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source: tags/ms_ra2q1/NTREE/NT_extern.cxx

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Last change on this file was 17262, checked in by westram, 6 years ago
partial merge from 'group' into 'trunk' fixes to arb_progress adds: log:branches/group@17191:17218,17220:17260 log:branches/progress@17195:17216,17218:17259
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 77.7 KB

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1	// =============================================================== //
2	// //
3	// File : NT_extern.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "map_viewer.h"
12	#include "NT_local.h"
13	#include "ad_trees.h"
14	#include "NT_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 <nds.h>
31	#include <db_query.h>
32	#include <dbui.h>
33	#include <refentries.h>
34	#include <insdel.h>
35
36	#include <awti_export.hxx>
37	#include <awti_import.hxx>
38
39	#include <awt.hxx>
40	#include <awt_input_mask.hxx>
41	#include <awt_sel_boxes.hxx>
42	#include <awt_www.hxx>
43	#include <awt_TreeAwars.hxx>
44	#include <awt_misc.hxx>
45
46	#include <aw_color_groups.hxx>
47	#include <aw_advice.hxx>
48	#include <aw_preset.hxx>
49	#include <aw_awars.hxx>
50	#include <aw_global_awars.hxx>
51	#include <aw_file.hxx>
52	#include <aw_msg.hxx>
53	#include <arb_progress.h>
54	#include <aw_root.hxx>
55	#include <aw_question.hxx>
56	#include <aw_select.hxx>
57	#include <rootAsWin.h>
58
59	#include <ad_cb.h>
60
61	#include <arb_strbuf.h>
62	#include <arb_strarray.h>
63	#include <arb_file.h>
64	#include <arb_version.h>
65
66	#if defined(DEVEL_RALF)
67	# define TRACE_GROUP_SELECTION
68	#endif
69
70	#define AWAR_EXPORT_NDS "tmp/export_nds"
71	#define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/separator"
72	#define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species"
73	#define AWAR_NTREE_TITLE_MODE "tmp/title_mode"
74
75	void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
76
77	void create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
78	AW_window create_insertDeleteColumn_window(AW_root root);
79	AW_window create_insertDeleteBySAI_window(AW_root root, GBDATA *gb_main);
80
81	AW_window create_tree_window(AW_root aw_root, AWT_graphic *awd);
82
83	static void nt_changesecurity(AW_root *aw_root) {
84	int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
85	GB_push_transaction(GLOBAL.gb_main);
86	GB_change_my_security(GLOBAL.gb_main, level);
87	GB_pop_transaction(GLOBAL.gb_main);
88	}
89
90	static void export_nds_cb(AW_window *aww, bool do_print) {
91	AW_root *aw_root = aww->get_root();
92	char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
93	FILE *out = fopen(name, "w");
94
95	if (!out) {
96	aw_message("Error: Cannot open and write to file");
97	}
98	else {
99	GB_transaction ta(GLOBAL.gb_main);
100
101	make_node_text_init(GLOBAL.gb_main);
102	NDS_Type nds_type = (NDS_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
103	char *tree_name = aw_root->awar(AWAR_TREE)->read_string();
104
105	for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
106	gb_species;
107	gb_species = GBT_next_marked_species(gb_species))
108	{
109	const char *buf = make_node_text_nds(GLOBAL.gb_main, gb_species, nds_type, NULp, tree_name);
110	fprintf(out, "%s\n", buf);
111	}
112	AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
113	fclose(out);
114	if (do_print) {
115	GB_ERROR error = GB_textprint(name);
116	if (error) aw_message(error);
117	}
118	free(tree_name);
119	}
120	free(name);
121	}
122
123	static AW_window create_nds_export_window(AW_root root) {
124	AW_window_simple *aws = new AW_window_simple;
125	aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
126	aws->load_xfig("sel_box_nds.fig");
127
128	aws->callback(AW_POPDOWN);
129	aws->at("close");
130	aws->create_button("CLOSE", "CLOSE", "C");
131
132	aws->callback(makeHelpCallback("arb_export_nds.hlp"));
133	aws->at("help");
134	aws->create_button("HELP", "HELP", "H");
135
136	aws->at("save");
137	aws->callback(makeWindowCallback(export_nds_cb, false));
138	aws->create_button("SAVE", "SAVE", "S");
139
140	aws->at("print");
141	aws->callback(makeWindowCallback(export_nds_cb, true));
142	aws->create_button("PRINT", "PRINT", "P");
143
144	aws->at("toggle1");
145	aws->label("Column output");
146	aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR, true);
147	aws->insert_default_option("Space padded", "S", NDS_OUTPUT_SPACE_PADDED);
148	aws->insert_option ("TAB separated", "T", NDS_OUTPUT_TAB_SEPARATED);
149	aws->insert_option ("Comma separated", "C", NDS_OUTPUT_COMMA_SEPARATED);
150	aws->update_option_menu();
151
152	AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS);
153
154	return aws;
155	}
156
157	static void create_export_nds_awars(AW_root *awr, AW_default def) {
158	AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds");
159	awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, NDS_OUTPUT_SPACE_PADDED, def);
160	}
161
162	static void selectedSpeciesChanged_cb(AW_root *awr) {
163	const char *value = awr->awar(AWAR_SPECIES_NAME)->read_char_pntr();
164	awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
165	if (value[0]) {
166	awr->awar(AWAR_GROUP)->write_pointer(NULp); // deselect group when species gets selected
167	#if defined(TRACE_GROUP_SELECTION)
168	fputs("clear AWAR_GROUP (because species selected)\n", stderr);
169	#endif
170	}
171	}
172
173	static void expert_mode_changed_cb(AW_root *aw_root) {
174	aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
175	}
176
177	static void NT_toggle_expert_mode(AW_window *aww) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
178	static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
179
180	static void nt_create_all_awars(AW_root *awr) {
181	// creates awars for all modules reachable from ARB_NT main window
182
183	awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT);
184	if (GB_read_clients(GLOBAL.gb_main)>=0) {
185	awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
186	}
187	else {
188	awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT);
189	}
190
191	awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main);
192	awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main);
193	awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main);
194	awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown", GLOBAL.gb_main);
195	awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main);
196	awr->awar(AWAR_SPECIES_NAME)->add_callback(selectedSpeciesChanged_cb);
197	awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
198
199	awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
200
201	GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
202	EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
203	#if defined(DEBUG)
204	AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT);
205	#endif // DEBUG
206
207	AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
208
209	awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT);
210	awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
211	#if defined(DEBUG) && 0
212	awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
213	#endif // DEBUG
214
215	create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT);
216	create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
217	create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
218	create_trees_var(awr, AW_ROOT_DEFAULT);
219	DBUI::create_dbui_awars(awr);
220	AP_create_consensus_var(awr, AW_ROOT_DEFAULT);
221	{
222	GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, NULp, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT);
223	if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
224	}
225	NT_create_transpro_variables(awr, AW_ROOT_DEFAULT);
226	NT_create_resort_awars(awr, AW_ROOT_DEFAULT);
227	NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT);
228	NT_create_trackAliChanges_Awars(awr, GLOBAL.gb_main);
229
230	NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
231	NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
232	create_nds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, false);
233	create_export_nds_awars(awr, AW_ROOT_DEFAULT);
234	create_group_search_awars(awr, AW_ROOT_DEFAULT);
235	TREE_create_awars(awr, GLOBAL.gb_main);
236
237	awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
238	awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
239
240	AWTC_create_submission_variables(awr, GLOBAL.gb_main);
241	NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
242	NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar
243	SQ_create_awars(awr, AW_ROOT_DEFAULT);
244	RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT);
245
246	NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT);
247
248	GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
249	if (!error) {
250	AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
251	awar_expert->add_callback(expert_mode_changed_cb);
252	awar_expert->touch();
253
254	awt_create_aww_vars(awr, AW_ROOT_DEFAULT);
255	}
256
257	if (error) aw_message(error);
258	}
259
260	// --------------------------------------------------------------------------------
261
262	bool nt_disconnect_from_db(AW_root aw_root, GBDATA& gb_main_ref) {
263	// ask user if DB was not saved
264	// returns true if user allows to quit
265
266	// @@@ code here could as well be applied to both merge DBs
267	// - question about saving only with target DB!
268
269	if (gb_main_ref) {
270	if (GB_read_clients(gb_main_ref)>=0) {
271	if (GB_read_clock(gb_main_ref) > GB_last_saved_clock(gb_main_ref)) {
272	long secs;
273	secs = GB_last_saved_time(gb_main_ref);
274
275	#if defined(DEBUG)
276	secs = GB_time_of_day(); // simulate "just saved"
277	#endif // DEBUG
278
279	const char *quit_buttons = "Quit ARB,Do NOT quit";
280	if (secs) {
281	secs = GB_time_of_day() - secs;
282	if (secs>10) {
283	char *question = GBS_global_string_copy("You last saved your data %li:%li minutes ago\nSure to quit ?", secs/60, secs%60);
284	int dontQuit = aw_question("quit_arb", question, quit_buttons);
285	free(question);
286	if (dontQuit) {
287	return false;
288	}
289	}
290	}
291	else {
292	if (aw_question("quit_arb", "You never saved any data\nSure to quit ???", quit_buttons)) {
293	return false;
294	}
295	}
296	}
297	}
298
299	GBCMS_shutdown(gb_main_ref);
300
301	GBDATA *gb_main = gb_main_ref;
302	gb_main_ref = NULp; // avoid further usage
303
304	nt_assert(aw_root);
305	#if defined(WARN_TODO)
306	#warning instead of directly calling the following functions, try to add them as GB_atclose_callback
307	#endif
308	aw_root->unlink_awars_from_DB(gb_main);
309	AWT_destroy_input_masks();
310	#if defined(DEBUG)
311	AWT_browser_forget_db(gb_main);
312	#endif // DEBUG
313
314	GB_close(gb_main);
315	}
316	return true;
317	}
318
319	static void nt_run(const char *command) {
320	GB_ERROR error = GBK_system(command);
321	if (error) {
322	fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
323	#if defined(DEBUG)
324	GBK_dump_backtrace(stderr, "nt_run-error");
325	#endif
326	}
327	}
328
329	void NT_start(const char *arb_ntree_args, bool restart_with_new_ARB_PID) {
330	char *command = GBS_global_string_copy("arb_launcher --async %s %s", restart_with_new_ARB_PID ? "arb" : "arb_ntree", arb_ntree_args);
331	nt_run(command);
332	free(command);
333	}
334
335	__ATTR__NORETURN static void really_exit(int exitcode, bool kill_my_clients) {
336	if (kill_my_clients) {
337	nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
338	}
339	exit(exitcode);
340	}
341
342	void NT_exit(AW_window *aws, int exitcode) {
343	AW_root *aw_root = aws->get_root();
344	AWTI_cleanup_importer();
345	shutdown_macro_recording(aw_root);
346	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
347	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
348	really_exit(exitcode, is_server_and_has_clients);
349	}
350	}
351	void NT_restart(AW_root aw_root, const char arb_ntree_args) {
352	// restarts arb_ntree (with new ARB_PID)
353	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
354	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
355	NT_start(arb_ntree_args, true);
356	really_exit(EXIT_SUCCESS, is_server_and_has_clients);
357	}
358	}
359
360	static void nt_start_2nd_arb(AW_window *aww, bool quit) {
361	// start 2nd arb with intro window
362	AW_root *aw_root = aww->get_root();
363	char *dir4intro;
364	GB_split_full_path(aw_root->awar(AWAR_DB_PATH)->read_char_pntr(), &dir4intro, NULp, NULp, NULp);
365	if (!dir4intro) {
366	dir4intro = ARB_strdup(".");
367	}
368
369	if (quit) {
370	NT_restart(aw_root, dir4intro);
371	}
372	else {
373	NT_start(dir4intro, true);
374	}
375	free(dir4intro);
376	}
377
378	// --------------------------------------------------------------------------------
379
380	static void NT_save_quick_cb(AW_window *aww) {
381	AW_root *awr = aww->get_root();
382	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
383
384	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
385
386	GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
387	free( filename);
388	if (error) aw_message(error);
389	else AW_refresh_fileselection(awr, AWAR_DBBASE);
390	}
391
392
393	static void NT_save_quick_as_cb(AW_window *aww) {
394	AW_root *awr = aww->get_root();
395	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
396	GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename);
397	if (!error) AW_refresh_fileselection(awr, AWAR_DBBASE);
398	aww->hide_or_notify(error);
399
400	free(filename);
401	}
402
403	#define AWAR_DB_TYPE AWAR_DBBASE "/type" // created by AWT_insert_DBsaveType_selector
404	#define AWAR_DB_COMPRESSION AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector
405	#define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name"
406
407	static void NT_save_as_cb(AW_window *aww) {
408	AW_root *awr = aww->get_root();
409	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
410	const char *atype = awr->awar(AWAR_DB_TYPE)->read_char_pntr();
411	const char *ctype = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr();
412	char *savetype = GBS_global_string_copy("%s%s", atype, ctype);
413
414	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
415	GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype);
416	if (!error) AW_refresh_fileselection(awr, AWAR_DBBASE);
417	aww->hide_or_notify(error);
418
419	free(savetype);
420	free(filename);
421	}
422
423	static AW_window NT_create_save_quick_as_window(AW_root aw_root, const char *base_name) {
424	static AW_window_simple *aws = NULp;
425	if (!aws) {
426	aws = new AW_window_simple;
427	aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as");
428	aws->load_xfig("save_as.fig");
429
430	aws->at("close");
431	aws->callback(AW_POPDOWN);
432	aws->create_button("CLOSE", "CLOSE", "C");
433
434	aws->callback(makeHelpCallback("save.hlp"));
435	aws->at("help");
436	aws->create_button("HELP", "HELP", "H");
437
438	AW_create_standard_fileselection(aws, base_name);
439
440	aws->at("comment");
441	aws->create_text_field(AWAR_DB_COMMENT);
442
443	aws->at("save");
444	aws->callback(NT_save_quick_as_cb);
445	aws->create_button("SAVE", "SAVE", "S");
446	}
447	return aws;
448	}
449
450	static void NT_database_optimization(AW_window *aww) {
451	arb_progress progress("Optimizing database compression", 2L);
452
453	GB_push_my_security(GLOBAL.gb_main);
454	GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
455	if (!error) {
456	ConstStrArray ali_names;
457	GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
458
459	arb_progress ali_progress("Optimizing sequence data", ali_names.size());
460	ali_progress.allow_title_reuse();
461
462	error = GBT_check_data(GLOBAL.gb_main, NULp);
463	error = GB_end_transaction(GLOBAL.gb_main, error);
464
465	if (!error) {
466	char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string();
467	for (int i = 0; ali_names[i]; ++i) {
468	error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
469	ali_progress.inc_and_check_user_abort(error);
470	}
471	free(tree_name);
472	}
473	}
474	progress.inc_and_check_user_abort(error);
475
476	if (!error) {
477	error = GB_optimize(GLOBAL.gb_main);
478	progress.inc_and_check_user_abort(error);
479	}
480
481	GB_pop_my_security(GLOBAL.gb_main);
482	aww->hide_or_notify(error);
483	}
484
485	static AW_window NT_create_database_optimization_window(AW_root aw_root) {
486	static AW_window_simple *aws = NULp;
487	if (aws) return aws;
488	GB_transaction ta(GLOBAL.gb_main);
489
490	const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
491	aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree);
492
493	aws = new AW_window_simple;
494	aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression");
495	aws->load_xfig("optimize.fig");
496
497	aws->at("trees");
498	awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME, true);
499
500	aws->at("close");
501	aws->callback(AW_POPDOWN);
502	aws->create_button("CLOSE", "CLOSE", "C");
503
504	aws->callback(makeHelpCallback("optimize.hlp"));
505	aws->at("help");
506	aws->create_button("HELP", "HELP", "H");
507
508	aws->at("go");
509	aws->callback(NT_database_optimization);
510	aws->create_button("GO", "GO");
511	return aws;
512	}
513
514	static AW_window NT_create_save_as(AW_root aw_root, const char *base_name) {
515	static AW_window_simple *aws = NULp;
516	if (aws) return aws;
517
518	aws = new AW_window_simple;
519	aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
520	aws->load_xfig("save_as.fig");
521
522	aws->at("close");
523	aws->callback(AW_POPDOWN);
524	aws->create_button("CLOSE", "CLOSE", "C");
525
526	aws->at("help");
527	aws->callback(makeHelpCallback("save.hlp"));
528	aws->create_button("HELP", "HELP", "H");
529
530	AW_create_standard_fileselection(aws, base_name);
531
532	aws->at("type");
533	AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE);
534
535	aws->at("compression");
536	AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION);
537
538	aws->at("optimize");
539	aws->callback(NT_create_database_optimization_window);
540	aws->help_text("optimize.hlp");
541	aws->create_autosize_button("OPTIMIZE", "Optimize database compression");
542
543	aws->at("save");
544	aws->callback(NT_save_as_cb);
545	aws->create_button("SAVE", "SAVE", "S");
546
547	aws->at("comment");
548	aws->create_text_field(AWAR_DB_COMMENT);
549
550	return aws;
551	}
552
553	static void NT_undo_cb(AW_window, GB_UNDO_TYPE undo_type, TREE_canvas ntw) {
554	GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type);
555	if (error) aw_message(error);
556	else {
557	GB_transaction ta(GLOBAL.gb_main);
558	AWT_auto_refresh allowed_on(ntw);
559	ntw->request_refresh();
560	}
561	}
562
563	enum streamSource { FROM_PIPE, FROM_FILE };
564	static char stream2str(streamSource source, const char commandOrFile) {
565	char *output = NULp;
566	FILE *in = NULp;
567
568	switch (source) {
569	case FROM_PIPE: in = popen(commandOrFile, "r"); break;
570	case FROM_FILE: in = fopen(commandOrFile, "rt"); break;
571	}
572
573	if (in) {
574	GBS_strstruct *out = GBS_stropen(2000);
575	int c;
576
577	while (EOF != (c = fgetc(in))) GBS_chrcat(out, c);
578
579	switch (source) {
580	case FROM_PIPE: pclose(in); break;
581	case FROM_FILE: fclose(in); break;
582	}
583
584	// skip trailing linefeeds
585	long offset = GBS_memoffset(out);
586	while (offset>0 && GBS_mempntr(out)[offset-1] == '\n') {
587	GBS_str_cut_tail(out, 1);
588	offset--;
589	}
590
591	output = GBS_strclose(out);
592	}
593	return output;
594	}
595
596	inline void removeTrailingNewlines(char *str) {
597	char *eos = strchr(str, 0)-1;
598	while (eos >= str && eos[0] == '\n') *eos-- = 0;
599	}
600
601	inline void append_named_value(GBS_strstruct out, const char prefix, const char *value) {
602	GBS_strcat(out, GBS_global_string("%-*s: %s\n", 12, prefix, value));
603	}
604	inline void append_command_output(GBS_strstruct out, const char prefix, const char *command) {
605	char *output = stream2str(FROM_PIPE, command);
606	if (output) {
607	removeTrailingNewlines(output);
608	if (strcmp(output, "unknown") != 0) append_named_value(out, prefix, output);
609	free(output);
610	}
611	}
612
613	static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) {
614	DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
615	nt_mode_event(NULp, canvas, mode);
616	}
617
618	static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) {
619	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
620	if (tree_root) {
621	AWT_auto_refresh allowed_on(ntw);
622	GB_transaction ta(ntw->gb_main);
623
624	NT_mark_all_cb(NULp, ntw, 0); // unmark all
625	tree_root->mark_duplicates();
626	ntw->request_structure_update();
627	}
628	}
629
630	static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) {
631	GB_transaction ta(ntw->gb_main);
632	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
633
634	if (tree_root) {
635	AWT_auto_refresh allowed_on(ntw);
636	tree_root->justify_branch_lenghs(ntw->gb_main);
637	ntw->request_save_and_zoom_reset();
638	}
639	}
640
641	#if defined(DEBUG)
642	static void NT_fix_database(AW_window *) {
643	GB_ERROR err = NULp;
644	err = GB_fix_database(GLOBAL.gb_main);
645	if (err) aw_message(err);
646	}
647	#endif
648
649	static void relink_pseudo_species_to_organisms(GBDATA &ref_gb_node, char &ref_name, GB_HASH *organism_hash) {
650	if (ref_gb_node) {
651	if (GEN_is_pseudo_gene_species(ref_gb_node)) {
652	GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
653
654	if (gb_organism) {
655	char *name = GBT_read_string(gb_organism, "name");
656
657	if (name) {
658	freeset(ref_name, name);
659	ref_gb_node = gb_organism;
660	}
661	}
662	}
663	}
664	}
665
666	static void NT_pseudo_species_to_organism(AW_window , TREE_canvas ntw) {
667	GB_transaction ta(ntw->gb_main);
668	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
669
670	if (tree_root) {
671	AWT_auto_refresh allowed_on(ntw);
672
673	GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
674	tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
675	GBS_free_hash(organism_hash);
676	ntw->request_save();
677	}
678	}
679
680
681	// #########################################
682	// #########################################
683	// ### ###
684	// ## user mask section ##
685	// ### ###
686	// #########################################
687	// #########################################
688
689	struct nt_item_type_species_selector FINAL_TYPE : public awt_item_type_selector {
690	nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
691	~nt_item_type_species_selector() OVERRIDE {}
692
693	const char *get_self_awar() const OVERRIDE {
694	return AWAR_SPECIES_NAME;
695	}
696	size_t get_self_awar_content_length() const OVERRIDE {
697	return 12; // should be enough for "nnaammee.999"
698	}
699	GBDATA current(AW_root root, GBDATA *gb_main) const OVERRIDE { // give the current item
700	char *species_name = root->awar(get_self_awar())->read_string();
701	GBDATA *gb_species = NULp;
702
703	if (species_name[0]) {
704	GB_transaction ta(gb_main);
705	gb_species = GBT_find_species(gb_main, species_name);
706	}
707
708	free(species_name);
709	return gb_species;
710	}
711	const char *getKeyPath() const OVERRIDE { // give the keypath for items
712	return CHANGE_KEY_PATH;
713	}
714	};
715
716	static nt_item_type_species_selector item_type_species;
717
718	static void NT_open_mask_window(AW_window aww, int id, GBDATA gb_main) {
719	const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
720	nt_assert(descriptor);
721	if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
722	}
723
724	static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
725	AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
726	}
727	static AW_window create_colorize_species_window(AW_root aw_root) {
728	return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
729	}
730
731	static void NT_update_marked_counter(GBDATA, AW_window aww) {
732	/*! Updates marked counter and issues redraw on tree if number of marked species changes.
733	* Called on any change of species_information container.
734	*/
735	long count = GBT_count_marked_species(GLOBAL.gb_main);
736	const char *buffer = count ? GBS_global_string("%li marked", count) : "";
737	AW_awar *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
738	char *oldval = counter->read_string();
739	if (strcmp(oldval, buffer)) {
740	counter->write_string(buffer);
741	aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
742	}
743	free(oldval);
744	}
745
746	// --------------------------------------------------------------------------------------------------
747
748	static void NT_alltree_remove_leafs(AW_window , GBT_TreeRemoveType mode, GBDATA gb_main) {
749	GB_ERROR error = NULp;
750	GB_transaction ta(gb_main);
751
752	ConstStrArray tree_names;
753	GBT_get_tree_names(tree_names, gb_main, false);
754
755	if (!tree_names.empty()) {
756	long treeCount = tree_names.size();
757
758	const char *whats_removed = NULp;
759	switch (mode) {
760	case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
761	case GBT_REMOVE_MARKED: whats_removed = "marked"; break;
762	default: nt_assert(0); break;
763	}
764
765	const char *task = GBS_global_string("Deleting %s from %li trees", whats_removed, treeCount);
766
767	arb_progress progress(task, treeCount);
768	GB_HASH *species_hash = GBT_create_species_hash(gb_main);
769
770	int modified = 0;
771
772	for (int t = 0; t<treeCount && !error; t++) {
773	progress.subtitle(tree_names[t]);
774	TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
775	if (!tree) {
776	aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
777	}
778	else {
779	int removed = 0;
780	int groups_removed = 0;
781
782	tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
783
784	nt_assert(removed >= groups_removed);
785
786	if (!tree) {
787	aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
788	}
789	else {
790	if (removed>0) {
791	error = GBT_write_tree(gb_main, tree_names[t], tree);
792	if (error) {
793	aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
794	}
795	else {
796	if (groups_removed>0) {
797	aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
798	}
799	else {
800	aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
801	}
802	modified++;
803	}
804	}
805	UNCOVERED();
806	destroy(tree);
807	}
808	}
809	progress.inc_and_check_user_abort(error);
810	}
811
812	if (modified) {
813	aw_message(GBS_global_string("Changed %i of %li trees.", modified, treeCount));
814	}
815	else {
816	aw_message("No tree modified");
817	}
818
819	GBS_free_hash(species_hash);
820	}
821
822	aw_message_if(ta.close(error));
823	}
824
825	TreeNode NT_get_tree_root_of_canvas(TREE_canvas ntw) {
826	AWT_graphic_tree *tree = AWT_TREE(ntw);
827	if (tree) {
828	AP_tree *root = tree->get_root_node();
829	if (root) return root;
830	}
831	return NULp;
832	}
833
834	// --------------------------------------------------------------------------------------------------
835
836	static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
837	GB_transaction ta(gb_main);
838	GBT_mark_all(gb_main, 0);
839
840	DBItemSetIter end = referred.end();
841	for (DBItemSetIter s = referred.begin(); s != end; ++s) {
842	GB_write_flag(*s, 1);
843	}
844	return ARB_ERROR();
845	}
846
847	static AW_window create_mark_by_refentries_window(AW_root awr, GBDATA *gbmain) {
848	static AW_window *aws = NULp;
849	if (!aws) {
850	static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
851	aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULp, "Mark referenced", mark_referred_species);
852	}
853	return aws;
854	}
855
856	// --------------------------------------------------------------------------------------------------
857
858	static void merge_from_to(AW_root awr, const char db_awar_name, bool merge_to) {
859	const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
860	char *quotedDB = GBK_singlequote(db_name);
861
862	AWT_system_cb(
863	GBS_global_string(
864	merge_to
865	? "arb_ntree : %s &"
866	: "arb_ntree %s : &",
867	quotedDB)
868	);
869
870	free(quotedDB);
871	}
872
873	static void merge_from_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, false); }
874	static void merge_into_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, true); }
875
876	static AW_window NT_create_merge_from_window(AW_root awr) {
877	static char *awar_name = NULp; // do not free, bound to callback
878	AW_window *aw_from =
879	awt_create_load_box(awr, "Merge data from", "other ARB database",
880	".", ".arb", &awar_name,
881	makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
882	return aw_from;
883	}
884	static AW_window NT_create_merge_to_window(AW_root awr) {
885	static char *awar_name = NULp; // do not free, bound to callback
886	AW_window *aw_to =
887	awt_create_load_box(awr, "Merge data to", "other ARB database",
888	".", ".arb", &awar_name,
889	makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
890	makeWindowCallback(AW_POPDOWN), NULp);
891	return aw_to;
892	}
893
894	// --------------------------------------------------------------------------------------------------
895
896	static void update_main_window_title(AW_root* awr, AW_window_menu_modes* aww, int clone) {
897	const char* filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
898	if (clone) {
899	aww->set_window_title(GBS_global_string("%s - ARB (%i)", filename, clone));
900	}
901	else {
902	aww->set_window_title(GBS_global_string("%s - ARB", filename));
903	}
904	}
905
906	static void canvas_tree_awar_changed_cb(AW_awar , bool, TREE_canvas ntw) {
907	NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
908	AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
909	TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_TREE);
910	}
911
912	class TREE_canvas_registry {
913	int count;
914	TREE_canvas *canvas[MAX_NT_WINDOWS];
915
916	static TREE_canvas_registry *SINGLETON;
917
918	TREE_canvas_registry() : count(0) {
919	AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
920	}
921
922	public:
923	static TREE_canvas_registry& instance() {
924	if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
925	return *SINGLETON;
926	}
927
928	void register_canvas(TREE_canvas *ntw) {
929	nt_assert(count<MAX_NT_WINDOWS);
930	nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
931	canvas[count++] = ntw;
932	ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
933	}
934
935	int get_count() const { return count; }
936
937	TREE_canvas *get_canvas(int idx) const {
938	if (idx<0 \|\| idx>=count) return NULp;
939	return canvas[idx];
940	}
941	};
942
943	TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULp;
944
945	TREE_canvas *NT_get_canvas_by_index(int idx) {
946	/! return canvas with index 'idx' [0...MAX_NT_WINDOWS-1] /
947	nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
948	return TREE_canvas_registry::instance().get_canvas(idx);
949	}
950
951	#if defined(TRACE_GROUP_SELECTION)
952	static TREE_canvas find_canvas_showing(AWT_graphic_tree agt) {
953	// look for (registered) canvas showing given AWT_graphic_tree
954	// returns NULp if none found
955	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
956
957	int maxIdx = reg.get_count();
958	for (int32_t i = 0; i<maxIdx; ++i) {
959	TREE_canvas *ntw = reg.get_canvas(i);
960	if (ntw->gfx == agt) return ntw;
961	}
962	return NULp;
963	}
964	#endif
965
966	void NT_fill_canvas_selection_list(class AW_selection_list sellst, TREE_canvas to_skip) {
967	/*! insert canvases into selection list (using canvas-indices as values)
968	*/
969	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
970
971	int maxIdx = reg.get_count();
972	for (int32_t i = 0; i<maxIdx; ++i) {
973	TREE_canvas *ntw = reg.get_canvas(i);
974	if (ntw && ntw != to_skip) {
975	nt_assert(ntw->get_awar_tree());
976	const char *treename = ntw->get_awar_tree()->read_char_pntr();
977	const char *description = i
978	? GBS_global_string("ARB (%i): %s", i, treename)
979	: GBS_global_string("ARB main: %s", treename);
980	sellst->insert(description, i);
981	}
982	}
983	}
984
985	// ----------------------------------
986	// group-selection handlers
987
988	void NT_deselect_group(AW_root *awr) {
989	awr->awar(AWAR_GROUP)->write_pointer(NULp);
990	}
991
992	static bool track_group_selection_by_canvas = true;
993
994	static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) {
995	const Group& group = gfx->get_selected_group();
996
997	#if defined(TRACE_GROUP_SELECTION)
998	fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track");
999	TREE_canvas *ntw = find_canvas_showing(gfx);
1000	if (group.is_valid()) {
1001	fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name());
1002	}
1003	else {
1004	fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index());
1005	}
1006	#endif
1007
1008	if (track_group_selection_by_canvas) {
1009	// set group-awar:
1010	gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULp if !group.is_valid()
1011	}
1012	}
1013
1014	static void group_awar_changed_cb(AW_root *awr) {
1015	AW_awar *awar_group = awr->awar(AWAR_GROUP);
1016	GBDATA *gb_wanted_group = awar_group->read_pointer();
1017
1018	GBDATA *gb_wanted_tree = NULp;
1019	{
1020	if (gb_wanted_group) {
1021	GB_transaction ta(gb_wanted_group);
1022	gb_wanted_tree = GB_get_father(gb_wanted_group);
1023	awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected
1024	#if defined(TRACE_GROUP_SELECTION)
1025	fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr);
1026	#endif
1027	}
1028	#if defined(TRACE_GROUP_SELECTION)
1029	const char *group_name = NULp;
1030	if (gb_wanted_group) {
1031	GB_transaction ta(gb_wanted_group);
1032	GBDATA *gb_name = GB_entry(gb_wanted_group, "group_name");
1033	if (gb_name) group_name = GB_read_char_pntr(gb_name);
1034	}
1035	fprintf(stderr, "group awar changed to %p", gb_wanted_group);
1036	if (group_name) fprintf(stderr, " (='%s')", group_name);
1037	fputc('\n', stderr);
1038	#endif
1039	}
1040
1041	LocallyModify<bool> ignore_group_selection_by_canvas(track_group_selection_by_canvas, false);
1042
1043	{
1044	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1045
1046	int maxIdx = reg.get_count();
1047	for (int32_t i = 0; i<maxIdx; ++i) {
1048	TREE_canvas *ntw = reg.get_canvas(i);
1049	AWT_graphic_tree *agt = AWT_TREE(ntw);
1050	const Group& curr_group = agt->get_selected_group();
1051
1052	GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree();
1053	if (gb_curr_tree == gb_wanted_tree) {
1054	AWT_auto_refresh allowed_on(ntw);
1055	if (!curr_group.is_valid() \|\| // no group selected
1056	curr_group.get_group_data() != gb_wanted_group) // wrong group selected
1057	{
1058	agt->select_group(gb_wanted_group);
1059	ntw->request_refresh();
1060	}
1061	// perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group)
1062	TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_GROUP);
1063	}
1064	else {
1065	if (curr_group.is_valid()) {
1066	AWT_auto_refresh allowed_on(ntw);
1067	agt->deselect_group();
1068	ntw->request_refresh();
1069	}
1070	}
1071	}
1072	}
1073	}
1074
1075	// ----------------------------
1076	// create main window
1077
1078	static AW_window popup_new_main_window(AW_root awr, int clone, TREE_canvas **result_ntw) {
1079	/*! create ARB_NTREE main window
1080	* @param awr application root
1081	* @param clone == 0 -> first window (full functionality); >0 -> additional tree views (restricted functionality)
1082	* @param result_ntw is set to the created TREE_canvas (passed pointer may be NULp if result is not needed)
1083	*/
1084	GB_push_transaction(GLOBAL.gb_main);
1085
1086	char window_title[256];
1087	const char *awar_tree = NULp;
1088
1089	if (clone) {
1090	awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
1091	sprintf(window_title, "ARB_NT_%i", clone);
1092	}
1093	else {
1094	awar_tree = AWAR_TREE;
1095	sprintf(window_title, "ARB_NT");
1096	}
1097	AW_window_menu_modes *awm = new AW_window_menu_modes;
1098	awm->init(awr, window_title, window_title, 0, 0);
1099
1100	awr->awar(AWAR_DB_NAME)
1101	->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1102	->update();
1103
1104	awm->button_length(5);
1105
1106	if (!clone) AW_init_color_group_defaults("arb_ntree");
1107
1108	AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1109
1110	if (!clone) { // while creating initial window
1111	AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb));
1112	awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb);
1113	}
1114
1115	TREE_canvas *ntw;
1116	{
1117	AW_awar *tree_awar = awr->awar_string(awar_tree);
1118	{
1119	AP_tree_display_style prev_style = tree->get_tree_style();
1120	tree->set_tree_style(AP_LIST_SIMPLE, NULp); // avoid NDS warnings during startup
1121
1122	ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1123	tree->set_tree_style(prev_style, ntw);
1124	ntw->set_mode(AWT_MODE_SELECT);
1125	}
1126
1127	if (result_ntw) *result_ntw = ntw;
1128
1129	{
1130	const char *tree_name = tree_awar->read_char_pntr();
1131	const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1132
1133	if (existing_tree_name) {
1134	tree_awar->write_string(existing_tree_name);
1135	NT_reload_tree_event(awr, ntw, true); // load first tree
1136	}
1137	else {
1138	AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, NULp, "no_tree.hlp");
1139	tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list
1140	}
1141
1142	TREE_canvas_registry::instance().register_canvas(ntw);
1143	AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1144	}
1145	}
1146
1147	TREE_install_update_callbacks(ntw);
1148
1149	bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1150
1151	WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1152
1153	// --------------
1154	// File
1155
1156	#if defined(DEBUG)
1157	AWT_create_debug_menu(awm);
1158	#endif // DEBUG
1159
1160	bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1161
1162	if (clone) {
1163	awm->create_menu("File", "F", AWM_ALL);
1164	if (allow_new_window) {
1165	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));
1166	}
1167	awm->insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN);
1168	}
1169	else {
1170	#if defined(DEBUG)
1171	// add more to debug-menu
1172	awm->sep______________();
1173	awm->insert_menu_topic("fix_db", "Fix database", "F", NULp, AWM_ALL, NT_fix_database);
1174	awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", NULp, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1175	awm->insert_menu_topic("test_compr", "Test compression", "T", NULp, AWM_ALL, makeWindowCallback(GBT_compression_test, GLOBAL.gb_main));
1176	#endif // DEBUG
1177
1178	awm->create_menu("File", "F", AWM_ALL);
1179	{
1180	// keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1181	awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, NT_save_quick_cb);
1182	awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1183	if (allow_new_window) {
1184	awm->sep______________();
1185	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));
1186	}
1187	awm->sep______________();
1188	awm->insert_menu_topic("optimize_db", "Optimize database compression", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window);
1189	awm->sep______________();
1190
1191	awm->insert_sub_menu("Import", "I");
1192	{
1193	awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1194	awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1195	GDE_load_menu(awm, AWM_EXP, "Import");
1196	}
1197	awm->close_sub_menu();
1198
1199	awm->insert_sub_menu("Export", "E");
1200	{
1201	awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1202	awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1203	GDE_load_menu(awm, AWM_ALL, "Export");
1204	awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window);
1205	}
1206	awm->close_sub_menu();
1207	awm->sep______________();
1208
1209	insert_macro_menu_entry(awm, false);
1210
1211	awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1212	{
1213	awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp"));
1214	awm->insert_menu_topic("bug_report", "Report bug", "b", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1215	awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1216	}
1217	awm->close_sub_menu();
1218	awm->sep______________();
1219
1220	awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1221	awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1222	awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_exit, EXIT_SUCCESS));
1223	}
1224
1225	// -----------------
1226	// Species
1227
1228	awm->create_menu("Species", "c", AWM_ALL);
1229	{
1230	awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1231	awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb);
1232
1233	awm->sep______________();
1234
1235	NT_insert_mark_submenus(awm, ntw, 1);
1236	awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1237	awm->insert_menu_topic("species_colors", "Colors ...", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window);
1238	awm->insert_menu_topic("selection_admin", "Selections ...", "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1239
1240	awm->sep______________();
1241
1242	awm->insert_sub_menu("Database fields admin", "f");
1243	DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1244	awm->close_sub_menu();
1245	NT_create_mask_submenu(awm);
1246
1247	awm->sep______________();
1248
1249	awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1250
1251	awm->insert_sub_menu("Sort Species", "s");
1252	{
1253	awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window);
1254	awm->insert_menu_topic("$sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1255	}
1256	awm->close_sub_menu();
1257
1258	awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1259	{
1260	awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1261	awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "species_join.hlp", AWM_EXP, NT_create_species_join_window);
1262	}
1263	awm->close_sub_menu();
1264
1265	awm->sep______________();
1266
1267	awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1268
1269	awm->sep______________();
1270
1271	awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1272
1273	awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1274	{
1275	awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames);
1276	awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames);
1277	awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1278	awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window);
1279	}
1280	awm->close_sub_menu();
1281	}
1282
1283	// ----------------------------
1284	// Genes + Experiment
1285
1286	if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1287
1288	// ------------------
1289	// Sequence
1290
1291	awm->create_menu("Sequence", "S", AWM_ALL);
1292	{
1293	awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)NULp));
1294	awm->insert_sub_menu("Insert/delete", "I");
1295	{
1296	awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window);
1297	awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main));
1298	}
1299	awm->close_sub_menu();
1300	awm->sep______________();
1301
1302	awm->insert_sub_menu("Edit Sequences", "E");
1303	{
1304	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));
1305	awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1306	awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1307	}
1308	awm->close_sub_menu();
1309
1310	awm->sep______________();
1311
1312	awm->insert_sub_menu("Align Sequences", "S");
1313	{
1314	awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1315	GDE_load_menu(awm, AWM_ALL, "Align");
1316	}
1317	awm->close_sub_menu();
1318	awm->insert_menu_topic("seq_concat", "Concatenate Sequences/Alignments", "C", "concatenate.hlp", AWM_ALL, NT_createConcatenationWindow);
1319	awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1320	awm->sep______________();
1321
1322	awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1323	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1324	awm->sep______________();
1325
1326	awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1327	awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1328
1329	awm->sep______________();
1330
1331	GDE_load_menu(awm, AWM_ALL, "Print");
1332	}
1333
1334	// -------------
1335	// SAI
1336
1337	awm->create_menu("SAI", "A", AWM_ALL);
1338	{
1339	awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1340	awm->insert_sub_menu("Create SAI using ...", "C");
1341	{
1342	awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window);
1343	awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window);
1344	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);
1345	awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_phylo &"));
1346	awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold);
1347
1348	GDE_load_menu(awm, AWM_EXP, "SAI");
1349	}
1350	awm->close_sub_menu();
1351
1352	awm->insert_sub_menu("Other functions", "O");
1353	{
1354	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));
1355	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));
1356	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);
1357	}
1358	awm->close_sub_menu();
1359	}
1360
1361	// ----------------
1362	// Probes
1363
1364	awm->create_menu("Probes", "P", AWM_ALL);
1365	{
1366	awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1367	awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1368	awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1369	awm->sep______________();
1370	awm->insert_menu_topic("probe_match_sp", "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window, ntw));
1371	awm->sep______________();
1372	awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1373	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));
1374	awm->sep______________();
1375	awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1376	}
1377
1378	}
1379
1380	// --------------
1381	// Tree
1382
1383	awm->create_menu("Tree", "T", AWM_ALL);
1384	{
1385	if (!clone) {
1386	awm->insert_sub_menu("Add Species to Existing Tree", "A");
1387	{
1388	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 &"));
1389	awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_pars &"));
1390	GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1391	}
1392	awm->close_sub_menu();
1393	}
1394
1395	awm->insert_sub_menu("Remove Species from Tree", "R");
1396	{
1397	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));
1398	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));
1399	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));
1400	awm->sep______________();
1401	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));
1402	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));
1403	}
1404	awm->close_sub_menu();
1405
1406	if (!clone) {
1407	awm->insert_sub_menu("Build tree from sequence data", "B");
1408	{
1409	awm->insert_sub_menu("Distance matrix methods", "D");
1410	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1411	GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1412	awm->close_sub_menu();
1413
1414	awm->insert_sub_menu("Maximum Parsimony methods", "P");
1415	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1416	awm->close_sub_menu();
1417
1418	awm->insert_sub_menu("Maximum Likelihood methods", "L");
1419	GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1420	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1421	awm->close_sub_menu();
1422
1423	awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1424	GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1425	awm->close_sub_menu();
1426	}
1427	awm->close_sub_menu();
1428	}
1429
1430	awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1431
1432	awm->sep______________();
1433
1434	awm->insert_sub_menu("Reset zoom", "z");
1435	{
1436	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));
1437	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));
1438	}
1439	awm->close_sub_menu();
1440
1441	awm->sep______________();
1442
1443	// taxonomic groups
1444	NT_insert_collapse_submenu(awm, ntw);
1445	if (!clone) {
1446	awm->insert_menu_topic("group_search", "Search groups...", "g", "group_search.hlp", AWM_ALL, makeWindowCallback (popup_group_search_window, GLOBAL.gb_main));
1447	awm->insert_menu_topic("compare_taxonomy", "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1448	awm->insert_menu_topic("move_groups", "Move groups...", "n", "move_groups.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_moveGroupInfo_window));
1449	}
1450
1451	awm->sep______________();
1452
1453	if (!clone) {
1454	awm->insert_menu_topic("compare_topology", "Compare topology...", "p", "compare_topo.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compareTopologies_window));
1455	}
1456
1457	awm->insert_sub_menu("Modify branches", "M");
1458	{
1459	awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw));
1460	awm->insert_menu_topic(awm->local_id("tree_toggle_bootstraps"), "Toggle 100% bootstraps", "1", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_toggle_bootstrap100, ntw));
1461	awm->sep______________();
1462	awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw));
1463	awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1464	awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw));
1465	awm->sep______________();
1466	awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1467	awm->sep______________();
1468	awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1469	awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1470
1471	}
1472	awm->close_sub_menu();
1473	awm->insert_sub_menu("Beautify tree", "e");
1474	{
1475	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));
1476	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));
1477	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));
1478	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));
1479	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));
1480	awm->sep______________();
1481	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));
1482	}
1483	awm->close_sub_menu();
1484
1485	awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "h", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1486	awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "u", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback(NT_mark_duplicates, ntw));
1487
1488	awm->sep______________();
1489
1490	awm->insert_menu_topic(awm->local_id("shade"), "Tree shading...", "s", "tree_shading.hlp", AWM_ALL, makeWindowCallback (NT_configure_treeShader));
1491	awm->insert_menu_topic(awm->local_id("syncscroll"), "Sync tree scrolling..", "o", "syncscroll.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1492
1493	awm->sep______________();
1494
1495	awm->insert_menu_topic(awm->local_id("tree_select"), "Select Tree", "T", NULp, AWM_ALL, makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1496	awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", NULp, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1497
1498	if (!clone) {
1499	awm->sep______________();
1500	awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1501	awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_nds_window, GLOBAL.gb_main));
1502	}
1503
1504	awm->sep______________();
1505	awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1506
1507	if (!clone) {
1508	awm->sep______________();
1509	awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1510	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)));
1511	}
1512
1513	if (is_genome_db) {
1514	awm->sep______________();
1515	awm->insert_sub_menu("Other..", "O", AWM_EXP);
1516	{
1517	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));
1518	}
1519	awm->close_sub_menu();
1520	}
1521	}
1522
1523	if (!clone) {
1524	// ---------------
1525	// Tools
1526
1527	awm->create_menu("Tools", "o", AWM_ALL);
1528	{
1529	awm->insert_menu_topic("names_admin", "Name server admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_namesadmin_window, GLOBAL.gb_main));
1530	awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1531	{
1532	awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1533	}
1534	awm->close_sub_menu();
1535	awm->insert_sub_menu("Network", "N", AWM_EXP);
1536	{
1537	GDE_load_menu(awm, AWM_EXP, "Network");
1538	}
1539	awm->close_sub_menu();
1540	awm->sep______________();
1541
1542	awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1543	{
1544	GDE_load_menu(awm, AWM_EXP, NULp);
1545	}
1546	awm->close_sub_menu();
1547
1548	awm->sep______________();
1549	awm->insert_menu_topic("xterm", "Start XTERM", "X", "xterm.hlp", AWM_ALL, AWT_console);
1550	awm->insert_menu_topic("viewlog", "View ARB log", "l", "console.hlp", AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_show_log.pl run", XCMD_ASYNC_WAIT_ON_ERROR)); // ../SH/arb_show_log.pl
1551	awm->insert_menu_topic("viewserv", "View server log", "V", "console.hlp", AWM_ALL, makeWindowCallback(AWT_system_in_console_cb, "arb_show_log.pl server", XCMD_ASYNC_WAIT_ON_ERROR));
1552	awm->sep______________();
1553	GDE_load_menu(awm, AWM_EXP, "User");
1554	}
1555	// --------------------
1556	// Properties
1557
1558	awm->create_menu("Properties", "r", AWM_ALL);
1559	{
1560	awm->insert_menu_topic("props_menu", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1561	awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1562	awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1563	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));
1564	awm->sep______________();
1565	awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", NULp, AWM_ALL, NT_toggle_expert_mode);
1566	awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", NULp, AWM_ALL, NT_toggle_focus_policy);
1567	awm->sep______________();
1568	AW_insert_common_property_menu_entries(awm);
1569	awm->sep______________();
1570	awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1571	}
1572	}
1573
1574	awm->insert_help_topic("ARB_NT help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1575
1576	// ----------------------
1577	// mode buttons
1578	//
1579	// keep them synchronized as far as possible with those in ARB_PARSIMONY
1580	// see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1581
1582	awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1583	awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1584	awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1585	awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1586	awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1587
1588	awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1589	awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW));
1590
1591	// topology-modification-modes
1592	awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1593	awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1594	awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1595	awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1596	awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1597
1598	// layout-modes
1599	awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1600	awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1601	awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1602
1603	awm->set_info_area_height(250);
1604	awm->at(5, 2);
1605	awm->auto_space(-2, -2);
1606	awm->shadow_width(1);
1607
1608	// -------------------------
1609	// create top area
1610
1611	int first_liney;
1612	int leftx;
1613	awm->get_at_position(&leftx, &first_liney);
1614
1615	// ---------------------
1616	// quit + help
1617
1618	awm->button_length(0);
1619
1620	if (clone) {
1621	awm->callback(AW_POPDOWN);
1622	awm->create_button("CLOSE", "#close.xpm");
1623	}
1624	else {
1625	awm->callback(makeWindowCallback(NT_exit, EXIT_SUCCESS));
1626	awm->help_text("quit.hlp");
1627	awm->create_button("QUIT", "#quit.xpm");
1628	}
1629
1630	int db_pathx = awm->get_at_xposition();
1631
1632	// now fetch the yposition for the 2nd button line
1633	awm->at_newline();
1634	int second_liney = awm->get_at_yposition();
1635
1636	awm->callback(AW_help_entry_pressed);
1637	awm->help_text("arb_ntree.hlp");
1638	awm->create_button("?", "#help.xpm");
1639
1640	// --------------------------
1641	// save + undo/redo
1642
1643	awm->callback(NT_save_quick_cb);
1644	awm->help_text("save.hlp");
1645	awm->create_button("SAVE", "#save.xpm");
1646
1647	awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1648	awm->help_text("save.hlp");
1649	awm->create_button("SAVE_AS", "#saveAs.xpm");
1650
1651	// undo/redo:
1652	awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1653	awm->help_text("undo.hlp");
1654	awm->create_button("UNDO", "#undo.xpm");
1655
1656	awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1657	awm->help_text("undo.hlp");
1658	awm->create_button("REDO", "#redo.xpm");
1659
1660	int db_pathx2 = awm->get_at_xposition();
1661
1662	// fetch position for mode help-line:
1663	awm->at_newline();
1664	int third_liney = awm->get_at_yposition();
1665
1666	awm->at(db_pathx, first_liney);
1667	// size of DB-name button is determined by buttons below:
1668	awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1669	awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1670	awm->help_text("save.hlp");
1671	awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1672
1673	// -----------------------------
1674	// tree + tree display
1675
1676	#define TREE_BUTTON_OVERSIZE 6
1677
1678	int db_treex = awm->get_at_xposition();
1679	int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1680
1681	awm->at(db_treex, second_uppery);
1682	awm->button_length(0);
1683
1684	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1685	awm->help_text("tr_type_radial.hlp");
1686	awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1687
1688	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1689	awm->help_text("tr_type_list.hlp");
1690	awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1691
1692	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1693	awm->help_text("tr_type_irs.hlp");
1694	awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1695
1696	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1697	awm->help_text("tr_type_nds.hlp");
1698	awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1699
1700	int db_treex2 = awm->get_at_xposition();
1701
1702	awm->at(db_treex, first_liney);
1703	// size of tree-name button is determined by buttons below:
1704	awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1705	awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1706	awm->help_text("nt_tree_select.hlp");
1707	awm->create_button("SELECT_A_TREE", awar_tree);
1708
1709	// ---------------------------------------------------------------
1710	// protection, alignment + editor (and maybe Genome Map)
1711
1712	int db_alignx = awm->get_at_xposition();
1713
1714	// editor and genemap buttons have to be 44x24 sized
1715	#define EDIT_XSIZE 50
1716	#define EDIT_YSIZE 30 // same as 'save as' buttons
1717
1718	// first draw protection:
1719	int protectx = db_alignx + 2*EDIT_XSIZE;
1720
1721	awm->at(protectx+2, first_liney+1);
1722	awm->button_length(0);
1723	awm->create_button(NULp, "#protect.xpm");
1724
1725	awm->at(protectx, second_liney+2);
1726	awm->create_option_menu(AWAR_SECURITY_LEVEL, true);
1727	awm->insert_option ("0", NULp, 0);
1728	awm->insert_option ("1", NULp, 1);
1729	awm->insert_option ("2", NULp, 2);
1730	awm->insert_option ("3", NULp, 3);
1731	awm->insert_option ("4", NULp, 4);
1732	awm->insert_option ("5", NULp, 5);
1733	awm->insert_default_option("6", NULp, 6);
1734	awm->update_option_menu();
1735
1736	int db_searchx = awm->get_at_xposition() - 7;
1737
1738	// draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1739	awm->at(db_alignx, second_liney);
1740
1741	awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1742	awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1743	awm->help_text("arb_edit4.hlp");
1744	if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1745	else awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1746
1747	if (is_genome_db) {
1748	awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1749	awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1750	awm->help_text("gene_map.hlp");
1751	awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1752	}
1753
1754	int db_alignx2 = awm->get_at_xposition();
1755
1756	awm->at(db_alignx, first_liney);
1757	awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1758	awm->callback(NT_create_select_alignment_window);
1759	awm->help_text("nt_align_select.hlp");
1760	awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1761
1762	// -------------------------------
1763	// create mode-help line
1764
1765	awm->at(leftx, third_liney);
1766	awm->button_length(AWAR_FOOTER_MAX_LEN);
1767	awm->create_button(NULp, AWAR_FOOTER);
1768
1769	awm->at_newline();
1770	int bottomy = awm->get_at_yposition();
1771
1772	// ---------------------------------------
1773	// Info / marked / Search / Jump
1774
1775	awm->button_length(7);
1776
1777	awm->at(db_searchx, first_liney);
1778	awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1779	awm->help_text("sp_search.hlp");
1780	awm->create_button("SEARCH", "Search");
1781
1782	awm->at(db_searchx, second_uppery);
1783	awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1784	awm->help_text("tr_jump.hlp");
1785	awm->create_button("JUMP", "Jump");
1786
1787	int db_infox = awm->get_at_xposition();
1788
1789	awm->at(db_infox, first_liney);
1790	awm->button_length(13);
1791	awm->callback(popupinfo_wcb);
1792	awm->help_text("sp_search.hlp");
1793	awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1794
1795	awm->at(db_infox, second_uppery);
1796	awm->button_length(13);
1797	awm->help_text("species_configs.hlp");
1798	awm->callback(makeWindowCallback(NT_popup_configuration_admin, ntw));
1799	awm->create_button("selection_admin2", AWAR_MARKED_SPECIES_COUNTER);
1800	{
1801	GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1802	GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(NT_update_marked_counter, static_cast<AW_window*>(awm)));
1803	NT_update_marked_counter(NULp, awm);
1804	}
1805
1806	// set height of top area:
1807	awm->set_info_area_height(bottomy+2);
1808	awm->set_bottom_area_height(0);
1809
1810	NT_activate_configMarkers_display(ntw);
1811
1812	// ------------------------------------
1813	// Autostarts for development
1814
1815	#if defined(DEVEL_RALF)
1816	// if (is_genome_db) GEN_map_first(awr)->show();
1817	#endif // DEVEL_RALF
1818
1819	GB_pop_transaction(GLOBAL.gb_main);
1820
1821	#if defined(DEBUG)
1822	AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1823	#endif
1824
1825	return awm;
1826	}
1827
1828	TREE_canvas NT_create_main_window(AW_root aw_root) {
1829	GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1830	if (error) aw_message(error);
1831
1832	nt_create_all_awars(aw_root);
1833
1834	TREE_canvas *ntw = NULp;
1835	AW_window *aww = popup_new_main_window(aw_root, 0, &ntw);
1836	NT_install_treeShader(ntw, GLOBAL.gb_main);
1837	aww->show();
1838
1839	error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1840	if (error) aw_message(error);
1841
1842	return ntw;
1843	}

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