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source: tags/arb_5.5/NTREE/NT_main.cxx

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Last change on this file was 6143, checked in by westram, 15 years ago
backport [6141] (parts changing code, but only strings and comments)
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File size: 19.3 KB

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1	#include <string.h>
2	#include <stdio.h>
3	#include <stdlib.h>
4	#include <arbdb.h>
5	#include <arbdbt.h>
6	#include <adGene.h>
7
8	#include <servercntrl.h>
9	#include <aw_root.hxx>
10	#include <aw_device.hxx>
11	#include <aw_window.hxx>
12	#include <aw_awars.hxx>
13	#include <aw_question.hxx>
14	#include <aw_global.hxx>
15	#include <awt_canvas.hxx>
16	#include <awt_advice.hxx>
17
18	#include <awt_tree.hxx>
19	#include <awt_dtree.hxx>
20	#include <awt.hxx>
21	#include <awti_import.hxx>
22
23	#include <mg_merge.hxx>
24
25	#include "nt_internal.h"
26	#include "ntree.hxx"
27	#include "nt_cb.hxx"
28	#include "NT_dbrepair.hxx"
29
30	#include <arb_version.h>
31
32	using namespace std;
33
34	AW_HEADER_MAIN
35
36	#define nt_assert(bed) arb_assert(bed)
37
38	#define NT_SERVE_DB_TIMER 50
39	#define NT_CHECK_DB_TIMER 200
40
41	GBDATA *GLOBAL_gb_main; // global gb_main for arb_ntree
42	NT_global GLOBAL_NT = { 0, 0, 0, false };
43
44	// NT_format_all_alignments may be called after any operation which causes
45	// unformatted alignments (e.g importing sequences)
46	//
47	// It tests all alignments whether they need to be formatted
48	// and asks the user if they should be formatted.
49
50	GB_ERROR NT_format_all_alignments(GBDATA *gb_main) {
51	GB_ERROR err = 0;
52	GB_push_transaction(gb_main);
53	GB_push_my_security(gb_main);
54
55	aw_status("Checking alignments");
56	err = GBT_check_data(gb_main, 0);
57
58	AW_repeated_question question;
59	GBDATA *gb_presets = GB_entry(gb_main,"presets");
60
61	question.add_help("prompt/format_alignments.hlp");
62
63	for (GBDATA *gb_ali = GB_entry(gb_presets,"alignment"); gb_ali && !err; gb_ali = GB_nextEntry(gb_ali)) {
64	GBDATA *gb_aligned = GB_search(gb_ali, "aligned", GB_INT);
65
66	if (GB_read_int(gb_aligned) == 0) { // sequences in alignment are not formatted
67	enum FormatAction {
68	FA_ASK_USER = 0, // ask user
69	FA_FORMAT_ALL = 1, // format automatically w/o asking
70	FA_SKIP_ALL = 2, // skip automatically w/o asking
71	};
72	FormatAction format_action = FA_ASK_USER;
73	GBDATA *gb_ali_name = GB_entry(gb_ali,"alignment_name");
74	const char *ali_name = GB_read_char_pntr(gb_ali_name);
75
76	{
77	bool is_ali_genom = strcmp(ali_name, GENOM_ALIGNMENT) == 0;
78	GBDATA *gb_auto_format = GB_entry(gb_ali, "auto_format");
79
80	if (gb_auto_format) {
81	format_action = FormatAction(GB_read_int(gb_auto_format));
82	if (is_ali_genom) {
83	if (format_action != FA_SKIP_ALL) {
84	format_action = FA_SKIP_ALL; // always skip ali_genom
85	err = GB_write_int(gb_auto_format, FA_SKIP_ALL);
86	}
87	}
88	}
89	else if (is_ali_genom) {
90	format_action = FA_SKIP_ALL;
91	err = GBT_write_int(gb_ali, "auto_format", FA_SKIP_ALL); // always skip
92	}
93	}
94
95	bool perform_format = false;
96	if (!err) {
97	switch (format_action) {
98	case FA_FORMAT_ALL: perform_format = true; break;
99	case FA_SKIP_ALL: perform_format = false; break;
100	default: {
101	char *qtext = GBS_global_string_copy("Alignment '%s' is not formatted. Format?", ali_name);
102	int answer = question.get_answer(qtext, "Format,Skip,Always format,Always skip", "all", false);
103
104	switch (answer) {
105	case 2:
106	err = GBT_write_int(gb_ali, "auto_format", FA_FORMAT_ALL);
107	// fall-through
108	case 0:
109	perform_format = true;
110	break;
111
112	case 3:
113	err = GBT_write_int(gb_ali, "auto_format", FA_SKIP_ALL);
114	break;
115	}
116
117	free(qtext);
118	break;
119	}
120	}
121	}
122	if (!err && perform_format) {
123	aw_status(GBS_global_string("Formatting '%s'", ali_name));
124	GB_push_my_security(gb_main);
125	err = GBT_format_alignment(gb_main, ali_name);
126	GB_pop_my_security(gb_main);
127	}
128	}
129	}
130
131	GB_pop_my_security(gb_main);
132
133	return GB_end_transaction(gb_main, err);
134	}
135
136
137	// --------------------------------------------------------------------------------
138
139
140
141	// called once on ARB_NTREE startup
142	//
143	static GB_ERROR nt_check_database_consistency() {
144	aw_openstatus("Checking database...");
145
146	GB_ERROR err = NT_format_all_alignments(GLOBAL_gb_main);
147	if (!err) err = NT_repair_DB(GLOBAL_gb_main);
148
149	aw_closestatus();
150	return err;
151	}
152
153
154	void serve_db_interrupt(AW_root *awr){
155	GB_BOOL succes = GBCMS_accept_calls(GLOBAL_gb_main,GB_FALSE);
156	while (succes){
157	awr->check_for_remote_command((AW_default)GLOBAL_gb_main,AWAR_NT_REMOTE_BASE);
158	succes = GBCMS_accept_calls(GLOBAL_gb_main,GB_TRUE);
159	}
160
161	awr->add_timed_callback(NT_SERVE_DB_TIMER,(AW_RCB)serve_db_interrupt,0,0);
162	}
163
164	void check_db_interrupt(AW_root *awr){
165	awr->check_for_remote_command((AW_default)GLOBAL_gb_main,AWAR_NT_REMOTE_BASE);
166	awr->add_timed_callback(NT_CHECK_DB_TIMER,(AW_RCB)check_db_interrupt,0,0);
167	}
168
169	GB_ERROR create_nt_window(AW_root *aw_root){
170	AW_window *aww;
171	GB_ERROR error = GB_request_undo_type(GLOBAL_gb_main, GB_UNDO_NONE);
172	if (error) aw_message(error);
173	nt_create_all_awars(aw_root,AW_ROOT_DEFAULT);
174	aww = create_nt_main_window(aw_root,0);
175	aww->show();
176	error = GB_request_undo_type(GLOBAL_gb_main, GB_UNDO_UNDO);
177	if (error) aw_message(error);
178	return error;
179	}
180
181	// after intro
182	void nt_main_startup_main_window(AW_root *aw_root){
183	create_nt_window(aw_root);
184
185	if (GB_read_clients(GLOBAL_gb_main)==0) { // i am the server
186	GB_ERROR error = GBCMS_open(":",0,GLOBAL_gb_main);
187	if (error) {
188	aw_message(
189	"THIS PROGRAM HAS PROBLEMS TO OPEN INTERCLIENT COMMUNICATION !!!\n"
190	"(MAYBE THERE IS ALREADY ANOTHER SERVER RUNNING)\n\n"
191	"You cannot use any EDITOR or other external SOFTWARE with this dataset!\n\n"
192	"Advice: Close ARB again, open a console, type 'arb_clean' and restart arb.\n"
193	"Caution: Any unsaved data in an eventually running ARB will be lost!\n");
194	}else{
195	aw_root->add_timed_callback(NT_SERVE_DB_TIMER,(AW_RCB)serve_db_interrupt,0,0);
196	error = nt_check_database_consistency();
197	if (error) aw_message(error);
198	}
199	}else{
200	aw_root->add_timed_callback(NT_CHECK_DB_TIMER,(AW_RCB)check_db_interrupt,0,0);
201	}
202	}
203
204	int main_load_and_startup_main_window(AW_root *aw_root) // returns 0 when successfull
205	{
206
207	char *db_server = aw_root->awar(AWAR_DB_PATH)->read_string();
208	GLOBAL_gb_main = GBT_open(db_server,"rw","$(ARBHOME)/lib/pts/*");
209
210	if (!GLOBAL_gb_main) {
211	aw_popup_ok(GB_await_error());
212	return -1;
213	}
214
215	aw_root->awar(AWAR_DB_PATH)->write_string(db_server);
216
217	#define MAXNAMELEN 35
218	int len = strlen(db_server);
219	if (len>MAXNAMELEN) {
220	char *nameOnly = strrchr(db_server, '/');
221	if (nameOnly) {
222	nameOnly++;
223	len -= (nameOnly-db_server);
224	memmove(db_server, nameOnly, len+1);
225	if (len>MAXNAMELEN) {
226	strcpy(db_server+MAXNAMELEN-3, "...");
227	}
228	}
229	}
230	#if defined(DEBUG)
231	AWT_announce_db_to_browser(GLOBAL_gb_main, GBS_global_string("ARB database (%s)", db_server));
232	#endif // DEBUG
233
234	free(db_server);
235	nt_main_startup_main_window(aw_root);
236
237	return 0;
238	}
239
240	void nt_delete_database(AW_window *aww){
241	char *db_server = aww->get_root()->awar(AWAR_DB_PATH)->read_string();
242	if (strlen(db_server)){
243	if (aw_ask_sure(GBS_global_string("Are you sure to delete database %s\nNote: there is no way to undelete it afterwards", db_server))) {
244	GB_ERROR error = 0;
245	error = GB_delete_database(db_server);
246	if (error) {
247	aw_message(error);
248	}
249	else {
250	aww->get_root()->awar(AWAR_DB"filter")->touch();
251	}
252	}
253	}
254	else {
255	aw_message("No database selected");
256	}
257	free(db_server);
258	}
259
260	// after import !!!!!
261	void main3(AW_root *aw_root)
262	{
263
264	GLOBAL_NT.awr = aw_root;
265	create_nt_window(aw_root);
266
267	if (GB_read_clients(GLOBAL_gb_main)==0) {
268	GB_ERROR error = GBCMS_open(":",0,GLOBAL_gb_main);
269	if (error) {
270	aw_message("THIS PROGRAM IS NOT THE ONLY DB SERVER !!!\nDON'T USE ANY ARB PROGRAM !!!!");
271	}else{
272	aw_root->add_timed_callback(NT_SERVE_DB_TIMER, (AW_RCB)serve_db_interrupt,0,0);
273	error = nt_check_database_consistency();
274	if (error) aw_message(error);
275	}
276	}
277	return;
278	}
279
280	void nt_intro_start_old(AW_window *aws)
281	{
282	aws->hide();
283	if (main_load_and_startup_main_window(aws->get_root())) {
284	aws->show();
285	}
286	}
287
288	void nt_intro_start_merge(AW_window aws,AW_root awr){
289	if (aws) awr = aws->get_root();
290	create_MG_main_window(awr);
291	if (aws) aws->hide();
292	}
293
294	void nt_intro_start_import(AW_window *aws)
295	{
296	aws->hide();
297	aws->get_root()->awar_string( AWAR_DB_PATH )->write_string( "noname.arb");
298	aws->get_root()->awar_int(AWAR_READ_GENOM_DB, IMP_PLAIN_SEQUENCE); // Default toggle in window "Create&import" is Non-Genom
299	GLOBAL_gb_main = open_AWTC_import_window(aws->get_root(), "", true, 0, (AW_RCB)main3, 0, 0);
300	}
301
302	AW_window nt_create_intro_window(AW_root awr)
303	{
304	AW_window_simple *aws = new AW_window_simple;
305	aws->init( awr, "ARB_INTRO", "ARB INTRO");
306	aws->load_xfig("arb_intro.fig");
307
308	aws->callback( (AW_CB0)exit);
309	aws->at("close");
310	aws->create_button("CANCEL","CANCEL","C");
311
312	aws->at("help");
313	aws->callback(AW_POPUP_HELP,(AW_CL)"arb_intro.hlp");
314	aws->create_button("HELP","HELP","H");
315
316	awt_create_selection_box(aws,"tmp/nt/arbdb");
317
318	aws->button_length(0);
319
320	aws->at("logo");
321	aws->create_button(0,"#logo.xpm");
322
323	aws->at("version");
324	aws->create_button(0, GBS_global_string("Version " ARB_VERSION), 0); // version
325
326	aws->at("copyright");
327	aws->create_button(0, GBS_global_string("(C) 1993-" ARB_BUILD_YEAR), 0);
328
329	// aws->button_length(25);
330
331	aws->at("old");
332	aws->callback(nt_intro_start_old);
333	aws->create_autosize_button("OPEN_SELECTED","OPEN SELECTED","O");
334
335	aws->at("del");
336	aws->callback(nt_delete_database);
337	aws->create_autosize_button("DELETE_SELECTED","DELETE SELECTED");
338
339	aws->at("new_complex");
340	aws->callback(nt_intro_start_import);
341	aws->create_autosize_button("CREATE_AND_IMPORT","CREATE AND IMPORT","I");
342
343	aws->at("merge");
344	aws->callback((AW_CB1)nt_intro_start_merge,0);
345	aws->create_autosize_button("MERGE_TWO_DATABASES","MERGE TWO ARB DATABASES","O");
346
347	aws->at("expert");
348	aws->create_toggle(AWAR_EXPERT);
349
350	return (AW_window *)aws;
351	}
352
353	void AD_set_default_root(AW_root *aw_root);
354
355	// ----------------------------------------------------------
356	// static void AWAR_DB_PATH_changed_cb(AW_root *awr)
357	// ----------------------------------------------------------
358	static void AWAR_DB_PATH_changed_cb(AW_root *awr) {
359	static int avoid_recursion = 0;
360
361	if (!avoid_recursion) {
362	avoid_recursion = 1;
363
364	char *value = awr->awar(AWAR_DB_PATH)->read_string();
365	char *lslash = strrchr(value, '/');
366
367	char *name = lslash ? lslash+1 : value;
368	#if defined(DEBUG)
369	printf("writing '%s' to AWAR_DB_NAME\n", name);
370	#endif // DEBUG
371	awr->awar(AWAR_DB_NAME)->write_string(name);
372
373	if (lslash) { // update value of directory
374	lslash[0] = 0;
375	awr->awar(AWAR_DB"directory")->write_string(value);
376	lslash[0] = '/';
377	}
378
379	free(value);
380
381	avoid_recursion = 0;
382	}
383	}
384
385	// ---------------------------------------
386	// int main(int argc, char **argv)
387	// ---------------------------------------
388	int main(int argc, char **argv)
389	{
390	AW_root *aw_root;
391	AW_default aw_default;
392
393	const char *db_server =":";
394
395	unsigned long mtime = GB_time_of_file("$(ARBHOME)/lib/message");
396	unsigned long rtime = GB_time_of_file("$(HOME)/.arb_prop/msgtime");
397	if (mtime > rtime){
398	AWT_edit("${ARBHOME}/lib/message");
399	system("touch ${HOME}/.arb_prop/msgtime");
400	}
401	aw_initstatus();
402	GB_set_verbose();
403
404	aw_root = new AW_root;
405	GLOBAL_NT.awr = aw_root;
406	AD_set_default_root(aw_root); // set default for AD_map_viewer (as long as no info-box was opened)
407
408	aw_default = aw_root->open_default(".arb_prop/ntree.arb");
409	aw_root->init_variables(aw_default);
410	aw_root->init_root("ARB_NT", false);
411
412	// create some early awars
413	// Note: normally you don't like to add your awar-init-function here, but into nt_create_all_awars()
414
415	aw_create_selection_box_awars(aw_root, AWAR_DB, "", ".arb", "noname.arb", aw_default);
416	aw_root->awar_string( AWAR_DB"type", "b", aw_default);
417
418	aw_root->awar_int(AWAR_EXPERT, 0, aw_default);
419
420	aw_root->awar_string(AWAR_DB_NAME, "noname.arb", aw_default);
421	aw_root->awar(AWAR_DB_PATH)->add_callback(AWAR_DB_PATH_changed_cb);
422
423	init_Advisor(aw_root, aw_default);
424
425	if (argc==3) { // looks like merge
426	if (argv[1][0] != '-') { // not if first argument is a switch
427	MG_create_all_awars(aw_root,aw_default,argv[1],argv[2]);
428	nt_intro_start_merge(0,aw_root);
429	aw_root->main_loop();
430	}
431	}
432
433	bool abort = false;
434	bool start_db_browser = true;
435	char *browser_startdir = strdup(".");
436
437	if (argc>=2) {
438	start_db_browser = false;
439
440	if (strcmp(argv[1], "--help")==0 \|\|
441	strcmp(argv[1], "-help")==0 \|\|
442	strcmp(argv[1], "-h")==0)
443	{
444	fprintf(stderr,
445	"\n"
446	"arb_ntree version " ARB_VERSION "\n"
447	"(C) 1993-" ARB_BUILD_YEAR " Lehrstuhl fuer Mikrobiologie - TU Muenchen\n"
448	"http://www.arb-home.de/\n"
449	#if defined(SHOW_WHERE_BUILD)
450	"(version build by: " ARB_BUILD_USER "@" ARB_BUILD_HOST ")\n"
451	#endif // SHOW_WHERE_BUILD
452	"\n"
453	"Known command line arguments:\n"
454	"\n"
455	"db.arb => start ARB_NTREE with database db.arb\n"
456	": => start ARB_NTREE and connect to existing db_server\n"
457	"db1.arb db2.arb => merge databases db1.arb and db2.arb\n"
458	"-export => connect to existing ARB server and export database to noname.arb\n"
459	"-import file => import 'file' into new database\n"
460	"w/o arguments => start database browser\n"
461	"\n"
462	);
463
464	exit(1);
465	}
466
467	if ( strcmp(argv[1],"-export")==0) {
468	MG_create_all_awars(aw_root,aw_default,":","noname.arb");
469	GLOBAL_gb_merge = GBT_open(":","rw",0);
470	if (!GLOBAL_gb_merge) {
471	aw_popup_ok(GB_await_error());
472	exit(0);
473	}
474	#if defined(DEBUG)
475	AWT_announce_db_to_browser(GLOBAL_gb_merge, "Current database (:)");
476	#endif // DEBUG
477
478	GLOBAL_gb_dest = GBT_open("noname.arb","cw",0);
479	#if defined(DEBUG)
480	AWT_announce_db_to_browser(GLOBAL_gb_dest, "New database (noname.arb)");
481	#endif // DEBUG
482
483	MG_start_cb2(NULL, aw_root, true, true);
484	aw_root->main_loop();
485	}
486
487	bool run_importer = false;
488	if (strcmp(argv[1], "-import") == 0) {
489	argv++;
490	run_importer = true;
491	}
492
493	db_server = argv[1];
494	GB_ERROR load_file_err = 0;
495	if (!run_importer) load_file_err = GBT_check_arb_file(db_server);
496
497	if (load_file_err) {
498	int answer = -1;
499	char *full_path = AWT_unfold_path(db_server);
500
501	printf("load_file_err='%s'\n", load_file_err);
502
503	if (AWT_is_dir(full_path)) answer = 2; // autoselect browser
504
505	if (answer == -1) {
506	if (!AWT_is_file(full_path)) {
507	const char *msg = GBS_global_string("'%s' is neither a known option nor a legal file- or directory-name.\n(Error: %s)",
508	full_path, load_file_err);
509	answer = aw_question(msg, "Browser,Exit");
510
511	switch (answer) { // map answer to codes used by aw_message below
512	case 0: answer = 2; break; // Browse
513	case 1: answer = 3; break; // Exit
514	default : nt_assert(0);
515	}
516	}
517	else {
518	const char *msg = GBS_global_string("Your file is not an original arb file\n(%s)", load_file_err);
519	answer = aw_question(msg, "Continue (dangerous),Start Converter,Browser,Exit");
520	}
521	}
522
523	switch (answer) {
524	case 0: { // Continue
525	break;
526	}
527	case 1: { // Start converter
528	run_importer = true;
529	break;
530	}
531	case 2: { // Browse
532	char *dir = nulldup(full_path);
533	while (dir && !AWT_is_dir(dir)) freeset(dir, AWT_extract_directory(dir));
534
535	if (dir) {
536	nt_assert(AWT_is_dir(dir));
537	reassign(browser_startdir, dir);
538	start_db_browser = true;
539	}
540	free(dir);
541	break;
542	}
543	case 3: { // Exit
544	abort = true;
545	break;
546	}
547	default: {
548	break;
549	}
550	}
551	free(full_path);
552	}
553
554	if (run_importer) {
555	aw_root->awar_int(AWAR_READ_GENOM_DB, IMP_PLAIN_SEQUENCE);
556	GLOBAL_gb_main = open_AWTC_import_window(aw_root, db_server, true, 0, (AW_RCB)main3, 0, 0);
557	aw_root->main_loop();
558	}
559	}
560
561
562	if (start_db_browser) {
563	aw_root->awar(AWAR_DB"directory")->write_string(browser_startdir);
564	char *latest = GB_find_latest_file(browser_startdir, "/\\.(arb\|a[0-9]{2})$/");
565	if (latest){
566	int l = strlen(latest);
567	latest[l-1] = 'b';
568	latest[l-2] = 'r';
569	latest[l-3] = 'a';
570	aw_root->awar(AWAR_DB_PATH)->write_string(latest);
571	free(latest);
572	}
573	AW_window *iws;
574	if (GLOBAL_NT.window_creator){
575	iws = GLOBAL_NT.window_creator(aw_root,0);
576	}else{
577	iws = nt_create_intro_window(aw_root);
578	}
579	iws->show();
580	aw_root->main_loop();
581	}
582
583	if (abort) {
584	printf("Aborting.\n");
585	}
586	else {
587	aw_root->awar(AWAR_DB_PATH)->write_string(db_server);
588	if (main_load_and_startup_main_window(aw_root)) return -1;
589	aw_root->main_loop();
590	}
591
592	return 0;
593	}

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