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NT_extern.cxx

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Last change on this file was 18126, checked in by westram, 5 years ago
full update from 'trunk' into 'alilink' adds: log:branches/cleanup@17627:17650,18105:18112 log:branches/clone@17813:17835 log:branches/config@17733:17737 log:branches/dbui@17881:17889 log:branches/fix@17380:17395,17480:17592,17597:17617 log:branches/fts@17653:18088,18090:18094 log:branches/gcc@17850:17876 log:branches/group@17162:17341 log:branches/gui@17754:18092 log:branches/mix@17631:17633,17637:17640 log:branches/optional@17481:17568 log:branches/progress@17195:17259 log:branches/svalues@17357:17477 log:trunk@17179:18123
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File size: 77.5 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 <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_file.h>
63	#include <arb_version.h>
64
65	#if defined(DEVEL_RALF)
66	# define TRACE_GROUP_SELECTION
67	#endif
68
69	#define AWAR_EXPORT_NDS "tmp/export_nds"
70	#define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/separator"
71	#define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species"
72	#define AWAR_NTREE_TITLE_MODE "tmp/title_mode"
73
74	void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
75
76	void create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
77	AW_window create_insertDeleteColumn_window(AW_root root);
78	AW_window create_insertDeleteBySAI_window(AW_root root, GBDATA *gb_main);
79
80	AW_window create_tree_window(AW_root aw_root, AWT_graphic *awd);
81
82	static void nt_changesecurity(AW_root *aw_root) {
83	int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
84	GB_push_transaction(GLOBAL.gb_main);
85	GB_change_my_security(GLOBAL.gb_main, level); // changes user security
86	GB_pop_transaction(GLOBAL.gb_main);
87	}
88
89	static void export_nds_cb(AW_window *aww, bool do_print) {
90	AW_root *aw_root = aww->get_root();
91	char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
92	FILE *out = fopen(name, "w");
93
94	if (!out) {
95	aw_message("Error: Cannot open and write to file");
96	}
97	else {
98	GB_transaction ta(GLOBAL.gb_main);
99
100	make_node_text_init(GLOBAL.gb_main);
101	NDS_Type nds_type = (NDS_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
102	char *tree_name = aw_root->awar(AWAR_TREE)->read_string();
103
104	for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
105	gb_species;
106	gb_species = GBT_next_marked_species(gb_species))
107	{
108	const char *buf = make_node_text_nds(GLOBAL.gb_main, gb_species, nds_type, NULp, tree_name);
109	fprintf(out, "%s\n", buf);
110	}
111	AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
112	fclose(out);
113	if (do_print) {
114	GB_ERROR error = GB_textprint(name);
115	if (error) aw_message(error);
116	}
117	free(tree_name);
118	}
119	free(name);
120	}
121
122	static AW_window create_nds_export_window(AW_root root) {
123	AW_window_simple *aws = new AW_window_simple;
124	aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
125	aws->load_xfig("sel_box_nds.fig");
126
127	aws->callback(AW_POPDOWN);
128	aws->at("close");
129	aws->create_button("CLOSE", "CLOSE", "C");
130
131	aws->callback(makeHelpCallback("arb_export_nds.hlp"));
132	aws->at("help");
133	aws->create_button("HELP", "HELP", "H");
134
135	aws->at("save");
136	aws->callback(makeWindowCallback(export_nds_cb, false));
137	aws->create_button("SAVE", "SAVE", "S");
138
139	aws->at("print");
140	aws->callback(makeWindowCallback(export_nds_cb, true));
141	aws->create_button("PRINT", "PRINT", "P");
142
143	aws->at("toggle1");
144	aws->label("Column output");
145	aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR, true);
146	aws->insert_default_option("Space padded", "S", NDS_OUTPUT_SPACE_PADDED);
147	aws->insert_option ("TAB separated", "T", NDS_OUTPUT_TAB_SEPARATED);
148	aws->insert_option ("Comma separated", "C", NDS_OUTPUT_COMMA_SEPARATED);
149	aws->update_option_menu();
150
151	AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS);
152
153	return aws;
154	}
155
156	static void create_export_nds_awars(AW_root *awr, AW_default def) {
157	AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds");
158	awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, NDS_OUTPUT_SPACE_PADDED, def);
159	}
160
161	static void selectedSpeciesChanged_cb(AW_root *awr) {
162	const char *value = awr->awar(AWAR_SPECIES_NAME)->read_char_pntr();
163	awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
164	if (value[0]) {
165	awr->awar(AWAR_GROUP)->write_pointer(NULp); // deselect group when species gets selected
166	#if defined(TRACE_GROUP_SELECTION)
167	fputs("clear AWAR_GROUP (because species selected)\n", stderr);
168	#endif
169	}
170	}
171
172	static void expert_mode_changed_cb(AW_root *aw_root) {
173	aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
174	}
175
176	static void NT_toggle_expert_mode(AW_window *aww) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
177	static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
178
179	static void nt_create_all_awars(AW_root *awr) {
180	// creates awars for all modules reachable from ARB_NT main window
181
182	awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT);
183	if (GB_read_clients(GLOBAL.gb_main)>=0) {
184	awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
185	}
186	else {
187	awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT);
188	}
189
190	awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main);
191	awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main);
192	awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main);
193	awr->awar_string(AWAR_MARKED_SPECIES_COUNTER, "unknown", GLOBAL.gb_main);
194	awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main);
195	awr->awar(AWAR_SPECIES_NAME)->add_callback(selectedSpeciesChanged_cb);
196	awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
197
198	awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
199
200	GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
201	EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
202	#if defined(DEBUG)
203	AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT);
204	#endif // DEBUG
205
206	AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
207
208	awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT);
209	awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
210	#if defined(DEBUG) && 0
211	awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
212	#endif // DEBUG
213
214	create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT);
215	create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
216	create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
217	create_trees_var(awr, AW_ROOT_DEFAULT);
218	DBUI::create_dbui_awars(awr);
219	AP_create_consensus_var(awr, AW_ROOT_DEFAULT);
220	{
221	GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, NULp, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT);
222	if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
223	}
224	NT_create_transpro_variables(awr, AW_ROOT_DEFAULT);
225	NT_create_resort_awars(awr, AW_ROOT_DEFAULT);
226	NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT);
227	NT_create_trackAliChanges_Awars(awr, GLOBAL.gb_main);
228
229	NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
230	NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
231	create_nds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, false);
232	create_export_nds_awars(awr, AW_ROOT_DEFAULT);
233	create_group_search_awars(awr, AW_ROOT_DEFAULT);
234	TREE_create_awars(awr, GLOBAL.gb_main);
235
236	awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
237	awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
238
239	AWTC_create_submission_variables(awr, GLOBAL.gb_main);
240	NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
241	NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar
242	SQ_create_awars(awr, AW_ROOT_DEFAULT);
243	RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT);
244
245	NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT);
246
247	GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
248	if (!error) {
249	AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
250	awar_expert->add_callback(expert_mode_changed_cb);
251	awar_expert->touch();
252
253	awt_create_aww_vars(awr, AW_ROOT_DEFAULT);
254	}
255
256	if (error) aw_message(error);
257	}
258
259	// --------------------------------------------------------------------------------
260
261	static bool nt_disconnect_from_db(AW_root aw_root, GBDATA& gb_main_ref) {
262	// ask user if DB was not saved
263	// returns true if user allows to quit
264
265	// @@@ code here could as well be applied to both merge DBs
266	// - question about saving only with target DB!
267
268	if (gb_main_ref) {
269	if (GB_read_clients(gb_main_ref)>=0) {
270	if (GB_read_clock(gb_main_ref) > GB_last_saved_clock(gb_main_ref)) {
271	long secs;
272	secs = GB_last_saved_time(gb_main_ref);
273
274	#if defined(DEBUG)
275	secs = GB_time_of_day(); // simulate "just saved"
276	#endif // DEBUG
277
278	const char *quit_buttons = "Quit ARB,Do NOT quit";
279	if (secs) {
280	secs = GB_time_of_day() - secs;
281	if (secs>10) {
282	char *question = GBS_global_string_copy("You last saved your data %li:%li minutes ago\nSure to quit ?", secs/60, secs%60);
283	int dontQuit = aw_question("quit_arb", question, quit_buttons);
284	free(question);
285	if (dontQuit) {
286	return false;
287	}
288	}
289	}
290	else {
291	if (aw_question("quit_arb", "You never saved any data\nSure to quit ???", quit_buttons)) {
292	return false;
293	}
294	}
295	}
296	}
297
298	GBCMS_shutdown(gb_main_ref);
299
300	GBDATA *gb_main = gb_main_ref;
301	gb_main_ref = NULp; // avoid further usage
302
303	nt_assert(aw_root);
304	#if defined(WARN_TODO)
305	#warning instead of directly calling the following functions, try to add them as GB_atclose_callback
306	#endif
307	aw_root->unlink_awars_from_DB(gb_main);
308	AWT_destroy_input_masks();
309	#if defined(DEBUG)
310	AWT_browser_forget_db(gb_main);
311	#endif // DEBUG
312
313	GB_close(gb_main);
314	}
315	return true;
316	}
317
318	static void nt_run(const char *command) {
319	GB_ERROR error = GBK_system(command);
320	if (error) {
321	fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
322	#if defined(DEBUG)
323	GBK_dump_backtrace(stderr, "nt_run-error");
324	#endif
325	}
326	}
327
328	void NT_start(const char *arb_ntree_args, bool restart_with_new_ARB_PID) {
329	char *command = GBS_global_string_copy("arb_launcher --async %s %s", restart_with_new_ARB_PID ? "arb" : "arb_ntree", arb_ntree_args);
330	nt_run(command);
331	free(command);
332	}
333
334	__ATTR__NORETURN static void really_exit(int exitcode, bool kill_my_clients) {
335	if (kill_my_clients) {
336	nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
337	}
338	exit(exitcode);
339	}
340
341	void NT_exit(AW_window *aws, int exitcode) {
342	AW_root *aw_root = aws->get_root();
343	AWTI_cleanup_importer();
344	shutdown_macro_recording(aw_root);
345	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
346	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
347	really_exit(exitcode, is_server_and_has_clients);
348	}
349	}
350	void NT_restart(AW_root aw_root, const char arb_ntree_args) {
351	// restarts arb_ntree (with new ARB_PID)
352	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
353	if (nt_disconnect_from_db(aw_root, GLOBAL.gb_main)) {
354	NT_start(arb_ntree_args, true);
355	really_exit(EXIT_SUCCESS, is_server_and_has_clients);
356	}
357	}
358
359	static void nt_start_2nd_arb(AW_window *aww, bool quit) {
360	// start 2nd arb with intro window
361	AW_root *aw_root = aww->get_root();
362	char *dir4intro;
363	GB_split_full_path(aw_root->awar(AWAR_DB_PATH)->read_char_pntr(), &dir4intro, NULp, NULp, NULp);
364	if (!dir4intro) {
365	dir4intro = ARB_strdup(".");
366	}
367
368	if (quit) {
369	NT_restart(aw_root, dir4intro);
370	}
371	else {
372	NT_start(dir4intro, true);
373	}
374	free(dir4intro);
375	}
376
377	// --------------------------------------------------------------------------------
378
379	static void NT_save_quick_cb(AW_window *aww) {
380	AW_root *awr = aww->get_root();
381	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
382
383	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
384
385	GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
386	free( filename);
387	if (error) aw_message(error);
388	else AW_refresh_fileselection(awr, AWAR_DBBASE);
389	}
390
391
392	static void NT_save_quick_as_cb(AW_window *aww) {
393	AW_root *awr = aww->get_root();
394	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
395	GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename);
396	if (!error) AW_refresh_fileselection(awr, AWAR_DBBASE);
397	aww->hide_or_notify(error);
398
399	free(filename);
400	}
401
402	#define AWAR_DB_TYPE AWAR_DBBASE "/type" // created by AWT_insert_DBsaveType_selector
403	#define AWAR_DB_COMPRESSION AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector
404	#define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name"
405
406	static void NT_save_as_cb(AW_window *aww) {
407	AW_root *awr = aww->get_root();
408	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
409	const char *atype = awr->awar(AWAR_DB_TYPE)->read_char_pntr();
410	const char *ctype = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr();
411	char *savetype = GBS_global_string_copy("%s%s", atype, ctype);
412
413	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
414	GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype);
415	if (!error) AW_refresh_fileselection(awr, AWAR_DBBASE);
416	aww->hide_or_notify(error);
417
418	free(savetype);
419	free(filename);
420	}
421
422	static AW_window NT_create_save_quick_as_window(AW_root aw_root, const char *base_name) {
423	static AW_window_simple *aws = NULp;
424	if (!aws) {
425	aws = new AW_window_simple;
426	aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as");
427	aws->load_xfig("save_as.fig");
428
429	aws->at("close");
430	aws->callback(AW_POPDOWN);
431	aws->create_button("CLOSE", "CLOSE", "C");
432
433	aws->callback(makeHelpCallback("save.hlp"));
434	aws->at("help");
435	aws->create_button("HELP", "HELP", "H");
436
437	AW_create_standard_fileselection(aws, base_name);
438
439	aws->at("comment");
440	aws->create_text_field(AWAR_DB_COMMENT);
441
442	aws->at("save");
443	aws->callback(NT_save_quick_as_cb);
444	aws->create_button("SAVE", "SAVE", "S");
445	}
446	return aws;
447	}
448
449	static void NT_database_optimization(AW_window *aww) {
450	arb_progress progress("Optimizing database compression", 2L);
451	GB_topSecurityLevel unsecured(GLOBAL.gb_main);
452
453	GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
454	if (!error) {
455	ConstStrArray ali_names;
456	GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
457
458	arb_progress ali_progress("Optimizing sequence data", ali_names.size());
459	ali_progress.allow_title_reuse();
460
461	error = GBT_check_data(GLOBAL.gb_main, NULp);
462	error = GB_end_transaction(GLOBAL.gb_main, error);
463
464	if (!error) {
465	char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string();
466	for (int i = 0; ali_names[i]; ++i) {
467	error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
468	ali_progress.inc_and_check_user_abort(error);
469	}
470	free(tree_name);
471	}
472	}
473	progress.inc_and_check_user_abort(error);
474
475	if (!error) {
476	error = GB_optimize(GLOBAL.gb_main);
477	progress.inc_and_check_user_abort(error);
478	}
479	aww->hide_or_notify(error);
480	}
481
482	static AW_window NT_create_database_optimization_window(AW_root aw_root) {
483	static AW_window_simple *aws = NULp;
484	if (aws) return aws;
485	GB_transaction ta(GLOBAL.gb_main);
486
487	const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
488	aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree);
489
490	aws = new AW_window_simple;
491	aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression");
492	aws->load_xfig("optimize.fig");
493
494	aws->at("trees");
495	awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME, true);
496
497	aws->at("close");
498	aws->callback(AW_POPDOWN);
499	aws->create_button("CLOSE", "CLOSE", "C");
500
501	aws->callback(makeHelpCallback("optimize.hlp"));
502	aws->at("help");
503	aws->create_button("HELP", "HELP", "H");
504
505	aws->at("go");
506	aws->callback(NT_database_optimization);
507	aws->create_button("GO", "GO");
508	return aws;
509	}
510
511	static AW_window NT_create_save_as(AW_root aw_root, const char *base_name) {
512	static AW_window_simple *aws = NULp;
513	if (aws) return aws;
514
515	aws = new AW_window_simple;
516	aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
517	aws->load_xfig("save_as.fig");
518
519	aws->at("close");
520	aws->callback(AW_POPDOWN);
521	aws->create_button("CLOSE", "CLOSE", "C");
522
523	aws->at("help");
524	aws->callback(makeHelpCallback("save.hlp"));
525	aws->create_button("HELP", "HELP", "H");
526
527	AW_create_standard_fileselection(aws, base_name);
528
529	aws->at("type");
530	AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE);
531
532	aws->at("compression");
533	AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION);
534
535	aws->at("optimize");
536	aws->callback(NT_create_database_optimization_window);
537	aws->help_text("optimize.hlp");
538	aws->create_autosize_button("OPTIMIZE", "Optimize database compression");
539
540	aws->at("save");
541	aws->callback(NT_save_as_cb);
542	aws->create_button("SAVE", "SAVE", "S");
543
544	aws->at("comment");
545	aws->create_text_field(AWAR_DB_COMMENT);
546
547	return aws;
548	}
549
550	static void NT_undo_cb(AW_window, GB_UNDO_TYPE undo_type, TREE_canvas ntw) {
551	GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type);
552	if (error) aw_message(error);
553	else {
554	GB_transaction ta(GLOBAL.gb_main);
555	AWT_auto_refresh allowed_on(ntw);
556	ntw->request_refresh();
557	}
558	}
559
560	enum streamSource { FROM_PIPE, FROM_FILE };
561	static char stream2str(streamSource source, const char commandOrFile) {
562	char *output = NULp;
563	FILE *in = NULp;
564
565	switch (source) {
566	case FROM_PIPE: in = popen(commandOrFile, "r"); break;
567	case FROM_FILE: in = fopen(commandOrFile, "rt"); break;
568	}
569
570	if (in) {
571	GBS_strstruct *out = GBS_stropen(2000);
572	int c;
573
574	while (EOF != (c = fgetc(in))) GBS_chrcat(out, c);
575
576	switch (source) {
577	case FROM_PIPE: pclose(in); break;
578	case FROM_FILE: fclose(in); break;
579	}
580
581	// skip trailing linefeeds
582	long offset = GBS_memoffset(out);
583	while (offset>0 && GBS_mempntr(out)[offset-1] == '\n') {
584	GBS_str_cut_tail(out, 1);
585	offset--;
586	}
587
588	output = GBS_strclose(out);
589	}
590	return output;
591	}
592
593	inline void removeTrailingNewlines(char *str) {
594	char *eos = strchr(str, 0)-1;
595	while (eos >= str && eos[0] == '\n') *eos-- = 0;
596	}
597
598	inline void append_named_value(GBS_strstruct out, const char prefix, const char *value) {
599	GBS_strcat(out, GBS_global_string("%-*s: %s\n", 12, prefix, value));
600	}
601	inline void append_command_output(GBS_strstruct out, const char prefix, const char *command) {
602	char *output = stream2str(FROM_PIPE, command);
603	if (output) {
604	removeTrailingNewlines(output);
605	if (strcmp(output, "unknown") != 0) append_named_value(out, prefix, output);
606	free(output);
607	}
608	}
609
610	static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) {
611	DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
612	nt_mode_event(NULp, canvas, mode);
613	}
614
615	static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) {
616	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
617	if (tree_root) {
618	AWT_auto_refresh allowed_on(ntw);
619	GB_transaction ta(ntw->gb_main);
620
621	NT_mark_all_cb(NULp, ntw, 0); // unmark all
622	tree_root->mark_duplicates();
623	ntw->request_structure_update();
624	}
625	}
626
627	static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) {
628	GB_transaction ta(ntw->gb_main);
629	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
630
631	if (tree_root) {
632	AWT_auto_refresh allowed_on(ntw);
633	tree_root->justify_branch_lenghs(ntw->gb_main);
634	ntw->request_save_and_zoom_reset();
635	}
636	}
637
638	#if defined(DEBUG)
639	static void NT_fix_database(AW_window *) {
640	GB_ERROR err = NULp;
641	err = GB_fix_database(GLOBAL.gb_main);
642	if (err) aw_message(err);
643	}
644	#endif
645
646	static void relink_pseudo_species_to_organisms(GBDATA &ref_gb_node, char &ref_name, GB_HASH *organism_hash) {
647	if (ref_gb_node) {
648	if (GEN_is_pseudo_gene_species(ref_gb_node)) {
649	GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
650
651	if (gb_organism) {
652	char *name = GBT_read_string(gb_organism, "name");
653
654	if (name) {
655	freeset(ref_name, name);
656	ref_gb_node = gb_organism;
657	}
658	}
659	}
660	}
661	}
662
663	static void NT_pseudo_species_to_organism(AW_window , TREE_canvas ntw) {
664	GB_transaction ta(ntw->gb_main);
665	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
666
667	if (tree_root) {
668	AWT_auto_refresh allowed_on(ntw);
669
670	GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
671	tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
672	GBS_free_hash(organism_hash);
673	ntw->request_save();
674	}
675	}
676
677
678	// #########################################
679	// #########################################
680	// ### ###
681	// ## user mask section ##
682	// ### ###
683	// #########################################
684	// #########################################
685
686	struct nt_item_type_species_selector FINAL_TYPE : public awt_item_type_selector {
687	nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
688	~nt_item_type_species_selector() OVERRIDE {}
689
690	const char *get_self_awar() const OVERRIDE {
691	return AWAR_SPECIES_NAME;
692	}
693	size_t get_self_awar_content_length() const OVERRIDE {
694	return 12; // should be enough for "nnaammee.999"
695	}
696	GBDATA current(AW_root root, GBDATA *gb_main) const OVERRIDE { // give the current item
697	char *species_name = root->awar(get_self_awar())->read_string();
698	GBDATA *gb_species = NULp;
699
700	if (species_name[0]) {
701	GB_transaction ta(gb_main);
702	gb_species = GBT_find_species(gb_main, species_name);
703	}
704
705	free(species_name);
706	return gb_species;
707	}
708	const char *getKeyPath() const OVERRIDE { // give the keypath for items
709	return CHANGE_KEY_PATH;
710	}
711	};
712
713	static nt_item_type_species_selector item_type_species;
714
715	static void NT_open_mask_window(AW_window aww, int id, GBDATA gb_main) {
716	const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
717	nt_assert(descriptor);
718	if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
719	}
720
721	static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
722	AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
723	}
724	static AW_window create_colorize_species_window(AW_root aw_root) {
725	return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
726	}
727
728	static void NT_update_marked_counter(GBDATA, AW_window aww) {
729	/*! Updates marked counter and issues redraw on tree if number of marked species changes.
730	* Called on any change of species_information container.
731	*/
732	long count = GBT_count_marked_species(GLOBAL.gb_main);
733	const char *buffer = count ? GBS_global_string("%li marked", count) : "";
734	AW_awar *counter = aww->get_root()->awar(AWAR_MARKED_SPECIES_COUNTER);
735	char *oldval = counter->read_string();
736	if (strcmp(oldval, buffer)) {
737	counter->write_string(buffer);
738	aww->get_root()->awar(AWAR_TREE_REFRESH)->touch();
739	}
740	free(oldval);
741	}
742
743	// --------------------------------------------------------------------------------------------------
744
745	static void NT_alltree_remove_leafs(AW_window , GBT_TreeRemoveType mode, GBDATA gb_main) {
746	GB_ERROR error = NULp;
747	GB_transaction ta(gb_main);
748
749	ConstStrArray tree_names;
750	GBT_get_tree_names(tree_names, gb_main, false);
751
752	if (!tree_names.empty()) {
753	long treeCount = tree_names.size();
754
755	const char *whats_removed = NULp;
756	switch (mode) {
757	case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
758	case GBT_REMOVE_MARKED: whats_removed = "marked"; break;
759	default: nt_assert(0); break;
760	}
761
762	const char *task = GBS_global_string("Deleting %s from %li trees", whats_removed, treeCount);
763
764	arb_progress progress(task, treeCount);
765	GB_HASH *species_hash = GBT_create_species_hash(gb_main);
766
767	int modified = 0;
768
769	for (int t = 0; t<treeCount && !error; t++) {
770	progress.subtitle(tree_names[t]);
771	TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
772	if (!tree) {
773	aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
774	}
775	else {
776	int removed = 0;
777	int groups_removed = 0;
778
779	tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
780
781	nt_assert(removed >= groups_removed);
782
783	if (!tree) {
784	aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
785	}
786	else {
787	if (removed>0) {
788	error = GBT_write_tree(gb_main, tree_names[t], tree);
789	if (error) {
790	aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
791	}
792	else {
793	if (groups_removed>0) {
794	aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
795	}
796	else {
797	aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
798	}
799	modified++;
800	}
801	}
802	UNCOVERED();
803	destroy(tree);
804	}
805	}
806	progress.inc_and_check_user_abort(error);
807	}
808
809	if (modified) {
810	aw_message(GBS_global_string("Changed %i of %li trees.", modified, treeCount));
811	}
812	else {
813	aw_message("No tree modified");
814	}
815
816	GBS_free_hash(species_hash);
817	}
818
819	aw_message_if(ta.close(error));
820	}
821
822	TreeNode NT_get_tree_root_of_canvas(TREE_canvas ntw) {
823	AWT_graphic_tree *tree = AWT_TREE(ntw);
824	if (tree) {
825	AP_tree *root = tree->get_root_node();
826	if (root) return root;
827	}
828	return NULp;
829	}
830
831	// --------------------------------------------------------------------------------------------------
832
833	static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
834	GB_transaction ta(gb_main);
835	GBT_mark_all(gb_main, 0);
836
837	DBItemSetIter end = referred.end();
838	for (DBItemSetIter s = referred.begin(); s != end; ++s) {
839	GB_write_flag(*s, 1);
840	}
841	return ARB_ERROR();
842	}
843
844	static AW_window create_mark_by_refentries_window(AW_root awr, GBDATA *gbmain) {
845	static AW_window *aws = NULp;
846	if (!aws) {
847	static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
848	aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULp, "Mark referenced", mark_referred_species);
849	}
850	return aws;
851	}
852
853	// --------------------------------------------------------------------------------------------------
854
855	static void merge_from_to(AW_root awr, const char db_awar_name, bool merge_to) {
856	const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
857	char *quotedDB = GBK_singlequote(db_name);
858
859	AWT_system_cb(
860	GBS_global_string(
861	merge_to
862	? "arb_ntree : %s &"
863	: "arb_ntree %s : &",
864	quotedDB)
865	);
866
867	free(quotedDB);
868	}
869
870	static void merge_from_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, false); }
871	static void merge_into_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, true); }
872
873	static AW_window NT_create_merge_from_window(AW_root awr) {
874	static char *awar_name = NULp; // do not free, bound to callback
875	AW_window *aw_from =
876	awt_create_load_box(awr, "Merge data from", "other ARB database",
877	".", ".arb", &awar_name,
878	makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
879	return aw_from;
880	}
881	static AW_window NT_create_merge_to_window(AW_root awr) {
882	static char *awar_name = NULp; // do not free, bound to callback
883	AW_window *aw_to =
884	awt_create_load_box(awr, "Merge data to", "other ARB database",
885	".", ".arb", &awar_name,
886	makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
887	makeWindowCallback(AW_POPDOWN), NULp);
888	return aw_to;
889	}
890
891	// --------------------------------------------------------------------------------------------------
892
893	static void update_main_window_title(AW_root* awr, AW_window_menu_modes* aww, int clone) {
894	const char* filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
895	if (clone) {
896	aww->set_window_title(GBS_global_string("%s - ARB (%i)", filename, clone));
897	}
898	else {
899	aww->set_window_title(GBS_global_string("%s - ARB", filename));
900	}
901	}
902
903	static void canvas_tree_awar_changed_cb(AW_awar , bool, TREE_canvas ntw) {
904	NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
905	AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
906	TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_TREE);
907	}
908
909	class TREE_canvas_registry {
910	int count;
911	TREE_canvas *canvas[MAX_NT_WINDOWS];
912
913	static TREE_canvas_registry *SINGLETON;
914
915	TREE_canvas_registry() : count(0) {
916	AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
917	}
918
919	public:
920	static TREE_canvas_registry& instance() {
921	if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
922	return *SINGLETON;
923	}
924
925	void register_canvas(TREE_canvas *ntw) {
926	nt_assert(count<MAX_NT_WINDOWS);
927	nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
928	canvas[count++] = ntw;
929	ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
930	}
931
932	int get_count() const { return count; }
933
934	TREE_canvas *get_canvas(int idx) const {
935	if (idx<0 \|\| idx>=count) return NULp;
936	return canvas[idx];
937	}
938	};
939
940	TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULp;
941
942	TREE_canvas *NT_get_canvas_by_index(int idx) {
943	/! return canvas with index 'idx' [0...MAX_NT_WINDOWS-1] /
944	nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
945	return TREE_canvas_registry::instance().get_canvas(idx);
946	}
947
948	#if defined(TRACE_GROUP_SELECTION)
949	static TREE_canvas find_canvas_showing(AWT_graphic_tree agt) {
950	// look for (registered) canvas showing given AWT_graphic_tree
951	// returns NULp if none found
952	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
953
954	int maxIdx = reg.get_count();
955	for (int32_t i = 0; i<maxIdx; ++i) {
956	TREE_canvas *ntw = reg.get_canvas(i);
957	if (ntw->gfx == agt) return ntw;
958	}
959	return NULp;
960	}
961	#endif
962
963	void NT_fill_canvas_selection_list(class AW_selection_list sellst, TREE_canvas to_skip) {
964	/*! insert canvases into selection list (using canvas-indices as values)
965	*/
966	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
967
968	int maxIdx = reg.get_count();
969	for (int32_t i = 0; i<maxIdx; ++i) {
970	TREE_canvas *ntw = reg.get_canvas(i);
971	if (ntw && ntw != to_skip) {
972	nt_assert(ntw->get_awar_tree());
973	const char *treename = ntw->get_awar_tree()->read_char_pntr();
974	const char *description = i
975	? GBS_global_string("ARB (%i): %s", i, treename)
976	: GBS_global_string("ARB main: %s", treename);
977	sellst->insert(description, i);
978	}
979	}
980	}
981
982	// ----------------------------------
983	// group-selection handlers
984
985	void NT_deselect_group(AW_root *awr) {
986	awr->awar(AWAR_GROUP)->write_pointer(NULp);
987	}
988
989	static bool track_group_selection_by_canvas = true;
990
991	static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) {
992	const Group& group = gfx->get_selected_group();
993
994	#if defined(TRACE_GROUP_SELECTION)
995	fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track");
996	TREE_canvas *ntw = find_canvas_showing(gfx);
997	if (group.is_valid()) {
998	fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name());
999	}
1000	else {
1001	fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index());
1002	}
1003	#endif
1004
1005	if (track_group_selection_by_canvas) {
1006	// set group-awar:
1007	gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULp if !group.is_valid()
1008	}
1009	}
1010
1011	static void group_awar_changed_cb(AW_root *awr) {
1012	AW_awar *awar_group = awr->awar(AWAR_GROUP);
1013	GBDATA *gb_wanted_group = awar_group->read_pointer();
1014
1015	GBDATA *gb_wanted_tree = NULp;
1016	{
1017	if (gb_wanted_group) {
1018	GB_transaction ta(gb_wanted_group);
1019	gb_wanted_tree = GB_get_father(gb_wanted_group);
1020	awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected
1021	#if defined(TRACE_GROUP_SELECTION)
1022	fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr);
1023	#endif
1024	}
1025	#if defined(TRACE_GROUP_SELECTION)
1026	const char *group_name = NULp;
1027	if (gb_wanted_group) {
1028	GB_transaction ta(gb_wanted_group);
1029	GBDATA *gb_name = GB_entry(gb_wanted_group, "group_name");
1030	if (gb_name) group_name = GB_read_char_pntr(gb_name);
1031	}
1032	fprintf(stderr, "group awar changed to %p", gb_wanted_group);
1033	if (group_name) fprintf(stderr, " (='%s')", group_name);
1034	fputc('\n', stderr);
1035	#endif
1036	}
1037
1038	LocallyModify<bool> ignore_group_selection_by_canvas(track_group_selection_by_canvas, false);
1039
1040	{
1041	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1042
1043	int maxIdx = reg.get_count();
1044	for (int32_t i = 0; i<maxIdx; ++i) {
1045	TREE_canvas *ntw = reg.get_canvas(i);
1046	AWT_graphic_tree *agt = AWT_TREE(ntw);
1047	const Group& curr_group = agt->get_selected_group();
1048
1049	GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree();
1050	if (gb_curr_tree == gb_wanted_tree) {
1051	AWT_auto_refresh allowed_on(ntw);
1052	if (!curr_group.is_valid() \|\| // no group selected
1053	curr_group.get_group_data() != gb_wanted_group) // wrong group selected
1054	{
1055	agt->select_group(gb_wanted_group);
1056	ntw->request_refresh();
1057	}
1058	// perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group)
1059	TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_GROUP);
1060	}
1061	else {
1062	if (curr_group.is_valid()) {
1063	AWT_auto_refresh allowed_on(ntw);
1064	agt->deselect_group();
1065	ntw->request_refresh();
1066	}
1067	}
1068	}
1069	}
1070	}
1071
1072	// ----------------------------
1073	// create main window
1074
1075	static AW_window popup_new_main_window(AW_root awr, int clone, TREE_canvas **result_ntw) {
1076	/*! create ARB_NTREE main window
1077	* @param awr application root
1078	* @param clone == 0 -> first window (full functionality); >0 -> additional tree views (restricted functionality)
1079	* @param result_ntw is set to the created TREE_canvas (passed pointer may be NULp if result is not needed)
1080	*/
1081	GB_push_transaction(GLOBAL.gb_main);
1082
1083	char window_title[256];
1084	const char *awar_tree = NULp;
1085
1086	if (clone) {
1087	awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
1088	sprintf(window_title, "ARB_NT_%i", clone);
1089	}
1090	else {
1091	awar_tree = AWAR_TREE;
1092	sprintf(window_title, "ARB_NT");
1093	}
1094	AW_window_menu_modes *awm = new AW_window_menu_modes;
1095	awm->init(awr, window_title, window_title, 0, 0);
1096
1097	awr->awar(AWAR_DB_NAME)
1098	->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1099	->update();
1100
1101	awm->button_length(5);
1102
1103	if (!clone) AW_init_color_group_defaults("arb_ntree");
1104
1105	AWT_graphic_tree *tree = NT_generate_tree(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1106
1107	if (!clone) { // while creating initial window
1108	AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb));
1109	awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb);
1110	}
1111
1112	TREE_canvas *ntw;
1113	{
1114	AW_awar *tree_awar = awr->awar_string(awar_tree);
1115	{
1116	AP_tree_display_style prev_style = tree->get_tree_style();
1117	tree->set_tree_style(AP_LIST_SIMPLE, NULp); // avoid NDS warnings during startup
1118
1119	ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1120	tree->set_tree_style(prev_style, ntw);
1121	ntw->set_mode(AWT_MODE_SELECT);
1122	}
1123
1124	if (result_ntw) *result_ntw = ntw;
1125
1126	{
1127	const char *tree_name = tree_awar->read_char_pntr();
1128	const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1129
1130	if (existing_tree_name) {
1131	tree_awar->write_string(existing_tree_name);
1132	NT_reload_tree_event(awr, ntw, true); // load first tree
1133	}
1134	else {
1135	AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, NULp, "no_tree.hlp");
1136	tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list
1137	}
1138
1139	TREE_canvas_registry::instance().register_canvas(ntw);
1140	AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1141	}
1142	}
1143
1144	TREE_install_update_callbacks(ntw);
1145
1146	bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1147
1148	WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1149
1150	// --------------
1151	// File
1152
1153	#if defined(DEBUG)
1154	AWT_create_debug_menu(awm);
1155	#endif // DEBUG
1156
1157	bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1158
1159	if (clone) {
1160	awm->create_menu("File", "F", AWM_ALL);
1161	if (allow_new_window) {
1162	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));
1163	}
1164	awm->insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN);
1165	}
1166	else {
1167	#if defined(DEBUG)
1168	// add more to debug-menu
1169	awm->sep______________();
1170	awm->insert_menu_topic("fix_db", "Fix database", "F", NULp, AWM_ALL, NT_fix_database);
1171	awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", NULp, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1172	awm->insert_menu_topic("test_compr", "Test compression", "T", NULp, AWM_ALL, makeWindowCallback(GBT_compression_test, GLOBAL.gb_main));
1173	#endif // DEBUG
1174
1175	awm->create_menu("File", "F", AWM_ALL);
1176	{
1177	// keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1178	awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, NT_save_quick_cb);
1179	awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1180	if (allow_new_window) {
1181	awm->sep______________();
1182	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));
1183	}
1184	awm->sep______________();
1185	awm->insert_menu_topic("optimize_db", "Optimize database compression", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window);
1186	awm->sep______________();
1187
1188	awm->insert_sub_menu("Import", "I");
1189	{
1190	awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1191	awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1192	GDE_load_menu(awm, AWM_EXP, "Import");
1193	}
1194	awm->close_sub_menu();
1195
1196	awm->insert_sub_menu("Export", "E");
1197	{
1198	awm->insert_menu_topic("export_to_ARB", "Merge to (new) ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1199	awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1200	GDE_load_menu(awm, AWM_ALL, "Export");
1201	awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window);
1202	}
1203	awm->close_sub_menu();
1204	awm->sep______________();
1205
1206	insert_macro_menu_entry(awm, false);
1207
1208	awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1209	{
1210	awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp"));
1211	awm->insert_menu_topic("bug_report", "Report bug", "b", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1212	awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1213	}
1214	awm->close_sub_menu();
1215	awm->sep______________();
1216
1217	awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1218	awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1219	awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_exit, EXIT_SUCCESS));
1220	}
1221
1222	// -----------------
1223	// Species
1224
1225	awm->create_menu("Species", "c", AWM_ALL);
1226	{
1227	awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1228	awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb);
1229
1230	awm->sep______________();
1231
1232	NT_insert_mark_submenus(awm, ntw, 1);
1233	awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1234	awm->insert_menu_topic("species_colors", "Colors ...", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window);
1235	awm->insert_menu_topic("selection_admin", "Selections ...", "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1236
1237	awm->sep______________();
1238
1239	awm->insert_sub_menu("Database fields admin", "f");
1240	DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1241	awm->close_sub_menu();
1242	NT_create_mask_submenu(awm);
1243
1244	awm->sep______________();
1245
1246	awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1247
1248	awm->insert_sub_menu("Sort Species", "s");
1249	{
1250	awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window);
1251	awm->insert_menu_topic("$sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1252	}
1253	awm->close_sub_menu();
1254
1255	awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1256	{
1257	awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1258	awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "species_join.hlp", AWM_EXP, NT_create_species_join_window);
1259	}
1260	awm->close_sub_menu();
1261
1262	awm->sep______________();
1263
1264	awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1265
1266	awm->sep______________();
1267
1268	awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1269
1270	awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1271	{
1272	awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames);
1273	awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames);
1274	awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1275	awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window);
1276	}
1277	awm->close_sub_menu();
1278	}
1279
1280	// ----------------------------
1281	// Genes + Experiment
1282
1283	if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1284
1285	// ------------------
1286	// Sequence
1287
1288	awm->create_menu("Sequence", "S", AWM_ALL);
1289	{
1290	awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)NULp));
1291	awm->insert_sub_menu("Insert/delete", "I");
1292	{
1293	awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window);
1294	awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main));
1295	}
1296	awm->close_sub_menu();
1297	awm->sep______________();
1298
1299	awm->insert_sub_menu("Edit Sequences", "E");
1300	{
1301	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));
1302	awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1303	awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1304	}
1305	awm->close_sub_menu();
1306
1307	awm->sep______________();
1308
1309	awm->insert_sub_menu("Align Sequences", "S");
1310	{
1311	awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1312	GDE_load_menu(awm, AWM_ALL, "Align");
1313	}
1314	awm->close_sub_menu();
1315	awm->insert_menu_topic("seq_concat", "Concatenate Sequences/Alignments", "C", "concatenate.hlp", AWM_ALL, NT_createConcatenationWindow);
1316	awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1317	awm->sep______________();
1318
1319	awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1320	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1321	awm->sep______________();
1322
1323	awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1324	awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1325
1326	awm->sep______________();
1327
1328	GDE_load_menu(awm, AWM_ALL, "Print");
1329	}
1330
1331	// -------------
1332	// SAI
1333
1334	awm->create_menu("SAI", "A", AWM_ALL);
1335	{
1336	awm->insert_menu_topic("sai_admin", "Manage SAIs", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1337	awm->insert_sub_menu("Create SAI using ...", "C");
1338	{
1339	awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window);
1340	awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window);
1341	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);
1342	awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_phylo &"));
1343	awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold);
1344
1345	GDE_load_menu(awm, AWM_EXP, "SAI");
1346	}
1347	awm->close_sub_menu();
1348
1349	awm->insert_sub_menu("Other functions", "O");
1350	{
1351	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));
1352	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));
1353	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);
1354	}
1355	awm->close_sub_menu();
1356	}
1357
1358	// ----------------
1359	// Probes
1360
1361	awm->create_menu("Probes", "P", AWM_ALL);
1362	{
1363	awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1364	awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1365	awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1366	awm->sep______________();
1367	awm->insert_menu_topic("probe_match_sp", "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window, ntw));
1368	awm->sep______________();
1369	awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1370	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));
1371	awm->sep______________();
1372	awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1373	}
1374
1375	}
1376
1377	// --------------
1378	// Tree
1379
1380	awm->create_menu("Tree", "T", AWM_ALL);
1381	{
1382	if (!clone) {
1383	awm->insert_sub_menu("Add Species to Existing Tree", "A");
1384	{
1385	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 &"));
1386	awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_pars &"));
1387	GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1388	}
1389	awm->close_sub_menu();
1390	}
1391
1392	awm->insert_sub_menu("Remove Species from Tree", "R");
1393	{
1394	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));
1395	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));
1396	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));
1397	awm->sep______________();
1398	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));
1399	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));
1400	}
1401	awm->close_sub_menu();
1402
1403	if (!clone) {
1404	awm->insert_sub_menu("Build tree from sequence data", "B");
1405	{
1406	awm->insert_sub_menu("Distance matrix methods", "D");
1407	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AWT_system_cb, "arb_dist &"));
1408	GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1409	awm->close_sub_menu();
1410
1411	awm->insert_sub_menu("Maximum Parsimony methods", "P");
1412	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1413	awm->close_sub_menu();
1414
1415	awm->insert_sub_menu("Maximum Likelihood methods", "L");
1416	GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1417	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1418	awm->close_sub_menu();
1419
1420	awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1421	GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1422	awm->close_sub_menu();
1423	}
1424	awm->close_sub_menu();
1425	}
1426
1427	awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1428
1429	awm->sep______________();
1430
1431	awm->insert_sub_menu("Reset zoom", "z");
1432	{
1433	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));
1434	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));
1435	}
1436	awm->close_sub_menu();
1437
1438	awm->sep______________();
1439
1440	// taxonomic groups
1441	NT_insert_collapse_submenu(awm, ntw);
1442	if (!clone) {
1443	awm->insert_menu_topic("group_search", "Search groups...", "g", "group_search.hlp", AWM_ALL, makeWindowCallback (popup_group_search_window, GLOBAL.gb_main));
1444	awm->insert_menu_topic("compare_taxonomy", "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1445	awm->insert_menu_topic("move_groups", "Move groups...", "n", "move_groups.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_moveGroupInfo_window));
1446	}
1447
1448	awm->sep______________();
1449
1450	if (!clone) {
1451	awm->insert_menu_topic("compare_topology", "Compare topology...", "p", "compare_topo.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compareTopologies_window));
1452	}
1453
1454	awm->insert_sub_menu("Modify branches", "M");
1455	{
1456	awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw));
1457	awm->sep______________();
1458	awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw));
1459	awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1460	awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw));
1461	awm->sep______________();
1462	awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1463	awm->sep______________();
1464	awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1465	awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1466
1467	}
1468	awm->close_sub_menu();
1469	awm->insert_sub_menu("Beautify tree", "e");
1470	{
1471	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));
1472	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));
1473	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));
1474	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));
1475	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));
1476	awm->sep______________();
1477	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));
1478	}
1479	awm->close_sub_menu();
1480
1481	awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "h", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1482	awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "u", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback(NT_mark_duplicates, ntw));
1483
1484	awm->sep______________();
1485
1486	awm->insert_menu_topic(awm->local_id("shade"), "Tree shading...", "s", "tree_shading.hlp", AWM_ALL, makeWindowCallback (NT_configure_treeShader));
1487	awm->insert_menu_topic(awm->local_id("syncscroll"), "Sync tree scrolling..", "o", "syncscroll.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1488
1489	awm->sep______________();
1490
1491	awm->insert_menu_topic(awm->local_id("tree_select"), "Select Tree", "T", NULp, AWM_ALL, makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1492	awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", NULp, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1493
1494	if (!clone) {
1495	awm->sep______________();
1496	awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1497	awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_nds_window, GLOBAL.gb_main));
1498	}
1499
1500	awm->sep______________();
1501	awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1502
1503	if (!clone) {
1504	awm->sep______________();
1505	awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1506	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)));
1507	}
1508
1509	if (is_genome_db) {
1510	awm->sep______________();
1511	awm->insert_sub_menu("Other..", "O", AWM_EXP);
1512	{
1513	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));
1514	}
1515	awm->close_sub_menu();
1516	}
1517	}
1518
1519	if (!clone) {
1520	// ---------------
1521	// Tools
1522
1523	awm->create_menu("Tools", "o", AWM_ALL);
1524	{
1525	awm->insert_menu_topic("names_admin", "Name server admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_namesadmin_window, GLOBAL.gb_main));
1526	awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1527	{
1528	awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1529	}
1530	awm->close_sub_menu();
1531	awm->insert_sub_menu("Network", "N", AWM_EXP);
1532	{
1533	GDE_load_menu(awm, AWM_EXP, "Network");
1534	}
1535	awm->close_sub_menu();
1536	awm->sep______________();
1537
1538	awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1539	{
1540	GDE_load_menu(awm, AWM_EXP, NULp);
1541	}
1542	awm->close_sub_menu();
1543
1544	awm->sep______________();
1545	awm->insert_menu_topic("xterm", "Start XTERM", "X", "xterm.hlp", AWM_ALL, AWT_console);
1546	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
1547	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));
1548	awm->sep______________();
1549	GDE_load_menu(awm, AWM_EXP, "User");
1550	}
1551	// --------------------
1552	// Properties
1553
1554	awm->create_menu("Properties", "r", AWM_ALL);
1555	{
1556	awm->insert_menu_topic("props_menu", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1557	awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1558	awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1559	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));
1560	awm->sep______________();
1561	awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", NULp, AWM_ALL, NT_toggle_expert_mode);
1562	awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", NULp, AWM_ALL, NT_toggle_focus_policy);
1563	awm->sep______________();
1564	AW_insert_common_property_menu_entries(awm);
1565	awm->sep______________();
1566	awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1567	}
1568	}
1569
1570	awm->insert_help_topic("ARB_NT help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1571
1572	// ----------------------
1573	// mode buttons
1574	//
1575	// keep them synchronized as far as possible with those in ARB_PARSIMONY
1576	// see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1577
1578	awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1579	awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1580	awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1581	awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1582	awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1583
1584	awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1585	awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW));
1586
1587	// topology-modification-modes
1588	awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1589	awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1590	awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1591	awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1592	awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1593
1594	// layout-modes
1595	awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1596	awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1597	awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1598
1599	awm->set_info_area_height(250);
1600	awm->at(5, 2);
1601	awm->auto_space(-2, -2);
1602	awm->shadow_width(1);
1603
1604	// -------------------------
1605	// create top area
1606
1607	int first_liney;
1608	int leftx;
1609	awm->get_at_position(&leftx, &first_liney);
1610
1611	// ---------------------
1612	// quit + help
1613
1614	awm->button_length(0);
1615
1616	if (clone) {
1617	awm->callback(AW_POPDOWN);
1618	awm->create_button("CLOSE", "#close.xpm");
1619	}
1620	else {
1621	awm->callback(makeWindowCallback(NT_exit, EXIT_SUCCESS));
1622	awm->help_text("quit.hlp");
1623	awm->create_button("QUIT", "#quit.xpm");
1624	}
1625
1626	int db_pathx = awm->get_at_xposition();
1627
1628	// now fetch the yposition for the 2nd button line
1629	awm->at_newline();
1630	int second_liney = awm->get_at_yposition();
1631
1632	awm->callback(AW_help_entry_pressed);
1633	awm->help_text("arb_ntree.hlp");
1634	awm->create_button("?", "#help.xpm");
1635
1636	// --------------------------
1637	// save + undo/redo
1638
1639	awm->callback(NT_save_quick_cb);
1640	awm->help_text("save.hlp");
1641	awm->create_button("SAVE", "#save.xpm");
1642
1643	awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1644	awm->help_text("save.hlp");
1645	awm->create_button("SAVE_AS", "#saveAs.xpm");
1646
1647	// undo/redo:
1648	awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1649	awm->help_text("undo.hlp");
1650	awm->create_button("UNDO", "#undo.xpm");
1651
1652	awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1653	awm->help_text("undo.hlp");
1654	awm->create_button("REDO", "#redo.xpm");
1655
1656	int db_pathx2 = awm->get_at_xposition();
1657
1658	// fetch position for mode help-line:
1659	awm->at_newline();
1660	int third_liney = awm->get_at_yposition();
1661
1662	awm->at(db_pathx, first_liney);
1663	// size of DB-name button is determined by buttons below:
1664	awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1665	awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1666	awm->help_text("save.hlp");
1667	awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1668
1669	// -----------------------------
1670	// tree + tree display
1671
1672	#define TREE_BUTTON_OVERSIZE 6
1673
1674	int db_treex = awm->get_at_xposition();
1675	int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1676
1677	awm->at(db_treex, second_uppery);
1678	awm->button_length(0);
1679
1680	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1681	awm->help_text("tr_type_radial.hlp");
1682	awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1683
1684	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1685	awm->help_text("tr_type_list.hlp");
1686	awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1687
1688	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1689	awm->help_text("tr_type_irs.hlp");
1690	awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1691
1692	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1693	awm->help_text("tr_type_nds.hlp");
1694	awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1695
1696	int db_treex2 = awm->get_at_xposition();
1697
1698	awm->at(db_treex, first_liney);
1699	// size of tree-name button is determined by buttons below:
1700	awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1701	awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree));
1702	awm->help_text("nt_tree_select.hlp");
1703	awm->create_button("SELECT_A_TREE", awar_tree);
1704
1705	// ---------------------------------------------------------------
1706	// protection, alignment + editor (and maybe Genome Map)
1707
1708	int db_alignx = awm->get_at_xposition();
1709
1710	// editor and genemap buttons have to be 44x24 sized
1711	#define EDIT_XSIZE 50
1712	#define EDIT_YSIZE 30 // same as 'save as' buttons
1713
1714	// first draw protection:
1715	int protectx = db_alignx + 2*EDIT_XSIZE;
1716
1717	awm->at(protectx+2, first_liney+1);
1718	awm->button_length(0);
1719	awm->create_button(NULp, "#protect.xpm");
1720
1721	awm->at(protectx, second_liney+2);
1722	awm->create_option_menu(AWAR_SECURITY_LEVEL, true);
1723	awm->insert_option ("0", NULp, 0);
1724	awm->insert_option ("1", NULp, 1);
1725	awm->insert_option ("2", NULp, 2);
1726	awm->insert_option ("3", NULp, 3);
1727	awm->insert_option ("4", NULp, 4);
1728	awm->insert_option ("5", NULp, 5);
1729	awm->insert_default_option("6", NULp, 6);
1730	awm->update_option_menu();
1731
1732	int db_searchx = awm->get_at_xposition() - 7;
1733
1734	// draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1735	awm->at(db_alignx, second_liney);
1736
1737	awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1738	awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1739	awm->help_text("arb_edit4.hlp");
1740	if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1741	else awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1742
1743	if (is_genome_db) {
1744	awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1745	awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1746	awm->help_text("gene_map.hlp");
1747	awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1748	}
1749
1750	int db_alignx2 = awm->get_at_xposition();
1751
1752	awm->at(db_alignx, first_liney);
1753	awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1754	awm->callback(NT_create_select_alignment_window);
1755	awm->help_text("nt_align_select.hlp");
1756	awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1757
1758	// -------------------------------
1759	// create mode-help line
1760
1761	awm->at(leftx, third_liney);
1762	awm->button_length(AWAR_FOOTER_MAX_LEN);
1763	awm->create_button(NULp, AWAR_FOOTER);
1764
1765	awm->at_newline();
1766	int bottomy = awm->get_at_yposition();
1767
1768	// ---------------------------------------
1769	// Info / marked / Search / Jump
1770
1771	awm->button_length(7);
1772
1773	awm->at(db_searchx, first_liney);
1774	awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1775	awm->help_text("sp_search.hlp");
1776	awm->create_button("SEARCH", "Search");
1777
1778	awm->at(db_searchx, second_uppery);
1779	awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1780	awm->help_text("tr_jump.hlp");
1781	awm->create_button("JUMP", "Jump");
1782
1783	int db_infox = awm->get_at_xposition();
1784
1785	awm->at(db_infox, first_liney);
1786	awm->button_length(13);
1787	awm->callback(popupinfo_wcb);
1788	awm->help_text("sp_search.hlp");
1789	awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1790
1791	awm->at(db_infox, second_uppery);
1792	awm->button_length(13);
1793	awm->help_text("species_configs.hlp");
1794	awm->callback(makeWindowCallback(NT_popup_configuration_admin, ntw));
1795	awm->create_button("selection_admin2", AWAR_MARKED_SPECIES_COUNTER);
1796	{
1797	GBDATA *gb_species_data = GBT_get_species_data(GLOBAL.gb_main);
1798	GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(NT_update_marked_counter, static_cast<AW_window*>(awm)));
1799	NT_update_marked_counter(NULp, awm);
1800	}
1801
1802	// set height of top area:
1803	awm->set_info_area_height(bottomy+2);
1804	awm->set_bottom_area_height(0);
1805
1806	NT_activate_configMarkers_display(ntw);
1807
1808	// ------------------------------------
1809	// Autostarts for development
1810
1811	#if defined(DEVEL_RALF)
1812	// if (is_genome_db) GEN_map_first(awr)->show();
1813	#endif // DEVEL_RALF
1814
1815	GB_pop_transaction(GLOBAL.gb_main);
1816
1817	#if defined(DEBUG)
1818	AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1819	#endif
1820
1821	return awm;
1822	}
1823
1824	TREE_canvas NT_create_main_window(AW_root aw_root) {
1825	GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1826	if (error) aw_message(error);
1827
1828	nt_create_all_awars(aw_root);
1829
1830	TREE_canvas *ntw = NULp;
1831	AW_window *aww = popup_new_main_window(aw_root, 0, &ntw);
1832	NT_install_treeShader(ntw, GLOBAL.gb_main);
1833	aww->show();
1834
1835	error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1836	if (error) aw_message(error);
1837
1838	return ntw;
1839	}

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source: branches/alilink/NTREE/NT_extern.cxx

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