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source: branches/help/SECEDIT/SEC_main.cxx

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Last change on this file was 18665, checked in by westram, 3 years ago
change many WARN_TODO triggered warnings into todo markers.
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 30.8 KB

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1	// =============================================================== //
2	// //
3	// File : SEC_main.cxx //
4	// Purpose : main part of SECEDIT //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include "SEC_root.hxx"
12	#include "SEC_graphic.hxx"
13	#include "SEC_helix.hxx"
14	#include "SEC_drawn_pos.hxx"
15	#include "SEC_toggle.hxx"
16
17	#include <BufferedFileReader.h>
18
19	#include <aw_awars.hxx>
20	#include <aw_preset.hxx>
21	#include <aw_file.hxx>
22	#include <aw_msg.hxx>
23	#include <aw_root.hxx>
24	#include <aw_question.hxx>
25
26	#include <mode_text.h>
27
28	#include <arb_file.h>
29	#include <awt_config_manager.hxx>
30	#include <ad_cb_prot.h>
31
32	#ifndef sec_assert // happens in NDEBUG mode
33	#define sec_assert(cond) arb_assert(cond)
34	#endif
35
36	void SEC_root::invalidate_base_positions() {
37	if (root_loop) {
38	SEC_base_part *start_part = root_loop->get_fixpoint_strand();
39	SEC_base_part *part = start_part;
40
41	do {
42	part->get_region()->invalidate_base_count();
43	part = part->next();
44	}
45	while (part != start_part);
46	}
47	}
48
49	// ------------------------------------------------------
50	// auto-scrolling (triggered by structure self)
51
52	void SEC_root::nail_position(size_t absPos) {
53	if (drawnPositions) {
54	nailedAbsPos = absPos;
55	drawnAbsPos = *drawnPositions->drawn_at(absPos);
56	}
57	}
58
59	void SEC_root::nail_cursor() { // re-position on cursor
60	if (cursorAbsPos >= 0) {
61	if (drawnPositions && !drawnPositions->empty()) {
62	size_t abs;
63	drawnAbsPos = drawnPositions->drawn_after(cursorAbsPos-1, &abs);
64	nailedAbsPos = abs;
65	}
66	}
67	}
68
69	void SEC_root::add_autoscroll(const Vector& scroll) {
70	if (autoscroll) *autoscroll += scroll;
71	else autoscroll = new Vector(scroll);
72	}
73
74	bool SEC_root::perform_autoscroll() {
75	bool scrolled = false;
76	AWT_canvas *canvas = db->canvas();
77
78	if (canvas && (nailedAbsPos != -1 \|\| autoscroll)) {
79	AW_device *device = canvas->aww->get_device(AW_MIDDLE_AREA);
80
81	if (nailedAbsPos != -1) {
82	{
83	int absPos = nailedAbsPos;
84	Vector *scroll = autoscroll;
85
86	// avoid endless recursion:
87	nailedAbsPos = -1;
88	autoscroll = NULp;
89
90	// @@@ make the refresh invisible
91
92	{
93	// hack: we may be inside or outside sync_DB_model_and_view() here (be permissive about flags here)
94	LocallyModify<int> allow_flag_modify(canvas->gfx->exports.get_modifying_flag_ref(), -1);
95	canvas->gfx->exports.update_display_as_requested(canvas, true);
96	}
97
98	nailedAbsPos = absPos;
99	autoscroll = scroll;
100	}
101	const Position *newPos = drawnPositions->drawn_at(nailedAbsPos);
102	if (newPos) {
103	Vector old2new(drawnAbsPos, *newPos);
104	#if defined(DEBUG) && 0
105	printf("drawnAbsPos=%.2f/%.2f newPos=%.2f/%.2f old2new=%.2f/%.2f\n",
106	drawnAbsPos.xpos(), drawnAbsPos.ypos(),
107	newPos->xpos(), newPos->ypos(),
108	old2new.x(), old2new.y());
109	#endif // DEBUG
110	add_autoscroll(old2new);
111	}
112	nailedAbsPos = -1;
113	}
114	if (autoscroll) {
115	canvas->init_device(device); // loads correct zoom
116	Vector screen_scroll = device->transform(*autoscroll);
117
118	#if defined(DEBUG) && 0
119	printf("autoscroll=%.2f/%.2f screen_scroll=%.2f/%.2f\n",
120	autoscroll->x(), autoscroll->y(),
121	screen_scroll.x(), screen_scroll.y());
122	#endif // DEBUG
123
124	delete autoscroll;
125	autoscroll = NULp;
126
127	device->clear(-1);
128	{
129	// hack: we may be inside sync_DB_model_and_view() here, but scroll() instanciates an AWT_auto_refresh. Permit!
130	LocallyModify<int> allow_flag_modify(canvas->gfx->exports.get_modifying_flag_ref(), 0);
131	canvas->scroll(screen_scroll);
132	}
133	scrolled = true;
134	}
135	}
136	return scrolled;
137	}
138	// --------------------------------------------------------------------------------
139
140	void SEC_root::position_cursor(bool toCenter, bool evenIfVisible) {
141	// centers the cursor in display (or scrolls it into view)
142	// if 'evenIfVisible' is true, always do it, otherwise only if not (fully) visible
143
144	const LineVector& cursorLine = get_last_drawed_cursor_position();
145	sec_assert(cursorLine.valid());
146
147	AWT_canvas *scr = db->canvas();
148	AW_device *device = scr->aww->get_device(AW_MIDDLE_AREA);
149
150	Rectangle cursor(device->transform(cursorLine));
151	Rectangle screen(device->get_area_size(), INCLUSIVE_OUTLINE);
152
153	if (evenIfVisible \|\| !screen.contains(cursor)) {
154	if (!toCenter) {
155	if (perform_autoscroll()) {
156	cursor = Rectangle(device->transform(cursorLine));
157	if (!screen.contains(cursor)) {
158	toCenter = true;
159	}
160	}
161	else { // if autoscroll didn't work
162	toCenter = true; // center cursor
163	}
164	}
165
166	if (toCenter) {
167	AWT_auto_refresh allowed_on(scr);
168	Vector scroll(cursor.centroid(), screen.centroid());
169
170	#if defined(DEBUG) && 1
171	printf("Auto-scroll: scroll = (%f, %f) [Center cursor]\n", scroll.x(), scroll.y());
172	#endif
173	scr->scroll(-scroll);
174	scr->request_refresh();
175	}
176	}
177	}
178
179	static void SEC_toggle_cb(AW_window, const SEC_db_interface db) {
180	AWT_auto_refresh allowed_on(db->canvas());
181	GB_ERROR error = db->structure()->next();
182	if (error) aw_message(error);
183	db->canvas()->request_refresh();
184	}
185
186	static void SEC_center_cb(AW_window , SEC_root root) {
187	root->position_cursor(true, true);
188	}
189
190	static void SEC_fit_window_cb(AW_window, const SEC_db_interface db) {
191	AWT_auto_refresh allowed_on(db->canvas());
192	db->canvas()->request_zoom_reset();
193	}
194
195	static void sec_mode_event(AW_window aws, SEC_root sec_root, AWT_COMMAND_MODE mode) {
196	const char *text = NULp;
197	switch (mode) {
198	case AWT_MODE_ZOOM: text = MODE_TEXT_STANDARD_ZOOMMODE(); break;
199
200	case AWT_MODE_EDIT: text = MODE_TEXT_1BUTTON("CONSTRAINT", "modify constraint"); break;
201	case AWT_MODE_CURSOR: text = MODE_TEXT_1BUTTON("SET CURSOR", "set cursor in ARB_EDIT4"); break;
202
203	case AWT_MODE_FOLD: text = MODE_TEXT_2BUTTONS("FOLD", "fold helix", "unfold helix"); break;
204	case AWT_MODE_SETROOT: text = MODE_TEXT_2BUTTONS("SET ROOT", "set logical center of structure", "reset angles on sub-structure"); break;
205	case AWT_MODE_ROTATE: text = MODE_TEXT_2BUTTONS("ROTATE", "rotate helix/loop", "same w/o substructure"); break;
206	case AWT_MODE_STRETCH: text = MODE_TEXT_2BUTTONS("STRETCH", "click and drag to stretch helices/loops", "reset"); break;
207	case AWT_MODE_PINFO: text = MODE_TEXT_2BUTTONS("PROBE INFO", "display PROBE information", "undisplay"); break;
208
209	default: text = no_mode_text_defined(); break;
210	}
211
212	sec_root->set_show_constraints((mode == AWT_MODE_STRETCH \|\| mode == AWT_MODE_EDIT)
213	? SEC_ANY_TYPE
214	: SEC_NO_TYPE);
215
216	sec_assert(strlen(text) < AWAR_FOOTER_MAX_LEN); // text too long!
217
218	aws->get_root()->awar(AWAR_FOOTER)->write_string(text);
219
220	AWT_canvas *scr = sec_root->get_db()->canvas();
221	AWT_auto_refresh allowed_on(scr);
222	scr->set_mode(mode);
223	scr->request_refresh();
224	}
225
226	static void SEC_undo_cb(AW_window , const SEC_db_interface db, GB_UNDO_TYPE undo_type) {
227	GBDATA *gb_main = db->gbmain();
228	GB_ERROR error = GB_undo(gb_main, undo_type);
229	if (error) {
230	aw_message(error);
231	}
232	else {
233	GB_begin_transaction(gb_main);
234	GB_commit_transaction(gb_main);
235	AWT_auto_refresh allowed_on(db->canvas());
236	db->canvas()->request_refresh();
237	}
238	}
239
240	// --------------------------------------------------------------------------------
241
242	#define ASS "ARB secondary structure v1" // don't change version here!
243	#define ASS_START "[" ASS "]"
244	#define ASS_EOS "[end of structure]"
245	#define ASS_EOF "[end of " ASS "]"
246
247	static void export_structure_to_file(AW_window , const SEC_db_interface db) {
248	GB_ERROR error = NULp;
249	SEC_root *sec_root = db->secroot();
250
251	if (!sec_root->get_root_loop()) {
252	error = "Please select a species (to display structure once) before saving";
253	}
254	else {
255	AW_root *aw_root = db->awroot();
256	char *filename = aw_root->awar(AWAR_SECEDIT_SAVEDIR"/file_name")->read_string();
257	FILE *out = fopen(filename, "wt");
258
259	if (out) {
260
261	fputs(ASS_START, out); fputc('\n', out);
262
263	char *strct = sec_root->buildStructureString();
264	fputs(strct, out);
265	delete [] strct;
266
267	fputs(ASS_EOS, out); fputc('\n', out);
268
269	const XString& xstr = sec_root->get_xString();
270	const char *x_string = xstr.get_x_string();
271
272	sec_assert(xstr.get_x_string_length() == strlen(x_string));
273
274	char *foldInfo = SEC_xstring_to_foldedHelixList(x_string, xstr.get_x_string_length(), sec_root->get_helixDef(), error);
275	if (foldInfo) {
276	fprintf(out, "foldedHelices=%s\n", foldInfo);
277	free(foldInfo);
278	}
279
280	fputs(ASS_EOF, out); fputc('\n', out);
281	fclose(out);
282
283	if (error) GB_unlink_or_warn(filename, &error);
284	}
285	else {
286	error = GB_export_errorf("Can't write secondary structure to '%s'", filename);
287	}
288
289	free(filename);
290	}
291	if (error) aw_message(error);
292	}
293
294	inline GB_ERROR expectedError(const char *expected) {
295	return GBS_global_string("expected '%s'", expected);
296	}
297	inline GB_ERROR expectContent(LineReader& file, const char *expected) {
298	GB_ERROR error = NULp;
299	string line;
300	if (!file.getLine(line) \|\| line != expected) {
301	error = expectedError(expected);
302	}
303	return error;
304	}
305
306	static string scanToken(LineReader& file, string& rest, GB_ERROR& error) {
307	string line;
308	string token;
309
310	sec_assert(!error);
311
312	if (file.getLine(line)) {
313	size_t equal = line.find('=');
314
315	if (equal == string::npos) {
316	error = "Expected '='";
317	}
318	else {
319	token = line.substr(0, equal);
320	rest = line.substr(equal+1);
321	}
322	}
323	else {
324	error = "Unexpected EOF";
325	}
326	return token;
327	}
328
329	static GB_ERROR expectToken(LineReader& file, const char *token, string& content) {
330	GB_ERROR error = NULp;
331	string foundToken = scanToken(file, content, error);
332	if (foundToken != token) error = expectedError(token);
333	return error;
334	}
335
336	static void import_structure_from_file(AW_window , const SEC_db_interface db) {
337	GB_ERROR error = NULp;
338	SEC_root *root = db->secroot();
339
340	if (!root->has_xString()) {
341	error = "Please select a species in EDIT4";
342	}
343	else {
344	char *filename = db->awroot()->awar(AWAR_SECEDIT_SAVEDIR"/file_name")->read_string();
345	FILE *in = fopen(filename, "rt"); // closed by FileBuffer
346
347	if (!in) {
348	error = GB_export_errorf("Can't open file '%s'", filename);
349	}
350	else {
351	BufferedFileReader file(filename, in);
352	error = expectContent(file, ASS_START);
353
354	string structure;
355	while (!error) {
356	string line;
357	if (!file.getLine(line)) error = expectedError(ASS_EOS);
358	else {
359	if (line == ASS_EOS) break;
360	structure += line + "\n";
361	}
362	}
363
364	char *x_string = NULp;
365	if (!error) {
366	string content;
367	string token = scanToken(file, content, error);
368
369	if (!error) {
370	// we already have an existing xstring, use it's length for new xstring
371	size_t xlength = root->get_xString().getLength();
372
373	if (token == "foldedHelices") { // new version
374	x_string = SEC_foldedHelixList_to_xstring(content.c_str(), xlength, root->get_helixDef(), error); // sets error
375	}
376	else if (token == "no of helices") { // old version
377	int saved_helices = atoi(content.c_str());
378
379	error = expectToken(file, "length of xstring", content); // ignore, using curr value
380	if (!error) error = expectToken(file, "xstring_rel_helix", content);
381	if (!error) {
382	int helices_in_db;
383	x_string = old_decode_xstring_rel_helix(content.c_str(), xlength, root->get_helixDef(), &helices_in_db);
384	if (helices_in_db != saved_helices) {
385	error = GBS_global_string("Number of helices does not match (file=%i, db=%i).\n"
386	"Saving the structure again from another DB with correct number of helices will work around this restriction.",
387	saved_helices, helices_in_db);
388	}
389	}
390	}
391	else {
392	error = "Expected 'foldedHelices' or 'no of helices'";
393	}
394	}
395	if (!error) error = expectContent(file, ASS_EOF);
396	}
397
398	if (error) {
399	error = GBS_static_string(file.lineError(error).c_str());
400	}
401	else {
402	AWT_auto_refresh allowed_on(db->canvas());
403	db->graphic()->write_data_to_db(structure.c_str(), x_string);
404	db->canvas()->request_refresh();
405	}
406	free(x_string);
407	}
408	free(filename);
409	}
410	if (error) aw_message(error);
411	}
412
413	#undef ASS
414	#undef ASS_START
415	#undef ASS_EOS
416	#undef ASS_EOF
417
418	static AW_window SEC_importExport(AW_root root, bool export_to_file, const SEC_db_interface *db) {
419	AW_window_simple *aws = new AW_window_simple;
420
421	if (export_to_file) aws->init(root, "export_secondary_structure", "Export secondary structure to ...");
422	else aws->init(root, "import_secondary_structure", "Import secondary structure from ...");
423
424	aws->load_xfig("sec_imexport.fig");
425
426	aws->at("close");
427	aws->callback(AW_POPDOWN);
428	aws->create_button("CLOSE", "CLOSE", "C");
429
430	aws->at("help");
431	aws->callback(makeHelpCallback("sec_imexport.hlp"));
432	aws->create_button("HELP", "HELP", "H");
433
434	AW_create_standard_fileselection(aws, AWAR_SECEDIT_SAVEDIR);
435
436	aws->at("save");
437	if (export_to_file) {
438	aws->callback(makeWindowCallback(export_structure_to_file, db));
439	aws->create_button("EXPORT", "EXPORT", "E");
440	}
441	else {
442	aws->callback(makeWindowCallback(import_structure_from_file, db));
443	aws->create_button("IMPORT", "IMPORT", "I");
444	}
445
446	return aws;
447	}
448
449	static void SEC_rename_structure(AW_window, const SEC_db_interface db) {
450	SEC_structure_toggler *structure = db->structure();
451
452	char *new_name = aw_input("Rename structure", "New name", structure->name());
453	if (new_name) {
454	structure->setName(new_name);
455	free(new_name);
456	AWT_auto_refresh allowed_on(db->canvas());
457	db->canvas()->request_refresh();
458	}
459	}
460
461	static void SEC_new_structure(AW_window, const SEC_db_interface db) {
462	SEC_structure_toggler *structure = db->structure();
463
464	if (!structure) {
465	db->init_toggler();
466	structure = db->structure();
467	sec_assert(structure);
468	}
469
470	GB_ERROR error = NULp;
471	bool done = false;
472
473	switch (aw_question(NULp, "Create new structure?", "Default bone,Copy current,Abort")) {
474	case 0: // default bone
475	error = structure->copyTo("Default");
476	if (!error) {
477	db->secroot()->create_default_bone();
478	db->graphic()->save_to_DB(NULp, NULp);
479	done = true;
480	}
481	break;
482
483	case 1: // copy current
484	error = structure->copyTo(GBS_global_string("%s(copy)", structure->name()));
485	done = !error;
486	break;
487
488	case 2: // abort
489	break;
490	}
491
492	if (done) {
493	{
494	AWT_auto_refresh allowed_on(db->canvas());
495	db->canvas()->request_zoom_reset();
496	}
497	SEC_rename_structure(NULp, db);
498	}
499	}
500
501	static void SEC_delete_structure(AW_window, const SEC_db_interface db) {
502	SEC_structure_toggler *structure = db->structure();
503
504	if (structure->getCount()>1) {
505	if (aw_ask_sure("delete_sec_structure", GBS_global_string("Are you sure to delete structure '%s'?", structure->name()))) {
506	AWT_auto_refresh allowed_on(db->canvas());
507	GB_ERROR error = structure->remove();
508	if (error) aw_message(error);
509	db->canvas()->request_refresh();
510	}
511	}
512	else {
513	aw_message("You cannot delete the last structure");
514	}
515	}
516
517	enum SyncColors {
518	COLOR_SYNC_SEARCH = 1,
519	COLOR_SYNC_RANGE = 2,
520	COLOR_SYNC_REST = 4,
521
522	COLOR_SYNC_ALL = (COLOR_SYNC_SEARCH\|COLOR_SYNC_RANGE\|COLOR_SYNC_REST),
523	};
524
525	static void SEC_sync_colors(AW_window *aww, SyncColors which) {
526	// overwrites color settings with those from EDIT4
527
528	if (which & COLOR_SYNC_SEARCH) {
529	AW_copy_GC_colors(aww->get_root(), "ARB_EDIT4", "ARB_SECEDIT",
530	"User1", "User2", "Probe",
531	"Primerl", "Primerr", "Primerg",
532	"Sigl", "Sigr", "Sigg",
533	"MISMATCHES",
534	NULp);
535	}
536	if (which & COLOR_SYNC_RANGE) {
537	AW_copy_GC_colors(aww->get_root(), "ARB_EDIT4", "ARB_SECEDIT",
538	"RANGE_0", "RANGE_1", "RANGE_2",
539	"RANGE_3", "RANGE_4", "RANGE_5",
540	"RANGE_6", "RANGE_7", "RANGE_8",
541	"RANGE_9",
542	NULp);
543	}
544	if (which & COLOR_SYNC_REST) {
545	AW_copy_GC_colors(aww->get_root(), "ARB_EDIT4", "ARB_SECEDIT",
546	"CURSOR",
547	NULp);
548	}
549	}
550
551	static AW_window SEC_create_bonddef_window(AW_root awr) {
552	AW_window_simple *aws = new AW_window_simple;
553
554	aws->init(awr, "SEC_BONDDEF", "Bond definitions");
555	aws->load_xfig("sec_bonddef.fig");
556
557	aws->at("close");
558	aws->callback(AW_POPDOWN);
559	aws->create_button("CLOSE", "CLOSE", "C");
560
561	aws->callback(makeHelpCallback("sec_bonddef.hlp"));
562	aws->at("help");
563	aws->create_button("HELP", "HELP", "H");
564
565	aws->at("label"); int x_label = aws->get_at_xposition();
566	aws->at("pairs"); int x_pairs = aws->get_at_xposition();
567	aws->at("chars"); int x_chars = aws->get_at_xposition();
568
569	aws->auto_space(0, 0);
570
571	#define INSERT_PAIR_FIELDS(label, pairname) \
572	aws->at_x(x_label); \
573	aws->create_button(NULp, label); \
574	aws->at_x(x_pairs); \
575	aws->create_input_field(AWAR_SECEDIT_##pairname##_PAIRS, 30); \
576	aws->at_x(x_chars); \
577	aws->create_input_field(AWAR_SECEDIT_##pairname##_PAIR_CHAR, 1); \
578	aws->at_newline();
579
580	INSERT_PAIR_FIELDS("Strong pairs", STRONG);
581	INSERT_PAIR_FIELDS("Normal pairs", NORMAL);
582	INSERT_PAIR_FIELDS("Weak pairs", WEAK);
583	INSERT_PAIR_FIELDS("No pairs", NO);
584	INSERT_PAIR_FIELDS("User pairs", USER);
585
586	#undef INSERT_PAIR_FIELDS
587
588	return aws;
589	}
590
591	#define INSERT_PAIR_MAPPING(pairname) \
592	{ AWAR_SECEDIT_##pairname##_PAIRS, "pairs_" #pairname }, \
593	{ AWAR_SECEDIT_##pairname##_PAIR_CHAR, "char_" #pairname }
594
595	static AWT_config_mapping_def secedit_display_config_mapping[] = {
596	{ AWAR_SECEDIT_HIDE_BASES, "hidebases" },
597	{ AWAR_SECEDIT_DIST_BETW_STRANDS, "stranddist" },
598	{ AWAR_SECEDIT_SHOW_BONDS, "showbonds" },
599
600	INSERT_PAIR_MAPPING(STRONG),
601	INSERT_PAIR_MAPPING(NORMAL),
602	INSERT_PAIR_MAPPING(WEAK),
603	INSERT_PAIR_MAPPING(NO),
604	INSERT_PAIR_MAPPING(USER),
605
606	{ AWAR_SECEDIT_BOND_THICKNESS, "bondthickness" },
607	{ AWAR_SECEDIT_SHOW_CURPOS, "showposition" },
608	{ AWAR_SECEDIT_SHOW_HELIX_NRS, "showhelixnrs" },
609	{ AWAR_SECEDIT_SHOW_ECOLI_POS, "showecolipos" },
610	{ AWAR_SECEDIT_DISPLAY_SEARCH, "showsearch" },
611	{ AWAR_SECEDIT_DISPLAY_SAI, "showsai" },
612	{ AWAR_SECEDIT_DISPPOS_BINDING, "disppos_helix" },
613	{ AWAR_SECEDIT_DISPPOS_ECOLI, "disppos_ecoli" },
614	{ AWAR_SECEDIT_SHOW_STR_SKELETON, "skeleton" },
615	{ AWAR_SECEDIT_SKELETON_THICKNESS, "skeleton_thickness" },
616
617	{ NULp, NULp }
618	};
619
620	#undef INSERT_PAIR_MAPPING
621
622	static AW_window SEC_create_display_window(AW_root awr) {
623	AW_window_simple *aws = new AW_window_simple;
624
625	const int SCALED_TEXT_COLUMNS = 7;
626	const int SCALER_WIDTH = 200;
627
628	aws->auto_space(5, 5);
629
630	aws->init(awr, "SEC_DISPLAY_OPTS", "Display options");
631	aws->load_xfig("sec_display.fig");
632
633	aws->at("close");
634	aws->callback(AW_POPDOWN);
635	aws->create_button("CLOSE", "CLOSE", "C");
636
637	aws->callback(makeHelpCallback("sec_display.hlp"));
638	aws->at("help");
639	aws->create_button("HELP", "HELP", "H");
640
641	// ----------------------------------------
642
643	aws->at("bases");
644	aws->label("Display bases :");
645	aws->create_inverse_toggle(AWAR_SECEDIT_HIDE_BASES);
646
647	aws->at("strand_dist");
648	aws->label("Distance between strands :");
649	aws->create_input_field_with_scaler(AWAR_SECEDIT_DIST_BETW_STRANDS, SCALED_TEXT_COLUMNS, SCALER_WIDTH, AW_SCALER_EXP_LOWER);
650
651	aws->at("bonds");
652	aws->label("Display bonds");
653	aws->create_option_menu(AWAR_SECEDIT_SHOW_BONDS, true);
654	aws->insert_option("None", "n", SHOW_NO_BONDS);
655	aws->insert_option("Helix", "h", SHOW_HELIX_BONDS);
656	aws->insert_option("+Non-helix", "o", SHOW_NHELIX_BONDS);
657	aws->update_option_menu();
658
659	aws->at("bonddef");
660	aws->callback(makeCreateWindowCallback(SEC_create_bonddef_window));
661	aws->create_button("sec_bonddef", "Define");
662
663	aws->at("bondThickness");
664	aws->label("Bond thickness :");
665	aws->create_input_field_with_scaler(AWAR_SECEDIT_BOND_THICKNESS, SCALED_TEXT_COLUMNS, SCALER_WIDTH, AW_SCALER_EXP_LOWER);
666
667	// ----------------------------------------
668
669	aws->at("cursor");
670	aws->label("Annotate cursor :");
671	aws->create_option_menu(AWAR_SECEDIT_SHOW_CURPOS, true);
672	aws->insert_option("None", "n", SHOW_NO_CURPOS);
673	aws->insert_option("Absolute", "a", SHOW_ABS_CURPOS);
674	aws->insert_option("Ecoli", "e", SHOW_ECOLI_CURPOS);
675	aws->insert_option("Base", "b", SHOW_BASE_CURPOS);
676	aws->update_option_menu();
677
678	aws->at("helixNrs");
679	aws->label("Annotate helices :");
680	aws->create_toggle(AWAR_SECEDIT_SHOW_HELIX_NRS);
681
682	aws->at("ecoli");
683	aws->label("Annotate ecoli positions :");
684	aws->create_toggle(AWAR_SECEDIT_SHOW_ECOLI_POS);
685
686	aws->at("search");
687	aws->label("Visualize search results :");
688	aws->create_toggle(AWAR_SECEDIT_DISPLAY_SEARCH);
689
690	aws->at("sai");
691	aws->label("Visualize SAI :");
692	aws->create_toggle(AWAR_SECEDIT_DISPLAY_SAI);
693
694	// ----------------------------------------
695
696	aws->at("binding");
697	aws->label("Binding helix positions :");
698	aws->create_toggle(AWAR_SECEDIT_DISPPOS_BINDING);
699
700	aws->at("ecoli2");
701	aws->label("Ecoli base positions :");
702	aws->create_toggle(AWAR_SECEDIT_DISPPOS_ECOLI);
703
704	// ----------------------------------------
705
706	aws->at("strSkeleton");
707	aws->label("Display structure skeleton :");
708	aws->create_toggle(AWAR_SECEDIT_SHOW_STR_SKELETON);
709
710	aws->at("skelThickness");
711	aws->label("Skeleton thickness :");
712	aws->create_input_field_with_scaler(AWAR_SECEDIT_SKELETON_THICKNESS, SCALED_TEXT_COLUMNS, SCALER_WIDTH, AW_SCALER_EXP_LOWER);
713
714	#ifdef DEBUG
715	aws->at("show_debug");
716	aws->label("Show debug info:");
717	aws->create_toggle(AWAR_SECEDIT_SHOW_DEBUG);
718	#endif
719
720	aws->at("config");
721	AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "secedit_display", secedit_display_config_mapping);
722
723	return aws;
724	}
725
726	static void SEC_exit(GBDATA , SEC_root sec_root) {
727	// @@@ use popdown callback for SEC_exit and valgrind open/close/open secedit
728	delete sec_root;
729	}
730
731	static AW_window SEC_create_gc_window(AW_root awr, AW_gc_manager *gcman) {
732	return AW_create_gc_window_named(awr, gcman, "SECEDIT_COLOR_DEF2", "SECEDIT colors and fonts");
733	}
734
735	AW_window *start_SECEDIT_plugin(ED4_plugin_host& host) {
736	AW_root *awr = host.get_application_root();
737	GBDATA *gb_main = host.get_database();
738
739	SEC_graphic *gfx = new SEC_graphic(awr, gb_main); // never freed
740	SEC_root *root = gfx->sec_root;
741
742	AW_window_menu_modes *awm = new AW_window_menu_modes;
743	awm->init(awr, "ARB_SECEDIT", "ARB_SECEDIT: Secondary structure editor", 200, 200);
744
745	AWT_canvas *scr = new AWT_canvas(gb_main, awm, awm->get_window_id(), gfx);
746	{
747	AWT_auto_refresh allowed_on(scr);
748	root->init(gfx, scr, host);
749	scr->request_resize();
750	}
751	scr->set_mode(AWT_MODE_ZOOM); // Default-Mode
752
753	const SEC_db_interface *db = root->get_db();
754
755	GB_atclose_callback(gb_main, makeDatabaseCallback(SEC_exit, root));
756
757	awm->create_menu("File", "F", AWM_ALL);
758
759	awm->insert_menu_topic("secedit_new", "New structure", "N", NULp, AWM_ALL, makeWindowCallback(SEC_new_structure, db));
760	awm->insert_menu_topic("secedit_rename", "Rename structure", "R", NULp, AWM_ALL, makeWindowCallback(SEC_rename_structure, db));
761	awm->insert_menu_topic("secedit_delete", "Delete structure", "D", NULp, AWM_ALL, makeWindowCallback(SEC_delete_structure, db));
762	awm->sep______________();
763	awm->insert_menu_topic("secedit_import", "Load structure", "L", "secedit_imexport.hlp", AWM_ALL, makeCreateWindowCallback(SEC_importExport, false, db));
764	awm->insert_menu_topic("secedit_export", "Save structure", "S", "secedit_imexport.hlp", AWM_ALL, makeCreateWindowCallback(SEC_importExport, true, db));
765	awm->sep______________();
766	awm->insert_menu_topic("secStruct2xfig", "Export structure to XFIG", "X", "tree2file.hlp", AWM_ALL, makeWindowCallback(AWT_popup_sec_export_window, scr));
767	awm->insert_menu_topic("print_secedit", "Print Structure", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, scr));
768	awm->sep______________();
769
770	awm->insert_menu_topic("close", "Close", "C", "quit.hlp", AWM_ALL, AW_POPDOWN);
771
772	awm->create_menu("Properties", "P", AWM_ALL);
773	awm->insert_menu_topic("sec_display", "Display options", "D", "sec_display.hlp", AWM_ALL, SEC_create_display_window);
774	awm->sep______________();
775	awm->insert_menu_topic("props_secedit", "Change Colors and Fonts", "C", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(SEC_create_gc_window, scr->gc_manager));
776	awm->sep______________();
777	awm->insert_menu_topic("sync_search_colors", "Sync search colors with EDIT4", "s", "sync_colors.hlp", AWM_ALL, makeWindowCallback(SEC_sync_colors, COLOR_SYNC_SEARCH));
778	awm->insert_menu_topic("sync_range_colors", "Sync range colors with EDIT4", "r", "sync_colors.hlp", AWM_ALL, makeWindowCallback(SEC_sync_colors, COLOR_SYNC_RANGE));
779	awm->insert_menu_topic("sync_other_colors", "Sync other colors with EDIT4", "o", "sync_colors.hlp", AWM_ALL, makeWindowCallback(SEC_sync_colors, COLOR_SYNC_REST));
780	awm->insert_menu_topic("sync_all_colors", "Sync all colors with EDIT4", "a", "sync_colors.hlp", AWM_ALL, makeWindowCallback(SEC_sync_colors, COLOR_SYNC_ALL));
781	awm->sep______________();
782	awm->insert_menu_topic("sec_save_props", "How to save properties", "p", "savedef.hlp", AWM_ALL, makeHelpCallback("sec_props.hlp"));
783
784	awm->create_mode("mode_zoom.xpm", "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_ZOOM));
785	awm->create_mode("mode_fold.xpm", "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_FOLD));
786	awm->create_mode("mode_setroot.xpm", "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_SETROOT));
787	awm->create_mode("mode_rotate.xpm", "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_ROTATE));
788	awm->create_mode("mode_stretch.xpm", "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_STRETCH));
789	awm->create_mode("mode_edit.xpm", "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_EDIT));
790	awm->create_mode("mode_cursor.xpm", "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_CURSOR));
791	awm->create_mode("mode_pinfo.xpm", "sec_mode.hlp", AWM_ALL, makeWindowCallback(sec_mode_event, root, AWT_MODE_PINFO));
792
793	awm->set_info_area_height(250);
794	awm->at(5, 2);
795	awm->auto_space(0, -2);
796
797	awm->button_length(0);
798	awm->help_text("quit.hlp");
799	awm->callback(AW_POPDOWN);
800	awm->create_button("Close", "#quit.xpm"); // use quit button, cause users regard secedit as separate program
801
802	awm->callback(AW_help_entry_pressed);
803	awm->help_text("arb_secedit.hlp");
804	awm->create_button("HELP", "#help.xpm");
805
806	awm->callback(makeWindowCallback(SEC_undo_cb, db, GB_UNDO_UNDO));
807	awm->help_text("undo.hlp");
808	awm->create_button("Undo", "#undo.xpm");
809
810	awm->callback(makeWindowCallback(SEC_undo_cb, db, GB_UNDO_REDO));
811	awm->help_text("undo.hlp");
812	awm->create_button("Redo", "#redo.xpm");
813
814	awm->callback(makeWindowCallback(SEC_toggle_cb, db));
815	awm->help_text("sec_main.hlp");
816	awm->create_button("Toggle", "Toggle");
817
818	awm->callback(makeWindowCallback(SEC_center_cb, root));
819	awm->help_text("sec_main.hlp");
820	awm->create_button("Center", "Center");
821
822	awm->callback(makeWindowCallback(SEC_fit_window_cb, db));
823	awm->help_text("sec_main.hlp");
824	awm->create_button("fitWindow", "Fit");
825
826	awm->at_newline();
827
828	{
829	SmartPtr<AW_at_storage> maxSize(AW_at_storage::make(awm, AW_AT_MAXSIZE));
830
831	awm->button_length(AWAR_FOOTER_MAX_LEN);
832	awm->create_button(NULp, AWAR_FOOTER);
833	awm->at_newline();
834	awm->restore_at_from(*maxSize);
835	}
836
837	awm->set_info_area_height(awm->get_at_yposition());
838
839	return awm;
840	}
841

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