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source: tags/ms_r16q3/NTREE/NT_extern.cxx

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Last change on this file was 15340, checked in by westram, 8 years ago
reintegrates 'sync' into 'trunk' implements #683 adds: log:branches/sync@15291,15301:15312,15315:15318,15320:15329,15331:15339
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 72.5 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
15	#include <seq_quality.h>
16	#include <multi_probe.hxx>
17	#include <st_window.hxx>
18	#include <GEN.hxx>
19	#include <EXP.hxx>
20
21	#include <TreeCallbacks.hxx>
22	#include <AW_rename.hxx>
23	#include <probe_gui.hxx>
24	#include <primer_design.hxx>
25	#include <gde.hxx>
26	#include <awtc_submission.hxx>
27
28	#include <macros.hxx>
29	#include <nds.h>
30	#include <db_query.h>
31	#include <dbui.h>
32	#include <refentries.h>
33	#include <insdel.h>
34
35	#include <awti_export.hxx>
36	#include <awti_import.hxx>
37
38	#include <awt.hxx>
39	#include <awt_input_mask.hxx>
40	#include <awt_sel_boxes.hxx>
41	#include <awt_www.hxx>
42	#include <awt_TreeAwars.hxx>
43	#include <awt_misc.hxx>
44
45	#include <aw_color_groups.hxx>
46	#include <aw_advice.hxx>
47	#include <aw_preset.hxx>
48	#include <aw_awars.hxx>
49	#include <aw_global_awars.hxx>
50	#include <aw_file.hxx>
51	#include <aw_msg.hxx>
52	#include <arb_progress.h>
53	#include <aw_root.hxx>
54	#include <aw_question.hxx>
55	#include <aw_select.hxx>
56	#include <rootAsWin.h>
57
58	#include <ad_cb.h>
59
60	#include <arb_strbuf.h>
61	#include <arb_strarray.h>
62	#include <arb_file.h>
63	#include <arb_version.h>
64
65	#define AWAR_EXPORT_NDS "tmp/export_nds"
66	#define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/separator"
67	#define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species"
68	#define AWAR_NTREE_TITLE_MODE "tmp/title_mode"
69
70	void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
71
72	void create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
73	AW_window create_insertDeleteColumn_window(AW_root root);
74	AW_window create_insertDeleteBySAI_window(AW_root root, GBDATA *gb_main);
75
76	AW_window create_tree_window(AW_root aw_root, AWT_graphic *awd);
77
78	static void nt_changesecurity(AW_root *aw_root) {
79	int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
80	GB_push_transaction(GLOBAL.gb_main);
81	GB_change_my_security(GLOBAL.gb_main, level);
82	GB_pop_transaction(GLOBAL.gb_main);
83	}
84
85	static void export_nds_cb(AW_window *aww, bool do_print) {
86	AW_root *aw_root = aww->get_root();
87	char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
88	FILE *out = fopen(name, "w");
89
90	if (!out) {
91	aw_message("Error: Cannot open and write to file");
92	}
93	else {
94	GB_transaction ta(GLOBAL.gb_main);
95
96	make_node_text_init(GLOBAL.gb_main);
97	NDS_Type nds_type = (NDS_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
98	char *tree_name = aw_root->awar(AWAR_TREE)->read_string();
99
100	for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
101	gb_species;
102	gb_species = GBT_next_marked_species(gb_species))
103	{
104	const char *buf = make_node_text_nds(GLOBAL.gb_main, gb_species, nds_type, 0, tree_name);
105	fprintf(out, "%s\n", buf);
106	}
107	AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
108	fclose(out);
109	if (do_print) {
110	GB_ERROR error = GB_textprint(name);
111	if (error) aw_message(error);
112	}
113	free(tree_name);
114	}
115	free(name);
116	}
117
118	static AW_window create_nds_export_window(AW_root root) {
119	AW_window_simple *aws = new AW_window_simple;
120	aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
121	aws->load_xfig("sel_box_nds.fig");
122
123	aws->callback(AW_POPDOWN);
124	aws->at("close");
125	aws->create_button("CLOSE", "CLOSE", "C");
126
127	aws->callback(makeHelpCallback("arb_export_nds.hlp"));
128	aws->at("help");
129	aws->create_button("HELP", "HELP", "H");
130
131	aws->at("save");
132	aws->callback(makeWindowCallback(export_nds_cb, false));
133	aws->create_button("SAVE", "SAVE", "S");
134
135	aws->at("print");
136	aws->callback(makeWindowCallback(export_nds_cb, true));
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) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
169	#if defined(ARB_MOTIF)
170	static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
171	#endif
172
173	static void nt_create_all_awars(AW_root *awr) {
174	// creates awars for all modules reachable from ARB_NT main window
175
176	awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT);
177	if (GB_read_clients(GLOBAL.gb_main)>=0) {
178	awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
179	}
180	else {
181	awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT);
182	}
183
184	awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main);
185	awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main);
186	awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main);
187	awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown", GLOBAL.gb_main);
188	awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main);
189	awr->awar(AWAR_SPECIES_NAME)->add_callback(AWAR_INFO_BUTTON_TEXT_change_cb);
190	awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
191
192	awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
193
194	GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
195	EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
196	#if defined(DEBUG)
197	AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT);
198	#endif // DEBUG
199
200	AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
201
202	awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT);
203	awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
204	#if defined(DEBUG) && 0
205	awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
206	#endif // DEBUG
207
208	create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT);
209	create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
210	create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
211	create_trees_var(awr, AW_ROOT_DEFAULT);
212	DBUI::create_dbui_awars(awr);
213	AP_create_consensus_var(awr, AW_ROOT_DEFAULT);
214	{
215	GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, 0, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT);
216	if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
217	}
218	NT_create_transpro_variables(awr, AW_ROOT_DEFAULT);
219	NT_create_resort_awars(awr, AW_ROOT_DEFAULT);
220	NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT);
221	NT_create_trackAliChanges_Awars(awr, GLOBAL.gb_main);
222
223	NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
224	NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
225	create_nds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, false);
226	create_export_nds_awars(awr, AW_ROOT_DEFAULT);
227	TREE_create_awars(awr, GLOBAL.gb_main);
228
229	awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
230	awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
231
232	AWTC_create_submission_variables(awr, GLOBAL.gb_main);
233	NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
234	NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar
235	SQ_create_awars(awr, AW_ROOT_DEFAULT);
236	RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT);
237
238	NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT);
239
240	GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
241	if (!error) {
242	AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
243	awar_expert->add_callback(expert_mode_changed_cb);
244	awar_expert->touch();
245
246	awt_create_aww_vars(awr, AW_ROOT_DEFAULT);
247	}
248
249	if (error) aw_message(error);
250	}
251
252	// --------------------------------------------------------------------------------
253
254	bool nt_disconnect_from_db(AW_root aw_root, GBDATA& gb_main_ref) {
255	// ask user if DB was not saved
256	// returns true if user allows to quit
257
258	// @@@ code here could as well be applied to both merge DBs
259	// - question about saving only with target DB!
260
261	if (gb_main_ref) {
262	if (GB_read_clients(gb_main_ref)>=0) {
263	if (GB_read_clock(gb_main_ref) > GB_last_saved_clock(gb_main_ref)) {
264	long secs;
265	secs = GB_last_saved_time(gb_main_ref);
266
267	#if defined(DEBUG)
268	secs = GB_time_of_day(); // simulate "just saved"
269	#endif // DEBUG
270
271	const char *quit_buttons = "Quit ARB,Do NOT quit";
272	if (secs) {
273	secs = GB_time_of_day() - secs;
274	if (secs>10) {
275	char *question = GBS_global_string_copy("You last saved your data %li:%li minutes ago\nSure to quit ?", secs/60, secs%60);
276	int dontQuit = aw_question("quit_arb", question, quit_buttons);
277	free(question);
278	if (dontQuit) {
279	return false;
280	}
281	}
282	}
283	else {
284	if (aw_question("quit_arb", "You never saved any data\nSure to quit ???", quit_buttons)) {
285	return false;
286	}
287	}
288	}
289	}
290
291	GBCMS_shutdown(gb_main_ref);
292
293	GBDATA *gb_main = gb_main_ref;
294	gb_main_ref = NULL; // avoid further usage
295
296	nt_assert(aw_root);
297	#if defined(WARN_TODO)
298	#warning instead of directly calling the following functions, try to add them as GB_atclose-callbacks
299	#endif
300	aw_root->unlink_awars_from_DB(gb_main);
301	AWT_destroy_input_masks();
302	#if defined(DEBUG)
303	AWT_browser_forget_db(gb_main);
304	#endif // DEBUG
305
306	GB_close(gb_main);
307	}
308	return true;
309	}
310
311	static void nt_run(const char *command) {
312	GB_ERROR error = GBK_system(command);
313	if (error) {
314	fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
315	#if defined(DEBUG)
316	GBK_dump_backtrace(stderr, "nt_run-error");
317	#endif
318	}
319	}
320
321	void NT_start(const char *arb_ntree_args, bool restart_with_new_ARB_PID) {
322	char *command = GBS_global_string_copy("arb_launcher --async %s %s", restart_with_new_ARB_PID ? "arb" : "arb_ntree", arb_ntree_args);
323	nt_run(command);
324	free(command);
325	}
326
327	__ATTR__NORETURN static void really_exit(int exitcode, bool kill_my_clients) {
328	if (kill_my_clients) {
329	nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
330	}
331	exit(exitcode);
332	}
333
334	void NT_exit(AW_window *aws, int exitcode) {
335	AW_root *aw_root = aws->get_root();
336	AWTI_cleanup_importer();
337	shutdown_macro_recording(aw_root);
338	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
339	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
340	really_exit(exitcode, is_server_and_has_clients);
341	}
342	}
343	void NT_restart(AW_root aw_root, const char arb_ntree_args) {
344	// restarts arb_ntree (with new ARB_PID)
345	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
346	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
347	NT_start(arb_ntree_args, true);
348	really_exit(EXIT_SUCCESS, is_server_and_has_clients);
349	}
350	}
351
352	static void nt_start_2nd_arb(AW_window *aww, bool quit) {
353	// start 2nd arb with intro window
354	AW_root *aw_root = aww->get_root();
355	char *dir4intro;
356	GB_split_full_path(aw_root->awar(AWAR_DB_PATH)->read_char_pntr(), &dir4intro, NULL, NULL, NULL);
357	if (!dir4intro) {
358	dir4intro = ARB_strdup(".");
359	}
360
361	if (quit) {
362	NT_restart(aw_root, dir4intro);
363	}
364	else {
365	NT_start(dir4intro, true);
366	}
367	free(dir4intro);
368	}
369
370	// --------------------------------------------------------------------------------
371
372	static void NT_save_quick_cb(AW_window *aww) {
373	AW_root *awr = aww->get_root();
374	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
375
376	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
377
378	GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
379	free( filename);
380	if (error) aw_message(error);
381	else AW_refresh_fileselection(awr, AWAR_DBBASE);
382	}
383
384
385	static void NT_save_quick_as_cb(AW_window *aww) {
386	AW_root *awr = aww->get_root();
387	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
388	GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename);
389	if (!error) AW_refresh_fileselection(awr, AWAR_DBBASE);
390	aww->hide_or_notify(error);
391
392	free(filename);
393	}
394
395	#define AWAR_DB_TYPE AWAR_DBBASE "/type" // created by AWT_insert_DBsaveType_selector
396	#define AWAR_DB_COMPRESSION AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector
397	#define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name"
398
399	static void NT_save_as_cb(AW_window *aww) {
400	AW_root *awr = aww->get_root();
401	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
402	const char *atype = awr->awar(AWAR_DB_TYPE)->read_char_pntr();
403	const char *ctype = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr();
404	char *savetype = GBS_global_string_copy("%s%s", atype, ctype);
405
406	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
407	GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype);
408	if (!error) AW_refresh_fileselection(awr, AWAR_DBBASE);
409	aww->hide_or_notify(error);
410
411	free(savetype);
412	free(filename);
413	}
414
415	static AW_window NT_create_save_quick_as_window(AW_root aw_root, const char *base_name) {
416	static AW_window_simple *aws = 0;
417	if (!aws) {
418	aws = new AW_window_simple;
419	aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as");
420	aws->load_xfig("save_as.fig");
421
422	aws->at("close");
423	aws->callback(AW_POPDOWN);
424	aws->create_button("CLOSE", "CLOSE", "C");
425
426	aws->callback(makeHelpCallback("save.hlp"));
427	aws->at("help");
428	aws->create_button("HELP", "HELP", "H");
429
430	AW_create_standard_fileselection(aws, base_name);
431
432	aws->at("comment");
433	aws->create_text_field(AWAR_DB_COMMENT);
434
435	aws->at("save");
436	aws->callback(NT_save_quick_as_cb);
437	aws->create_button("SAVE", "SAVE", "S");
438	}
439	return aws;
440	}
441
442	static void NT_database_optimization(AW_window *aww) {
443	arb_progress progress("Optimizing database compression", 2);
444
445	GB_push_my_security(GLOBAL.gb_main);
446	GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
447	if (!error) {
448	ConstStrArray ali_names;
449	GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
450
451	arb_progress ali_progress("Optimizing sequence data", ali_names.size());
452	ali_progress.allow_title_reuse();
453
454	error = GBT_check_data(GLOBAL.gb_main, 0);
455	error = GB_end_transaction(GLOBAL.gb_main, error);
456
457	if (!error) {
458	char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string();
459	for (int i = 0; ali_names[i]; ++i) {
460	error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
461	ali_progress.inc_and_check_user_abort(error);
462	}
463	free(tree_name);
464	}
465	}
466	progress.inc_and_check_user_abort(error);
467
468	if (!error) {
469	error = GB_optimize(GLOBAL.gb_main);
470	progress.inc_and_check_user_abort(error);
471	}
472
473	GB_pop_my_security(GLOBAL.gb_main);
474	aww->hide_or_notify(error);
475	}
476
477	static AW_window NT_create_database_optimization_window(AW_root aw_root) {
478	static AW_window_simple *aws = 0;
479	if (aws) return (AW_window *)aws;
480	GB_transaction ta(GLOBAL.gb_main);
481
482	const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
483	aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree);
484
485	aws = new AW_window_simple;
486	aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression");
487	aws->load_xfig("optimize.fig");
488
489	aws->at("trees");
490	awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME, true);
491
492	aws->at("close");
493	aws->callback(AW_POPDOWN);
494	aws->create_button("CLOSE", "CLOSE", "C");
495
496	aws->callback(makeHelpCallback("optimize.hlp"));
497	aws->at("help");
498	aws->create_button("HELP", "HELP", "H");
499
500	aws->at("go");
501	aws->callback(NT_database_optimization);
502	aws->create_button("GO", "GO");
503	return aws;
504	}
505
506	static AW_window NT_create_save_as(AW_root aw_root, const char *base_name)
507	{
508	static AW_window_simple *aws = 0;
509	if (aws) return (AW_window *)aws;
510
511	aws = new AW_window_simple;
512	aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
513	aws->load_xfig("save_as.fig");
514
515	aws->at("close");
516	aws->callback(AW_POPDOWN);
517	aws->create_button("CLOSE", "CLOSE", "C");
518
519	aws->at("help");
520	aws->callback(makeHelpCallback("save.hlp"));
521	aws->create_button("HELP", "HELP", "H");
522
523	AW_create_standard_fileselection(aws, base_name);
524
525	aws->at("type");
526	AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE);
527
528	aws->at("compression");
529	AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION);
530
531	aws->at("optimize");
532	aws->callback(NT_create_database_optimization_window);
533	aws->help_text("optimize.hlp");
534	aws->create_autosize_button("OPTIMIZE", "Optimize database compression");
535
536	aws->at("save");
537	aws->callback(NT_save_as_cb);
538	aws->create_button("SAVE", "SAVE", "S");
539
540	aws->at("comment");
541	aws->create_text_field(AWAR_DB_COMMENT);
542
543	return aws;
544	}
545
546	static void NT_undo_cb(AW_window, GB_UNDO_TYPE undo_type, TREE_canvas ntw) {
547	GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type);
548	if (error) aw_message(error);
549	else {
550	GB_transaction ta(GLOBAL.gb_main);
551	ntw->refresh();
552	}
553	}
554
555	enum streamSource { FROM_PIPE, FROM_FILE };
556	static char stream2str(streamSource source, const char commandOrFile) {
557	char *output = 0;
558	FILE *in = 0;
559
560	switch (source) {
561	case FROM_PIPE: in = popen(commandOrFile, "r"); break;
562	case FROM_FILE: in = fopen(commandOrFile, "rt"); break;
563	}
564
565	if (in) {
566	GBS_strstruct *out = GBS_stropen(2000);
567	int c;
568
569	while (EOF != (c = fgetc(in))) GBS_chrcat(out, c);
570
571	switch (source) {
572	case FROM_PIPE: pclose(in); break;
573	case FROM_FILE: fclose(in); break;
574	}
575
576	// skip trailing linefeeds
577	long offset = GBS_memoffset(out);
578	while (offset>0 && GBS_mempntr(out)[offset-1] == '\n') {
579	GBS_str_cut_tail(out, 1);
580	offset--;
581	}
582
583	output = GBS_strclose(out);
584	}
585	return output;
586	}
587
588	inline void removeTrailingNewlines(char *str) {
589	char *eos = strchr(str, 0)-1;
590	while (eos >= str && eos[0] == '\n') *eos-- = 0;
591	}
592
593	inline void append_named_value(GBS_strstruct out, const char prefix, const char *value) {
594	GBS_strcat(out, GBS_global_string("%-*s: %s\n", 12, prefix, value));
595	}
596	inline void append_command_output(GBS_strstruct out, const char prefix, const char *command) {
597	char *output = stream2str(FROM_PIPE, command);
598	if (output) {
599	removeTrailingNewlines(output);
600	if (strcmp(output, "unknown") != 0) append_named_value(out, prefix, output);
601	free(output);
602	}
603	}
604
605	static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) {
606	DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
607	nt_mode_event(NULL, canvas, mode);
608	}
609
610	static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) {
611	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
612	if (tree_root) {
613	GB_transaction ta(ntw->gb_main);
614	NT_mark_all_cb(NULL, ntw, 0);
615
616	tree_root->mark_duplicates();
617	tree_root->compute_tree();
618	ntw->refresh();
619	}
620	}
621
622	static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) {
623	GB_transaction ta(ntw->gb_main);
624	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
625
626	if (tree_root) {
627	tree_root->justify_branch_lenghs(ntw->gb_main);
628	tree_root->compute_tree();
629	GB_ERROR error = AWT_TREE(ntw)->save(ntw->gb_main, NULL);
630	if (error) aw_message(error);
631	ntw->refresh();
632	}
633	}
634
635	#if defined(DEBUG)
636	static void NT_fix_database(AW_window *) {
637	GB_ERROR err = 0;
638	err = GB_fix_database(GLOBAL.gb_main);
639	if (err) aw_message(err);
640	}
641	#endif
642
643	static void relink_pseudo_species_to_organisms(GBDATA &ref_gb_node, char &ref_name, GB_HASH *organism_hash) {
644	if (ref_gb_node) {
645	if (GEN_is_pseudo_gene_species(ref_gb_node)) {
646	GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
647
648	if (gb_organism) {
649	char *name = GBT_read_string(gb_organism, "name");
650
651	if (name) {
652	freeset(ref_name, name);
653	ref_gb_node = gb_organism;
654	}
655	}
656	}
657	}
658	}
659
660	static void NT_pseudo_species_to_organism(AW_window , TREE_canvas ntw) {
661	GB_transaction ta(ntw->gb_main);
662	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
663
664	if (tree_root) {
665	GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
666	tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
667	tree_root->compute_tree();
668	GB_ERROR error = AWT_TREE(ntw)->save(ntw->gb_main, NULL);
669	if (error) aw_message(error);
670	ntw->refresh();
671	GBS_free_hash(organism_hash);
672	}
673	}
674
675
676	// #########################################
677	// #########################################
678	// ### ###
679	// ## user mask section ##
680	// ### ###
681	// #########################################
682	// #########################################
683
684	struct nt_item_type_species_selector : public awt_item_type_selector {
685	nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
686	~nt_item_type_species_selector() OVERRIDE {}
687
688	const char *get_self_awar() const OVERRIDE {
689	return AWAR_SPECIES_NAME;
690	}
691	size_t get_self_awar_content_length() const OVERRIDE {
692	return 12; // should be enough for "nnaammee.999"
693	}
694	GBDATA current(AW_root root, GBDATA *gb_main) const OVERRIDE { // give the current item
695	char *species_name = root->awar(get_self_awar())->read_string();
696	GBDATA *gb_species = 0;
697
698	if (species_name[0]) {
699	GB_transaction ta(gb_main);
700	gb_species = GBT_find_species(gb_main, species_name);
701	}
702
703	free(species_name);
704	return gb_species;
705	}
706	const char *getKeyPath() const OVERRIDE { // give the keypath for items
707	return CHANGE_KEY_PATH;
708	}
709	};
710
711	static nt_item_type_species_selector item_type_species;
712
713	static void NT_open_mask_window(AW_window aww, int id, GBDATA gb_main) {
714	const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
715	nt_assert(descriptor);
716	if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
717	}
718
719	static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
720	AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
721	}
722	static AW_window create_colorize_species_window(AW_root aw_root) {
723	return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
724	}
725
726	static void NT_update_marked_counter(GBDATA, AW_window aww) {
727	/*! Updates marked counter and issues redraw on tree if number of marked species changes.
728	* Called on any change of species_information container.
729	*/
730	long count = GBT_count_marked_species(GLOBAL.gb_main);
731	const char *buffer = count ? GBS_global_string("%li marked", count) : "";
732	AW_awar *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
733	char *oldval = counter->read_string();
734	if (strcmp(oldval, buffer)) {
735	counter->write_string(buffer);
736	aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
737	}
738	free(oldval);
739	}
740
741	// --------------------------------------------------------------------------------------------------
742
743	static void NT_alltree_remove_leafs(AW_window , GBT_TreeRemoveType mode, GBDATA gb_main) {
744	GB_ERROR error = 0;
745	GB_transaction ta(gb_main);
746
747	ConstStrArray tree_names;
748	GBT_get_tree_names(tree_names, gb_main, false);
749
750	if (!tree_names.empty()) {
751	int treeCount = tree_names.size();
752
753	const char *whats_removed = NULL;
754	switch (mode) {
755	case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
756	case GBT_REMOVE_MARKED: whats_removed = "marked"; break;
757	default: nt_assert(0); break;
758	}
759
760	const char *task = GBS_global_string("Deleting %s from %i trees", whats_removed, treeCount);
761
762	arb_progress progress(task, treeCount);
763	GB_HASH *species_hash = GBT_create_species_hash(gb_main);
764
765	int modified = 0;
766
767	for (int t = 0; t<treeCount && !error; t++) {
768	progress.subtitle(tree_names[t]);
769	TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
770	if (!tree) {
771	aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
772	}
773	else {
774	int removed = 0;
775	int groups_removed = 0;
776
777	tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
778
779	nt_assert(removed >= groups_removed);
780
781	if (!tree) {
782	aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
783	}
784	else {
785	if (removed>0) {
786	error = GBT_write_tree(gb_main, tree_names[t], tree);
787	if (error) {
788	aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
789	}
790	else {
791	if (groups_removed>0) {
792	aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
793	}
794	else {
795	aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
796	}
797	modified++;
798	}
799	}
800	UNCOVERED();
801	destroy(tree);
802	}
803	}
804	progress.inc_and_check_user_abort(error);
805	}
806
807	if (modified) {
808	aw_message(GBS_global_string("Changed %i of %i trees.", modified, treeCount));
809	}
810	else {
811	aw_message("No tree modified");
812	}
813
814	GBS_free_hash(species_hash);
815	}
816
817	aw_message_if(ta.close(error));
818	}
819
820	TreeNode NT_get_tree_root_of_canvas(TREE_canvas ntw) {
821	AWT_graphic_tree *tree = AWT_TREE(ntw);
822	if (tree) {
823	AP_tree *root = tree->get_root_node();
824	if (root) return root;
825	}
826	return NULL;
827	}
828
829	// --------------------------------------------------------------------------------------------------
830
831	static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
832	GB_transaction ta(gb_main);
833	GBT_mark_all(gb_main, 0);
834
835	DBItemSetIter end = referred.end();
836	for (DBItemSetIter s = referred.begin(); s != end; ++s) {
837	GB_write_flag(*s, 1);
838	}
839	return ARB_ERROR();
840	}
841
842	static AW_window create_mark_by_refentries_window(AW_root awr, GBDATA *gbmain) {
843	static AW_window *aws = NULL;
844	if (!aws) {
845	static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
846	aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULL, "Mark referenced", mark_referred_species);
847	}
848	return aws;
849	}
850
851	// --------------------------------------------------------------------------------------------------
852
853	static void merge_from_to(AW_root awr, const char db_awar_name, bool merge_to) {
854	const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
855	char *quotedDB = GBK_singlequote(db_name);
856
857	AWT_system_cb(
858	GBS_global_string(
859	merge_to
860	? "arb_ntree : %s &"
861	: "arb_ntree %s : &",
862	quotedDB)
863	);
864
865	free(quotedDB);
866	}
867
868	static void merge_from_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, false); }
869	static void merge_into_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, true); }
870
871	static AW_window NT_create_merge_from_window(AW_root awr) {
872	static char *awar_name = NULL; // do not free, bound to callback
873	AW_window *aw_from =
874	awt_create_load_box(awr, "Merge data from", "other ARB database",
875	".", ".arb", &awar_name,
876	makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
877	return aw_from;
878	}
879	static AW_window NT_create_merge_to_window(AW_root awr) {
880	static char *awar_name = NULL; // do not free, bound to callback
881	AW_window *aw_to =
882	awt_create_load_box(awr, "Merge data to", "other ARB database",
883	".", ".arb", &awar_name,
884	makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
885	makeWindowCallback(AW_POPDOWN), NULL);
886	return aw_to;
887	}
888
889	// --------------------------------------------------------------------------------------------------
890
891	static void update_main_window_title(AW_root* awr, AW_window_menu_modes* aww, int clone) {
892	const char* filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
893	if (clone) {
894	aww->set_window_title(GBS_global_string("%s - ARB (%i)", filename, clone));
895	}
896	else {
897	aww->set_window_title(GBS_global_string("%s - ARB", filename));
898	}
899	}
900
901	static void canvas_tree_awar_changed_cb(AW_awar , bool, TREE_canvas ntw) {
902	NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
903	AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
904	}
905
906	class TREE_canvas_registry {
907	int count;
908	TREE_canvas *canvas[MAX_NT_WINDOWS];
909
910	static TREE_canvas_registry *SINGLETON;
911
912	TREE_canvas_registry() : count(0) {
913	AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
914	}
915
916	public:
917	static TREE_canvas_registry& instance() {
918	if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
919	return *SINGLETON;
920	}
921
922	void register_canvas(TREE_canvas *ntw) {
923	nt_assert(count<MAX_NT_WINDOWS);
924	nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
925	canvas[count++] = ntw;
926	ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
927	}
928
929	int get_count() const { return count; }
930
931	TREE_canvas *get_canvas(int idx) const {
932	if (idx<0 \|\| idx>=count) return NULL;
933	return canvas[idx];
934	}
935	};
936
937	TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULL;
938
939	TREE_canvas *NT_get_canvas_by_index(int idx) {
940	/! return canvas with index 'idx' [0...MAX_NT_WINDOWS-1] /
941	nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
942	return TREE_canvas_registry::instance().get_canvas(idx);
943	}
944
945	void NT_fill_canvas_selection_list(class AW_selection_list sellst, TREE_canvas to_skip) {
946	/*! insert canvases into selection list (using canvas-indices as values)
947	*/
948	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
949
950	int maxIdx = reg.get_count();
951	for (int32_t i = 0; i<maxIdx; ++i) {
952	TREE_canvas *ntw = reg.get_canvas(i);
953	if (ntw && ntw != to_skip) {
954	nt_assert(ntw->get_awar_tree());
955	const char *treename = ntw->get_awar_tree()->read_char_pntr();
956	const char *description = i
957	? GBS_global_string("ARB (%i): %s", i, treename)
958	: GBS_global_string("ARB main: %s", treename);
959	sellst->insert(description, i);
960	}
961	}
962	}
963
964	// ----------------------------
965	// create main window
966
967	static AW_window popup_new_main_window(AW_root awr, int clone, TREE_canvas **result_ntw) {
968	/*! create ARB_NTREE main window
969	* @param awr application root
970	* @param clone == 0 -> first window (full functionality); >0 -> additional tree views (restricted functionality)
971	* @param result_ntw is set to the created TREE_canvas (passed pointer may be NULL if result is not needed)
972	*/
973	GB_push_transaction(GLOBAL.gb_main);
974
975	char window_title[256];
976	const char *awar_tree = NULL;
977
978	if (clone) {
979	awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
980	sprintf(window_title, "ARB_NT_%i", clone);
981	}
982	else {
983	awar_tree = AWAR_TREE;
984	sprintf(window_title, "ARB_NT");
985	}
986	AW_window_menu_modes *awm = new AW_window_menu_modes;
987	awm->init(awr, window_title, window_title, 0, 0);
988
989	awr->awar(AWAR_DB_NAME)
990	->add_callback(makeRootCallback(update_main_window_title, awm, clone))
991	->update();
992
993	awm->button_length(5);
994
995	if (!clone) AW_init_color_group_defaults("arb_ntree");
996
997	AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
998
999	TREE_canvas *ntw;
1000	{
1001	AW_awar *tree_awar = awr->awar_string(awar_tree);
1002	{
1003	AP_tree_display_type old_sort_type = tree->tree_sort;
1004	tree->set_tree_type(AP_LIST_SIMPLE, NULL); // avoid NDS warnings during startup
1005
1006	ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1007	tree->set_tree_type(old_sort_type, ntw);
1008	ntw->set_mode(AWT_MODE_SELECT);
1009	}
1010
1011	if (result_ntw) *result_ntw = ntw;
1012
1013	{
1014	const char *tree_name = tree_awar->read_char_pntr();
1015	const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1016
1017	if (existing_tree_name) {
1018	tree_awar->write_string(existing_tree_name);
1019	NT_reload_tree_event(awr, ntw, true); // load first tree
1020	}
1021	else {
1022	AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, 0, "no_tree.hlp");
1023	tree->set_tree_type(AP_LIST_NDS, ntw); // no tree -> show NDS list
1024	}
1025
1026	TREE_canvas_registry::instance().register_canvas(ntw);
1027	AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1028	}
1029	}
1030
1031	TREE_install_update_callbacks(ntw);
1032	awr->awar(AWAR_TREE_NAME)->add_callback(makeRootCallback(TREE_auto_jump_cb, ntw, true)); // NT specific (tree name never changes in parsimony!)
1033
1034	bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1035
1036	WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1037
1038	// --------------
1039	// File
1040
1041	#if defined(DEBUG)
1042	AWT_create_debug_menu(awm);
1043	#endif // DEBUG
1044
1045	bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1046
1047	if (clone) {
1048	awm->create_menu("File", "F", AWM_ALL);
1049	if (allow_new_window) {
1050	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, (TREE_canvas**)NULL));
1051	}
1052	awm->insert_menu_topic("close", "Close", "C", 0, AWM_ALL, AW_POPDOWN);
1053	}
1054	else {
1055	#if defined(DEBUG)
1056	// add more to debug-menu
1057	awm->sep______________();
1058	awm->insert_menu_topic("fix_db", "Fix database", "F", 0, AWM_ALL, NT_fix_database);
1059	awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", 0, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1060	awm->insert_menu_topic("test_compr", "Test compression", "T", 0, AWM_ALL, makeWindowCallback(GBT_compression_test, GLOBAL.gb_main));
1061	#endif // DEBUG
1062
1063	awm->create_menu("File", "F", AWM_ALL);
1064	{
1065	// keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1066	awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, NT_save_quick_cb);
1067	awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1068	if (allow_new_window) {
1069	awm->sep______________();
1070	awm->insert_menu_topic("new_window", "New window (same database)", "N", "newwindow.hlp", AWM_ALL, makeCreateWindowCallback(popup_new_main_window, clone+1, (TREE_canvas**)NULL));
1071	}
1072	awm->sep______________();
1073	awm->insert_menu_topic("optimize_db", "Optimize database compression", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window);
1074	awm->sep______________();
1075
1076	awm->insert_sub_menu("Import", "I");
1077	{
1078	awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1079	awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1080	GDE_load_menu(awm, AWM_EXP, "Import");
1081	}
1082	awm->close_sub_menu();
1083
1084	awm->insert_sub_menu("Export", "E");
1085	{
1086	awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1087	awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1088	GDE_load_menu(awm, AWM_ALL, "Export");
1089	awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window);
1090	}
1091	awm->close_sub_menu();
1092	awm->sep______________();
1093
1094	insert_macro_menu_entry(awm, false);
1095
1096	awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1097	{
1098	awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp"));
1099	awm->insert_menu_topic("bug_report", "Report bug", "b", NULL, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1100	awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULL, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1101	}
1102	awm->close_sub_menu();
1103	awm->sep______________();
1104
1105	awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1106	awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1107	awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_exit, EXIT_SUCCESS));
1108	}
1109
1110	// -----------------
1111	// Species
1112
1113	awm->create_menu("Species", "c", AWM_ALL);
1114	{
1115	awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1116	awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb);
1117
1118	awm->sep______________();
1119
1120	NT_insert_mark_submenus(awm, ntw, 1);
1121	awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1122	awm->insert_menu_topic("species_colors", "Colors ...", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window);
1123	awm->insert_menu_topic("selection_admin", "Selections ...", "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1124
1125	awm->sep______________();
1126
1127	awm->insert_sub_menu("Database fields admin", "f");
1128	DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1129	awm->close_sub_menu();
1130	NT_create_mask_submenu(awm);
1131
1132	awm->sep______________();
1133
1134	awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1135
1136	awm->insert_sub_menu("Sort Species", "s");
1137	{
1138	awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window);
1139	awm->insert_menu_topic("$sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1140	}
1141	awm->close_sub_menu();
1142
1143	awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1144	{
1145	awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1146	awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "species_join.hlp", AWM_EXP, NT_create_species_join_window);
1147	}
1148	awm->close_sub_menu();
1149
1150	awm->sep______________();
1151
1152	awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1153
1154	awm->sep______________();
1155
1156	awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1157
1158	awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1159	{
1160	awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames);
1161	awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames);
1162	awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1163	awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window);
1164	}
1165	awm->close_sub_menu();
1166	}
1167
1168	// ----------------------------
1169	// Genes + Experiment
1170
1171	if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1172
1173	// ------------------
1174	// Sequence
1175
1176	awm->create_menu("Sequence", "S", AWM_ALL);
1177	{
1178	awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)0));
1179	awm->insert_sub_menu("Insert/delete", "I");
1180	{
1181	awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window);
1182	awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main));
1183	}
1184	awm->close_sub_menu();
1185	awm->sep______________();
1186
1187	awm->insert_sub_menu("Edit Sequences", "E");
1188	{
1189	awm->insert_menu_topic("new_arb_edit4", "Using marked species and tree", "m", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1190	awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1191	awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1192	}
1193	awm->close_sub_menu();
1194
1195	awm->sep______________();
1196
1197	awm->insert_sub_menu("Align Sequences", "S");
1198	{
1199	awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1200	GDE_load_menu(awm, AWM_ALL, "Align");
1201	}
1202	awm->close_sub_menu();
1203	awm->insert_menu_topic("seq_concat", "Concatenate Sequences/Alignments", "C", "concatenate.hlp", AWM_ALL, NT_createConcatenationWindow);
1204	awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1205	awm->sep______________();
1206
1207	awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1208	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1209	awm->sep______________();
1210
1211	awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1212	awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1213
1214	awm->sep______________();
1215
1216	GDE_load_menu(awm, AWM_ALL, "Print");
1217	}
1218
1219	// -------------
1220	// SAI
1221
1222	awm->create_menu("SAI", "A", AWM_ALL);
1223	{
1224	awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1225	awm->insert_sub_menu("Create SAI using ...", "C");
1226	{
1227	awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window);
1228	awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window);
1229	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);
1230	awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_phylo &"));
1231	awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, makeWindowCallback(NT_create_sai_from_pfold, ntw));
1232
1233	GDE_load_menu(awm, AWM_EXP, "SAI");
1234	}
1235	awm->close_sub_menu();
1236
1237	awm->insert_sub_menu("Other functions", "O");
1238	{
1239	awm->insert_menu_topic("count_different_chars", "Count different chars/column", "C", "count_chars.hlp", AWM_EXP, makeWindowCallback(NT_count_different_chars, GLOBAL.gb_main));
1240	awm->insert_menu_topic("corr_mutat_analysis", "Compute clusters of correlated positions", "m", "", AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_rnacma", XCMD_ASYNC_WAIT_ON_ERROR));
1241	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);
1242	}
1243	awm->close_sub_menu();
1244	}
1245
1246	// ----------------
1247	// Probes
1248
1249	awm->create_menu("Probes", "P", AWM_ALL);
1250	{
1251	awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1252	awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1253	awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1254	awm->sep______________();
1255	awm->insert_menu_topic("probe_match_sp", "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window, ntw));
1256	awm->sep______________();
1257	awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1258	awm->insert_menu_topic("primer_design", "Design Sequencing Primers", "S", "primer.hlp", AWM_EXP, makeWindowCallback(AWT_system_in_console_cb, "arb_primer", XCMD_ASYNC_WAITKEY));
1259	awm->sep______________();
1260	awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1261	}
1262
1263	}
1264
1265	// --------------
1266	// Tree
1267
1268	awm->create_menu("Tree", "T", AWM_ALL);
1269	{
1270	if (!clone) {
1271	awm->insert_sub_menu("Add Species to Existing Tree", "A");
1272	{
1273	awm->insert_menu_topic("arb_pars_quick", "ARB Parsimony (Quick add marked)", "Q", "pars.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_pars -add_marked -quit &"));
1274	awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_pars &"));
1275	GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1276	}
1277	awm->close_sub_menu();
1278	}
1279
1280	awm->insert_sub_menu("Remove Species from Tree", "R");
1281	{
1282	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));
1283	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));
1284	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));
1285	awm->sep______________();
1286	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));
1287	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));
1288	}
1289	awm->close_sub_menu();
1290
1291	if (!clone) {
1292	awm->insert_sub_menu("Build tree from sequence data", "B");
1293	{
1294	awm->insert_sub_menu("Distance matrix methods", "D");
1295	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1296	GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1297	awm->close_sub_menu();
1298
1299	awm->insert_sub_menu("Maximum Parsimony methods", "P");
1300	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1301	awm->close_sub_menu();
1302
1303	awm->insert_sub_menu("Maximum Likelihood methods", "L");
1304	GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1305	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1306	awm->close_sub_menu();
1307
1308	awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1309	GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1310	awm->close_sub_menu();
1311	}
1312	awm->close_sub_menu();
1313	}
1314
1315	awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1316	awm->sep______________();
1317
1318	awm->insert_sub_menu("Reset zoom", "z");
1319	{
1320	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));
1321	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));
1322	}
1323	awm->close_sub_menu();
1324	NT_insert_collapse_submenu(awm, ntw);
1325	awm->insert_sub_menu("Beautify tree", "e");
1326	{
1327	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));
1328	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));
1329	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));
1330	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));
1331	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));
1332	awm->sep______________();
1333	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));
1334	}
1335	awm->close_sub_menu();
1336	awm->insert_sub_menu("Modify branches", "M");
1337	{
1338	awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw));
1339	awm->insert_menu_topic(awm->local_id("tree_toggle_bootstraps"), "Toggle 100% bootstraps", "1", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_toggle_bootstrap100, ntw));
1340	awm->sep______________();
1341	awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw));
1342	awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1343	awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw));
1344	awm->sep______________();
1345	awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1346	awm->sep______________();
1347	awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1348	awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1349
1350	}
1351	awm->close_sub_menu();
1352
1353	awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "s", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1354	awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "u", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback(NT_mark_duplicates, ntw));
1355
1356	awm->sep______________();
1357
1358	awm->insert_menu_topic(awm->local_id("compare_taxonomy"), "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1359	awm->insert_menu_topic(awm->local_id("shade"), "Tree shading...", "s", "tree_shading.hlp", AWM_ALL, makeWindowCallback (NT_configure_treeShader));
1360	awm->insert_menu_topic(awm->local_id("syncscroll"), "Sync tree scrolling..", "y", "syncscroll.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1361
1362	awm->sep______________();
1363
1364	awm->insert_menu_topic(awm->local_id("tree_select"), "Select Tree", "T", 0, AWM_ALL, makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1365	awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", 0, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1366
1367	if (!clone) {
1368	awm->sep______________();
1369	awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1370	awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_nds_window, GLOBAL.gb_main));
1371	}
1372
1373	awm->sep______________();
1374	awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1375
1376	if (!clone) {
1377	awm->sep______________();
1378	awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1379	awm->insert_menu_topic("tree_2_xfig", "Export tree to XFIG", "F", "tree2file.hlp", AWM_ALL, makeWindowCallback(AWT_popup_tree_export_window, static_cast<AWT_canvas*>(ntw)));
1380	}
1381
1382	if (is_genome_db) {
1383	awm->sep______________();
1384	awm->insert_sub_menu("Other..", "O", AWM_EXP);
1385	{
1386	awm->insert_menu_topic(awm->local_id("tree_pseudo_species_to_organism"), "Relink tree to organisms", "o", "tree_pseudo.hlp", AWM_EXP, makeWindowCallback(NT_pseudo_species_to_organism, ntw));
1387	}
1388	awm->close_sub_menu();
1389	}
1390	}
1391
1392	if (!clone) {
1393	// ---------------
1394	// Tools
1395
1396	awm->create_menu("Tools", "o", AWM_ALL);
1397	{
1398	awm->insert_menu_topic("names_admin", "Name server admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_namesadmin_window, GLOBAL.gb_main));
1399	awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1400	{
1401	awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1402	}
1403	awm->close_sub_menu();
1404	awm->insert_sub_menu("Network", "N", AWM_EXP);
1405	{
1406	GDE_load_menu(awm, AWM_EXP, "Network");
1407	}
1408	awm->close_sub_menu();
1409	awm->sep______________();
1410
1411	awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1412	{
1413	GDE_load_menu(awm, AWM_EXP, NULL);
1414	}
1415	awm->close_sub_menu();
1416
1417	awm->sep______________();
1418	awm->insert_menu_topic("xterm", "Start XTERM", "X", 0, AWM_ALL, AWT_console);
1419	awm->sep______________();
1420	GDE_load_menu(awm, AWM_EXP, "User");
1421	}
1422	// --------------------
1423	// Properties
1424
1425	awm->create_menu("Properties", "r", AWM_ALL);
1426	{
1427	#if defined(ARB_MOTIF)
1428	awm->insert_menu_topic("props_menu", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1429	#endif
1430	awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1431	awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1432	awm->insert_menu_topic("props_www", "Search world wide web (WWW)", "b", "props_www.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_www_window, GLOBAL.gb_main));
1433	awm->sep______________();
1434	awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", 0, AWM_ALL, NT_toggle_expert_mode);
1435	#if defined(ARB_MOTIF)
1436	awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", 0, AWM_ALL, NT_toggle_focus_policy);
1437	#endif
1438	awm->sep______________();
1439	AW_insert_common_property_menu_entries(awm);
1440	awm->sep______________();
1441	awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1442	}
1443	}
1444
1445	awm->insert_help_topic("ARB_NT help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1446
1447	// ----------------------
1448	// mode buttons
1449	//
1450	// keep them synchronized as far as possible with those in ARB_PARSIMONY
1451	// see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1452
1453	awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1454	awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1455	awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1456	awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1457	awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1458
1459	awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1460	awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW));
1461
1462	// topology-modification-modes
1463	awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1464	awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1465	awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1466	awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1467	awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1468
1469	// layout-modes
1470	awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1471	awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1472	awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1473
1474	awm->set_info_area_height(250);
1475	awm->at(5, 2);
1476	awm->auto_space(-2, -2);
1477	awm->shadow_width(1);
1478
1479	// -------------------------
1480	// create top area
1481
1482	int first_liney;
1483	int leftx;
1484	awm->get_at_position(&leftx, &first_liney);
1485
1486	// ---------------------
1487	// quit + help
1488
1489	awm->button_length(0);
1490
1491	if (clone) {
1492	awm->callback(AW_POPDOWN);
1493	awm->create_button("CLOSE", "#close.xpm");
1494	}
1495	else {
1496	awm->callback(makeWindowCallback(NT_exit, EXIT_SUCCESS));
1497	#if defined(ARB_GTK)
1498	awm->set_hide_on_close(false); //the main window should really close when closed
1499	#endif
1500	awm->help_text("quit.hlp");
1501	awm->create_button("QUIT", "#quit.xpm");
1502	#if defined(ARB_GTK)
1503	awm->set_close_action("QUIT");
1504	#endif
1505	}
1506
1507	int db_pathx = awm->get_at_xposition();
1508
1509	// now fetch the yposition for the 2nd button line
1510	awm->at_newline();
1511	int second_liney = awm->get_at_yposition();
1512
1513	awm->callback(AW_help_entry_pressed);
1514	awm->help_text("arb_ntree.hlp");
1515	awm->create_button("?", "#help.xpm");
1516
1517	// --------------------------
1518	// save + undo/redo
1519
1520	awm->callback(NT_save_quick_cb);
1521	awm->help_text("save.hlp");
1522	awm->create_button("SAVE", "#save.xpm");
1523
1524	awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1525	awm->help_text("save.hlp");
1526	awm->create_button("SAVE_AS", "#saveAs.xpm");
1527
1528	// undo/redo:
1529	awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1530	awm->help_text("undo.hlp");
1531	awm->create_button("UNDO", "#undo.xpm");
1532
1533	awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1534	awm->help_text("undo.hlp");
1535	awm->create_button("REDO", "#redo.xpm");
1536
1537	int db_pathx2 = awm->get_at_xposition();
1538
1539	// fetch position for mode help-line:
1540	awm->at_newline();
1541	int third_liney = awm->get_at_yposition();
1542
1543	awm->at(db_pathx, first_liney);
1544	// size of DB-name button is determined by buttons below:
1545	awm->at_set_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1546	awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1547	awm->help_text("save.hlp");
1548	awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1549
1550	// -----------------------------
1551	// tree + tree display
1552
1553	#define TREE_BUTTON_OVERSIZE 6
1554
1555	int db_treex = awm->get_at_xposition();
1556	int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1557
1558	awm->at(db_treex, second_uppery);
1559	awm->button_length(0);
1560
1561	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1562	awm->help_text("tr_type_radial.hlp");
1563	awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1564
1565	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1566	awm->help_text("tr_type_list.hlp");
1567	awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1568
1569	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1570	awm->help_text("tr_type_irs.hlp");
1571	awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1572
1573	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1574	awm->help_text("tr_type_nds.hlp");
1575	awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1576
1577	int db_treex2 = awm->get_at_xposition();
1578
1579	awm->at(db_treex, first_liney);
1580	// size of tree-name button is determined by buttons below:
1581	awm->at_set_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1582	awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1583	awm->help_text("nt_tree_select.hlp");
1584	awm->create_button("SELECT_A_TREE", awar_tree);
1585
1586	// ---------------------------------------------------------------
1587	// protection, alignment + editor (and maybe Genome Map)
1588
1589	int db_alignx = awm->get_at_xposition();
1590
1591	// editor and genemap buttons have to be 44x24 sized
1592	#define EDIT_XSIZE 50
1593	#define EDIT_YSIZE 30 // same as 'save as' buttons
1594
1595	// first draw protection:
1596	int protectx = db_alignx + 2*EDIT_XSIZE;
1597
1598	awm->at(protectx+2, first_liney+1);
1599	awm->button_length(0);
1600	awm->create_button(NULL, "#protect.xpm");
1601
1602	awm->at(protectx, second_liney+2);
1603	awm->create_option_menu(AWAR_SECURITY_LEVEL, true);
1604	awm->insert_option("0", 0, 0);
1605	awm->insert_option("1", 0, 1);
1606	awm->insert_option("2", 0, 2);
1607	awm->insert_option("3", 0, 3);
1608	awm->insert_option("4", 0, 4);
1609	awm->insert_option("5", 0, 5);
1610	awm->insert_default_option("6", 0, 6);
1611	awm->update_option_menu();
1612
1613	int db_searchx = awm->get_at_xposition() - 7;
1614
1615	// draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1616	awm->at(db_alignx, second_liney);
1617
1618	awm->at_set_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1619	awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1620	awm->help_text("arb_edit4.hlp");
1621	if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1622	else awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1623
1624	if (is_genome_db) {
1625	awm->at_set_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1626	awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1627	awm->help_text("gene_map.hlp");
1628	awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1629	}
1630
1631	int db_alignx2 = awm->get_at_xposition();
1632
1633	awm->at(db_alignx, first_liney);
1634	awm->at_set_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1635	awm->callback(NT_create_select_alignment_window);
1636	awm->help_text("nt_align_select.hlp");
1637	awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1638
1639	// -------------------------------
1640	// create mode-help line
1641
1642	awm->at(leftx, third_liney);
1643	awm->button_length(AWAR_FOOTER_MAX_LEN);
1644	awm->create_button(0, AWAR_FOOTER);
1645
1646	awm->at_newline();
1647	int bottomy = awm->get_at_yposition();
1648
1649	// ---------------------------------------
1650	// Info / marked / Search / Jump
1651
1652	awm->button_length(7);
1653
1654	awm->at(db_searchx, first_liney);
1655	awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1656	awm->help_text("sp_search.hlp");
1657	awm->create_button("SEARCH", "Search");
1658
1659	awm->at(db_searchx, second_uppery);
1660	awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1661	awm->help_text("tr_jump.hlp");
1662	awm->create_button("JUMP", "Jump");
1663
1664	int db_infox = awm->get_at_xposition();
1665
1666	awm->at(db_infox, first_liney);
1667	awm->button_length(13);
1668	awm->callback(popupinfo_wcb);
1669	awm->help_text("sp_search.hlp");
1670	awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1671
1672	awm->at(db_infox, second_uppery);
1673	awm->button_length(13);
1674	awm->help_text("species_configs.hlp");
1675	awm->callback(makeWindowCallback(NT_popup_configuration_admin, ntw));
1676	awm->create_button("selection_admin2", AWAR_MARKED_SPECIES_COUNTER);
1677	{
1678	GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1679	GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(NT_update_marked_counter, static_cast<AW_window*>(awm)));
1680	NT_update_marked_counter(NULL, awm);
1681	}
1682
1683	// set height of top area:
1684	awm->set_info_area_height(bottomy+2);
1685	awm->set_bottom_area_height(0);
1686
1687	NT_activate_configMarkers_display(ntw);
1688
1689	// ------------------------------------
1690	// Autostarts for development
1691
1692	#if defined(DEVEL_RALF)
1693	// if (is_genome_db) GEN_map_first(awr)->show();
1694	#endif // DEVEL_RALF
1695
1696	GB_pop_transaction(GLOBAL.gb_main);
1697
1698	#if defined(DEBUG)
1699	AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1700	#endif
1701
1702	return awm;
1703	}
1704
1705	TREE_canvas NT_create_main_window(AW_root aw_root) {
1706	GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1707	if (error) aw_message(error);
1708
1709	nt_create_all_awars(aw_root);
1710
1711	TREE_canvas *ntw = NULL;
1712	AW_window *aww = popup_new_main_window(aw_root, 0, &ntw);
1713	NT_install_treeShader(ntw, GLOBAL.gb_main);
1714	aww->show();
1715
1716	error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1717	if (error) aw_message(error);
1718
1719	return ntw;
1720	}

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