1684	awm->create_option_menu(AWAR_SECURITY_LEVEL, true);
1685	awm->insert_option("0", 0, 0);
1686	awm->insert_option("1", 0, 1);
1687	awm->insert_option("2", 0, 2);
1688	awm->insert_option("3", 0, 3);
1689	awm->insert_option("4", 0, 4);
1690	awm->insert_option("5", 0, 5);
1691	awm->insert_default_option("6", 0, 6);
1692	awm->update_option_menu();
1693
1694	int db_searchx = awm->get_at_xposition() - 7;
1695
1696	// draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1697	awm->at(db_alignx, second_liney);
1698
1699	awm->at_set_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1700	awm->callback(NT_start_editor_on_tree, 0, (AW_CL)ntw);
1701	awm->help_text("arb_edit4.hlp");
1702	awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1703
1704	if (is_genome_db) {
1705	awm->at_set_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1706	awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1707	awm->help_text("gene_map.hlp");
1708	awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1709	}
1710
1711	int db_alignx2 = awm->get_at_xposition();
1712
1713	awm->at(db_alignx, first_liney);
1714	awm->at_set_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1715	awm->callback(NT_create_select_alignment_window);
1716	awm->help_text("nt_align_select.hlp");
1717	awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1718
1719	// -------------------------------
1720	// create mode-help line
1721
1722	awm->at(leftx, third_liney);
1723	awm->button_length(AWAR_FOOTER_MAX_LEN);
1724	awm->create_button(0, AWAR_FOOTER);
1725
1726	awm->at_newline();
1727	int bottomy = awm->get_at_yposition();
1728
1729	// ---------------------------------------
1730	// Info / marked / Search / Jump
1731
1732	awm->button_length(7);
1733
1734	awm->at(db_searchx, first_liney);
1735	awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1736	awm->help_text("sp_search.hlp");
1737	awm->create_button("SEARCH", "Search");
1738
1739	awm->at(db_searchx, second_uppery);
1740	awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1741	awm->help_text("tr_jump.hlp");
1742	awm->create_button("JUMP", "Jump");
1743
1744	int db_infox = awm->get_at_xposition();
1745
1746	awm->at(db_infox, first_liney);
1747	awm->button_length(13);
1748	awm->callback(popupinfo_wcb);
1749	awm->help_text("sp_search.hlp");
1750	awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1751
1752	awm->at(db_infox, second_uppery);
1753	awm->button_length(13);
1754	awm->help_text("configuration.hlp");
1755	awm->callback(NT_popup_configuration_admin, (AW_CL)ntw, 0);
1756	awm->create_button("selection_admin2", AWAR_MARKED_SPECIES_COUNTER);
1757	{
1758	GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1759	GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(NT_update_marked_counter, static_cast<AW_window*>(awm)));
1760	NT_update_marked_counter(NULL, awm);
1761	}
1762
1763	// set height of top area:
1764	awm->set_info_area_height(bottomy+2);
1765	awm->set_bottom_area_height(0);
1766
1767	// ------------------------------------
1768	// Autostarts for development
1769
1770	#if defined(DEVEL_RALF)
1771	// if (is_genome_db) GEN_map_first(awr)->show();
1772	#endif // DEVEL_RALF
1773
1774	GB_pop_transaction(GLOBAL.gb_main);
1775
1776	#if defined(DEBUG)
1777	AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1778	#endif
1779
1780	return awm;
1781	}
1782
1783	void nt_create_main_window(AW_root *aw_root) {
1784	GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1785	if (error) aw_message(error);
1786
1787	nt_create_all_awars(aw_root, AW_ROOT_DEFAULT);
1788
1789	AW_window *aww = popup_new_main_window(aw_root, 0);
1790	aww->show();
1791
1792	error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1793	if (error) aw_message(error);
1794	}

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