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NT_extern.cxx

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Last change on this file was 19575, checked in by westram, 3 weeks ago
reintegrates 'help' into 'trunk' preformatted text gets checked for width now (to enforce it fits into the arb help window). fixed help following these checks, using the following steps: ignore problems in foreign documentation. increase default help window width. introduce control comments to accept oversized preformatted sections. enforce preformatted style for whole sections. simply define single-line preformatted sections Used intensive for definition of internal script languages. fixed several non-related problems found in documentation. minor layout changes for HTML version of arb help (more compacted; highlight anchored/all sections). refactor system interface (GUI version) and use it from help module. adds: log:branches/help@19532:19574
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 82.5 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	#include "NT_group_search.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_gui.hxx>
25	#include <primer_design.hxx>
26	#include <gde.hxx>
27	#include <awtc_submission.hxx>
28
29	#include <macros.hxx>
30	#include <xcmd.hxx>
31	#include <nds.h>
32	#include <db_query.h>
33	#include <dbui.h>
34	#include <refentries.h>
35	#include <insdel.h>
36
37	#include <awti_export.hxx>
38	#include <awti_import.hxx>
39
40	#include <awt.hxx>
41	#include <awt_input_mask.hxx>
42	#include <awt_sel_boxes.hxx>
43	#include <awt_www.hxx>
44	#include <awt_TreeAwars.hxx>
45	#include <awt_misc.hxx>
46
47	#include <aw_color_groups.hxx>
48	#include <aw_advice.hxx>
49	#include <aw_preset.hxx>
50	#include <aw_awars.hxx>
51	#include <aw_global_awars.hxx>
52	#include <aw_file.hxx>
53	#include <aw_msg.hxx>
54	#include <arb_progress.h>
55	#include <aw_root.hxx>
56	#include <aw_question.hxx>
57	#include <aw_select.hxx>
58	#include <aw_system.hxx>
59	#include <rootAsWin.h>
60
61	#include <ad_cb.h>
62
63	#include <arb_strbuf.h>
64	#include <arb_file.h>
65	#include <arb_version.h>
66	#include <arb_sleep.h>
67
68	#include <saicalc.h>
69
70	#if defined(DEVEL_RALF)
71	# define TRACE_GROUP_SELECTION
72	#endif
73
74	#define AWAR_EXPORT_NDS "tmp/export_nds"
75	#define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/delimiter"
76	#define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species"
77	#define AWAR_NTREE_TITLE_MODE "tmp/title_mode"
78
79	void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
80
81	void create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
82	AW_window create_insertDeleteColumn_window(AW_root root);
83	AW_window create_insertDeleteBySAI_window(AW_root root, GBDATA *gb_main);
84
85	AW_window create_tree_window(AW_root aw_root, AWT_graphic *awd);
86
87	enum Export_Type {
88	EXPORT_SPACE_PADDED_RIGHT_ALIGNED = 1, // format info (using spaces). slow - uses one extra pass for column width detection.
89	EXPORT_SPACE_PADDED_LEFT_ALIGNED = 4, // dito, but left aligned
90	EXPORT_TAB_SEPARATED = 2, // format info (using 1 tab per column - for easy import into star-calc, excel, etc. )
91	EXPORT_COMMA_SEPARATED = 3, // like EXPORT_TAB_SEPARATED, but using commas
92	};
93
94	static void nt_changesecurity(AW_root *aw_root) {
95	int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
96	GB_push_transaction(GLOBAL.gb_main);
97	GB_change_my_security(GLOBAL.gb_main, level); // changes user security
98	GB_pop_transaction(GLOBAL.gb_main);
99	}
100
101	static void export_nds_cb(AW_window *aww, bool do_print) {
102	AW_root *aw_root = aww->get_root();
103	char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
104	FILE *out = fopen(name, "w");
105
106	if (!out) {
107	aw_message("Error: Cannot open and write to file");
108	}
109	else {
110	GB_transaction ta(GLOBAL.gb_main);
111
112	char *tree_name = aw_root->awar(AWAR_TREE)->read_string();
113	const Export_Type export_type = (Export_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
114	const NDS_Type nds_type = export_type == EXPORT_COMMA_SEPARATED ? NDS_OUTPUT_COMMA_SEPARATED : NDS_OUTPUT_TAB_SEPARATED;
115	const bool spacePadded = export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED \|\| export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED;
116	const int passesNeeded = spacePadded ? 2 : 1;
117	NDS_Labeler labeler(nds_type);
118
119	arb_progress progress("Exporting data using NDS", passesNeeded*GBT_count_marked_species(GLOBAL.gb_main));
120
121	const size_t max_col = std::max(labeler.max_columns(GLOBAL.gb_main), 1L);
122	size_t col_max_len[max_col];
123
124	const char *col_format = NULp;
125
126	if (spacePadded) {
127	for (size_t i = 0; i<max_col; ++i) {
128	col_max_len[i] = 0;
129	}
130	if (export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED) {
131	col_format = "%*s";
132	}
133	else {
134	col_format = "%-*s";
135	}
136	}
137
138	for (int pass = 1; pass<=passesNeeded; ++pass) {
139	for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
140	gb_species;
141	gb_species = GBT_next_marked_species(gb_species))
142	{
143	const char *label = labeler.speciesLabel(GLOBAL.gb_main, gb_species, NULp, tree_name);
144
145	if (spacePadded) {
146	ConstStrArray parts;
147	GBT_split_string(parts, label, "\t", SPLIT_KEEPEMPTY);
148
149	size_t col_count = parts.size();
150	nt_assert(col_count<=max_col);
151
152	if (pass == 1) { // track maximum used width for all columns
153	for (size_t i = 0; i<col_count; ++i) {
154	col_max_len[i] = std::max(col_max_len[i], strlen(parts[i]));
155	}
156	}
157	else { // format according to tracked widths
158	for (size_t i = 0; i<col_count; ++i) {
159	if (i) fputc(' ', out);
160
161	arb_assert(col_max_len[i]>0); // otherwise empty, unused column (might be ok, but might need different handling)
162	arb_assert(col_max_len[i]<=INT_MAX); // (protect cast below)
163
164	if (export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED && i == (col_count-1)) { // left aligned and last column
165	fputs(parts[i], out);
166	}
167	else {
168	fprintf(out, col_format, int(col_max_len[i]), parts[i]);
169	}
170	}
171	fputc('\n', out);
172	}
173	}
174	else {
175	fprintf(out, "%s\n", label);
176	}
177	++progress;
178	}
179	}
180
181	AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
182	fclose(out);
183	if (do_print) {
184	GB_ERROR error = GB_textprint(name);
185	if (error) aw_message(error);
186	}
187	free(tree_name);
188	}
189	free(name);
190	}
191
192	static AW_window create_nds_export_window(AW_root root) {
193	AW_window_simple *aws = new AW_window_simple;
194	aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
195	aws->load_xfig("sel_box_nds.fig");
196
197	aws->callback(AW_POPDOWN);
198	aws->at("close");
199	aws->create_button("CLOSE", "CLOSE", "C");
200
201	aws->callback(makeHelpCallback("arb_export_nds.hlp"));
202	aws->at("help");
203	aws->create_button("HELP", "HELP", "H");
204
205	aws->at("save");
206	aws->callback(makeWindowCallback(export_nds_cb, false));
207	aws->create_button("SAVE", "SAVE", "S");
208
209	aws->at("print");
210	aws->callback(makeWindowCallback(export_nds_cb, true));
211	aws->create_button("PRINT", "PRINT", "P");
212
213	aws->at("toggle1");
214	aws->label("Column output");
215	aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR);
216	aws->insert_option ("Space padded (left aligned)", "S", EXPORT_SPACE_PADDED_LEFT_ALIGNED);
217	aws->insert_option ("Space padded (right aligned)", "r", EXPORT_SPACE_PADDED_RIGHT_ALIGNED);
218	aws->insert_default_option("TAB separated", "T", EXPORT_TAB_SEPARATED);
219	aws->insert_option ("Comma separated", "C", EXPORT_COMMA_SEPARATED);
220	aws->update_option_menu();
221
222	AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS);
223
224	return aws;
225	}
226
227	static void create_export_nds_awars(AW_root *awr, AW_default def) {
228	AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds");
229	awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, EXPORT_TAB_SEPARATED, def);
230	}
231
232	static void selectedSpeciesChanged_cb(AW_root *awr) {
233	const char *value = awr->awar(AWAR_SPECIES_NAME)->read_char_pntr();
234	awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
235	if (value[0]) {
236	awr->awar(AWAR_GROUP)->write_pointer(NULp); // deselect group when species gets selected
237	#if defined(TRACE_GROUP_SELECTION)
238	fputs("clear AWAR_GROUP (because species selected)\n", stderr);
239	#endif
240	}
241	}
242
243	static void expert_mode_changed_cb(AW_root *aw_root) {
244	aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
245	}
246
247	static void NT_toggle_expert_mode(AW_window *aww) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
248	static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
249
250	static void nt_create_all_awars(AW_root *awr) {
251	// creates awars for all modules reachable from ARB_NT main window
252
253	awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT);
254	if (GB_read_clients(GLOBAL.gb_main)>=0) {
255	awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
256	}
257	else {
258	awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT);
259	}
260
261	awr->awar_string(AWAR_TOPAREA_SAIS, "ECOLI;HELIX;HELIX_NR", AW_ROOT_DEFAULT);
262
263	awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main);
264	awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main);
265	awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main);
266	awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown", GLOBAL.gb_main);
267	awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main);
268	awr->awar(AWAR_SPECIES_NAME)->add_callback(selectedSpeciesChanged_cb);
269	awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
270
271	awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
272
273	GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
274	EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
275	#if defined(DEBUG)
276	AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT);
277	#endif // DEBUG
278
279	AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
280
281	awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT);
282	awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
283	#if defined(DEBUG) && 0
284	awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
285	#endif // DEBUG
286
287	create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT);
288	create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
289	create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
290	create_trees_var(awr, AW_ROOT_DEFAULT);
291	DBUI::create_dbui_awars(awr);
292	AP_create_consensus_var(awr, AW_ROOT_DEFAULT);
293	{
294	GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, NULp, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT);
295	if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
296	}
297	NT_create_transpro_variables(awr, AW_ROOT_DEFAULT);
298	NT_create_resort_awars(awr, AW_ROOT_DEFAULT);
299	NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT);
300	NT_create_trackAliChanges_Awars(awr, AW_ROOT_DEFAULT);
301
302	NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
303	NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
304	NDS_create_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
305	create_export_nds_awars(awr, AW_ROOT_DEFAULT);
306	create_group_search_awars(awr, AW_ROOT_DEFAULT);
307	TREE_create_awars(awr, GLOBAL.gb_main);
308
309	awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
310	awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
311
312	AWTC_create_submission_variables(awr, GLOBAL.gb_main);
313	NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
314	NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar
315	SQ_create_awars(awr, AW_ROOT_DEFAULT);
316	RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT);
317
318	NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT);
319
320	GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
321	if (!error) {
322	AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
323	awar_expert->add_callback(expert_mode_changed_cb);
324	awar_expert->touch();
325
326	awt_create_aww_vars(awr, AW_ROOT_DEFAULT);
327	}
328
329	if (error) aw_message(error);
330	}
331
332	// --------------------------------------------------------------------------------
333
334	static bool nt_disconnect_from_db(AW_root aw_root, GBDATA& gb_main_ref, bool quitWithoutSaveQuestion) {
335	// ask user if DB was not saved in the last 15 seconds (dont ask if quitWithoutSaveQuestion is true).
336	// returns true if user allows to quit.
337
338	// @@@ code here could as well be applied to both merge DBs
339	// - question about saving only with target DB!
340
341	#if defined(DEBUG)
342	quitWithoutSaveQuestion = true; // do not ask about saving while developing
343	#endif
344
345	if (gb_main_ref) {
346	if (GB_read_clients(gb_main_ref) >= 0 && // only in server
347	GB_read_clock(gb_main_ref) > GB_last_saved_clock(gb_main_ref) &&
348	quitWithoutSaveQuestion == false)
349	{
350	long secs = GB_last_saved_time(gb_main_ref);
351	const char *quit_buttons = "Quit ARB,Do NOT quit";
352	if (secs) {
353	secs = GB_time_of_day() - secs;
354	if (secs>15) {
355	char *question = GBS_global_string_copy("You last saved your data %li:%02li minutes ago\nSure to quit?", secs/60, secs%60);
356	int dontQuit = aw_question("quit_arb", question, quit_buttons);
357	free(question);
358	if (dontQuit) {
359	return false;
360	}
361	}
362	}
363	else {
364	if (aw_question("quit_arb", "You never saved any data.\nSure to quit?", quit_buttons)) {
365	return false;
366	}
367	}
368	}
369
370	GBCMS_shutdown(gb_main_ref);
371
372	GBDATA *gb_main = gb_main_ref;
373	gb_main_ref = NULp; // avoid further usage
374
375	nt_assert(aw_root);
376
377	// @@@ instead of directly calling the following functions, try to add them as GB_atclose_callback
378	aw_root->unlink_awars_from_DB(gb_main);
379	AWT_destroy_input_masks();
380	#if defined(DEBUG)
381	AWT_browser_forget_db(gb_main);
382	#endif // DEBUG
383
384	GB_close(gb_main);
385	}
386	return true;
387	}
388
389	static void nt_run(const char *command) {
390	GB_ERROR error = GBK_system(command);
391	if (error) {
392	fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
393	#if defined(DEBUG)
394	GBK_dump_backtrace(stderr, "nt_run-error");
395	#endif
396	}
397	}
398
399	void NT_start(const char *arb_ntree_args, bool restart_with_new_ARB_PID) {
400	char *command = GBS_global_string_copy("arb_launcher --async %s %s", restart_with_new_ARB_PID ? "arb" : "arb_ntree", arb_ntree_args);
401	nt_run(command);
402	free(command);
403	}
404
405	__ATTR__NORETURN static void really_exit(int exitcode, bool kill_my_clients) {
406	if (kill_my_clients) {
407	nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
408	}
409	exit(exitcode);
410	}
411
412	static void exit_ignoring_running_macro(AW_root *aw_root, int exitcode, bool quitWithoutSaveQuestion) {
413	AWTI_cleanup_importer();
414	shutdown_macro_recording(aw_root);
415
416	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
417	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main, quitWithoutSaveQuestion)) {
418	really_exit(exitcode, is_server_and_has_clients);
419	}
420	}
421
422	#define TRY_TO_QUIT_ARB_FREQUENCY 250 // ms
423
424	static unsigned NT_exit_when_macros_did_finish(AW_root *aw_root, int exitcode) {
425	if (is_server_and_executing_macro(aw_root)) {
426	static long milliSeconds = 0;
427	static int lastDecaSeconds = 0;
428
429	milliSeconds += TRY_TO_QUIT_ARB_FREQUENCY;
430	int seconds = milliSeconds/1000;
431	int decaSeconds = seconds/10;
432
433	if (decaSeconds != lastDecaSeconds) {
434	const char *msg = GBS_global_string("waited %i seconds for macro termination", seconds);
435	if (decaSeconds>3) {
436	int after = (10-decaSeconds)*10;
437	msg = GBS_global_string("%s. Will terminate unconditionally in %i seconds", msg, after);
438	}
439	aw_message(GBS_global_string("[%s]", msg));
440	lastDecaSeconds = decaSeconds;
441	}
442
443	if (decaSeconds<10) {
444	return TRY_TO_QUIT_ARB_FREQUENCY;
445	}
446	// reached after 100s
447	aw_message("[forcing arb quit]");
448	}
449	else {
450	aw_message("[all macros have terminated. arb quits now]");
451	}
452	ARB_sleep(1, SEC);
453	exit_ignoring_running_macro(aw_root, exitcode, true); // never ask if sure to quit!
454	return 0;
455	}
456
457	void NT_exit(AW_window *aws, int exitcode) {
458	AW_root *aw_root = aws->get_root();
459	if (is_server_and_executing_macro(aw_root)) {
460	static int suppressed = 0;
461	if (!suppressed) {
462	aw_message("[did not quit arb yet, because macro is still running. Would crash. Will retry ASAP]");
463	suppressed = 1;
464	}
465	else {
466	aw_message("[macro is still running. But time will pass faster because you are in a hurry]");
467	}
468
469	// Note: this branch effectively suppresses the 'sure to quit?' question
470	aw_root->add_timed_callback(TRY_TO_QUIT_ARB_FREQUENCY,
471	makeTimedCallback(NT_exit_when_macros_did_finish, exitcode));
472	}
473	else {
474	exit_ignoring_running_macro(aw_root, exitcode, false);
475	}
476	}
477
478	void NT_restart(AW_root aw_root, const char arb_ntree_args) {
479	// restarts arb_ntree (with new ARB_PID)
480	// @@@ do we need to call AWTI_cleanup_importer and/or shutdown_macro_recording here?
481	// consider to delegate to normal exit-code (NT_exit, exit_ignoring_running_macro)
482	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
483	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main, false)) {
484	NT_start(arb_ntree_args, true);
485	really_exit(EXIT_SUCCESS, is_server_and_has_clients);
486	}
487	}
488
489	static void nt_start_2nd_arb(AW_window *aww, bool quit) {
490	// start 2nd arb with intro window
491	AW_root *aw_root = aww->get_root();
492	char *dir4intro;
493	GB_split_full_path(aw_root->awar(AWAR_SAVED_DB_PATH)->read_char_pntr(), &dir4intro, NULp, NULp, NULp);
494	if (!dir4intro) {
495	dir4intro = ARB_strdup(".");
496	}
497
498	if (quit) {
499	NT_restart(aw_root, dir4intro);
500	}
501	else {
502	NT_start(dir4intro, true);
503	}
504	free(dir4intro);
505	}
506
507	// --------------------------------------------------------------------------------
508
509	static void NT_save_quick_cb(AW_window *aww) {
510	AW_root *awr = aww->get_root();
511	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
512
513	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
514
515	GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
516	if (error) aw_message(error);
517	else {
518	awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
519	AW_refresh_fileselection(awr, AWAR_DBBASE);
520	}
521
522	free(filename);
523	}
524
525
526	static void NT_save_quick_as_cb(AW_window *aww) {
527	AW_root *awr = aww->get_root();
528	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
529
530	// @@@ also use dont_save_awars_with_default_value here?
531
532	GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename);
533	if (!error) {
534	awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
535	AW_refresh_fileselection(awr, AWAR_DBBASE);
536	}
537	aww->hide_or_notify(error);
538
539	free(filename);
540	}
541
542	#define AWAR_DB_TYPE AWAR_DBBASE "/type" // created by AWT_insert_DBsaveType_selector
543	#define AWAR_DB_COMPRESSION AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector
544	#define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name"
545
546	static void NT_save_as_cb(AW_window *aww) {
547	AW_root *awr = aww->get_root();
548	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
549	const char *atype = awr->awar(AWAR_DB_TYPE)->read_char_pntr();
550	const char *ctype = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr();
551	char *savetype = GBS_global_string_copy("%s%s", atype, ctype);
552
553	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
554
555	GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype);
556	if (!error) {
557	awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
558	AW_refresh_fileselection(awr, AWAR_DBBASE);
559	}
560	aww->hide_or_notify(error);
561
562	free(savetype);
563	free(filename);
564	}
565
566	static AW_window NT_create_save_quick_as_window(AW_root aw_root, const char *base_name) {
567	static AW_window_simple *aws = NULp;
568	if (!aws) {
569	aws = new AW_window_simple;
570	aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as");
571	aws->load_xfig("save_as.fig");
572
573	aws->at("close");
574	aws->callback(AW_POPDOWN);
575	aws->create_button("CLOSE", "CLOSE", "C");
576
577	aws->callback(makeHelpCallback("save.hlp"));
578	aws->at("help");
579	aws->create_button("HELP", "HELP", "H");
580
581	AW_create_standard_fileselection(aws, base_name);
582
583	aws->at("comment");
584	aws->create_text_field(AWAR_DB_COMMENT);
585
586	aws->at("save");
587	aws->callback(NT_save_quick_as_cb);
588	aws->create_button("SAVE", "SAVE", "S");
589	}
590	return aws;
591	}
592
593	static void NT_database_optimization(AW_window *aww) {
594	arb_progress progress(WEIGHTED, "Optimizing database compression", 0.38);
595	// 38% for seq-compression is just a rough guess made with silvaNR99138
596	// (a real guess would have to depend on ali-count, ali-length + field-count)
597
598	GB_topSecurityLevel unsecured(GLOBAL.gb_main);
599
600	GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
601	if (!error) {
602	ConstStrArray ali_names;
603	GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
604
605	arb_progress ali_progress("Optimizing sequence data", ali_names.size());
606	ali_progress.allow_title_reuse();
607
608	error = GBT_check_data(GLOBAL.gb_main, NULp);
609	error = GB_end_transaction(GLOBAL.gb_main, error);
610
611	if (!error) {
612	char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string();
613	for (int i = 0; ali_names[i]; ++i) {
614	error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
615	ali_progress.inc_and_check_user_abort(error);
616	}
617	free(tree_name);
618	}
619	}
620	progress.inc_and_check_user_abort(error);
621
622	if (!error) {
623	error = GB_optimize(GLOBAL.gb_main);
624	progress.inc_and_check_user_abort(error);
625	}
626	aww->hide_or_notify(error);
627	}
628
629	static AW_window NT_create_database_optimization_window(AW_root aw_root) {
630	static AW_window_simple *aws = NULp;
631	if (aws) return aws;
632	GB_transaction ta(GLOBAL.gb_main);
633
634	const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
635	aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree);
636
637	aws = new AW_window_simple;
638	aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression");
639	aws->load_xfig("optimize.fig");
640
641	aws->at("trees");
642	awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME);
643
644	aws->at("close");
645	aws->callback(AW_POPDOWN);
646	aws->create_button("CLOSE", "CLOSE", "C");
647
648	aws->callback(makeHelpCallback("optimize.hlp"));
649	aws->at("help");
650	aws->create_button("HELP", "HELP", "H");
651
652	aws->at("go");
653	aws->callback(NT_database_optimization);
654	aws->create_button("GO", "GO");
655	return aws;
656	}
657
658	static AW_window NT_create_save_as(AW_root aw_root, const char *base_name) {
659	static AW_window_simple *aws = NULp;
660	if (aws) return aws;
661
662	aws = new AW_window_simple;
663	aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
664	aws->load_xfig("save_as.fig");
665
666	aws->at("close");
667	aws->callback(AW_POPDOWN);
668	aws->create_button("CLOSE", "CLOSE", "C");
669
670	aws->at("help");
671	aws->callback(makeHelpCallback("save.hlp"));
672	aws->create_button("HELP", "HELP", "H");
673
674	AW_create_standard_fileselection(aws, base_name);
675
676	aws->at("type");
677	AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE);
678
679	aws->at("compression");
680	AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION);
681
682	aws->at("optimize");
683	aws->callback(NT_create_database_optimization_window);
684	aws->help_text("optimize.hlp");
685	aws->create_autosize_button("OPTIMIZE", "Optimize database compression");
686
687	aws->at("save");
688	aws->callback(NT_save_as_cb);
689	aws->create_button("SAVE", "SAVE", "S");
690
691	aws->at("comment");
692	aws->create_text_field(AWAR_DB_COMMENT);
693
694	return aws;
695	}
696
697	static void NT_undo_cb(AW_window, GB_UNDO_TYPE undo_type, TREE_canvas ntw) {
698	GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type);
699	if (error) aw_message(error);
700	else {
701	GB_transaction ta(GLOBAL.gb_main);
702	AWT_auto_refresh allowed_on(ntw);
703	ntw->request_refresh();
704	}
705	}
706
707	static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) {
708	DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
709	nt_mode_event(NULp, canvas, mode);
710	}
711
712	static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) {
713	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
714	if (tree_root) {
715	AWT_auto_refresh allowed_on(ntw);
716	GB_transaction ta(ntw->gb_main);
717
718	NT_mark_all_cb(NULp, ntw, 0); // unmark all
719	tree_root->mark_duplicates();
720	ntw->request_structure_update();
721	}
722	}
723
724	static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) {
725	GB_transaction ta(ntw->gb_main);
726	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
727
728	if (tree_root) {
729	AWT_auto_refresh allowed_on(ntw);
730	tree_root->justify_branch_lenghs(ntw->gb_main);
731	ntw->request_save_and_zoom_reset();
732	}
733	}
734
735	#if defined(DEBUG)
736	static void NT_fix_database(AW_window *) {
737	GB_ERROR err = NULp;
738	err = GB_fix_database(GLOBAL.gb_main);
739	if (err) aw_message(err);
740	}
741	#endif
742
743	static void relink_pseudo_species_to_organisms(GBDATA &ref_gb_node, char &ref_name, GB_HASH *organism_hash) {
744	if (ref_gb_node) {
745	if (GEN_is_pseudo_gene_species(ref_gb_node)) {
746	GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
747
748	if (gb_organism) {
749	char *name = GBT_read_string(gb_organism, "name");
750
751	if (name) {
752	freeset(ref_name, name);
753	ref_gb_node = gb_organism;
754	}
755	}
756	}
757	}
758	}
759
760	static void NT_pseudo_species_to_organism(AW_window , TREE_canvas ntw) {
761	GB_transaction ta(ntw->gb_main);
762	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
763
764	if (tree_root) {
765	AWT_auto_refresh allowed_on(ntw);
766
767	GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
768	tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
769	GBS_free_hash(organism_hash);
770	ntw->request_save();
771	}
772	}
773
774
775	// #########################################
776	// #########################################
777	// ### ###
778	// ## user mask section ##
779	// ### ###
780	// #########################################
781	// #########################################
782
783	struct nt_item_type_species_selector FINAL_TYPE : public awt_item_type_selector {
784	nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
785	~nt_item_type_species_selector() OVERRIDE {}
786
787	const char *get_self_awar() const OVERRIDE {
788	return AWAR_SPECIES_NAME;
789	}
790	size_t get_self_awar_content_length() const OVERRIDE {
791	return 12; // should be enough for "nnaammee.999"
792	}
793	GBDATA current(AW_root root, GBDATA *gb_main) const OVERRIDE { // give the current item
794	char *species_name = root->awar(get_self_awar())->read_string();
795	GBDATA *gb_species = NULp;
796
797	if (species_name[0]) {
798	GB_transaction ta(gb_main);
799	gb_species = GBT_find_species(gb_main, species_name);
800	}
801
802	free(species_name);
803	return gb_species;
804	}
805	const char *getKeyPath() const OVERRIDE { // give the keypath for items
806	return CHANGE_KEY_PATH;
807	}
808	};
809
810	static nt_item_type_species_selector item_type_species;
811
812	static void NT_open_mask_window(AW_window aww, int id, GBDATA gb_main) {
813	const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
814	nt_assert(descriptor);
815	if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
816	}
817
818	static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
819	AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
820	}
821	static AW_window create_colorize_species_window(AW_root aw_root) {
822	return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
823	}
824
825	static void NT_update_marked_counter(GBDATA, AW_window aww) {
826	/*! Updates marked counter and issues redraw on tree if number of marked species changes.
827	* Called on any change of species_information container.
828	*/
829	long count = GBT_count_marked_species(GLOBAL.gb_main);
830	const char *buffer = count ? GBS_global_string("%li marked", count) : "";
831	AW_awar *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
832	char *oldval = counter->read_string();
833	if (strcmp(oldval, buffer)) {
834	counter->write_string(buffer);
835	aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
836	}
837	free(oldval);
838	}
839
840	// --------------------------------------------------------------------------------------------------
841
842	static void NT_alltree_remove_leafs(AW_window , GBT_TreeRemoveType mode, GBDATA gb_main) {
843	GB_ERROR error = NULp;
844	GB_transaction ta(gb_main);
845
846	ConstStrArray tree_names;
847	GBT_get_tree_names(tree_names, gb_main, false);
848
849	if (!tree_names.empty()) {
850	long treeCount = tree_names.size();
851
852	const char *whats_removed = NULp;
853	switch (mode) {
854	case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
855	case GBT_REMOVE_MARKED: whats_removed = "marked"; break;
856	default: nt_assert(0); break;
857	}
858
859	const char *task = GBS_global_string("Deleting %s from %li trees", whats_removed, treeCount);
860
861	arb_progress progress(task, treeCount);
862	GB_HASH *species_hash = GBT_create_species_hash(gb_main);
863
864	int modified = 0;
865
866	for (int t = 0; t<treeCount && !error; t++) {
867	progress.subtitle(tree_names[t]);
868	TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
869	if (!tree) {
870	aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
871	}
872	else {
873	int removed = 0;
874	int groups_removed = 0;
875
876	tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
877
878	nt_assert(removed >= groups_removed);
879
880	if (!tree) {
881	aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
882	}
883	else {
884	if (removed>0) {
885	error = GBT_write_tree(gb_main, tree_names[t], tree);
886	if (error) {
887	aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
888	}
889	else {
890	if (groups_removed>0) {
891	aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
892	}
893	else {
894	aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
895	}
896	modified++;
897	}
898	}
899	UNCOVERED();
900	destroy(tree);
901	}
902	}
903	progress.inc_and_check_user_abort(error);
904	}
905
906	if (modified) {
907	aw_message(GBS_global_string("Changed %i of %li trees.", modified, treeCount));
908	}
909	else {
910	aw_message("No tree modified");
911	}
912
913	GBS_free_hash(species_hash);
914	}
915
916	aw_message_if(ta.close(error));
917	}
918
919	TreeNode NT_get_tree_root_of_canvas(TREE_canvas ntw) {
920	AWT_graphic_tree *tree = AWT_TREE(ntw);
921	if (tree) {
922	AP_tree *root = tree->get_root_node();
923	if (root) return root;
924	}
925	return NULp;
926	}
927
928	// --------------------------------------------------------------------------------------------------
929
930	static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
931	GB_transaction ta(gb_main);
932	GBT_mark_all(gb_main, 0);
933
934	DBItemSetIter end = referred.end();
935	for (DBItemSetIter s = referred.begin(); s != end; ++s) {
936	GB_write_flag(*s, 1);
937	}
938	return ARB_ERROR();
939	}
940
941	static AW_window create_mark_by_refentries_window(AW_root awr, GBDATA *gbmain) {
942	static AW_window *aws = NULp;
943	if (!aws) {
944	static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
945	aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULp, "Mark referenced", mark_referred_species);
946	}
947	return aws;
948	}
949
950	// --------------------------------------------------------------------------------------------------
951
952	static void merge_from_to(AW_root awr, const char db_awar_name, bool merge_to) {
953	const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
954	char *quotedDB = GBK_singlequote(db_name);
955
956	AW_system(
957	GBS_global_string(
958	merge_to
959	? "arb_ntree : %s &"
960	: "arb_ntree %s : &",
961	quotedDB)
962	);
963
964	free(quotedDB);
965	}
966
967	static void merge_from_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, false); }
968	static void merge_into_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, true); }
969
970	static AW_window NT_create_merge_from_window(AW_root awr) {
971	static char *awar_name = NULp; // do not free, bound to callback
972	AW_window *aw_from =
973	awt_create_load_box(awr, "Merge data from", "other ARB database",
974	".", ".arb", &awar_name,
975	makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
976	return aw_from;
977	}
978	static AW_window NT_create_merge_to_window(AW_root awr) {
979	static char *awar_name = NULp; // do not free, bound to callback
980	AW_window *aw_to =
981	awt_create_load_box(awr, "Merge data to", "other ARB database",
982	".", ".arb", &awar_name,
983	makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
984	makeWindowCallback(AW_POPDOWN), NULp);
985	return aw_to;
986	}
987
988	// --------------------------------------------------------------------------------------------------
989
990	static void update_main_window_title(AW_root* awr, AW_window_menu_modes* aww, int clone) {
991	const char* filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
992	if (clone) {
993	aww->set_window_title(GBS_global_string("%s - ARB (%i)", filename, clone));
994	}
995	else {
996	aww->set_window_title(GBS_global_string("%s - ARB", filename));
997	}
998	}
999
1000	static void canvas_tree_awar_changed_cb(AW_awar , bool, TREE_canvas ntw) {
1001	NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
1002	AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
1003	TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_TREE);
1004	}
1005
1006	class TREE_canvas_registry {
1007	int count;
1008	TREE_canvas *canvas[MAX_NT_WINDOWS];
1009
1010	static TREE_canvas_registry *SINGLETON;
1011
1012	TREE_canvas_registry() : count(0) {
1013	AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
1014	}
1015
1016	public:
1017	static TREE_canvas_registry& instance() {
1018	if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
1019	return *SINGLETON;
1020	}
1021
1022	void register_canvas(TREE_canvas *ntw) {
1023	nt_assert(count<MAX_NT_WINDOWS);
1024	nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
1025	canvas[count++] = ntw;
1026	ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
1027	}
1028
1029	int get_count() const { return count; }
1030
1031	TREE_canvas *get_canvas(int idx) const {
1032	if (idx<0 \|\| idx>=count) return NULp;
1033	return canvas[idx];
1034	}
1035	};
1036
1037	TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULp;
1038
1039	TREE_canvas *NT_get_canvas_by_index(int idx) {
1040	/! return canvas with index 'idx' [0...MAX_NT_WINDOWS-1] /
1041	nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
1042	return TREE_canvas_registry::instance().get_canvas(idx);
1043	}
1044
1045	#if defined(TRACE_GROUP_SELECTION)
1046	static TREE_canvas find_canvas_showing(AWT_graphic_tree agt) {
1047	// look for (registered) canvas showing given AWT_graphic_tree
1048	// returns NULp if none found
1049	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1050
1051	int maxIdx = reg.get_count();
1052	for (int32_t i = 0; i<maxIdx; ++i) {
1053	TREE_canvas *ntw = reg.get_canvas(i);
1054	if (ntw->gfx == agt) return ntw;
1055	}
1056	return NULp;
1057	}
1058	#endif
1059
1060	void NT_fill_canvas_selection_list(class AW_selection_list sellst, TREE_canvas to_skip) {
1061	/*! insert canvases into selection list (using canvas-indices as values)
1062	*/
1063	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1064
1065	int maxIdx = reg.get_count();
1066	for (int32_t i = 0; i<maxIdx; ++i) {
1067	TREE_canvas *ntw = reg.get_canvas(i);
1068	if (ntw && ntw != to_skip) {
1069	nt_assert(ntw->get_awar_tree());
1070	const char *treename = ntw->get_awar_tree()->read_char_pntr();
1071	const char *description = i
1072	? GBS_global_string("ARB (%i): %s", i, treename)
1073	: GBS_global_string("ARB main: %s", treename);
1074	sellst->insert(description, i);
1075	}
1076	}
1077	}
1078
1079	// ----------------------------------
1080	// group-selection handlers
1081
1082	void NT_deselect_group(AW_root *awr) {
1083	awr->awar(AWAR_GROUP)->write_pointer(NULp);
1084	}
1085
1086	static bool track_group_selection_by_canvas = true;
1087
1088	static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) {
1089	const Group& group = gfx->get_selected_group();
1090
1091	#if defined(TRACE_GROUP_SELECTION)
1092	fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track");
1093	TREE_canvas *ntw = find_canvas_showing(gfx);
1094	if (group.is_valid()) {
1095	fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name());
1096	}
1097	else {
1098	fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index());
1099	}
1100	#endif
1101
1102	if (track_group_selection_by_canvas) {
1103	// set group-awar:
1104	gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULp if !group.is_valid()
1105	}
1106	}
1107
1108	static void group_awar_changed_cb(AW_root *awr) {
1109	AW_awar *awar_group = awr->awar(AWAR_GROUP);
1110	GBDATA *gb_wanted_group = awar_group->read_pointer();
1111
1112	GBDATA *gb_wanted_tree = NULp;
1113	{
1114	if (gb_wanted_group) {
1115	GB_transaction ta(gb_wanted_group);
1116	gb_wanted_tree = GB_get_father(gb_wanted_group);
1117	awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected
1118	#if defined(TRACE_GROUP_SELECTION)
1119	fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr);
1120	#endif
1121	}
1122	#if defined(TRACE_GROUP_SELECTION)
1123	const char *group_name = NULp;
1124	if (gb_wanted_group) {
1125	GB_transaction ta(gb_wanted_group);
1126	GBDATA *gb_name = GB_entry(gb_wanted_group, "group_name");
1127	if (gb_name) group_name = GB_read_char_pntr(gb_name);
1128	}
1129	fprintf(stderr, "group awar changed to %p", gb_wanted_group);
1130	if (group_name) fprintf(stderr, " (='%s')", group_name);
1131	fputc('\n', stderr);
1132	#endif
1133	}
1134
1135	LocallyModify<bool> ignore_group_selection_by_canvas(track_group_selection_by_canvas, false);
1136
1137	{
1138	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1139
1140	int maxIdx = reg.get_count();
1141	for (int32_t i = 0; i<maxIdx; ++i) {
1142	TREE_canvas *ntw = reg.get_canvas(i);
1143	AWT_graphic_tree *agt = AWT_TREE(ntw);
1144	const Group& curr_group = agt->get_selected_group();
1145
1146	GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree();
1147	if (gb_curr_tree == gb_wanted_tree) {
1148	AWT_auto_refresh allowed_on(ntw);
1149	if (!curr_group.is_valid() \|\| // no group selected
1150	curr_group.get_group_data() != gb_wanted_group) // wrong group selected
1151	{
1152	agt->select_group(gb_wanted_group);
1153	ntw->request_refresh();
1154	}
1155	// perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group)
1156	TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_GROUP);
1157	}
1158	else {
1159	if (curr_group.is_valid()) {
1160	AWT_auto_refresh allowed_on(ntw);
1161	agt->deselect_group();
1162	ntw->request_refresh();
1163	}
1164	}
1165	}
1166	}
1167	}
1168
1169	// ----------------------------
1170	// create main window
1171
1172	static AW_window popup_new_main_window(AW_root awr, int clone, TREE_canvas **result_ntw) {
1173	/*! create ARB_NTREE main window
1174	* @param awr application root
1175	* @param clone == 0 -> first window (full functionality); >0 -> additional tree views (restricted functionality)
1176	* @param result_ntw is set to the created TREE_canvas (passed pointer may be NULp if result is not needed)
1177	*/
1178	GB_push_transaction(GLOBAL.gb_main);
1179
1180	char window_title[256];
1181	const char *awar_tree = NULp;
1182
1183	if (clone) {
1184	awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
1185	sprintf(window_title, "ARB_NT_%i", clone);
1186	}
1187	else {
1188	awar_tree = AWAR_TREE;
1189	sprintf(window_title, "ARB_NT");
1190	}
1191	AW_window_menu_modes *awm = new AW_window_menu_modes;
1192	awm->init(awr, window_title, window_title, 0, 0);
1193
1194	awr->awar(AWAR_DB_NAME)
1195	->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1196	->update();
1197
1198	awm->button_length(5);
1199
1200	if (!clone) AW_init_color_group_defaults("arb_ntree");
1201
1202	AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1203
1204	if (!clone) { // while creating initial window
1205	AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb));
1206	awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb);
1207	}
1208
1209	TREE_canvas *ntw;
1210	{
1211	AW_awar *tree_awar = awr->awar_string(awar_tree);
1212	{
1213	AP_tree_display_style prev_style = tree->get_tree_style();
1214	tree->set_tree_style(AP_LIST_SIMPLE, NULp); // avoid NDS warnings during startup
1215
1216	ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1217	tree->set_tree_style(prev_style, ntw);
1218	ntw->set_mode(AWT_MODE_SELECT);
1219	}
1220
1221	if (result_ntw) *result_ntw = ntw;
1222
1223	{
1224	const char *tree_name = tree_awar->read_char_pntr();
1225	const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1226
1227	if (existing_tree_name) {
1228	tree_awar->write_string(existing_tree_name);
1229	NT_reload_tree_event(awr, ntw, true); // load first tree
1230	}
1231	else {
1232	AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, NULp, "no_tree.hlp");
1233	tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list
1234	}
1235
1236	TREE_canvas_registry::instance().register_canvas(ntw);
1237	AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1238	}
1239	}
1240
1241	TREE_install_update_callbacks(ntw);
1242
1243	bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1244
1245	WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1246
1247	// --------------
1248	// File
1249
1250	#if defined(DEBUG)
1251	AWT_create_debug_menu(awm);
1252	#endif // DEBUG
1253
1254	bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1255
1256	if (clone) {
1257	awm->create_menu("File", "F", AWM_ALL);
1258	if (allow_new_window) {
1259	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**)NULp));
1260	}
1261	awm->insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN);
1262	}
1263	else {
1264	#if defined(DEBUG)
1265	// add more to debug-menu
1266	awm->sep______________();
1267	awm->insert_menu_topic("fix_db", "Fix database", "F", NULp, AWM_ALL, NT_fix_database);
1268	awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", NULp, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1269	awm->insert_menu_topic("test_compr", "Test compression", "T", NULp, AWM_ALL, makeWindowCallback(GBT_compression_test, GLOBAL.gb_main));
1270	#endif // DEBUG
1271
1272	awm->create_menu("File", "F", AWM_ALL);
1273	{
1274	// keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1275	awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, NT_save_quick_cb);
1276	awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1277	if (allow_new_window) {
1278	awm->sep______________();
1279	awm->insert_menu_topic("new_window", "New window (same database)", "N", "newwindow.hlp", AWM_ALL, makeCreateWindowCallback(popup_new_main_window, clone+1, (TREE_canvas**)NULp));
1280	}
1281	awm->sep______________();
1282	awm->insert_menu_topic("optimize_db", "Optimize database compression", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window);
1283	awm->sep______________();
1284
1285	awm->insert_sub_menu("Import", "I");
1286	{
1287	awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1288	awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1289	GDE_load_menu(awm, AWM_EXP, "Import");
1290	}
1291	awm->close_sub_menu();
1292
1293	awm->insert_sub_menu("Export", "E");
1294	{
1295	awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1296	awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1297	GDE_load_menu(awm, AWM_ALL, "Export");
1298	awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window);
1299	}
1300	awm->close_sub_menu();
1301	awm->sep______________();
1302
1303	insert_macro_menu_entry(awm, false);
1304
1305	awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1306	{
1307	awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp"));
1308	awm->insert_menu_topic("bug_report", "Report bug", "b", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1309	awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1310	}
1311	awm->close_sub_menu();
1312	awm->sep______________();
1313
1314	awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1315	awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1316	awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_exit, EXIT_SUCCESS));
1317	}
1318
1319	// -----------------
1320	// Species
1321
1322	awm->create_menu("Species", "c", AWM_ALL);
1323	{
1324	awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1325	awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb);
1326
1327	awm->sep______________();
1328
1329	NT_insert_mark_submenus(awm, ntw, 1);
1330	awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1331	awm->insert_menu_topic("species_colors", "Colors ...", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window);
1332	awm->insert_menu_topic("selection_admin", "Selections ...", "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1333
1334	awm->sep______________();
1335
1336	awm->insert_sub_menu("Database fields admin", "f");
1337	DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1338	awm->close_sub_menu();
1339	NT_create_mask_submenu(awm);
1340
1341	awm->sep______________();
1342
1343	awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1344
1345	awm->insert_sub_menu("Sort Species", "s");
1346	{
1347	awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window);
1348	awm->insert_menu_topic("$sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1349	}
1350	awm->close_sub_menu();
1351
1352	awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1353	{
1354	awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1355	awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "species_join.hlp", AWM_EXP, NT_create_species_join_window);
1356	}
1357	awm->close_sub_menu();
1358
1359	awm->sep______________();
1360
1361	awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1362
1363	awm->sep______________();
1364
1365	awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1366
1367	awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1368	{
1369	awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames);
1370	awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames);
1371	awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1372	awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window);
1373	}
1374	awm->close_sub_menu();
1375	}
1376
1377	// ----------------------------
1378	// Genes + Experiment
1379
1380	if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1381
1382	// ------------------
1383	// Sequence
1384
1385	awm->create_menu("Sequence", "S", AWM_ALL);
1386	{
1387	awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)NULp));
1388	awm->insert_sub_menu("Insert/delete", "I");
1389	{
1390	awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window);
1391	awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main));
1392	}
1393	awm->close_sub_menu();
1394	awm->sep______________();
1395
1396	awm->insert_sub_menu("Edit Sequences", "E");
1397	{
1398	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));
1399	awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1400	awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1401	}
1402	awm->close_sub_menu();
1403
1404	awm->sep______________();
1405
1406	awm->insert_sub_menu("Align sequences", "l");
1407	{
1408	awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1409	GDE_load_menu(awm, AWM_ALL, "Align");
1410	}
1411	awm->close_sub_menu();
1412	awm->insert_menu_topic("seq_concat", "Concatenate sequences", "C", "concatenate.hlp", AWM_ALL, NT_createConcatenationWindow);
1413	awm->insert_menu_topic("seq_split", "Split sequences", "S", "split.hlp", AWM_ALL, NT_create_splitAlignment_window);
1414	awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1415	awm->sep______________();
1416
1417	awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1418	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist"));
1419	awm->sep______________();
1420
1421	awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1422	awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1423
1424	awm->sep______________();
1425
1426	GDE_load_menu(awm, AWM_ALL, "Print");
1427	}
1428
1429	// -------------
1430	// SAI
1431
1432	awm->create_menu("SAI", "A", AWM_ALL);
1433	{
1434	awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1435	awm->insert_menu_topic("sai_calc", "Combine SAIs", "b", "saicalc.hlp", AWM_ALL, makeWindowCallback(SAI_popup_calculator_window, GLOBAL.gb_main));
1436	awm->insert_sub_menu("Create SAI using ...", "C");
1437	{
1438	awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window);
1439	awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window);
1440	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);
1441	awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_phylo"));
1442	awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold);
1443
1444	GDE_load_menu(awm, AWM_EXP, "SAI");
1445	}
1446	awm->close_sub_menu();
1447
1448	awm->insert_sub_menu("Other functions", "O");
1449	{
1450	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));
1451	awm->insert_menu_topic("corr_mutat_analysis", "Compute clusters of correlated positions", "m", "", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_rnacma", new XCmdType(XCMD_SERVSYNC_WAIT_ON_ERROR, GLOBAL.gb_main)));
1452	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);
1453	}
1454	awm->close_sub_menu();
1455	}
1456
1457	// ----------------
1458	// Probes
1459
1460	awm->create_menu("Probes", "P", AWM_ALL);
1461	{
1462	awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1463	awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1464	awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1465	awm->sep______________();
1466	awm->insert_menu_topic("probe_match_sp", "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window, ntw));
1467	awm->sep______________();
1468	awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1469	awm->insert_menu_topic("primer_design", "Design Sequencing Primers", "S", "primer.hlp", AWM_EXP, makeWindowCallback(ARB_system_in_console_cb, "arb_primer", new XCmdType(XCMD_SERVSYNC_WAIT_ON_ERROR, GLOBAL.gb_main)));
1470	awm->sep______________();
1471	awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1472	}
1473
1474	}
1475
1476	// --------------
1477	// Tree
1478
1479	awm->create_menu("Tree", "T", AWM_ALL);
1480	{
1481	if (!clone) {
1482	awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1483	awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(NDS_create_window, GLOBAL.gb_main));
1484	awm->sep______________();
1485	awm->insert_sub_menu("Add Species to Existing Tree", "A");
1486	{
1487	awm->insert_menu_topic("arb_pars_quick", "ARB Parsimony (Quick add marked)", "Q", "pars.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_pars -add_marked -quit"));
1488	awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_pars"));
1489	GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1490	}
1491	awm->close_sub_menu();
1492	}
1493
1494	awm->insert_sub_menu("Remove Species from Tree", "R");
1495	{
1496	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));
1497	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));
1498	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));
1499	awm->sep______________();
1500	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));
1501	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));
1502	}
1503	awm->close_sub_menu();
1504
1505	if (!clone) {
1506	awm->insert_sub_menu("Build tree from sequence data", "B");
1507	{
1508	awm->insert_sub_menu("Distance matrix methods", "D");
1509	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist"));
1510	GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1511	awm->close_sub_menu();
1512
1513	awm->insert_sub_menu("Maximum Parsimony methods", "P");
1514	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1515	awm->close_sub_menu();
1516
1517	awm->insert_sub_menu("Maximum Likelihood methods", "L");
1518	GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1519	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1520	awm->close_sub_menu();
1521
1522	awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1523	GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1524	awm->close_sub_menu();
1525	}
1526	awm->close_sub_menu();
1527	}
1528
1529	awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1530
1531	awm->sep______________();
1532
1533	awm->insert_sub_menu("Reset zoom", "z");
1534	{
1535	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));
1536	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));
1537	}
1538	awm->close_sub_menu();
1539
1540	awm->sep______________();
1541
1542	// taxonomic groups
1543	NT_insert_collapse_submenu(awm, ntw);
1544	if (!clone) {
1545	awm->insert_menu_topic("group_search", "Search groups...", "g", "group_search.hlp", AWM_ALL, makeWindowCallback (popup_group_search_window, GLOBAL.gb_main));
1546	awm->insert_menu_topic("compare_taxonomy", "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1547	awm->insert_menu_topic("move_groups", "Move groups...", "v", "move_groups.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_moveGroupInfo_window));
1548	}
1549
1550	awm->sep______________();
1551
1552	if (!clone) {
1553	awm->insert_menu_topic("compare_topology", "Compare topology...", "o", "compare_topo.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compareTopologies_window));
1554	}
1555
1556	awm->insert_sub_menu("Modify branches", "M");
1557	{
1558	awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw));
1559	awm->insert_menu_topic(awm->local_id("tree_edit_remark"), "Edit bootstraps", "E", "ted_boot.hlp", AWM_ALL, makeWindowCallback(NT_edit_bootstrap, ntw));
1560	awm->sep______________();
1561	awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw));
1562	awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1563	awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw));
1564	awm->sep______________();
1565	awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1566	awm->sep______________();
1567	awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1568	awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1569
1570	}
1571	awm->close_sub_menu();
1572	awm->insert_sub_menu("Beautify tree", "u");
1573	{
1574	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));
1575	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));
1576	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));
1577	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));
1578	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));
1579	awm->sep______________();
1580	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));
1581	}
1582	awm->close_sub_menu();
1583
1584	awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "h", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1585	awm->insert_menu_topic(awm->local_id("syncroots"), "Adjust roots...", "j", "syncroots.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncroot_window, GLOBAL.gb_main));
1586	awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "k", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback (NT_mark_duplicates, ntw));
1587
1588	awm->sep______________();
1589	awm->insert_menu_topic(awm->local_id("shade"), "Tree shading...", "s", "tree_shading.hlp", AWM_ALL, makeWindowCallback (NT_configure_treeShader));
1590	awm->insert_menu_topic(awm->local_id("syncscroll"), "Sync tree scrolling..", "e", "syncscroll.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1591
1592	awm->sep______________();
1593	awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", NULp, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1594
1595	awm->sep______________();
1596	awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1597
1598	if (is_genome_db) {
1599	awm->sep______________();
1600	awm->insert_menu_topic(awm->local_id("tree_pseudo_species_to_organism"), "Relink tree to organisms", "i", "tree_pseudo.hlp", AWM_EXP, makeWindowCallback(NT_pseudo_species_to_organism, ntw));
1601	}
1602
1603	if (!clone) {
1604	awm->sep______________();
1605	awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1606	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)));
1607	}
1608
1609	}
1610
1611	if (!clone) {
1612	// ---------------
1613	// Tools
1614
1615	awm->create_menu("Tools", "o", AWM_ALL);
1616	{
1617	awm->insert_menu_topic("names_admin", "Nameserver admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeWindowCallback(AW_popup_namesadmin_window, GLOBAL.gb_main));
1618	awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1619	{
1620	awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1621	}
1622	awm->close_sub_menu();
1623	awm->sep______________();
1624
1625	awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1626	{
1627	GDE_load_menu(awm, AWM_EXP, NULp);
1628	}
1629	awm->close_sub_menu();
1630
1631	awm->sep______________();
1632	awm->insert_menu_topic("xterm", "Start XTERM", "X", "xterm.hlp", AWM_ALL, AW_console_cb);
1633	XCmdType *showlog_cmdtype = new XCmdType(XCMD_ASYNC_WAIT_ON_ERROR, GLOBAL.gb_main); // do not free (used in callback)
1634	awm->insert_menu_topic("viewlog", "View ARB log", "l", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl run", showlog_cmdtype)); // ../SH/arb_show_log.pl
1635	awm->insert_menu_topic("viewserv", "View server log", "V", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl server", showlog_cmdtype));
1636	awm->insert_menu_topic("viewsys", "View sysinfo", "i", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl sysinf", showlog_cmdtype));
1637	awm->sep______________();
1638	GDE_load_menu(awm, AWM_EXP, "User");
1639	}
1640	// --------------------
1641	// Properties
1642
1643	awm->create_menu("Properties", "r", AWM_ALL);
1644	{
1645	awm->insert_menu_topic("props_menu", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1646	awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1647	awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1648	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));
1649	awm->sep______________();
1650	awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", NULp, AWM_ALL, NT_toggle_expert_mode);
1651	awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", NULp, AWM_ALL, NT_toggle_focus_policy);
1652	awm->sep______________();
1653	AW_insert_common_property_menu_entries(awm);
1654	awm->sep______________();
1655	awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1656	}
1657	}
1658
1659	awm->insert_help_topic("ARB_NT help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1660
1661	// ----------------------
1662	// mode buttons
1663	//
1664	// keep them synchronized as far as possible with those in ARB_PARSIMONY
1665	// see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1666
1667	awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1668	awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1669	awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1670	awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1671	awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1672
1673	awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1674	awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW));
1675
1676	// topology-modification-modes
1677	awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1678	awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1679	awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1680	awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1681	awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1682
1683	// layout-modes
1684	awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1685	awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1686	awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1687
1688	awm->set_info_area_height(250);
1689	awm->at(5, 2);
1690	awm->auto_space(-2, -2);
1691	awm->shadow_width(1);
1692
1693	// -------------------------
1694	// create top area
1695
1696	int first_liney;
1697	int leftx;
1698	awm->get_at_position(&leftx, &first_liney);
1699
1700	// ---------------------
1701	// quit + help
1702
1703	awm->button_length(0);
1704
1705	if (clone) {
1706	awm->callback(AW_POPDOWN);
1707	awm->create_button("CLOSE", "#close.xpm");
1708	}
1709	else {
1710	awm->callback(makeWindowCallback(NT_exit, EXIT_SUCCESS));
1711	awm->help_text("quit.hlp");
1712	awm->create_button("QUIT", "#quit.xpm");
1713	}
1714
1715	int db_pathx = awm->get_at_xposition();
1716
1717	// now fetch the yposition for the 2nd button line
1718	awm->at_newline();
1719	int second_liney = awm->get_at_yposition();
1720
1721	awm->callback(AW_help_entry_pressed);
1722	awm->help_text("arb_ntree.hlp");
1723	awm->create_button("?", "#help.xpm");
1724
1725	// --------------------------
1726	// save + undo/redo
1727
1728	awm->callback(NT_save_quick_cb);
1729	awm->help_text("save.hlp");
1730	awm->create_button("SAVE", "#save.xpm");
1731
1732	awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1733	awm->help_text("save.hlp");
1734	awm->create_button("SAVE_AS", "#saveAs.xpm");
1735
1736	// undo/redo:
1737	awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1738	awm->help_text("undo.hlp");
1739	awm->create_button("UNDO", "#undo.xpm");
1740
1741	awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1742	awm->help_text("undo.hlp");
1743	awm->create_button("REDO", "#redo.xpm");
1744
1745	int db_pathx2 = awm->get_at_xposition();
1746
1747	// fetch position for mode help-line:
1748	awm->at_newline();
1749	int third_liney = awm->get_at_yposition();
1750
1751	awm->at(db_pathx, first_liney);
1752	// size of DB-name button is determined by buttons below:
1753	awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1754	awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1755	awm->help_text("save.hlp");
1756	awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1757
1758	// -----------------------------
1759	// tree + tree display
1760
1761	#define TREE_BUTTON_OVERSIZE 6
1762
1763	int db_treex = awm->get_at_xposition();
1764	int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1765
1766	awm->at(db_treex, second_uppery);
1767	awm->button_length(0);
1768
1769	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1770	awm->help_text("tr_type_radial.hlp");
1771	awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1772
1773	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1774	awm->help_text("tr_type_dendro.hlp");
1775	awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1776
1777	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1778	awm->help_text("tr_type_irs.hlp");
1779	awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1780
1781	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1782	awm->help_text("tr_type_nds.hlp");
1783	awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1784
1785	int db_treex2 = awm->get_at_xposition();
1786
1787	awm->at(db_treex, first_liney);
1788	// size of tree-name button is determined by buttons below:
1789	awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1790	awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1791	awm->help_text("nt_tree_select.hlp");
1792	awm->create_button("SELECT_A_TREE", awar_tree);
1793
1794	// ---------------------------------------------------------------
1795	// protection, alignment + editor (and maybe Genome Map)
1796
1797	int db_alignx = awm->get_at_xposition();
1798
1799	// editor and genemap buttons have to be 44x24 sized
1800	#define EDIT_XSIZE 50
1801	#define EDIT_YSIZE 30 // same as 'save as' buttons
1802
1803	// first draw protection:
1804	int protectx = db_alignx + 2*EDIT_XSIZE;
1805
1806	awm->at(protectx+2, first_liney+1);
1807	awm->button_length(0);
1808	awm->create_button(NULp, "#protect.xpm");
1809
1810	awm->at(protectx, second_liney+2);
1811	awm->create_option_menu(AWAR_SECURITY_LEVEL);
1812	awm->insert_option ("0", NULp, 0);
1813	awm->insert_option ("1", NULp, 1);
1814	awm->insert_option ("2", NULp, 2);
1815	awm->insert_option ("3", NULp, 3);
1816	awm->insert_option ("4", NULp, 4);
1817	awm->insert_option ("5", NULp, 5);
1818	awm->insert_default_option("6", NULp, 6);
1819	awm->update_option_menu();
1820
1821	int db_searchx = awm->get_at_xposition() - 7;
1822
1823	// draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1824	awm->at(db_alignx, second_liney);
1825
1826	awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1827	awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1828	awm->help_text("arb_edit4.hlp");
1829	if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1830	else awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1831
1832	if (is_genome_db) {
1833	awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1834	awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1835	awm->help_text("gene_map.hlp");
1836	awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1837	}
1838
1839	int db_alignx2 = awm->get_at_xposition();
1840
1841	awm->at(db_alignx, first_liney);
1842	awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1843	awm->callback(NT_create_select_alignment_window);
1844	awm->help_text("nt_align_select.hlp");
1845	awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1846
1847	// -------------------------------
1848	// create mode-help line
1849
1850	awm->at(leftx, third_liney);
1851	awm->button_length(AWAR_FOOTER_MAX_LEN);
1852	awm->create_button(NULp, AWAR_FOOTER);
1853
1854	awm->at_newline();
1855	int bottomy = awm->get_at_yposition();
1856
1857	// ---------------------------------------
1858	// Info / marked / Search / Jump
1859
1860	awm->button_length(7);
1861
1862	awm->at(db_searchx, first_liney);
1863	awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1864	awm->help_text("sp_search.hlp");
1865	awm->create_button("SEARCH", "Search");
1866
1867	awm->at(db_searchx, second_uppery);
1868	awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1869	awm->help_text("tr_jump.hlp");
1870	awm->create_button("JUMP", "Jump");
1871
1872	int db_infox = awm->get_at_xposition();
1873
1874	awm->at(db_infox, first_liney);
1875	awm->button_length(13);
1876	awm->callback(popupinfo_wcb);
1877	awm->help_text("sp_info.hlp");
1878	awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1879
1880	awm->at(db_infox, second_uppery);
1881	awm->button_length(13);
1882	awm->help_text("species_configs.hlp");
1883	awm->callback(makeWindowCallback(NT_popup_configuration_admin, ntw));
1884	awm->create_button("selection_admin2", AWAR_MARKED_SPECIES_COUNTER);
1885	{
1886	GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1887	GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(NT_update_marked_counter, static_cast<AW_window*>(awm)));
1888	NT_update_marked_counter(NULp, awm);
1889	}
1890
1891	// set height of top area:
1892	awm->set_info_area_height(bottomy+2);
1893	awm->set_bottom_area_height(0);
1894
1895	NT_activate_configMarkers_display(ntw);
1896
1897	// ------------------------------------
1898	// Autostarts for development
1899
1900	#if defined(DEVEL_RALF)
1901	// if (is_genome_db) GEN_map_first(awr)->show();
1902	#endif // DEVEL_RALF
1903
1904	GB_pop_transaction(GLOBAL.gb_main);
1905
1906	#if defined(DEBUG)
1907	AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1908	#endif
1909
1910	return awm;
1911	}
1912
1913	TREE_canvas NT_create_main_window(AW_root aw_root) {
1914	GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1915	if (error) aw_message(error);
1916
1917	nt_create_all_awars(aw_root);
1918
1919	TREE_canvas *ntw = NULp;
1920	AW_window *aww = popup_new_main_window(aw_root, 0, &ntw);
1921	NT_install_treeShader(ntw, GLOBAL.gb_main);
1922	aww->show();
1923
1924	error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1925	if (error) aw_message(error);
1926
1927	return ntw;
1928	}

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source: branches/lib/NTREE/NT_extern.cxx

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