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NT_extern.cxx

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Last change on this file was 19731, checked in by westram, 3 months ago
reintegrates 'species' into 'trunk' provides species selections in mergetool (#868) adds: log:branches/species@19693:19730
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 78.4 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 <MacroExitor.hxx>
31	#include <xcmd.hxx>
32	#include <nds.h>
33	#include <db_query.h>
34	#include <dbui.h>
35	#include <refentries.h>
36	#include <insdel.h>
37
38	#include <awti_export.hxx>
39	#include <awti_import.hxx>
40
41	#include <app.hxx>
42	#include <input_mask.hxx>
43	#include <sel_boxes.hxx>
44	#include <selection_admin.h>
45	#include <www.hxx>
46	#include <TreeAwars.hxx>
47	#include <arb_spec.hxx>
48
49	#include <aw_color_groups.hxx>
50	#include <aw_advice.hxx>
51	#include <aw_preset.hxx>
52	#include <aw_awars.hxx>
53	#include <aw_global_awars.hxx>
54	#include <aw_file.hxx>
55	#include <arb_progress.h>
56	#include <aw_select.hxx>
57	#include <aw_system.hxx>
58	#include <rootAsWin.h>
59
60	#include <ad_cb.h>
61
62	#include <arb_strbuf.h>
63	#include <arb_file.h>
64	#include <arb_version.h>
65
66	#include <saicalc.h>
67
68	#include <string>
69
70	#if defined(DEVEL_RALF)
71	# define TRACE_GROUP_SELECTION
72	#endif
73
74	#define AWAR_EXPORT_NDS "tmp/export_nds"
75	#define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/delimiter"
76	#define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species"
77	#define AWAR_NTREE_TITLE_MODE "tmp/title_mode"
78
79	void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global);
80
81	void create_insertDeleteColumn_variables(AW_root *root, AW_default db1);
82	AW_window create_insertDeleteColumn_window(AW_root root);
83	AW_window create_insertDeleteBySAI_window(AW_root root, GBDATA *gb_main);
84
85	AW_window create_tree_window(AW_root aw_root, AWT_graphic *awd);
86
87	enum Export_Type {
88	EXPORT_SPACE_PADDED_RIGHT_ALIGNED = 1, // format info (using spaces). slow - uses one extra pass for column width detection.
89	EXPORT_SPACE_PADDED_LEFT_ALIGNED = 4, // dito, but left aligned
90	EXPORT_TAB_SEPARATED = 2, // format info (using 1 tab per column - for easy import into star-calc, excel, etc. )
91	EXPORT_COMMA_SEPARATED = 3, // like EXPORT_TAB_SEPARATED, but using commas
92	};
93
94	static void nt_changesecurity(AW_root *aw_root) {
95	int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int();
96	GB_push_transaction(GLOBAL.gb_main);
97	GB_change_my_security(GLOBAL.gb_main, level); // changes user security
98	GB_pop_transaction(GLOBAL.gb_main);
99	}
100
101	static void export_nds_cb(AW_window *aww, bool do_print) {
102	AW_root *aw_root = aww->get_root();
103	char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string();
104	FILE *out = fopen(name, "w");
105
106	if (!out) {
107	aw_message("Error: Cannot open and write to file");
108	}
109	else {
110	GB_transaction ta(GLOBAL.gb_main);
111
112	char *tree_name = aw_root->awar(AWAR_TREE)->read_string();
113	const Export_Type export_type = (Export_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int();
114	const NDS_Type nds_type = export_type == EXPORT_COMMA_SEPARATED ? NDS_OUTPUT_COMMA_SEPARATED : NDS_OUTPUT_TAB_SEPARATED;
115	const bool spacePadded = export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED \|\| export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED;
116	const int passesNeeded = spacePadded ? 2 : 1;
117	NDS_Labeler labeler(nds_type);
118
119	arb_progress progress("Exporting data using NDS", passesNeeded*GBT_count_marked_species(GLOBAL.gb_main));
120
121	const size_t max_col = std::max(labeler.max_columns(GLOBAL.gb_main), 1L);
122	size_t col_max_len[max_col];
123
124	const char *col_format = NULp;
125
126	if (spacePadded) {
127	for (size_t i = 0; i<max_col; ++i) {
128	col_max_len[i] = 0;
129	}
130	if (export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED) {
131	col_format = "%*s";
132	}
133	else {
134	col_format = "%-*s";
135	}
136	}
137
138	for (int pass = 1; pass<=passesNeeded; ++pass) {
139	for (GBDATA *gb_species = GBT_first_marked_species(GLOBAL.gb_main);
140	gb_species;
141	gb_species = GBT_next_marked_species(gb_species))
142	{
143	const char *label = labeler.speciesLabel(GLOBAL.gb_main, gb_species, NULp, tree_name);
144
145	if (spacePadded) {
146	ConstStrArray parts;
147	GBT_split_string(parts, label, "\t", SPLIT_KEEPEMPTY);
148
149	size_t col_count = parts.size();
150	nt_assert(col_count<=max_col);
151
152	if (pass == 1) { // track maximum used width for all columns
153	for (size_t i = 0; i<col_count; ++i) {
154	col_max_len[i] = std::max(col_max_len[i], strlen(parts[i]));
155	}
156	}
157	else { // format according to tracked widths
158	for (size_t i = 0; i<col_count; ++i) {
159	if (i) fputc(' ', out);
160
161	arb_assert(col_max_len[i]>0); // otherwise empty, unused column (might be ok, but might need different handling)
162	arb_assert(col_max_len[i]<=INT_MAX); // (protect cast below)
163
164	if (export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED && i == (col_count-1)) { // left aligned and last column
165	fputs(parts[i], out);
166	}
167	else {
168	fprintf(out, col_format, int(col_max_len[i]), parts[i]);
169	}
170	}
171	fputc('\n', out);
172	}
173	}
174	else {
175	fprintf(out, "%s\n", label);
176	}
177	++progress;
178	}
179	}
180
181	AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS);
182	fclose(out);
183	if (do_print) {
184	GB_ERROR error = GB_textprint(name);
185	if (error) aw_message(error);
186	}
187	free(tree_name);
188	}
189	free(name);
190	}
191
192	static AW_window create_nds_export_window(AW_root root) {
193	AW_window_simple *aws = new AW_window_simple;
194	aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES");
195	aws->load_xfig("sel_box_nds.fig");
196
197	aws->callback(AW_POPDOWN);
198	aws->at("close");
199	aws->create_button("CLOSE", "CLOSE", "C");
200
201	aws->callback(makeHelpCallback("arb_export_nds.hlp"));
202	aws->at("help");
203	aws->create_button("HELP", "HELP", "H");
204
205	aws->at("save");
206	aws->callback(makeWindowCallback(export_nds_cb, false));
207	aws->create_button("SAVE", "SAVE", "S");
208
209	aws->at("print");
210	aws->callback(makeWindowCallback(export_nds_cb, true));
211	aws->create_button("PRINT", "PRINT", "P");
212
213	aws->at("toggle1");
214	aws->label("Column output");
215	aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR);
216	aws->insert_option ("Space padded (left aligned)", "S", EXPORT_SPACE_PADDED_LEFT_ALIGNED);
217	aws->insert_option ("Space padded (right aligned)", "r", EXPORT_SPACE_PADDED_RIGHT_ALIGNED);
218	aws->insert_default_option("TAB separated", "T", EXPORT_TAB_SEPARATED);
219	aws->insert_option ("Comma separated", "C", EXPORT_COMMA_SEPARATED);
220	aws->update_option_menu();
221
222	AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS);
223
224	return aws;
225	}
226
227	static void create_export_nds_awars(AW_root *awr, AW_default def) {
228	AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds");
229	awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, EXPORT_TAB_SEPARATED, def);
230	}
231
232	static void selectedSpeciesChanged_cb(AW_root *awr) {
233	const char *value = awr->awar(AWAR_SPECIES_NAME)->read_char_pntr();
234	awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info");
235	if (value[0]) {
236	awr->awar(AWAR_GROUP)->write_pointer(NULp); // deselect group when species gets selected
237	#if defined(TRACE_GROUP_SELECTION)
238	fputs("clear AWAR_GROUP (because species selected)\n", stderr);
239	#endif
240	}
241	}
242
243	static void expert_mode_changed_cb(AW_root *aw_root) {
244	aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally
245	}
246
247	static void NT_toggle_expert_mode(AW_window *aww) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); }
248	static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); }
249
250	static void nt_create_all_awars(AW_root *awr) {
251	// creates awars for all modules reachable from ARB_NT main window
252
253	awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT);
254	if (GB_read_clients(GLOBAL.gb_main)>=0) {
255	awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main);
256	}
257	else {
258	awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT);
259	}
260
261	awr->awar_string(AWAR_TOPAREA_SAIS, "ECOLI;HELIX;HELIX_NR", AW_ROOT_DEFAULT);
262
263	awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main);
264	awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main);
265	awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main);
266	awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main);
267	awr->awar(AWAR_SPECIES_NAME)->add_callback(selectedSpeciesChanged_cb);
268	awr->awar_int(AWAR_NTREE_TITLE_MODE, 1);
269
270	awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match
271
272	GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
273	EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
274	#if defined(DEBUG)
275	AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT);
276	#endif // DEBUG
277
278	AW_create_namesadmin_awars(awr, GLOBAL.gb_main);
279
280	awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT);
281	awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity);
282	#if defined(DEBUG) && 0
283	awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging..
284	#endif // DEBUG
285
286	create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT);
287	create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
288	create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
289	create_trees_var(awr, AW_ROOT_DEFAULT);
290	DBUI::create_dbui_awars(awr);
291	AP_create_consensus_var(awr, AW_ROOT_DEFAULT);
292	{
293	GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, NULp, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT);
294	if (gde_err) GBK_terminatef("Fatal: %s", gde_err);
295	}
296	NT_create_transpro_variables(awr, AW_ROOT_DEFAULT);
297	NT_create_resort_awars(awr, AW_ROOT_DEFAULT);
298	NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT);
299	NT_create_trackAliChanges_Awars(awr, AW_ROOT_DEFAULT);
300
301	NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
302	NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
303	NDS_create_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
304	create_export_nds_awars(awr, AW_ROOT_DEFAULT);
305	create_group_search_awars(awr, AW_ROOT_DEFAULT);
306	TREE_create_awars(awr, GLOBAL.gb_main);
307
308	awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main);
309	awr->awar_string(AWAR_DB_COMMENT, "<no description>", GLOBAL.gb_main);
310
311	AWTC_create_submission_variables(awr, GLOBAL.gb_main);
312	NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main);
313	NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar
314	SQ_create_awars(awr, AW_ROOT_DEFAULT);
315	RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT);
316
317	NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT);
318
319	GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main);
320	if (!error) {
321	AW_awar *awar_expert = awr->awar(AWAR_EXPERT);
322	awar_expert->add_callback(expert_mode_changed_cb);
323	awar_expert->touch();
324
325	awt_create_aww_vars(awr, AW_ROOT_DEFAULT);
326	}
327
328	if (error) aw_message(error);
329	}
330
331	// --------------------------------------------------------------------------------
332
333	static void nt_run(const char *command) {
334	GB_ERROR error = GBK_system(command);
335	if (error) {
336	fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error);
337	#if defined(DEBUG)
338	GBK_dump_backtrace(stderr, "nt_run-error");
339	#endif
340	}
341	}
342
343	void NT_start_if(const char *arb_ntree_args) {
344	if (arb_ntree_args && arb_ntree_args[0]) {
345	char *command = GBS_global_string_copy("arb_launcher --async arb %s", arb_ntree_args);
346	nt_run(command);
347	free(command);
348	}
349	}
350
351	void NT_exit_now_restart_if(AW_root aw_root, int exitcode, const char restart_ntree_args) { // goes to header: __ATTR__NORETURN
352	// Exit arb_ntree + optionally restart arb.
353	//
354	// 'exitcode': exit with this code.
355	// 'restart_ntree_args': if null or empty -> just exit;
356	// otherwise -> restarts arb_ntree (with new ARB_PID).
357
358	AWTI_cleanup_importer(aw_root);
359
360	bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0;
361	ARB_disconnect_from_db(aw_root, GLOBAL.gb_main);
362	NT_start_if(restart_ntree_args);
363	if (is_server_and_has_clients) {
364	nt_run("(arb_clean session; echo ARB done) &"); // kills all clients
365	}
366	exit(exitcode);
367	}
368
369	class NT_MacroExitor: public MacroExitor {
370	int exitcode;
371	std::string restart_ntree_args; // [if non-empty] restart arb with these arguments
372
373	__ATTR__NORETURN void perform_exit() OVERRIDE {
374	NT_exit_now_restart_if(get_root(), exitcode, restart_ntree_args.c_str());
375	}
376
377	GBDATA* get_gbmain_checked_for_save() OVERRIDE {
378	return GLOBAL.gb_main;
379	}
380
381	public:
382	NT_MacroExitor(AW_root aw_root_, int exitcode_, const char restart_ntree_args_)
383	: MacroExitor(aw_root_, "ARB"),
384	exitcode(exitcode_),
385	restart_ntree_args(null2empty(restart_ntree_args_)) // restart arb if not empty/null
386	{}
387	};
388
389	void NT_confirm_exit_restart_if(AW_root aw_root, int exitcode, const char restart_ntree_args) {
390	// finally (may) exit ARB using NT_exit_now_restart_if(). see there for arguments.
391	//
392	// Beforehand this will happen:
393	// - if no macro running -> asks user to confirm quit (and maybe aborts exit/restart).
394	// - otherwise waits for macro to finish, then quits w/o question.
395
396	static SmartPtr<NT_MacroExitor> exitor;
397	if (exitor.isNull()) exitor = new NT_MacroExitor(aw_root, exitcode, restart_ntree_args);
398	exitor->maybe_exit_delayed();
399	if (!exitor->is_performing_delayed_exit()) exitor.setNull();
400	}
401
402	void NT_confirm_exit(AW_window *aws, int exitcode) {
403	NT_confirm_exit_restart_if(aws->get_root(), exitcode, NULp);
404	}
405
406	static void nt_start_2nd_arb(AW_window *aww, bool quit) {
407	// start 2nd arb with intro window
408	AW_root *aw_root = aww->get_root();
409	char *dir4intro;
410	GB_split_full_path(aw_root->awar(AWAR_SAVED_DB_PATH)->read_char_pntr(), &dir4intro, NULp, NULp, NULp);
411	if (!dir4intro) {
412	dir4intro = ARB_strdup(".");
413	}
414
415	if (quit) {
416	NT_confirm_exit_restart_if(aww->get_root(), EXIT_SUCCESS, dir4intro);
417	}
418	else {
419	NT_start_if(dir4intro);
420	}
421	free(dir4intro);
422	}
423
424	// --------------------------------------------------------------------------------
425
426	static void NT_save_quick_cb(AW_window *aww) {
427	AW_root *awr = aww->get_root();
428	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
429
430	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
431
432	GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename);
433	if (error) aw_message(error);
434	else {
435	awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
436	AW_refresh_fileselection(awr, AWAR_DBBASE);
437	}
438
439	free(filename);
440	}
441
442
443	static void NT_save_quick_as_cb(AW_window *aww) {
444	AW_root *awr = aww->get_root();
445	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
446
447	// @@@ also use dont_save_awars_with_default_value here?
448
449	GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename);
450	if (!error) {
451	awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
452	AW_refresh_fileselection(awr, AWAR_DBBASE);
453	}
454	aww->hide_or_notify(error);
455
456	free(filename);
457	}
458
459	#define AWAR_DB_TYPE AWAR_DBBASE "/type" // created by AWT_insert_DBsaveType_selector
460	#define AWAR_DB_COMPRESSION AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector
461	#define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name"
462
463	static void NT_save_as_cb(AW_window *aww) {
464	AW_root *awr = aww->get_root();
465	char *filename = awr->awar(AWAR_DB_PATH)->read_string();
466	const char *atype = awr->awar(AWAR_DB_TYPE)->read_char_pntr();
467	const char *ctype = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr();
468	char *savetype = GBS_global_string_copy("%s%s", atype, ctype);
469
470	awr->dont_save_awars_with_default_value(GLOBAL.gb_main);
471
472	GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype);
473	if (!error) {
474	awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename);
475	AW_refresh_fileselection(awr, AWAR_DBBASE);
476	}
477	aww->hide_or_notify(error);
478
479	free(savetype);
480	free(filename);
481	}
482
483	static AW_window NT_create_save_quick_as_window(AW_root aw_root, const char *base_name) {
484	static AW_window_simple *aws = NULp;
485	if (!aws) {
486	aws = new AW_window_simple;
487	aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as");
488	aws->load_xfig("save_as.fig");
489
490	aws->at("close");
491	aws->callback(AW_POPDOWN);
492	aws->create_button("CLOSE", "CLOSE", "C");
493
494	aws->callback(makeHelpCallback("save.hlp"));
495	aws->at("help");
496	aws->create_button("HELP", "HELP", "H");
497
498	AW_create_standard_fileselection(aws, base_name);
499
500	aws->at("comment");
501	aws->create_text_field(AWAR_DB_COMMENT);
502
503	aws->at("save");
504	aws->callback(NT_save_quick_as_cb);
505	aws->create_button("SAVE", "SAVE", "S");
506	}
507	return aws;
508	}
509
510	static void NT_database_optimization(AW_window *aww) {
511	arb_progress progress(WEIGHTED, "Optimizing database compression", 0.38);
512	// 38% for seq-compression is just a rough guess made with silvaNR99138
513	// (a real guess would have to depend on ali-count, ali-length + field-count)
514
515	GB_topSecurityLevel unsecured(GLOBAL.gb_main);
516
517	GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main);
518	if (!error) {
519	ConstStrArray ali_names;
520	GBT_get_alignment_names(ali_names, GLOBAL.gb_main);
521
522	arb_progress ali_progress("Optimizing sequence data", ali_names.size());
523	ali_progress.allow_title_reuse();
524
525	error = GBT_check_data(GLOBAL.gb_main, NULp);
526	error = GB_end_transaction(GLOBAL.gb_main, error);
527
528	if (!error) {
529	char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string();
530	for (int i = 0; ali_names[i]; ++i) {
531	error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]);
532	ali_progress.inc_and_check_user_abort(error);
533	}
534	free(tree_name);
535	}
536	}
537	progress.inc_and_check_user_abort(error);
538
539	if (!error) {
540	error = GB_optimize(GLOBAL.gb_main);
541	progress.inc_and_check_user_abort(error);
542	}
543	aww->hide_or_notify(error);
544	}
545
546	static AW_window NT_create_database_optimization_window(AW_root aw_root) {
547	static AW_window_simple *aws = NULp;
548	if (aws) return aws;
549	GB_transaction ta(GLOBAL.gb_main);
550
551	const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main);
552	aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree);
553
554	aws = new AW_window_simple;
555	aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression");
556	aws->load_xfig("optimize.fig");
557
558	aws->at("trees");
559	awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME);
560
561	aws->at("close");
562	aws->callback(AW_POPDOWN);
563	aws->create_button("CLOSE", "CLOSE", "C");
564
565	aws->callback(makeHelpCallback("optimize.hlp"));
566	aws->at("help");
567	aws->create_button("HELP", "HELP", "H");
568
569	aws->at("go");
570	aws->callback(NT_database_optimization);
571	aws->create_button("GO", "GO");
572	return aws;
573	}
574
575	static AW_window NT_create_save_as(AW_root aw_root, const char *base_name) {
576	static AW_window_simple *aws = NULp;
577	if (aws) return aws;
578
579	aws = new AW_window_simple;
580	aws->init(aw_root, "SAVE_DB", "SAVE ARB DB");
581	aws->load_xfig("save_as.fig");
582
583	aws->at("close");
584	aws->callback(AW_POPDOWN);
585	aws->create_button("CLOSE", "CLOSE", "C");
586
587	aws->at("help");
588	aws->callback(makeHelpCallback("save.hlp"));
589	aws->create_button("HELP", "HELP", "H");
590
591	AW_create_standard_fileselection(aws, base_name);
592
593	aws->at("type");
594	AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE);
595
596	aws->at("compression");
597	AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION);
598
599	aws->at("optimize");
600	aws->callback(NT_create_database_optimization_window);
601	aws->help_text("optimize.hlp");
602	aws->create_autosize_button("OPTIMIZE", "Optimize database compression");
603
604	aws->at("save");
605	aws->callback(NT_save_as_cb);
606	aws->create_button("SAVE", "SAVE", "S");
607
608	aws->at("comment");
609	aws->create_text_field(AWAR_DB_COMMENT);
610
611	return aws;
612	}
613
614	static void NT_undo_cb(AW_window, GB_UNDO_TYPE undo_type, TREE_canvas ntw) {
615	GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type);
616	if (error) aw_message(error);
617	else {
618	GB_transaction ta(GLOBAL.gb_main);
619	AWT_auto_refresh allowed_on(ntw);
620	ntw->request_refresh();
621	}
622	}
623
624	static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) {
625	DBUI::popup_species_info_window(canvas->awr, canvas->gb_main);
626	nt_mode_event(NULp, canvas, mode);
627	}
628
629	static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) {
630	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
631	if (tree_root) {
632	AWT_auto_refresh allowed_on(ntw);
633	GB_transaction ta(ntw->gb_main);
634
635	NT_mark_all_cb(NULp, ntw, 0); // unmark all
636	tree_root->mark_duplicates();
637	ntw->request_structure_update();
638	}
639	}
640
641	static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) {
642	GB_transaction ta(ntw->gb_main);
643	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
644
645	if (tree_root) {
646	AWT_auto_refresh allowed_on(ntw);
647	tree_root->justify_branch_lenghs(ntw->gb_main);
648	ntw->request_save_and_zoom_reset();
649	}
650	}
651
652	#if defined(DEBUG)
653	static void NT_fix_database(AW_window *) {
654	GB_ERROR err = NULp;
655	err = GB_fix_database(GLOBAL.gb_main);
656	if (err) aw_message(err);
657	}
658	#endif
659
660	static void relink_pseudo_species_to_organisms(GBDATA &ref_gb_node, char &ref_name, GB_HASH *organism_hash) {
661	if (ref_gb_node) {
662	if (GEN_is_pseudo_gene_species(ref_gb_node)) {
663	GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash);
664
665	if (gb_organism) {
666	char *name = GBT_read_string(gb_organism, "name");
667
668	if (name) {
669	freeset(ref_name, name);
670	ref_gb_node = gb_organism;
671	}
672	}
673	}
674	}
675	}
676
677	static void NT_pseudo_species_to_organism(AW_window , TREE_canvas ntw) {
678	GB_transaction ta(ntw->gb_main);
679	AP_tree *tree_root = AWT_TREE(ntw)->get_root_node();
680
681	if (tree_root) {
682	AWT_auto_refresh allowed_on(ntw);
683
684	GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main);
685	tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash);
686	GBS_free_hash(organism_hash);
687	ntw->request_save();
688	}
689	}
690
691
692	// #########################################
693	// #########################################
694	// ### ###
695	// ## user mask section ##
696	// ### ###
697	// #########################################
698	// #########################################
699
700	struct nt_item_type_species_selector FINAL_TYPE : public awt_item_type_selector {
701	nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {}
702	~nt_item_type_species_selector() OVERRIDE {}
703
704	const char *get_self_awar() const OVERRIDE {
705	return AWAR_SPECIES_NAME;
706	}
707	size_t get_self_awar_content_length() const OVERRIDE {
708	return 12; // should be enough for "nnaammee.999"
709	}
710	GBDATA current(AW_root root, GBDATA *gb_main) const OVERRIDE { // give the current item
711	char *species_name = root->awar(get_self_awar())->read_string();
712	GBDATA *gb_species = NULp;
713
714	if (species_name[0]) {
715	GB_transaction ta(gb_main);
716	gb_species = GBT_find_species(gb_main, species_name);
717	}
718
719	free(species_name);
720	return gb_species;
721	}
722	const char *getKeyPath() const OVERRIDE { // give the keypath for items
723	return CHANGE_KEY_PATH;
724	}
725	};
726
727	static nt_item_type_species_selector item_type_species;
728
729	static void NT_open_mask_window(AW_window aww, int id, GBDATA gb_main) {
730	const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id);
731	nt_assert(descriptor);
732	if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask());
733	}
734
735	static void NT_create_mask_submenu(AW_window_menu_modes *awm) {
736	AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main);
737	}
738	static AW_window create_colorize_species_window(AW_root aw_root) {
739	return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector());
740	}
741
742	// --------------------------------------------------------------------------------------------------
743
744	static void NT_alltree_remove_leafs(AW_window , GBT_TreeRemoveType mode, GBDATA gb_main) {
745	GB_ERROR error = NULp;
746	GB_transaction ta(gb_main);
747
748	ConstStrArray tree_names;
749	GBT_get_tree_names(tree_names, gb_main, false);
750
751	if (!tree_names.empty()) {
752	long treeCount = tree_names.size();
753
754	const char *whats_removed = NULp;
755	switch (mode) {
756	case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break;
757	case GBT_REMOVE_MARKED: whats_removed = "marked"; break;
758	default: nt_assert(0); break;
759	}
760
761	const char *task = GBS_global_string("Deleting %s from %li trees", whats_removed, treeCount);
762
763	arb_progress progress(task, treeCount);
764	GB_HASH *species_hash = GBT_create_species_hash(gb_main);
765
766	int modified = 0;
767
768	for (int t = 0; t<treeCount && !error; t++) {
769	progress.subtitle(tree_names[t]);
770	TreeNode *tree = GBT_read_tree(gb_main, tree_names[t], new SimpleRoot);
771	if (!tree) {
772	aw_message(GBS_global_string("Can't load tree '%s' - skipped", tree_names[t]));
773	}
774	else {
775	int removed = 0;
776	int groups_removed = 0;
777
778	tree = GBT_remove_leafs(tree, mode, species_hash, &removed, &groups_removed);
779
780	nt_assert(removed >= groups_removed);
781
782	if (!tree) {
783	aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t]));
784	}
785	else {
786	if (removed>0) {
787	error = GBT_write_tree(gb_main, tree_names[t], tree);
788	if (error) {
789	aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error));
790	}
791	else {
792	if (groups_removed>0) {
793	aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t]));
794	}
795	else {
796	aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t]));
797	}
798	modified++;
799	}
800	}
801	UNCOVERED();
802	destroy(tree);
803	}
804	}
805	progress.inc_and_check_user_abort(error);
806	}
807
808	if (modified) {
809	aw_message(GBS_global_string("Changed %i of %li trees.", modified, treeCount));
810	}
811	else {
812	aw_message("No tree modified");
813	}
814
815	GBS_free_hash(species_hash);
816	}
817
818	aw_message_if(ta.close(error));
819	}
820
821	// --------------------------------------------------------------------------------------------------
822
823	static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) {
824	GB_transaction ta(gb_main);
825	GBT_mark_all(gb_main, 0);
826
827	DBItemSetIter end = referred.end();
828	for (DBItemSetIter s = referred.begin(); s != end; ++s) {
829	GB_write_flag(*s, 1);
830	}
831	return ARB_ERROR();
832	}
833
834	static AW_window create_mark_by_refentries_window(AW_root awr, GBDATA *gbmain) {
835	static AW_window *aws = NULp;
836	if (!aws) {
837	static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector());
838	aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULp, "Mark referenced", mark_referred_species);
839	}
840	return aws;
841	}
842
843	// --------------------------------------------------------------------------------------------------
844
845	static void merge_from_to(AW_root awr, const char db_awar_name, bool merge_to) {
846	const char *db_name = awr->awar(db_awar_name)->read_char_pntr();
847	char *quotedDB = GBK_singlequote(db_name);
848
849	AW_system(
850	GBS_global_string(
851	merge_to
852	? "arb_ntree : %s &"
853	: "arb_ntree %s : &",
854	quotedDB)
855	);
856
857	free(quotedDB);
858	}
859
860	static void merge_from_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, false); }
861	static void merge_into_cb(AW_window aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), (const char**)cl_awarNamePtr, true); }
862
863	static AW_window NT_create_merge_from_window(AW_root awr) {
864	static char *awar_name = NULp; // do not free, bound to callback
865	AW_window *aw_from =
866	awt_create_load_box(awr, "Merge data from", "other ARB database",
867	".", ".arb", &awar_name,
868	makeWindowCallback(merge_from_cb, AW_CL(&awar_name)));
869	return aw_from;
870	}
871	static AW_window NT_create_merge_to_window(AW_root awr) {
872	static char *awar_name = NULp; // do not free, bound to callback
873	AW_window *aw_to =
874	awt_create_load_box(awr, "Merge data to", "other or new ARB database",
875	".", ".arb", &awar_name,
876	makeWindowCallback(merge_into_cb, AW_CL(&awar_name)),
877	makeWindowCallback(AW_POPDOWN), NULp);
878	return aw_to;
879	}
880
881	// --------------------------------------------------------------------------------------------------
882
883	static void update_main_window_title(AW_root awr, AW_window_menu_modes aww, int clone) {
884	const char *filename = awr->awar(AWAR_DB_NAME)->read_char_pntr();
885	const char *base_title = GBS_global_string("%s - ARB", filename);
886	aww->set_window_title(TREE_canvas::suffixed_title_for_index(base_title, clone));
887	}
888
889	static void canvas_tree_awar_changed_cb(AW_awar , bool, TREE_canvas ntw) {
890	NT_reload_tree_event(AW_root::SINGLETON, ntw, true);
891	AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists
892	TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_TREE);
893	}
894
895	class TREE_canvas_registry {
896	int count;
897	TREE_canvas *canvas[MAX_NT_WINDOWS];
898
899	static TREE_canvas_registry *SINGLETON;
900
901	TREE_canvas_registry() : count(0) {
902	AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT);
903	}
904
905	public:
906	static TREE_canvas_registry& instance() {
907	if (!SINGLETON) SINGLETON = new TREE_canvas_registry;
908	return *SINGLETON;
909	}
910
911	void register_canvas(TREE_canvas *ntw) {
912	nt_assert(count<MAX_NT_WINDOWS);
913	nt_assert(count == ntw->get_index()); // you have to register TREE_canvas'es in order of creation!
914	canvas[count++] = ntw;
915	ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks
916	}
917
918	int get_count() const { return count; }
919
920	TREE_canvas *get_canvas(int idx) const {
921	if (idx<0 \|\| idx>=count) return NULp;
922	return canvas[idx];
923	}
924	};
925
926	TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULp;
927
928	TREE_canvas *NT_get_canvas_by_index(int idx) {
929	/! return canvas with index 'idx' [0...MAX_NT_WINDOWS-1] /
930	nt_assert(idx>=0 && idx<MAX_NT_WINDOWS);
931	return TREE_canvas_registry::instance().get_canvas(idx);
932	}
933
934	#if defined(TRACE_GROUP_SELECTION)
935	static TREE_canvas find_canvas_showing(AWT_graphic_tree agt) {
936	// look for (registered) canvas showing given AWT_graphic_tree
937	// returns NULp if none found
938	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
939
940	int maxIdx = reg.get_count();
941	for (int32_t i = 0; i<maxIdx; ++i) {
942	TREE_canvas *ntw = reg.get_canvas(i);
943	if (ntw->gfx == agt) return ntw;
944	}
945	return NULp;
946	}
947	#endif
948
949	void NT_fill_canvas_selection_list(class AW_selection_list sellst, TREE_canvas to_skip) {
950	/*! insert canvases into selection list (using canvas-indices as values)
951	*/
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 && ntw != to_skip) {
958	nt_assert(ntw->get_awar_tree());
959	const char *treename = ntw->get_awar_tree()->read_char_pntr();
960	const char *description = i
961	? GBS_global_string("%s: %s", TREE_canvas::suffixed_title_for_index("ARB", i), treename)
962	: GBS_global_string("ARB main: %s", treename);
963	sellst->insert(description, i);
964	}
965	}
966	}
967
968	// ----------------------------------
969	// group-selection handlers
970
971	void NT_deselect_group(AW_root *awr) {
972	awr->awar(AWAR_GROUP)->write_pointer(NULp);
973	}
974
975	static bool track_group_selection_by_canvas = true;
976
977	static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) {
978	const Group& group = gfx->get_selected_group();
979
980	#if defined(TRACE_GROUP_SELECTION)
981	fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track");
982	TREE_canvas *ntw = find_canvas_showing(gfx);
983	if (group.is_valid()) {
984	fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name());
985	}
986	else {
987	fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index());
988	}
989	#endif
990
991	if (track_group_selection_by_canvas) {
992	// set group-awar:
993	gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULp if !group.is_valid()
994	}
995	}
996
997	static void group_awar_changed_cb(AW_root *awr) {
998	AW_awar *awar_group = awr->awar(AWAR_GROUP);
999	GBDATA *gb_wanted_group = awar_group->read_pointer();
1000
1001	GBDATA *gb_wanted_tree = NULp;
1002	{
1003	if (gb_wanted_group) {
1004	GB_transaction ta(gb_wanted_group);
1005	gb_wanted_tree = GB_get_father(gb_wanted_group);
1006	awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected
1007	#if defined(TRACE_GROUP_SELECTION)
1008	fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr);
1009	#endif
1010	}
1011	#if defined(TRACE_GROUP_SELECTION)
1012	const char *group_name = NULp;
1013	if (gb_wanted_group) {
1014	GB_transaction ta(gb_wanted_group);
1015	GBDATA *gb_name = GB_entry(gb_wanted_group, "group_name");
1016	if (gb_name) group_name = GB_read_char_pntr(gb_name);
1017	}
1018	fprintf(stderr, "group awar changed to %p", gb_wanted_group);
1019	if (group_name) fprintf(stderr, " (='%s')", group_name);
1020	fputc('\n', stderr);
1021	#endif
1022	}
1023
1024	LocallyModify<bool> ignore_group_selection_by_canvas(track_group_selection_by_canvas, false);
1025
1026	{
1027	const TREE_canvas_registry& reg = TREE_canvas_registry::instance();
1028
1029	int maxIdx = reg.get_count();
1030	for (int32_t i = 0; i<maxIdx; ++i) {
1031	TREE_canvas *ntw = reg.get_canvas(i);
1032	AWT_graphic_tree *agt = AWT_TREE(ntw);
1033	const Group& curr_group = agt->get_selected_group();
1034
1035	GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree();
1036	if (gb_curr_tree == gb_wanted_tree) {
1037	AWT_auto_refresh allowed_on(ntw);
1038	if (!curr_group.is_valid() \|\| // no group selected
1039	curr_group.get_group_data() != gb_wanted_group) // wrong group selected
1040	{
1041	agt->select_group(gb_wanted_group);
1042	ntw->request_refresh();
1043	}
1044	// perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group)
1045	TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_GROUP);
1046	}
1047	else {
1048	if (curr_group.is_valid()) {
1049	AWT_auto_refresh allowed_on(ntw);
1050	agt->deselect_group();
1051	ntw->request_refresh();
1052	}
1053	}
1054	}
1055	}
1056	}
1057
1058	// ----------------------------
1059	// create main window
1060
1061	static AW_window popup_new_main_window(AW_root awr, int clone, TREE_canvas **result_ntw) {
1062	/*! create ARB_NTREE main window
1063	* @param awr application root
1064	* @param clone == 0 -> first window (full functionality); >0 -> additional tree views (restricted functionality)
1065	* @param result_ntw is set to the created TREE_canvas (passed pointer may be NULp if result is not needed)
1066	*/
1067	GB_push_transaction(GLOBAL.gb_main);
1068
1069	const char *awar_tree = NULp;
1070	AW_window_menu_modes *awm = new AW_window_menu_modes;
1071
1072	{
1073	char window_id[256];
1074	if (clone) {
1075	awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone));
1076	sprintf(window_id, "ARB_NT_%i", clone);
1077	}
1078	else {
1079	awar_tree = AWAR_TREE;
1080	sprintf(window_id, "ARB_NT");
1081	}
1082	awm->init(awr, window_id, "[starting arb]", 0, 0); // effective title is generated by update_main_window_title
1083	}
1084
1085	awr->awar(AWAR_DB_NAME)
1086	->add_callback(makeRootCallback(update_main_window_title, awm, clone))
1087	->update();
1088
1089	awm->button_length(5);
1090
1091	if (!clone) AW_init_color_group_defaults("arb_ntree");
1092
1093	AWT_graphic_tree *tree = TREE_generate_display(awr, GLOBAL.gb_main, launch_MapViewer_cb);
1094
1095	if (!clone) { // while creating initial window
1096	AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb));
1097	awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb);
1098	}
1099
1100	TREE_canvas *ntw;
1101	{
1102	AW_awar *tree_awar = awr->awar_string(awar_tree);
1103	{
1104	AP_tree_display_style prev_style = tree->get_tree_style();
1105	tree->set_tree_style(AP_LIST_SIMPLE, NULp); // avoid NDS warnings during startup
1106
1107	ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar);
1108	nt_assert(ntw->get_index() == clone); // required for proper title enumeration.
1109
1110	tree->set_tree_style(prev_style, ntw);
1111	ntw->set_mode(AWT_MODE_SELECT);
1112	}
1113
1114	if (result_ntw) *result_ntw = ntw;
1115
1116	{
1117	const char *tree_name = tree_awar->read_char_pntr();
1118	const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name);
1119
1120	if (existing_tree_name) {
1121	tree_awar->write_string(existing_tree_name);
1122	NT_reload_tree_event(awr, ntw, true); // load first tree
1123	}
1124	else {
1125	AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, NULp, "no_tree.hlp");
1126	tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list
1127	}
1128
1129	TREE_canvas_registry::instance().register_canvas(ntw);
1130	AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false);
1131	}
1132	}
1133
1134	TREE_install_update_callbacks(ntw);
1135
1136	bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db)
1137
1138	WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main);
1139
1140	// --------------
1141	// File
1142
1143	#if defined(DEBUG)
1144	AWT_create_debug_menu(awm);
1145	#endif // DEBUG
1146
1147	bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS;
1148
1149	if (clone) {
1150	awm->create_menu("File", "F", AWM_ALL);
1151	if (allow_new_window) {
1152	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));
1153	}
1154	awm->insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN);
1155	}
1156	else {
1157	#if defined(DEBUG)
1158	// add more to debug-menu
1159	awm->sep______________();
1160	awm->insert_menu_topic("fix_db", "Fix database", "F", NULp, AWM_ALL, NT_fix_database);
1161	awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", NULp, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main));
1162	awm->insert_menu_topic("test_compr", "Test compression", "T", NULp, AWM_ALL, makeWindowCallback(GBT_compression_test, GLOBAL.gb_main));
1163	#endif // DEBUG
1164
1165	awm->create_menu("File", "F", AWM_ALL);
1166	{
1167	// keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries
1168	awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, NT_save_quick_cb);
1169	awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1170	if (allow_new_window) {
1171	awm->sep______________();
1172	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));
1173	}
1174	awm->sep______________();
1175	awm->insert_menu_topic("optimize_db", "Optimize database compression", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window);
1176	awm->sep______________();
1177
1178	awm->insert_sub_menu("Import", "I");
1179	{
1180	awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window);
1181	awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, makeWindowCallback(NT_import_sequences, ntw));
1182	GDE_load_menu(awm, AWM_EXP, "Import");
1183	}
1184	awm->close_sub_menu();
1185
1186	awm->insert_sub_menu("Export", "E");
1187	{
1188	awm->insert_menu_topic("export_to_ARB", "Merge to other or new ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window);
1189	awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main));
1190	GDE_load_menu(awm, AWM_ALL, "Export");
1191	awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window);
1192	}
1193	awm->close_sub_menu();
1194	awm->sep______________();
1195
1196	insert_macro_menu_entry(awm, false);
1197
1198	awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V");
1199	{
1200	awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp"));
1201	awm->insert_menu_topic("bug_report", "Report bug", "b", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport"));
1202	awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList"));
1203	}
1204	awm->close_sub_menu();
1205	awm->sep______________();
1206
1207	awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false));
1208	awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true));
1209	awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_confirm_exit, EXIT_SUCCESS));
1210	}
1211
1212	// -----------------
1213	// Species
1214
1215	awm->create_menu("Species", "c", AWM_ALL);
1216	{
1217	awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1218	awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb);
1219
1220	awm->sep______________();
1221
1222	NT_insert_mark_submenus(awm, ntw, 1);
1223	awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main));
1224	awm->insert_menu_topic("species_colors", "Colors ...", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window);
1225	awm->insert_menu_topic("selection_admin", "Selections ...", "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw));
1226
1227	awm->sep______________();
1228
1229	awm->insert_sub_menu("Database fields admin", "f");
1230	DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main);
1231	awm->close_sub_menu();
1232	NT_create_mask_submenu(awm);
1233
1234	awm->sep______________();
1235
1236	awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw));
1237
1238	awm->insert_sub_menu("Sort Species", "s");
1239	{
1240	awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window);
1241	awm->insert_menu_topic("$sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw));
1242	}
1243	awm->close_sub_menu();
1244
1245	awm->insert_sub_menu("Merge Species", "g", AWM_EXP);
1246	{
1247	awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow);
1248	awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "species_join.hlp", AWM_EXP, NT_create_species_join_window);
1249	}
1250	awm->close_sub_menu();
1251
1252	awm->sep______________();
1253
1254	awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main));
1255
1256	awm->sep______________();
1257
1258	awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main));
1259
1260	awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP);
1261	{
1262	awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames);
1263	awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames);
1264	awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames);
1265	awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window);
1266	}
1267	awm->close_sub_menu();
1268	}
1269
1270	// ----------------------------
1271	// Genes + Experiment
1272
1273	if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true);
1274
1275	// ------------------
1276	// Sequence
1277
1278	awm->create_menu("Sequence", "S", AWM_ALL);
1279	{
1280	awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)NULp));
1281	awm->insert_sub_menu("Insert/delete", "I");
1282	{
1283	awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window);
1284	awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main));
1285	}
1286	awm->close_sub_menu();
1287	awm->sep______________();
1288
1289	awm->insert_sub_menu("Edit Sequences", "E");
1290	{
1291	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));
1292	awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw));
1293	awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window);
1294	}
1295	awm->close_sub_menu();
1296
1297	awm->sep______________();
1298
1299	awm->insert_sub_menu("Align sequences", "l");
1300	{
1301	awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window);
1302	GDE_load_menu(awm, AWM_ALL, "Align");
1303	}
1304	awm->close_sub_menu();
1305	awm->insert_menu_topic("seq_concat", "Concatenate sequences", "C", "concatenate.hlp", AWM_ALL, NT_createConcatenationWindow);
1306	awm->insert_menu_topic("seq_split", "Split sequences", "S", "split.hlp", AWM_ALL, NT_create_splitAlignment_window);
1307	awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window);
1308	awm->sep______________();
1309
1310	awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window);
1311	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist"));
1312	awm->sep______________();
1313
1314	awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main));
1315	awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main));
1316
1317	awm->sep______________();
1318
1319	GDE_load_menu(awm, AWM_ALL, "Print");
1320	}
1321
1322	// -------------
1323	// SAI
1324
1325	awm->create_menu("SAI", "A", AWM_ALL);
1326	{
1327	awm->insert_menu_topic("sai_admin", "SAI Admin", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window);
1328	awm->insert_menu_topic("sai_calc", "Combine SAIs", "b", "saicalc.hlp", AWM_ALL, makeWindowCallback(SAI_popup_calculator_window, GLOBAL.gb_main));
1329	awm->insert_sub_menu("Create SAI using ...", "C");
1330	{
1331	awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window);
1332	awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window);
1333	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);
1334	awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_phylo"));
1335	awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold);
1336
1337	GDE_load_menu(awm, AWM_EXP, "SAI");
1338	}
1339	awm->close_sub_menu();
1340
1341	awm->insert_sub_menu("Other functions", "O");
1342	{
1343	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));
1344	awm->insert_menu_topic("corr_mutat_analysis", "Compute clusters of correlated positions", "m", "", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_rnacma", new XCmdType(XCMD_SERVSYNC_WAIT_ON_ERROR, GLOBAL.gb_main)));
1345	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);
1346	}
1347	awm->close_sub_menu();
1348	}
1349
1350	// ----------------
1351	// Probes
1352
1353	awm->create_menu("Probes", "P", AWM_ALL);
1354	{
1355	awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main));
1356	awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw));
1357	awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main));
1358	awm->sep______________();
1359	awm->insert_menu_topic("probe_match_sp", "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window, ntw));
1360	awm->sep______________();
1361	awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main));
1362	awm->insert_menu_topic("primer_design", "Design Sequencing Primers", "S", "primer.hlp", AWM_EXP, makeWindowCallback(ARB_system_in_console_cb, "arb_primer", new XCmdType(XCMD_SERVSYNC_WAIT_ON_ERROR, GLOBAL.gb_main)));
1363	awm->sep______________();
1364	awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main));
1365	}
1366
1367	}
1368
1369	// --------------
1370	// Tree
1371
1372	awm->create_menu("Tree", "T", AWM_ALL);
1373	{
1374	if (!clone) {
1375	awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window);
1376	awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(NDS_create_window, GLOBAL.gb_main));
1377	awm->sep______________();
1378	awm->insert_sub_menu("Add Species to Existing Tree", "A");
1379	{
1380	awm->insert_menu_topic("arb_pars_quick", "ARB Parsimony (Quick add marked)", "Q", "pars.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_pars -add_marked -quit"));
1381	awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_pars"));
1382	GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny");
1383	}
1384	awm->close_sub_menu();
1385	}
1386
1387	awm->insert_sub_menu("Remove Species from Tree", "R");
1388	{
1389	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));
1390	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));
1391	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));
1392	awm->sep______________();
1393	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));
1394	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));
1395	}
1396	awm->close_sub_menu();
1397
1398	if (!clone) {
1399	awm->insert_sub_menu("Build tree from sequence data", "B");
1400	{
1401	awm->insert_sub_menu("Distance matrix methods", "D");
1402	awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist"));
1403	GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix");
1404	awm->close_sub_menu();
1405
1406	awm->insert_sub_menu("Maximum Parsimony methods", "P");
1407	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony");
1408	awm->close_sub_menu();
1409
1410	awm->insert_sub_menu("Maximum Likelihood methods", "L");
1411	GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP");
1412	GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood");
1413	awm->close_sub_menu();
1414
1415	awm->insert_sub_menu("Other methods", "O", AWM_EXP);
1416	GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)");
1417	awm->close_sub_menu();
1418	}
1419	awm->close_sub_menu();
1420	}
1421
1422	awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window);
1423
1424	awm->sep______________();
1425
1426	awm->insert_sub_menu("Reset zoom", "z");
1427	{
1428	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));
1429	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));
1430	}
1431	awm->close_sub_menu();
1432
1433	awm->sep______________();
1434
1435	// taxonomic groups
1436	NT_insert_collapse_submenu(awm, ntw);
1437	if (!clone) {
1438	awm->insert_menu_topic("group_search", "Search groups...", "g", "group_search.hlp", AWM_ALL, makeWindowCallback (popup_group_search_window, GLOBAL.gb_main));
1439	awm->insert_menu_topic("compare_taxonomy", "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw));
1440	awm->insert_menu_topic("move_groups", "Move groups...", "v", "move_groups.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_moveGroupInfo_window));
1441	}
1442
1443	awm->sep______________();
1444
1445	if (!clone) {
1446	awm->insert_menu_topic("compare_topology", "Compare topology...", "o", "compare_topo.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compareTopologies_window));
1447	}
1448
1449	awm->insert_sub_menu("Modify branches", "M");
1450	{
1451	awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw));
1452	awm->insert_menu_topic(awm->local_id("tree_edit_remark"), "Edit bootstraps", "E", "ted_boot.hlp", AWM_ALL, makeWindowCallback(NT_edit_bootstrap, ntw));
1453	awm->sep______________();
1454	awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw));
1455	awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw));
1456	awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw));
1457	awm->sep______________();
1458	awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw));
1459	awm->sep______________();
1460	awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0));
1461	awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1));
1462
1463	}
1464	awm->close_sub_menu();
1465	awm->insert_sub_menu("Beautify tree", "u");
1466	{
1467	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));
1468	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));
1469	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));
1470	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));
1471	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));
1472	awm->sep______________();
1473	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));
1474	}
1475	awm->close_sub_menu();
1476
1477	awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "h", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw));
1478	awm->insert_menu_topic(awm->local_id("syncroots"), "Adjust roots...", "j", "syncroots.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncroot_window, GLOBAL.gb_main));
1479	awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "k", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback (NT_mark_duplicates, ntw));
1480
1481	awm->sep______________();
1482	awm->insert_menu_topic(awm->local_id("shade"), "Tree shading...", "s", "tree_shading.hlp", AWM_ALL, makeWindowCallback (NT_configure_treeShader));
1483	awm->insert_menu_topic(awm->local_id("syncscroll"), "Sync tree scrolling..", "e", "syncscroll.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw));
1484
1485	awm->sep______________();
1486	awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", NULp, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree));
1487
1488	awm->sep______________();
1489	awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp"));
1490
1491	if (is_genome_db) {
1492	awm->sep______________();
1493	awm->insert_menu_topic(awm->local_id("tree_pseudo_species_to_organism"), "Relink tree to organisms", "i", "tree_pseudo.hlp", AWM_EXP, makeWindowCallback(NT_pseudo_species_to_organism, ntw));
1494	}
1495
1496	if (!clone) {
1497	awm->sep______________();
1498	awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast<AWT_canvas*>(ntw)));
1499	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)));
1500	}
1501
1502	}
1503
1504	if (!clone) {
1505	// ---------------
1506	// Tools
1507
1508	awm->create_menu("Tools", "o", AWM_ALL);
1509	{
1510	awm->insert_menu_topic("names_admin", "Nameserver admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeWindowCallback(AW_popup_namesadmin_window, GLOBAL.gb_main));
1511	awm->insert_sub_menu("DB admin", "D", AWM_EXP);
1512	{
1513	awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main));
1514	}
1515	awm->close_sub_menu();
1516	awm->sep______________();
1517
1518	awm->insert_sub_menu("GDE specials", "G", AWM_EXP);
1519	{
1520	GDE_load_menu(awm, AWM_EXP, NULp);
1521	}
1522	awm->close_sub_menu();
1523
1524	awm->sep______________();
1525	awm->insert_menu_topic("xterm", "Start XTERM", "X", "xterm.hlp", AWM_ALL, AW_console_cb);
1526	XCmdType *showlog_cmdtype = new XCmdType(XCMD_ASYNC_WAIT_ON_ERROR, GLOBAL.gb_main); // do not free (used in callback)
1527	awm->insert_menu_topic("viewlog", "View ARB log", "l", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl run", showlog_cmdtype)); // ../SH/arb_show_log.pl
1528	awm->insert_menu_topic("viewserv", "View server log", "V", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl server", showlog_cmdtype));
1529	awm->insert_menu_topic("viewsys", "View sysinfo", "i", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl sysinf", showlog_cmdtype));
1530	awm->sep______________();
1531	GDE_load_menu(awm, AWM_EXP, "User");
1532	}
1533	// --------------------
1534	// Properties
1535
1536	awm->create_menu("Properties", "r", AWM_ALL);
1537	{
1538	awm->insert_menu_topic("props_menu", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window);
1539	awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window);
1540	awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager));
1541	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));
1542	awm->sep______________();
1543	awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", NULp, AWM_ALL, NT_toggle_expert_mode);
1544	awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", NULp, AWM_ALL, NT_toggle_focus_policy);
1545	awm->sep______________();
1546	AW_insert_common_property_menu_entries(awm);
1547	awm->sep______________();
1548	awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties);
1549	}
1550	}
1551
1552	awm->insert_help_topic("ARB NTREE help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp"));
1553
1554	// ----------------------
1555	// mode buttons
1556	//
1557	// keep them synchronized as far as possible with those in ARB_PARSIMONY
1558	// see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized
1559
1560	awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT));
1561	awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK));
1562	awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP));
1563	awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM));
1564	awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM));
1565
1566	awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO));
1567	awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW));
1568
1569	// topology-modification-modes
1570	awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT));
1571	awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP));
1572	awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE));
1573	awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH));
1574	awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC));
1575
1576	// layout-modes
1577	awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE));
1578	awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE));
1579	awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD));
1580
1581	awm->set_info_area_height(250);
1582	awm->at(5, 2);
1583	awm->auto_space(-2, -2);
1584	awm->shadow_width(1);
1585
1586	// -------------------------
1587	// create top area
1588
1589	int first_liney;
1590	int leftx;
1591	awm->get_at_position(&leftx, &first_liney);
1592
1593	// ---------------------
1594	// quit + help
1595
1596	awm->button_length(0);
1597
1598	if (clone) {
1599	awm->callback(AW_POPDOWN);
1600	awm->create_button("CLOSE", "#close.xpm");
1601	}
1602	else {
1603	awm->callback(makeWindowCallback(NT_confirm_exit, EXIT_SUCCESS));
1604	awm->help_text("quit.hlp");
1605	awm->create_button("QUIT", "#quit.xpm");
1606	}
1607
1608	int db_pathx = awm->get_at_xposition();
1609
1610	// now fetch the yposition for the 2nd button line
1611	awm->at_newline();
1612	int second_liney = awm->get_at_yposition();
1613
1614	awm->callback(AW_help_entry_pressed);
1615	awm->help_text("arb_ntree.hlp");
1616	awm->create_button("?", "#help.xpm");
1617
1618	// --------------------------
1619	// save + undo/redo
1620
1621	awm->callback(NT_save_quick_cb);
1622	awm->help_text("save.hlp");
1623	awm->create_button("SAVE", "#save.xpm");
1624
1625	awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE));
1626	awm->help_text("save.hlp");
1627	awm->create_button("SAVE_AS", "#saveAs.xpm");
1628
1629	// undo/redo:
1630	awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw));
1631	awm->help_text("undo.hlp");
1632	awm->create_button("UNDO", "#undo.xpm");
1633
1634	awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw));
1635	awm->help_text("undo.hlp");
1636	awm->create_button("REDO", "#redo.xpm");
1637
1638	int db_pathx2 = awm->get_at_xposition();
1639
1640	// fetch position for mode help-line:
1641	awm->at_newline();
1642	int third_liney = awm->get_at_yposition();
1643
1644	awm->at(db_pathx, first_liney);
1645	// size of DB-name button is determined by buttons below:
1646	awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1);
1647	awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE));
1648	awm->help_text("save.hlp");
1649	awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME);
1650
1651	// -----------------------------
1652	// tree + tree display
1653
1654	#define TREE_BUTTON_OVERSIZE 6
1655
1656	int db_treex = awm->get_at_xposition();
1657	int second_uppery = second_liney-TREE_BUTTON_OVERSIZE;
1658
1659	awm->at(db_treex, second_uppery);
1660	awm->button_length(0);
1661
1662	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL));
1663	awm->help_text("tr_type_radial.hlp");
1664	awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm");
1665
1666	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL));
1667	awm->help_text("tr_type_dendro.hlp");
1668	awm->create_button("LIST_TREE_TYPE", "#dendro.xpm");
1669
1670	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS));
1671	awm->help_text("tr_type_irs.hlp");
1672	awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm");
1673
1674	awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS));
1675	awm->help_text("tr_type_nds.hlp");
1676	awm->create_button("NO_TREE_TYPE", "#listdisp.xpm");
1677
1678	int db_treex2 = awm->get_at_xposition();
1679
1680	awm->at(db_treex, first_liney);
1681	// size of tree-name button is determined by buttons below:
1682	awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1);
1683	awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree, ntw));
1684	awm->help_text("nt_tree_select.hlp");
1685	awm->create_button("SELECT_A_TREE", awar_tree);
1686
1687	// ---------------------------------------------------------------
1688	// protection, alignment + editor (and maybe Genome Map)
1689
1690	int db_alignx = awm->get_at_xposition();
1691
1692	// editor and genemap buttons have to be 44x24 sized
1693	#define EDIT_XSIZE 50
1694	#define EDIT_YSIZE 30 // same as 'save as' buttons
1695
1696	// first draw protection:
1697	int protectx = db_alignx + 2*EDIT_XSIZE;
1698
1699	awm->at(protectx+2, first_liney+1);
1700	awm->button_length(0);
1701	awm->create_button(NULp, "#protect.xpm");
1702
1703	awm->at(protectx, second_liney+2);
1704	awm->create_option_menu(AWAR_SECURITY_LEVEL);
1705	awm->insert_option ("0", NULp, 0);
1706	awm->insert_option ("1", NULp, 1);
1707	awm->insert_option ("2", NULp, 2);
1708	awm->insert_option ("3", NULp, 3);
1709	awm->insert_option ("4", NULp, 4);
1710	awm->insert_option ("5", NULp, 5);
1711	awm->insert_default_option("6", NULp, 6);
1712	awm->update_option_menu();
1713
1714	int db_searchx = awm->get_at_xposition() - 7;
1715
1716	// draw ali/editor buttons AFTER protect menu (to get rid of it's label)
1717	awm->at(db_alignx, second_liney);
1718
1719	awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE);
1720	awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw));
1721	awm->help_text("arb_edit4.hlp");
1722	if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm");
1723	else awm->create_button("EDIT_SEQUENCES", "#editor.xpm");
1724
1725	if (is_genome_db) {
1726	awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE);
1727	awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map
1728	awm->help_text("gene_map.hlp");
1729	awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm");
1730	}
1731
1732	int db_alignx2 = awm->get_at_xposition();
1733
1734	awm->at(db_alignx, first_liney);
1735	awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1);
1736	awm->callback(NT_create_select_alignment_window);
1737	awm->help_text("nt_align_select.hlp");
1738	awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT);
1739
1740	// -------------------------------
1741	// create mode-help line
1742
1743	awm->at(leftx, third_liney);
1744	awm->button_length(AWAR_FOOTER_MAX_LEN);
1745	awm->create_button(NULp, AWAR_FOOTER);
1746
1747	awm->at_newline();
1748	int bottomy = awm->get_at_yposition();
1749
1750	// ---------------------------------------
1751	// Info / marked / Search / Jump
1752
1753	awm->button_length(7);
1754
1755	awm->at(db_searchx, first_liney);
1756	awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main));
1757	awm->help_text("sp_search.hlp");
1758	awm->create_button("SEARCH", "Search");
1759
1760	awm->at(db_searchx, second_uppery);
1761	awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON));
1762	awm->help_text("tr_jump.hlp");
1763	awm->create_button("JUMP", "Jump");
1764
1765	int db_infox = awm->get_at_xposition();
1766
1767	awm->at(db_infox, first_liney);
1768	awm->button_length(13);
1769	awm->callback(popupinfo_wcb);
1770	awm->help_text("sp_info.hlp");
1771	awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT);
1772
1773	awm->at(db_infox, second_uppery);
1774	create_species_selection_button(awm, makeWindowCallback(NT_popup_configuration_admin, ntw), "selection_admin2", AWAR_MARKED_SPECIES_COUNTER, GLOBAL.gb_main);
1775
1776	// set height of top area:
1777	awm->set_info_area_height(bottomy+2);
1778	awm->set_bottom_area_height(0);
1779
1780	NT_activate_configMarkers_display(ntw);
1781
1782	// ------------------------------------
1783	// Autostarts for development
1784
1785	#if defined(DEVEL_RALF)
1786	// if (is_genome_db) GEN_map_first(awr)->show();
1787	#endif // DEVEL_RALF
1788
1789	GB_pop_transaction(GLOBAL.gb_main);
1790
1791	#if defined(DEBUG)
1792	AWT_check_action_ids(awr, is_genome_db ? "_genome" : "");
1793	#endif
1794
1795	return awm;
1796	}
1797
1798	TREE_canvas NT_create_main_window(AW_root aw_root) {
1799	GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE);
1800	if (error) aw_message(error);
1801
1802	nt_create_all_awars(aw_root);
1803
1804	TREE_canvas *ntw = NULp;
1805	AW_window *aww = popup_new_main_window(aw_root, 0, &ntw);
1806	NT_install_treeShader(ntw, GLOBAL.gb_main);
1807	aww->show();
1808
1809	error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO);
1810	if (error) aw_message(error);
1811
1812	return ntw;
1813	}

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source: branches/sina/NTREE/NT_extern.cxx

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