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source: tags/old_import_filter/EDIT4/ED4_cursor.cxx

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Last change on this file was 9539, checked in by westram, 11 years ago
remove local versions of min, max and abs
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 60.4 KB

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1	#include <cctype>
2	#include <climits>
3
4	#include <arbdbt.h>
5	#include <aw_awars.hxx>
6	#include <AW_helix.hxx>
7	#include <BI_basepos.hxx>
8	#include <aw_msg.hxx>
9	#include <arb_progress.h>
10	#include <aw_root.hxx>
11
12	#include <ed4_extern.hxx>
13
14	#include "ed4_class.hxx"
15	#include "ed4_edit_string.hxx"
16	#include "ed4_tools.hxx"
17	#include "ed4_awars.hxx"
18	#include "ed4_ProteinViewer.hxx"
19
20	#include <arb_strbuf.h>
21	#include <arb_defs.h>
22
23	/* --------------------------------------------------------------------------------
24	CursorShape
25	-------------------------------------------------------------------------------- */
26
27	#define MAXLINES 30
28	#define MAXPOINTS (2*MAXLINES)
29
30	class ED4_CursorShape {
31	int points;
32	int xpos[MAXPOINTS];
33	int ypos[MAXPOINTS];
34
35	int lines;
36	int start[MAXLINES];
37	int end[MAXLINES];
38
39	int char_width;
40
41	bool reverse;
42
43	int point(int x, int y) {
44	e4_assert(points<MAXPOINTS);
45	if (reverse) {
46	xpos[points] = char_width-x;
47	}
48	else {
49	xpos[points] = x;
50	}
51	ypos[points] = y;
52	return points++;
53	}
54	int line(int p1, int p2) {
55	e4_assert(p1>=0 && p1<points);
56	e4_assert(p2>=0 && p2<points);
57
58	e4_assert(lines<MAXLINES);
59	start[lines] = p1;
60	end[lines] = p2;
61
62	return lines++;
63	}
64	int horizontal_line(int x, int y, int half_width) {
65	return line(point(x-half_width, y), point(x+half_width, y));
66	}
67
68	public:
69
70	ED4_CursorShape(ED4_CursorType type, int term_height, int character_width, bool reverse_cursor);
71	~ED4_CursorShape() {}
72
73	void draw(AW_device *device, int x, int y) const {
74	e4_assert(lines);
75	for (int l=0; l<lines; l++) {
76	int p1 = start[l];
77	int p2 = end[l];
78	device->line(ED4_G_CURSOR, xpos[p1]+x, ypos[p1]+y, xpos[p2]+x, ypos[p2]+y, AW_SCREEN);
79	}
80	device->flush();
81	}
82
83	void get_bounding_box(int x, int y, int &xmin, int &ymin, int &xmax, int &ymax) const {
84	e4_assert(points);
85	xmin = ymin = INT_MAX;
86	xmax = ymax = INT_MIN;
87	for (int p=0; p<points; p++) {
88	if (xpos[p]<xmin) { xmin = xpos[p]; }
89	else if (xpos[p]>xmax) { xmax = xpos[p]; }
90	if (ypos[p]<ymin) { ymin = ypos[p]; }
91	else if (ypos[p]>ymax) { ymax = ypos[p]; }
92	}
93
94	xmin += x; xmax += x;
95	ymin += y; ymax += y;
96	}
97
98
99	};
100
101	ED4_CursorShape::ED4_CursorShape(ED4_CursorType typ, /* int x, int y, */ int term_height, int character_width, bool reverse_cursor)
102	{
103	lines = 0;
104	points = 0;
105	reverse = reverse_cursor;
106	char_width = character_width;
107
108	int x = 0;
109	int y = 0;
110
111	switch (typ) {
112	#define UPPER_OFFSET (-1)
113	#define LOWER_OFFSET (term_height-1)
114	#define CWIDTH (character_width)
115
116	case ED4_RIGHT_ORIENTED_CURSOR_THIN:
117	case ED4_RIGHT_ORIENTED_CURSOR: {
118	// --CWIDTH--
119	//
120	// 0--------1 UPPER_OFFSET (from top)
121	// \|3-------4
122	// \|\|
123	// \|\|
124	// \|\|
125	// \|\|
126	// \|\|
127	// \|\|
128	// 25 LOWER_OFFSET (from top)
129	//
130	//
131	// x
132
133	if (typ == ED4_RIGHT_ORIENTED_CURSOR) { // non-thin version
134	int p0 = point(x-1, y+UPPER_OFFSET);
135
136	line(p0, point(x+CWIDTH-1, y+UPPER_OFFSET)); // 0->1
137	line(p0, point(x-1, y+LOWER_OFFSET)); // 0->2
138	}
139
140	int p3 = point(x, y+UPPER_OFFSET+1);
141
142	line(p3, point(x+CWIDTH-1, y+UPPER_OFFSET+1)); // 3->4
143	line(p3, point(x, y+LOWER_OFFSET)); // 3->5
144
145	break;
146
147	#undef UPPER_OFFSET
148	#undef LOWER_OFFSET
149	#undef CWIDTH
150
151	}
152	case ED4_TRADITIONAL_CURSOR_CONNECTED:
153	case ED4_TRADITIONAL_CURSOR_BOTTOM:
154	case ED4_TRADITIONAL_CURSOR: {
155	int small_version = (term_height <= 10) ? 1 : 0;
156
157
158	#define UPPER_OFFSET 0
159	#define LOWER_OFFSET (term_height-1)
160	#define CWIDTH 3
161
162	// -----2*CWIDTH----
163	//
164	// 0---------------1 UPPER_OFFSET (from top)
165	// 4---------5
166	// 8---9
167	// C/C
168	//
169	// D/D
170	// A---B
171	// 6---------7
172	// 2---------------3 LOWER_OFFSET (from top)
173
174	bool draw_upper = typ != ED4_TRADITIONAL_CURSOR_BOTTOM;
175
176	if (draw_upper) horizontal_line(x, y+UPPER_OFFSET, CWIDTH-small_version); // 0/1
177	horizontal_line(x, y+LOWER_OFFSET, CWIDTH-small_version); // 2/3
178
179	if (draw_upper) horizontal_line(x, y+UPPER_OFFSET+1, (CWIDTH*2)/3-small_version); // 4/5
180	horizontal_line(x, y+LOWER_OFFSET-1, (CWIDTH*2)/3-small_version); // 6/7
181
182	if (!small_version) {
183	if (draw_upper) horizontal_line(x, y+UPPER_OFFSET+2, CWIDTH/3); // 8/9
184	horizontal_line(x, y+LOWER_OFFSET-2, CWIDTH/3); // A/B
185	}
186
187	int pu = point(x, y+UPPER_OFFSET+3-small_version);
188	int pl = point(x, y+LOWER_OFFSET-3+small_version);
189
190	if (draw_upper) line(pu, pu); // C/C
191	line(pl, pl); // D/D
192
193	if (typ == ED4_TRADITIONAL_CURSOR_CONNECTED) {
194	int pu2 = point(x, y+UPPER_OFFSET+5-small_version);
195	int pl2 = point(x, y+LOWER_OFFSET-5+small_version);
196	line(pu2, pl2);
197	}
198
199	break;
200
201	#undef UPPER_OFFSET
202	#undef LOWER_OFFSET
203	#undef CWIDTH
204
205	}
206	case ED4_FUCKING_BIG_CURSOR: {
207
208	#define OUTER_HEIGHT (term_height/4)
209	#define INNER_HEIGHT (term_height-1)
210	#define CWIDTH 12
211	#define STEPS 6
212	#define THICKNESS 2
213
214	#if (2*STEPS+THICKNESS > MAXLINES)
215	#error Bad definitions!
216	#endif
217
218	// 2 3 \|
219	// \ / \| OUTER_HEIGHT
220	// \ / \|
221	// 0 \| \|
222	// \| \| INNER_HEIGHT
223	// \| \|
224	// 1 \|
225	// / \ --
226	// / \ --
227	// 4 5
228	//
229	// -----------------
230	// 2*WIDTH
231
232	int s;
233	for (s=0; s<STEPS; s++) {
234	int size = ((STEPS-s)*CWIDTH)/STEPS;
235
236	horizontal_line(x, y-OUTER_HEIGHT+s, size);
237	horizontal_line(x, y+INNER_HEIGHT+OUTER_HEIGHT-s, size);
238	}
239
240	int y_upper = ypos[s-4];
241	int y_lower = ypos[s-2];
242
243	int t;
244	for (t=0; t<THICKNESS; t++) {
245	int xp = x-(THICKNESS/2)+t+1;
246	line(point(xp, y_upper), point(xp, y_lower));
247	}
248
249	break;
250
251	#undef OUTER_HEIGHT
252	#undef INNER_HEIGHT
253	#undef CWIDTH
254	#undef STEPS
255	#undef THICKNESS
256
257	}
258	default: {
259	e4_assert(0);
260	break;
261	}
262	}
263	}
264
265	/* --------------------------------------------------------------------------------
266	ED4_cursor
267	-------------------------------------------------------------------------------- */
268
269	ED4_returncode ED4_cursor::draw_cursor(AW_pos x, AW_pos y) { // @@@ remove return value
270	if (cursor_shape) {
271	delete cursor_shape;
272	cursor_shape = 0;
273	}
274
275	cursor_shape = new ED4_CursorShape(ctype,
276	SEQ_TERM_TEXT_YOFFSET+2,
277	ED4_ROOT->font_group.get_width(ED4_G_SEQUENCES),
278	!awar_edit_rightward);
279
280	cursor_shape->draw(window()->get_device(), int(x), int(y));
281
282	#if defined(TRACE_REFRESH)
283	printf("draw_cursor(%i, %i)\n", int(x), int(y));
284	#endif // TRACE_REFRESH
285
286	return ED4_R_OK;
287	}
288
289	ED4_returncode ED4_cursor::delete_cursor(AW_pos del_mark, ED4_base *target_terminal) {
290	AW_pos x, y;
291	target_terminal->calc_world_coords(&x, &y);
292	ED4_base *temp_parent = target_terminal->get_parent(ED4_L_SPECIES);
293	if (!temp_parent \|\| temp_parent->flag.hidden \|\| !is_partly_visible()) {
294	return ED4_R_BREAK;
295	}
296
297	x = del_mark;
298	win->world_to_win_coords(&x, &y);
299
300	// refresh own terminal + terminal above + terminal below
301
302	const int MAX_AFFECTED = 3;
303	int affected = 0;
304	ED4_terminal *affected_terminal[MAX_AFFECTED];
305
306	affected_terminal[affected++] = target_terminal->to_terminal();
307
308	{
309	ED4_terminal *term = target_terminal->to_terminal();
310	bool backward = true;
311
312	while (1) {
313	int done = 0;
314
315	term = backward ? term->get_prev_terminal() : term->get_next_terminal();
316	if (!term) done = 1;
317	else if ((term->is_sequence_terminal()) && !term->is_in_folded_group()) {
318	affected_terminal[affected++] = term;
319	done = 1;
320	}
321
322	if (done) {
323	if (!backward) break;
324	backward = false;
325	term = target_terminal->to_terminal();
326	}
327	}
328	}
329
330	bool refresh_was_requested[MAX_AFFECTED];
331	e4_assert(affected >= 1 && affected <= MAX_AFFECTED);
332	for (int a = 0; a<affected; ++a) {
333	ED4_terminal *term = affected_terminal[a];
334	// cppcheck-suppress unreadVariable
335	refresh_was_requested[a] = term->update_info.refresh;
336	term->request_refresh();
337	}
338
339	// clear rectangle where cursor is displayed
340
341	AW_device *dev = win->get_device();
342	dev->push_clip_scale();
343
344	int xmin, xmax, ymin, ymax;
345
346	e4_assert(cursor_shape);
347	cursor_shape->get_bounding_box(int(x), int(y), xmin, ymin, xmax, ymax);
348
349	#if defined(TRACE_REFRESH)
350	printf("delete_cursor(%i, %i)\n", int(x), int(y));
351	#endif // TRACE_REFRESH
352
353	dev->set_font_overlap(true);
354
355	#define EXPAND_SIZE 0
356	if (dev->reduceClipBorders(ymin-EXPAND_SIZE, ymax+EXPAND_SIZE, xmin-EXPAND_SIZE, xmax+EXPAND_SIZE)) {
357	dev->clear_part(xmin, ymin, xmax-xmin+1, ymax-ymin+1, AW_ALL_DEVICES);
358	// refresh terminal to hide cursor
359	ED4_LocalWinContext uses(window());
360	LocallyModify<bool> flag(allowed_to_draw, false);
361	ED4_ROOT->special_window_refresh(false);
362	}
363	dev->pop_clip_scale();
364
365	// restore old refresh flags (to avoid refresh of 3 complete terminals when cursor changes)
366	for (int a = 0; a<affected; ++a) {
367	affected_terminal[a]->update_info.refresh = refresh_was_requested[a];
368	}
369
370	return (ED4_R_OK);
371	}
372
373
374	ED4_cursor::ED4_cursor(ED4_window *win_) : win(win_) {
375	init();
376	allowed_to_draw = true;
377	cursor_shape = 0;
378
379	ctype = (ED4_CursorType)(ED4_ROOT->aw_root->awar(ED4_AWAR_CURSOR_TYPE)->read_int()%ED4_CURSOR_TYPES);
380	}
381	void ED4_cursor::init() {
382	// used by ED4_terminal-d-tor
383	owner_of_cursor = NULL;
384	cursor_abs_x = 0;
385	screen_position = 0;
386	}
387	ED4_cursor::~ED4_cursor() {
388	delete cursor_shape;
389	}
390
391	int ED4_cursor::get_sequence_pos() const {
392	ED4_remap *remap = ED4_ROOT->root_group_man->remap();
393	size_t max_scrpos = remap->get_max_screen_pos();
394
395	return remap->screen_to_sequence(size_t(screen_position)<=max_scrpos ? screen_position : max_scrpos);
396	}
397
398	bool ED4_species_manager::setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfold_groups, ED4_CursorJumpType jump_type)
399	{
400	ED4_group_manager *group_manager_to_unfold = is_in_folded_group();
401
402	if (unfold_groups) {
403	bool did_unfold = false;
404
405	while (group_manager_to_unfold && unfold_groups) {
406	ED4_base *base = group_manager_to_unfold->search_spec_child_rek(ED4_L_BRACKET);
407	if (!base) break;
408
409	base->to_bracket_terminal()->unfold();
410	did_unfold = true;
411
412	group_manager_to_unfold = is_in_folded_group();
413	}
414
415	if (did_unfold) ED4_ROOT->refresh_all_windows(1); // needed to recalculate world cache of target terminal
416	}
417
418	if (!group_manager_to_unfold) { // species manager is visible (now)
419	ED4_terminal *terminal = search_spec_child_rek(ED4_L_SEQUENCE_STRING)->to_terminal();
420	if (terminal) {
421	if (seq_pos == -1) seq_pos = cursor->get_sequence_pos();
422	cursor->set_to_terminal(terminal, seq_pos, jump_type);
423	return true;
424	}
425	}
426
427	return false;
428	}
429
430	static void jump_to_species(ED4_species_name_terminal *name_term, int seq_pos, bool unfold_groups, ED4_CursorJumpType jump_type)
431	{
432	ED4_species_manager *species_manager = name_term->get_parent(ED4_L_SPECIES)->to_species_manager();
433	ED4_cursor *cursor = &current_cursor();
434	bool jumped = false;
435
436	if (species_manager) jumped = species_manager->setCursorTo(cursor, seq_pos, unfold_groups, jump_type);
437	if (!jumped) cursor->HideCursor();
438	}
439
440	static bool ignore_selected_species_changes_cb = false;
441	static bool ignore_selected_SAI_changes_cb = false;
442
443	static void select_named_sequence_terminal(const char *name) {
444	GB_transaction ta(GLOBAL_gb_main);
445	ED4_species_name_terminal *name_term = ED4_find_species_name_terminal(name);
446	if (name_term) {
447	ED4_MostRecentWinContext context; // use the last used window for selection
448
449	// lookup current name term
450	ED4_species_name_terminal *cursor_name_term = 0;
451	{
452	ED4_cursor *cursor = &current_cursor();
453	if (cursor) {
454	ED4_sequence_terminal *cursor_seq_term = 0;
455
456	if (cursor->owner_of_cursor) {
457	ED4_terminal *cursor_term = cursor->owner_of_cursor->to_text_terminal();
458	if (cursor_term->is_sequence_terminal()) {
459	cursor_seq_term = cursor_term->to_sequence_terminal();
460	}
461	else { // cursor is in a non-sequence text terminal -> search for corresponding sequence terminal
462	ED4_multi_sequence_manager *seq_man = cursor_term->get_parent(ED4_L_MULTI_SEQUENCE)->to_multi_sequence_manager();
463	if (seq_man) {
464	cursor_seq_term = seq_man->search_spec_child_rek(ED4_L_SEQUENCE_STRING)->to_sequence_terminal();
465	}
466	}
467	}
468	if (cursor_seq_term) {
469	cursor_name_term = cursor_seq_term->corresponding_species_name_terminal();
470	}
471	}
472	}
473
474	if (name_term!=cursor_name_term) { // do not change if already there!
475	#if defined(TRACE_JUMPS)
476	printf("Jumping to species/SAI '%s'\n", name);
477	#endif
478	jump_to_species(name_term, -1, false, ED4_JUMP_KEEP_POSITION);
479	}
480	else {
481	#if defined(TRACE_JUMPS)
482	printf("Change ignored because same name term!\n");
483	#endif
484	}
485	}
486	}
487
488	void ED4_selected_SAI_changed_cb(AW_root * /* aw_root */) {
489	if (!ignore_selected_SAI_changes_cb) {
490	char *name = GBT_read_string(GLOBAL_gb_main, AWAR_SAI_NAME);
491
492	if (name && name[0]) {
493	#if defined(TRACE_JUMPS)
494	printf("Selected SAI is '%s'\n", name);
495	#endif // DEBUG
496	LocallyModify<bool> flag(ED4_update_global_cursor_awars_allowed, false);
497	select_named_sequence_terminal(name);
498	free(name);
499	}
500	}
501	}
502
503	void ED4_selected_species_changed_cb(AW_root * /* aw_root */) {
504	if (!ignore_selected_species_changes_cb) {
505	char *name = GBT_read_string(GLOBAL_gb_main, AWAR_SPECIES_NAME);
506	if (name && name[0]) {
507	#if defined(TRACE_JUMPS)
508	printf("Selected species is '%s'\n", name);
509	#endif
510	LocallyModify<bool> flag(ED4_update_global_cursor_awars_allowed, false);
511	select_named_sequence_terminal(name);
512	}
513	free(name);
514	}
515	else {
516	#if defined(TRACE_JUMPS)
517	printf("Change ignored because ignore_selected_species_changes_cb!\n");
518	#endif
519	}
520	}
521
522	void ED4_jump_to_current_species(AW_window *aww, AW_CL) {
523	ED4_LocalWinContext uses(aww);
524	char *name = GBT_read_string(GLOBAL_gb_main, AWAR_SPECIES_NAME);
525	if (name && name[0]) {
526	GB_transaction dummy(GLOBAL_gb_main);
527	#if defined(TRACE_JUMPS)
528	printf("Jump to selected species (%s)\n", name);
529	#endif
530	ED4_species_name_terminal *name_term = ED4_find_species_name_terminal(name);
531
532	if (name_term) {
533	jump_to_species(name_term, -1, true, ED4_JUMP_KEEP_POSITION);
534	}
535	else {
536	aw_message(GBS_global_string("Species '%s' is not loaded - use GET to load it.", name));
537	}
538	}
539	else {
540	aw_message("Please select a species");
541	}
542	}
543
544	static bool multi_species_man_consensus_id_starts_with(ED4_base *base, AW_CL cl_start) { // TRUE if consensus id starts with 'start'
545	ED4_multi_species_manager *ms_man = base->to_multi_species_manager();
546	char start = (char)cl_start;
547	ED4_base *consensus = ms_man->search_spec_child_rek(ED4_L_SPECIES);
548
549	if (consensus) {
550	ED4_base *consensus_name = consensus->search_spec_child_rek(ED4_L_SPECIES_NAME);
551
552	if (consensus_name) {
553	if (strncmp(consensus_name->id, start, strlen(start))==0) {
554	ED4_multi_species_manager *cons_ms_man = consensus_name->get_parent(ED4_L_MULTI_SPECIES)->to_multi_species_manager();
555	return cons_ms_man==ms_man;
556	}
557	}
558	}
559
560	return false;
561	}
562
563	ED4_multi_species_manager *ED4_new_species_multi_species_manager() { // returns manager into which new species should be inserted
564	ED4_base *manager = ED4_ROOT->root_group_man->find_first_that(ED4_L_MULTI_SPECIES, multi_species_man_consensus_id_starts_with, (AW_CL)"More Sequences");
565	return manager ? manager->to_multi_species_manager() : 0;
566	}
567
568	void ED4_init_notFoundMessage() {
569	not_found_counter = 0;
570	not_found_message = GBS_stropen(10000);
571	// GBS_strcat(not_found_message,"Species not found: ");
572	}
573	void ED4_finish_and_show_notFoundMessage() {
574	if (not_found_counter != 0) {
575	if (not_found_counter>MAX_SHOWN_MISSING_SPECIES) {
576	GBS_strcat(not_found_message, GBS_global_string("(skipped display of %zu more species)\n", not_found_counter-MAX_SHOWN_MISSING_SPECIES));
577	}
578	char *out_message = GBS_strclose(not_found_message);
579	aw_message(out_message);
580	aw_message(GBS_global_string("Couldn't load %zu species:", not_found_counter));
581	free(out_message);
582	}
583	else {
584	GBS_strforget(not_found_message);
585	}
586	not_found_message = 0;
587	}
588
589	void ED4_get_and_jump_to_species(GB_CSTR species_name)
590	{
591	e4_assert(species_name && species_name[0]);
592
593	GB_transaction dummy(GLOBAL_gb_main);
594	ED4_species_name_terminal *name_term = ED4_find_species_name_terminal(species_name);
595	int loaded = 0;
596
597	if (!name_term) { // insert new species
598	ED4_multi_species_manager *insert_into_manager = ED4_new_species_multi_species_manager();
599	ED4_group_manager *group_man = insert_into_manager->get_parent(ED4_L_GROUP)->to_group_manager();
600	char string = (char)GB_calloc(strlen(species_name)+3, sizeof(*string));
601	int index = 0;
602	ED4_index y = 0;
603	ED4_index lot = 0;
604
605	ED4_init_notFoundMessage();
606
607	sprintf(string, "-L%s", species_name);
608	ED4_ROOT->database->fill_species(insert_into_manager,
609	ED4_ROOT->ref_terminals.get_ref_sequence_info(), ED4_ROOT->ref_terminals.get_ref_sequence(),
610	string, &index, &y, 0, &lot, insert_into_manager->calc_group_depth(), NULL);
611	loaded = 1;
612
613	ED4_finish_and_show_notFoundMessage();
614
615	{
616	GBDATA *gb_species = GBT_find_species(GLOBAL_gb_main, species_name);
617	GBDATA *gbd = GBT_read_sequence(gb_species, ED4_ROOT->alignment_name);
618
619	if (gbd) {
620	char *data = GB_read_string(gbd);
621	int len = GB_read_string_count(gbd);
622
623	group_man->update_bases(0, 0, data, len);
624	}
625	}
626
627	name_term = ED4_find_species_name_terminal(species_name);
628	if (name_term) {
629	// new AAseqTerminals should be created if it is in ProtView mode
630	if (ED4_ROOT->alignment_type == GB_AT_DNA) {
631	PV_AddCorrespondingOrfTerminals(name_term);
632	}
633	ED4_ROOT->main_manager->request_resize(); // @@@ instead needs to be called whenever adding or deleting PV-terminals
634	// it should create new AA Sequence terminals if the protein viewer is enabled
635	}
636	delete string;
637
638	insert_into_manager->invalidate_species_counters();
639	}
640	if (name_term) {
641	jump_to_species(name_term, -1, true, ED4_JUMP_KEEP_POSITION);
642	if (!loaded) {
643	aw_message(GBS_global_string("'%s' is already loaded.", species_name));
644	}
645	}
646	else {
647	aw_message(GBS_global_string("Cannot get species '%s'", species_name));
648	}
649	}
650
651	void ED4_get_and_jump_to_current(AW_window *aww, AW_CL) {
652	ED4_LocalWinContext uses(aww);
653	char *name = GBT_read_string(GLOBAL_gb_main, AWAR_SPECIES_NAME);
654	if (name && name[0]) {
655	ED4_get_and_jump_to_species(name);
656	}
657	else {
658	aw_message("Please select a species");
659	}
660	}
661
662	void ED4_get_and_jump_to_current_from_menu(AW_window *aw, AW_CL cl, AW_CL) {
663	ED4_get_and_jump_to_current(aw, cl);
664	}
665
666	void ED4_get_marked_from_menu(AW_window *, AW_CL, AW_CL) {
667	#define BUFFERSIZE 1000
668	GB_transaction dummy(GLOBAL_gb_main);
669	int marked = GBT_count_marked_species(GLOBAL_gb_main);
670
671	if (marked) {
672	GBDATA *gb_species = GBT_first_marked_species(GLOBAL_gb_main);
673	char *buffer = new char[BUFFERSIZE+1];
674	char *bp = buffer;
675
676	ED4_multi_species_manager *insert_into_manager = ED4_new_species_multi_species_manager();
677	ED4_group_manager *group_man = insert_into_manager->get_parent(ED4_L_GROUP)->to_group_manager();
678
679	int group_depth = insert_into_manager->calc_group_depth();
680	int index = 0;
681	ED4_index y = 0;
682	ED4_index lot = 0;
683	int inserted = 0;
684	char *default_alignment = GBT_get_default_alignment(GLOBAL_gb_main);
685
686	arb_progress progress("Loading species", marked);
687
688	ED4_init_notFoundMessage();
689
690	while (gb_species) {
691	const char *name = GBT_read_name(gb_species);
692	ED4_species_name_terminal *name_term = ED4_find_species_name_terminal(name);
693
694	if (!name_term) { // species not found -> insert
695	{
696	int namelen = strlen(name);
697	int buffree = BUFFERSIZE-int(bp-buffer);
698
699	if ((namelen+2)>buffree) {
700	*bp = 0;
701	ED4_ROOT->database->fill_species(insert_into_manager,
702	ED4_ROOT->ref_terminals.get_ref_sequence_info(), ED4_ROOT->ref_terminals.get_ref_sequence(),
703	buffer, &index, &y, 0, &lot, group_depth, NULL);
704	bp = buffer;
705	index = 0;
706	}
707
708	*bp++ = 1;
709	*bp++ = 'L';
710	memcpy(bp, name, namelen);
711	bp += namelen;
712	}
713
714	{
715	GBDATA *gbd = GBT_read_sequence(gb_species, default_alignment);
716
717	if (gbd) {
718	char *data = GB_read_string(gbd);
719	int len = GB_read_string_count(gbd);
720	group_man->table().add(data, len);
721	}
722	}
723
724	inserted++;
725	}
726	gb_species = GBT_next_marked_species(gb_species);
727	progress.inc();
728	}
729
730	if (bp>buffer) {
731	*bp++ = 0;
732	ED4_ROOT->database->fill_species(insert_into_manager,
733	ED4_ROOT->ref_terminals.get_ref_sequence_info(), ED4_ROOT->ref_terminals.get_ref_sequence(),
734	buffer, &index, &y, 0, &lot, group_depth, NULL);
735	}
736
737	aw_message(GBS_global_string("Loaded %i of %i marked species.", inserted, marked));
738
739	ED4_finish_and_show_notFoundMessage();
740
741	if (inserted) {
742	// new AAseqTerminals should be created if it is in ProtView mode
743	if (ED4_ROOT->alignment_type == GB_AT_DNA) {
744	PV_AddOrfTerminalsToLoadedSpecies();
745	}
746	ED4_ROOT->main_manager->request_resize(); // @@@ instead needs to be called whenever adding or deleting PV-terminals
747	}
748
749	delete [] buffer;
750	free(default_alignment);
751	}
752	else {
753	aw_message("No species marked.");
754	}
755
756	#undef BUFFERSIZE
757	}
758
759	ED4_returncode ED4_cursor::HideCursor()
760	{
761	if (owner_of_cursor) {
762	if (is_partly_visible()) {
763	delete_cursor(cursor_abs_x, owner_of_cursor);
764	}
765	owner_of_cursor = 0;
766	}
767
768	return ED4_R_OK;
769	}
770
771	void ED4_cursor::changeType(ED4_CursorType typ)
772	{
773	if (owner_of_cursor) {
774	ED4_terminal *old_owner_of_cursor = owner_of_cursor;
775
776	HideCursor();
777	ctype = typ;
778	ED4_ROOT->aw_root->awar(ED4_AWAR_CURSOR_TYPE)->write_int(int(ctype));
779	owner_of_cursor = old_owner_of_cursor;
780	ShowCursor(0, ED4_C_NONE, 0);
781	}
782	else {
783	ctype = typ;
784	}
785	}
786
787	bool ED4_update_global_cursor_awars_allowed = true;
788
789	static void trace_termChange_in_global_awar(ED4_terminal term, char& last_value, bool& ignore_flag, const char *awar_name) {
790	char *species_name = term->get_name_of_species();
791
792	if (!last_value \|\| strcmp(last_value, species_name) != 0) {
793	freeset(last_value, species_name);
794	LocallyModify<bool> raise(ignore_flag, true);
795	#if defined(TRACE_JUMPS)
796	fprintf(stderr, "Writing '%s' to awar '%s'\n", species_name, awar_name);
797	#endif
798	GBT_write_string(GLOBAL_gb_main, awar_name, species_name);
799	}
800	else {
801	free(species_name);
802	}
803	}
804
805	void ED4_cursor::updateAwars(bool new_term_selected) {
806	AW_root *aw_root = ED4_ROOT->aw_root;
807	int seq_pos = get_sequence_pos();
808
809	if (ED4_update_global_cursor_awars_allowed && new_term_selected) {
810	// @@@ last_set_XXX has to be window-specific (or better cursor specific)
811	if (in_SAI_terminal()) {
812	static char *last_set_SAI = 0;
813	trace_termChange_in_global_awar(owner_of_cursor, last_set_SAI, ignore_selected_SAI_changes_cb, AWAR_SAI_NAME);
814	}
815	else if (in_species_seq_terminal()) {
816	static char *last_set_species = 0;
817	trace_termChange_in_global_awar(owner_of_cursor, last_set_species, ignore_selected_species_changes_cb, AWAR_SPECIES_NAME);
818	}
819	}
820
821	// update awars for cursor position:
822	aw_root->awar(win->awar_path_for_cursor)->write_int(info2bio(seq_pos));
823	if (ED4_update_global_cursor_awars_allowed) {
824	aw_root->awar(AWAR_CURSOR_POSITION)->write_int(info2bio(seq_pos)); // update ARB-global cursor position
825	}
826
827	// look if we have a commented search result under the cursor:
828
829	if (owner_of_cursor && owner_of_cursor->is_sequence_terminal()) {
830	ED4_sequence_terminal *seq_term = owner_of_cursor->to_sequence_terminal();
831	ED4_SearchResults &results = seq_term->results();
832	ED4_SearchPosition *pos = results.get_shown_at(seq_pos);
833
834	if (pos) {
835	GB_CSTR comment = pos->get_comment();
836
837	if (comment) {
838	char *buffer = GB_give_buffer(strlen(comment)+30);
839
840	sprintf(buffer, "%s: %s", ED4_SearchPositionTypeId[pos->get_whatsFound()], comment);
841	aw_message(buffer);
842	}
843	}
844	}
845
846	// update awar for ecoli position:
847	BI_ecoli_ref *ecoli = ED4_ROOT->ecoli_ref;
848	if (ecoli->gotData()) {
849	int ecoli_pos = ecoli->abs_2_rel(seq_pos+1); // inclusive position behind cursor
850	aw_root->awar(win->awar_path_for_Ecoli)->write_int(ecoli_pos);
851	}
852
853	// update awar for base position:
854	int base_pos = base_position.get_base_position(owner_of_cursor, seq_pos+1); // inclusive position behind cursor
855	aw_root->awar(win->awar_path_for_basePos)->write_int(base_pos);
856
857	// update awar for IUPAC:
858
859	#define MAXIUPAC 6
860
861	char iupac[MAXIUPAC+1];
862	strcpy(iupac, ED4_IUPAC_EMPTY);
863
864	{
865	char at[2] = "\0";
866
867	if (in_consensus_terminal()) {
868	ED4_group_manager *group_manager = owner_of_cursor->get_parent(ED4_L_GROUP)->to_group_manager();
869	ED4_char_table& groupTab = group_manager->table();
870	if (seq_pos<groupTab.size()) {
871	groupTab.build_consensus_string_to(at, ExplicitRange(seq_pos, seq_pos));
872	}
873	}
874	else if (in_species_seq_terminal() \|\| in_SAI_terminal()) {
875	int len;
876	const char *seq = owner_of_cursor->resolve_pointer_to_char_pntr(&len);
877
878	if (seq_pos<len) at[0] = seq[seq_pos];
879	}
880
881	if (at[0]) {
882	char base = at[0];
883	const char *i = ED4_decode_iupac(base, ED4_ROOT->alignment_type);
884
885	e4_assert(strlen(i)<=MAXIUPAC);
886	strcpy(iupac, i);
887	}
888	}
889
890	#undef MAXIUPAC
891
892	aw_root->awar(win->awar_path_for_IUPAC)->write_string(iupac);
893
894	// update awar for helix#:
895	const char *helixNr = ED4_ROOT->helix->helixNr(seq_pos);
896	aw_root->awar(win->awar_path_for_helixNr)->write_string(helixNr ? helixNr : "");
897	}
898
899	int ED4_cursor::get_screen_relative_pos() const {
900	const ED4_coords& coords = window()->coords;
901	return cursor_abs_x - coords.window_left_clip_point;
902	}
903	void ED4_cursor::set_screen_relative_pos(int scroll_to_relpos) {
904	int curr_rel_pos = get_screen_relative_pos();
905	int scroll_amount = curr_rel_pos-scroll_to_relpos;
906
907	int length_of_char = ED4_ROOT->font_group.get_width(ED4_G_SEQUENCES);
908	scroll_amount = (scroll_amount/length_of_char)*length_of_char; // align to char-size
909
910	if (scroll_amount != 0) {
911	AW_window *aww = window()->aww;
912	aww->set_horizontal_scrollbar_position(aww->slider_pos_horizontal + scroll_amount);
913	#if defined(TRACE_JUMPS)
914	printf("set_screen_relative_pos(%i) auto-scrolls %i\n", scroll_to_relpos, scroll_amount);
915	#endif
916	ED4_horizontal_change_cb(aww, 0, 0);
917	}
918	}
919
920
921	void ED4_cursor::jump_screen_pos(int screen_pos, ED4_CursorJumpType jump_type) {
922	if (!owner_of_cursor) {
923	aw_message("First you have to place the cursor");
924	return;
925	}
926
927	if (owner_of_cursor->is_hidden()) return; // do not jump if cursor terminal is hidden
928
929	AW_pos terminal_x, terminal_y;
930	owner_of_cursor->calc_world_coords(&terminal_x, &terminal_y);
931
932	#if defined(TRACE_JUMPS)
933	printf("jump_screen_pos(%i)\n", screen_pos);
934	#endif
935
936	ED4_terminal *term = owner_of_cursor;
937	ED4_window *ed4w = window();
938
939	term->scroll_into_view(ed4w); // correct y-position of terminal
940
941	int cursor_diff = screen_pos-screen_position;
942	if (cursor_diff == 0) { // cursor position did not change
943	if (jump_type == ED4_JUMP_KEEP_VISIBLE) return; // nothing special -> done
944	}
945
946	int terminal_pixel_length = ed4w->get_device()->get_string_size(ED4_G_SEQUENCES, 0, owner_of_cursor->to_text_terminal()->get_length());
947	int length_of_char = ED4_ROOT->font_group.get_width(ED4_G_SEQUENCES);
948	int abs_x_new = cursor_abs_x+cursor_diff*length_of_char; // position in terminal
949
950	if (abs_x_new > terminal_x+terminal_pixel_length+CHARACTEROFFSET \|\| abs_x_new < terminal_x+CHARACTEROFFSET) {
951	return; // don`t move out of terminal
952	}
953
954	ED4_coords *coords = &ed4w->coords;
955
956	int screen_width = coords->window_right_clip_point-coords->window_left_clip_point;
957	int scroll_new_to = -1; // if >0 -> scroll abs_x_new to this screen-relative position
958
959	if (jump_type != ED4_JUMP_KEEP_VISIBLE) {
960	int rel_x = cursor_abs_x-coords->window_left_clip_point;
961
962	if (jump_type == ED4_JUMP_KEEP_POSITION) {
963	bool was_in_screen = rel_x >= 0 && rel_x <= screen_width;
964	if (!was_in_screen) {
965	jump_type = ED4_JUMP_KEEP_VISIBLE; // // don't have useful relative position -> scroll
966	}
967	}
968
969	switch (jump_type) {
970	case ED4_JUMP_CENTERED: scroll_new_to = screen_width/2; break;
971	case ED4_JUMP_KEEP_POSITION: scroll_new_to = rel_x; break;
972	case ED4_JUMP_KEEP_VISIBLE: break; // handled below
973	default: e4_assert(0); break;
974	}
975	}
976
977	if (jump_type == ED4_JUMP_KEEP_VISIBLE) {
978	int margin = length_of_char * ED4_ROOT->aw_root->awar(ED4_AWAR_SCROLL_MARGIN)->read_int();
979
980	int right_margin = coords->window_right_clip_point - margin;
981	int left_margin = coords->window_left_clip_point + margin;
982
983	if (left_margin >= right_margin) scroll_new_to = screen_width/2; // margins too big -> center
984	else if (abs_x_new > right_margin) scroll_new_to = screen_width-margin;
985	else if (abs_x_new < left_margin) scroll_new_to = margin;
986	}
987
988	delete_cursor(cursor_abs_x, owner_of_cursor);
989
990	if (scroll_new_to >= 0) { // scroll
991	int rel_x_new = abs_x_new-coords->window_left_clip_point;
992	int scroll_amount = rel_x_new-scroll_new_to;
993
994	if (scroll_amount>0) scroll_amount += length_of_char/2;
995	else if (scroll_amount<0) scroll_amount -= length_of_char/2;
996
997	scroll_amount = (scroll_amount/length_of_char)*length_of_char; // align to char-size
998	if (scroll_amount != 0) {
999	AW_window *aww = ed4w->aww;
1000	aww->set_horizontal_scrollbar_position(aww->slider_pos_horizontal + scroll_amount);
1001	#if defined(TRACE_JUMPS)
1002	printf("jump_screen_pos auto-scrolls %i\n", scroll_amount);
1003	#endif
1004	LocallyModify<bool> flag(allowed_to_draw, false);
1005	ED4_horizontal_change_cb(aww, 0, 0);
1006	}
1007	}
1008
1009	LocallyModify<bool> flag(allowed_to_draw, true);
1010	if (cursor_diff >= 0) {
1011	ShowCursor(cursor_diff*length_of_char, ED4_C_RIGHT, abs(cursor_diff));
1012	}
1013	else {
1014	ShowCursor(cursor_diff*length_of_char, ED4_C_LEFT, abs(cursor_diff));
1015	}
1016	}
1017
1018	void ED4_cursor::jump_sequence_pos(int seq_pos, ED4_CursorJumpType jump_type) {
1019	int screen_pos = ED4_ROOT->root_group_man->remap()->sequence_to_screen(seq_pos);
1020	jump_screen_pos(screen_pos, jump_type);
1021	}
1022
1023	void ED4_cursor::jump_base_pos(int base_pos, ED4_CursorJumpType jump_type) {
1024	int seq_pos = base2sequence_position(base_pos);
1025	jump_sequence_pos(seq_pos, jump_type);
1026	}
1027
1028	class has_base_at : public ED4_TerminalPredicate {
1029	int seq_pos;
1030	bool want_base;
1031	public:
1032	has_base_at(int seq_pos_, bool want_base_) : seq_pos(seq_pos_), want_base(want_base_) {}
1033	bool fulfilled_by(const ED4_terminal *terminal) const OVERRIDE {
1034	bool test_succeeded = false;
1035
1036	if (terminal->is_sequence_terminal()) {
1037	const ED4_sequence_terminal *seqTerm = terminal->to_sequence_terminal();
1038	int len;
1039	char *seq = seqTerm->resolve_pointer_to_string_copy(&len);
1040	if (seq) {
1041	test_succeeded = len>seq_pos && bool(ADPP_IS_ALIGN_CHARACTER(seq[seq_pos]))!=want_base;
1042	}
1043	free(seq);
1044	}
1045
1046	return test_succeeded;
1047	}
1048	};
1049
1050	struct acceptAnyTerminal : public ED4_TerminalPredicate {
1051	bool fulfilled_by(const ED4_terminal *) const OVERRIDE { return true; }
1052	};
1053
1054	static ED4_terminal get_upper_lower_cursor_pos(ED4_manager starting_point, ED4_cursor_move cursor_move, AW_pos current_y, bool isScreen, const ED4_TerminalPredicate& predicate) {
1055	// current_y is y-position of terminal at which search starts.
1056	// It may be in world or screen coordinates (isScreen marks which is used)
1057	// This is needed to move the cursor from top- to middle-area w/o scrolling middle-area to top-position.
1058
1059	ED4_terminal *result = 0;
1060
1061	int m = 0;
1062	int last_m = starting_point->children->members()-1;
1063	int incr = 1;
1064
1065	if (cursor_move == ED4_C_UP) {
1066	std::swap(m, last_m); incr = -1; // revert search direction
1067	e4_assert(!isScreen); // use screen coordinates for ED4_C_DOWN only!
1068	}
1069
1070	while (!result) {
1071	ED4_base *member = starting_point->children->member(m);
1072
1073	if (member->is_manager()) {
1074	if (!member->flag.hidden) { // step over hidden managers (e.g. folded groups)
1075	result = get_upper_lower_cursor_pos(member->to_manager(), cursor_move, current_y, isScreen, predicate);
1076	}
1077	}
1078	else {
1079	if (member->dynamic_prop & ED4_P_CURSOR_ALLOWED) {
1080	AW_pos x, y;
1081	member->calc_world_coords(&x, &y);
1082	if (isScreen) current_ed4w()->world_to_win_coords(&x, &y); // if current_y is screen, convert x/y to screen-coordinates as well
1083
1084	bool pos_beyond = (cursor_move == ED4_C_UP) ? y<current_y : y>current_y;
1085	if (pos_beyond) {
1086	bool skip_top_scrolled = false;
1087	if (isScreen) {
1088	ED4_multi_species_manager *marea_man = NULL;
1089	if (member->get_area_level(&marea_man) == ED4_A_MIDDLE_AREA) {
1090	// previous position was in top-area -> avoid selecting scrolled-out terminals
1091	AW_pos y_area = marea_man->parent->extension.position[Y_POS];
1092	skip_top_scrolled = y<y_area;
1093	}
1094	}
1095
1096	if (!skip_top_scrolled) {
1097	ED4_terminal *term = member->to_terminal();
1098	if (predicate.fulfilled_by(term)) result = term;
1099	}
1100	}
1101	}
1102	}
1103
1104	if (m == last_m) break;
1105	m += incr;
1106	}
1107
1108	return result;
1109	}
1110
1111	struct acceptConsensusTerminal : public ED4_TerminalPredicate {
1112	bool fulfilled_by(const ED4_terminal *term) const OVERRIDE { return term->is_consensus_terminal(); }
1113	};
1114
1115	ED4_returncode ED4_cursor::move_cursor(AW_event *event) {
1116	// move cursor up down
1117	ED4_cursor_move dir = ED4_C_NONE;
1118	ED4_returncode result = ED4_R_OK;
1119	bool endHome = false;
1120
1121	switch (event->keycode) {
1122	case AW_KEY_UP: dir = ED4_C_UP; break;
1123	case AW_KEY_DOWN: dir = ED4_C_DOWN; break;
1124	case AW_KEY_HOME: dir = ED4_C_UP; endHome = true; break;
1125	case AW_KEY_END: dir = ED4_C_DOWN; endHome = true; break;
1126	default: e4_assert(0); break; // illegal call of move_cursor()
1127	}
1128
1129	if (dir != ED4_C_NONE) {
1130	if (owner_of_cursor->is_hidden()) result = ED4_R_IMPOSSIBLE; // don't move cursor if terminal is hidden
1131
1132	if (result == ED4_R_OK) {
1133	AW_pos x_dummy, y_world;
1134
1135	owner_of_cursor->calc_world_coords(&x_dummy, &y_world);
1136
1137	int seq_pos = get_sequence_pos();
1138	ED4_terminal *target_terminal = 0;
1139
1140	// stay in current area
1141	ED4_multi_species_manager *start_at_manager = 0;
1142	ED4_AREA_LEVEL area_level = owner_of_cursor->get_area_level(&start_at_manager);
1143
1144	if (event->keymodifier & AW_KEYMODE_CONTROL) {
1145	bool has_base = has_base_at(seq_pos, true).fulfilled_by(owner_of_cursor);
1146
1147	if (!endHome) { // not End or Home
1148	target_terminal = get_upper_lower_cursor_pos(start_at_manager, dir, y_world, false, has_base_at(seq_pos, !has_base));
1149	if (target_terminal && !has_base && ED4_ROOT->aw_root->awar(ED4_AWAR_FAST_CURSOR_JUMP)->read_int()) { // if jump_over group
1150	target_terminal->calc_world_coords(&x_dummy, &y_world);
1151	target_terminal = get_upper_lower_cursor_pos(start_at_manager, dir, y_world, false, has_base_at(seq_pos, false));
1152	}
1153	}
1154
1155	if (target_terminal == 0) {
1156	// either already in last group (or no space behind last group) -> jump to end (or start)
1157	target_terminal = get_upper_lower_cursor_pos(start_at_manager,
1158	dir == ED4_C_UP ? ED4_C_DOWN : ED4_C_UP, // use opposite movement direction
1159	dir == ED4_C_UP ? 0 : INT_MAX, false, // search for top-/bottom-most terminal
1160	acceptAnyTerminal());
1161	}
1162	}
1163	else {
1164	e4_assert(!endHome); // END and HOME w/o Ctrl should not call move_cursor()
1165	if (event->keymodifier & AW_KEYMODE_ALT) {
1166	target_terminal = get_upper_lower_cursor_pos(start_at_manager, dir, y_world, false, acceptConsensusTerminal());
1167	}
1168	else {
1169	bool isScreen = false;
1170	if (dir == ED4_C_DOWN) {
1171	if (area_level == ED4_A_TOP_AREA) {
1172	window()->world_to_win_coords(&x_dummy, &y_world); // special handling to move cursor from top to bottom area
1173	isScreen = true;
1174	}
1175	}
1176	target_terminal = get_upper_lower_cursor_pos(ED4_ROOT->main_manager, dir, y_world, isScreen, acceptAnyTerminal());
1177	}
1178	}
1179
1180	if (target_terminal) {
1181	set_to_terminal(target_terminal, seq_pos, ED4_JUMP_KEEP_VISIBLE);
1182	}
1183	}
1184	}
1185
1186	return result;
1187	}
1188
1189	void ED4_cursor::set_abs_x() {
1190	AW_pos x, y;
1191	owner_of_cursor->calc_world_coords(&x, &y);
1192	cursor_abs_x = int(get_sequence_pos()*ED4_ROOT->font_group.get_width(ED4_G_SEQUENCES) + CHARACTEROFFSET + x);
1193	}
1194
1195
1196	ED4_returncode ED4_cursor::ShowCursor(ED4_index offset_x, ED4_cursor_move move, int move_pos) {
1197	AW_pos x=0, y=0, x_help = 0, y_help;
1198
1199	owner_of_cursor->calc_world_coords(&x, &y);
1200
1201	switch (move) {
1202	case ED4_C_RIGHT: screen_position += move_pos; break;
1203	case ED4_C_LEFT: screen_position -= move_pos; break;
1204	case ED4_C_NONE: break; // no move - only redisplay
1205	default: e4_assert(0); break;
1206	}
1207
1208	{
1209	LocallyModify<bool> flag(ED4_update_global_cursor_awars_allowed, ED4_update_global_cursor_awars_allowed && move != ED4_C_NONE);
1210	updateAwars(false);
1211	}
1212
1213	x_help = cursor_abs_x + offset_x;
1214	y_help = y;
1215
1216	window()->world_to_win_coords(&x_help, &y_help);
1217
1218	if (allowed_to_draw) draw_cursor(x_help, y_help);
1219	#if defined(DEBUG) && 0
1220	else printf("Skip draw_cursor (allowed_to_draw=false)\n");
1221	#endif // DEBUG
1222
1223	cursor_abs_x += offset_x;
1224
1225	return (ED4_R_OK);
1226	}
1227
1228	bool ED4_cursor::is_hidden_inside_group() const {
1229	if (!owner_of_cursor) return false;
1230	if (!owner_of_cursor->is_in_folded_group()) return false;
1231	if (in_consensus_terminal()) {
1232	ED4_base *group_man = owner_of_cursor->get_parent(ED4_L_GROUP);
1233	e4_assert(group_man);
1234	return group_man->is_in_folded_group();
1235	}
1236	return true;
1237	}
1238
1239	bool ED4_cursor::is_partly_visible() const {
1240	e4_assert(owner_of_cursor);
1241	e4_assert(cursor_shape); // cursor is not drawn, cannot test visibility
1242
1243	if (is_hidden_inside_group()) {
1244	printf("is_hidden_inside_group=true\n");
1245	return false;
1246	}
1247
1248	AW_pos x, y;
1249	owner_of_cursor->calc_world_coords(&x, &y);
1250
1251	int x1, y1, x2, y2;
1252	cursor_shape->get_bounding_box(cursor_abs_x, int(y), x1, y1, x2, y2);
1253
1254	bool visible = false;
1255
1256	switch (owner_of_cursor->get_area_level(0)) {
1257	case ED4_A_TOP_AREA: visible = win->shows_xpos(x1) \|\| win->shows_xpos(x2); break;
1258	case ED4_A_MIDDLE_AREA: visible = win->partly_shows(x1, y1, x2, y2); break;
1259	default: break;
1260	}
1261
1262	return visible;
1263	}
1264
1265	bool ED4_cursor::is_completely_visible() const {
1266	e4_assert(owner_of_cursor);
1267	e4_assert(cursor_shape); // cursor is not drawn, cannot test visibility
1268
1269	if (is_hidden_inside_group()) return false;
1270
1271	AW_pos x, y;
1272	owner_of_cursor->calc_world_coords(&x, &y);
1273
1274	int x1, y1, x2, y2;
1275	cursor_shape->get_bounding_box(cursor_abs_x, int(y), x1, y1, x2, y2);
1276
1277	bool visible = false;
1278
1279	switch (owner_of_cursor->get_area_level(0)) {
1280	case ED4_A_TOP_AREA: visible = win->shows_xpos(x1) && win->shows_xpos(x2); break;
1281	case ED4_A_MIDDLE_AREA: visible = win->completely_shows(x1, y1, x2, y2); break;
1282	default: break;
1283	}
1284
1285	return visible;
1286	}
1287
1288	#if defined(DEBUG) && 0
1289	#define DUMP_SCROLL_INTO_VIEW
1290	#endif
1291
1292	void ED4_terminal::scroll_into_view(ED4_window *ed4w) { // scroll y-position only
1293	ED4_LocalWinContext uses(ed4w);
1294
1295	AW_pos termw_x, termw_y;
1296	calc_world_coords(&termw_x, &termw_y);
1297
1298	ED4_coords *coords = &current_ed4w()->coords;
1299
1300	int term_height = int(extension.size[1]);
1301	int win_ysize = coords->window_lower_clip_point - coords->window_upper_clip_point + 1;
1302
1303	bool scroll = false;
1304	int slider_pos_y;
1305
1306	ED4_cursor_move direction = ED4_C_NONE;
1307
1308	AW_pos termw_y_upper = termw_y; // upper border of terminal
1309	AW_pos termw_y_lower = termw_y + term_height; // lower border of terminal
1310
1311	if (termw_y_upper > coords->top_area_height) { // don't scroll if terminal is in top area (always visible)
1312	if (termw_y_upper < coords->window_upper_clip_point) { // scroll up
1313	#ifdef DUMP_SCROLL_INTO_VIEW
1314	printf("termw_y_upper(%i) < window_upper_clip_point(%i)\n",
1315	int(termw_y_upper), int(coords->window_upper_clip_point));
1316	#endif // DEBUG
1317	slider_pos_y = int(termw_y_upper - coords->top_area_height - term_height);
1318	scroll = true;
1319	direction = ED4_C_UP;
1320	}
1321	else if (termw_y_lower > coords->window_lower_clip_point) { // scroll down
1322	#ifdef DUMP_SCROLL_INTO_VIEW
1323	printf("termw_y_lower(%i) > window_lower_clip_point(%i)\n",
1324	int(termw_y_lower), int(coords->window_lower_clip_point));
1325	#endif // DEBUG
1326	slider_pos_y = int(termw_y_upper - coords->top_area_height - win_ysize);
1327	scroll = true;
1328	direction = ED4_C_DOWN;
1329	}
1330	}
1331
1332	#ifdef DUMP_SCROLL_INTO_VIEW
1333	if (!scroll) {
1334	printf("No scroll needed (termw_y_upper=%i termw_y_lower=%i term_height=%i window_upper_clip_point=%i window_lower_clip_point=%i)\n",
1335	int(termw_y_upper), int(termw_y_lower), term_height,
1336	int(coords->window_upper_clip_point), int(coords->window_lower_clip_point));
1337	}
1338	#endif // DEBUG
1339
1340	if (scroll) {
1341	AW_window *aww = ed4w->aww;
1342
1343	int pic_ysize = int(aww->get_scrolled_picture_height());
1344	int slider_pos_yrange = pic_ysize - win_ysize;
1345
1346	if (slider_pos_yrange<0) { // win_ysize > pic_ysize
1347	slider_pos_y = 0;
1348	}
1349	else {
1350	ED4_multi_species_manager *start_at_manager = 0;
1351	get_area_level(&start_at_manager);
1352
1353	ED4_terminal *nextTerm = get_upper_lower_cursor_pos(start_at_manager, direction, termw_y, false, acceptAnyTerminal());
1354	if (!nextTerm) { // no next term in this area
1355	slider_pos_y = direction == ED4_C_UP ? 0 : slider_pos_yrange; // scroll to limit
1356	}
1357	}
1358
1359	if (slider_pos_y>slider_pos_yrange) slider_pos_y = slider_pos_yrange;
1360	if (slider_pos_y<0) slider_pos_y = 0;
1361
1362	aww->set_vertical_scrollbar_position(slider_pos_y);
1363	ED4_scrollbar_change_cb(aww, 0, 0);
1364	}
1365	}
1366
1367	void ED4_cursor::set_to_terminal(ED4_terminal *terminal, int seq_pos, ED4_CursorJumpType jump_type) {
1368	if (seq_pos == -1) seq_pos = get_sequence_pos();
1369
1370	bool new_term_selected = owner_of_cursor != terminal;
1371	if (new_term_selected) {
1372	if (owner_of_cursor) {
1373	if (get_sequence_pos() != seq_pos) {
1374	jump_sequence_pos(seq_pos, jump_type); // position to wanted column -- scrolls horizontally
1375	}
1376	}
1377
1378	int scr_pos = ED4_ROOT->root_group_man->remap()->sequence_to_screen(seq_pos);
1379	show_cursor_at(terminal, scr_pos);
1380
1381	if (!is_completely_visible()) {
1382	jump_sequence_pos(seq_pos, jump_type);
1383	}
1384	}
1385	else {
1386	jump_sequence_pos(seq_pos, jump_type);
1387	}
1388
1389	GB_transaction ta(GLOBAL_gb_main);
1390	updateAwars(new_term_selected);
1391	}
1392
1393	ED4_returncode ED4_cursor::show_cursor_at(ED4_terminal *target_terminal, ED4_index scr_pos) {
1394	bool new_term_selected = owner_of_cursor != target_terminal;
1395
1396	if (owner_of_cursor) {
1397	if (is_partly_visible()) {
1398	delete_cursor(cursor_abs_x, owner_of_cursor);
1399	}
1400	owner_of_cursor = NULL;
1401	DRAW = 1;
1402	}
1403
1404	target_terminal->scroll_into_view(window());
1405
1406	AW_pos termw_x, termw_y;
1407	target_terminal->calc_world_coords(&termw_x, &termw_y);
1408
1409	screen_position = scr_pos;
1410
1411	int length_of_char = ED4_ROOT->font_group.get_width(ED4_G_SEQUENCES);
1412
1413	AW_pos world_x = termw_x + length_of_char*screen_position + CHARACTEROFFSET;
1414	AW_pos world_y = termw_y;
1415
1416	AW_pos win_x = world_x;
1417	AW_pos win_y = world_y;
1418	window()->world_to_win_coords(&win_x, &win_y);
1419
1420	cursor_abs_x = (long int)world_x;
1421	owner_of_cursor = target_terminal;
1422
1423	draw_cursor(win_x, win_y);
1424
1425	GB_transaction gb_dummy(GLOBAL_gb_main);
1426	updateAwars(new_term_selected);
1427
1428	return ED4_R_OK;
1429	}
1430
1431	ED4_returncode ED4_cursor::show_clicked_cursor(AW_pos click_xpos, ED4_terminal *target_terminal)
1432	{
1433	AW_pos termw_x, termw_y;
1434	target_terminal->calc_world_coords(&termw_x, &termw_y);
1435
1436	ED4_index scr_pos = ED4_ROOT->pixel2pos(click_xpos - termw_x);
1437	return show_cursor_at(target_terminal, scr_pos);
1438	}
1439
1440
1441	/* --------------------------------------------------------------------------------
1442	ED4_base_position
1443	-------------------------------------------------------------------------------- */
1444
1445	ED4_base_position::ED4_base_position()
1446	: calced4term(0)
1447	{
1448	}
1449
1450	ED4_base_position::~ED4_base_position() {
1451	invalidate();
1452	}
1453
1454	static void ed4_bp_sequence_changed_cb(ED4_species_manager *, AW_CL cl_base_pos) {
1455	ED4_base_position base_pos = (ED4_base_position)cl_base_pos;
1456	base_pos->invalidate();
1457	}
1458
1459	void ED4_base_position::invalidate() {
1460	if (calced4term) {
1461	ED4_species_manager *species_manager = calced4term->get_parent(ED4_L_SPECIES)->to_species_manager();
1462	species_manager->remove_sequence_changed_cb(ed4_bp_sequence_changed_cb, (AW_CL)this); // @@@ removes cb called later -> ED4_base.cxx@INVALID_CB_HANDLING
1463
1464	calced4term = 0;
1465	}
1466	}
1467
1468	static bool is_gap(char c) { return ED4_is_align_character[safeCharIndex(c)]; }
1469	static bool is_consensus_gap(char c) { return ED4_is_align_character[safeCharIndex(c)] \|\| c == '='; }
1470
1471	void ED4_base_position::calc4term(const ED4_terminal *base)
1472	{
1473	e4_assert(base);
1474
1475	ED4_species_manager *species_manager = base->get_parent(ED4_L_SPECIES)->to_species_manager();
1476	int len;
1477	char *seq;
1478
1479	if (calced4term) {
1480	ED4_species_manager *prev_species_manager = calced4term->get_parent(ED4_L_SPECIES)->to_species_manager();
1481	prev_species_manager->remove_sequence_changed_cb(ed4_bp_sequence_changed_cb, (AW_CL)this);
1482	}
1483
1484	species_manager->add_sequence_changed_cb(ed4_bp_sequence_changed_cb, (AW_CL)this);
1485
1486	bool (*isGap_fun)(char);
1487	if (species_manager->is_consensus_manager()) {
1488	ED4_group_manager *group_manager = base->get_parent(ED4_L_GROUP)->to_group_manager();
1489
1490	seq = group_manager->table().build_consensus_string();
1491	len = strlen(seq);
1492	isGap_fun = is_consensus_gap;
1493	}
1494	else {
1495	seq = base->resolve_pointer_to_string_copy(&len);
1496	e4_assert((int)strlen(seq) == len);
1497	isGap_fun = is_gap;
1498	}
1499
1500	e4_assert(seq);
1501
1502	#if defined(WARN_TODO)
1503	#warning ED4_is_align_character is kinda CharPredicate - refactor
1504	#endif
1505	CharPredicate pred_is_gap(isGap_fun);
1506	initialize(seq, len, pred_is_gap);
1507	calced4term = base;
1508
1509	free(seq);
1510	}
1511	int ED4_base_position::get_base_position(const ED4_terminal *term, int sequence_position) {
1512	if (!term) return 0;
1513	set_term(term);
1514	return abs_2_rel(sequence_position);
1515	}
1516	int ED4_base_position::get_sequence_position(const ED4_terminal *term, int base_pos) {
1517	if (!term) return 0;
1518	set_term(term);
1519	return rel_2_abs(base_pos);
1520	}
1521
1522	/* --------------------------------------------------------------------------------
1523	Store/Restore Cursorpositions
1524	-------------------------------------------------------------------------------- */
1525
1526	class CursorPos : virtual Noncopyable {
1527	ED4_terminal *terminal;
1528	int seq_pos;
1529
1530	CursorPos *next;
1531
1532	static CursorPos *head;
1533
1534	public:
1535
1536	static void clear()
1537	{
1538	while (head) {
1539	CursorPos *p = head->next;
1540
1541	delete head;
1542	head = p;
1543	}
1544	}
1545	static CursorPos *get_head() { return head; }
1546
1547	CursorPos(ED4_terminal *t, int p)
1548	{
1549	terminal = t;
1550	seq_pos = p;
1551	next = head;
1552	head = this;
1553	}
1554	~CursorPos() {}
1555
1556	ED4_terminal *get_terminal() const { return terminal; }
1557	int get_seq_pos() const { return seq_pos; }
1558
1559	void moveToEnd()
1560	{
1561	e4_assert(this==head);
1562
1563	if (next) {
1564	CursorPos *p = head = next;
1565
1566	while (p->next) {
1567	p = p->next;
1568	}
1569
1570	p->next = this;
1571	this->next = 0;
1572	}
1573	}
1574	};
1575
1576	CursorPos *CursorPos::head = 0;
1577
1578	void ED4_store_curpos(AW_window aww, AW_CL / cd1 /, AW_CL / cd2 */) {
1579	GB_transaction dummy(GLOBAL_gb_main);
1580	ED4_LocalWinContext uses(aww);
1581	ED4_cursor *cursor = &current_cursor();
1582
1583	if (!cursor->owner_of_cursor) {
1584	aw_message("First you have to place the cursor.");
1585	}
1586	else {
1587	new CursorPos(cursor->owner_of_cursor, cursor->get_sequence_pos());
1588	}
1589	}
1590
1591	void ED4_restore_curpos(AW_window aww, AW_CL / cd1 /, AW_CL / cd2 */) {
1592	GB_transaction dummy(GLOBAL_gb_main);
1593	ED4_LocalWinContext uses(aww);
1594	ED4_cursor *cursor = &current_cursor();
1595
1596	CursorPos *pos = CursorPos::get_head();
1597	if (!pos) {
1598	aw_message("No cursor position stored.");
1599	return;
1600	}
1601
1602	pos->get_terminal()->setCursorTo(cursor, pos->get_seq_pos(), true, ED4_JUMP_KEEP_VISIBLE);
1603	pos->moveToEnd();
1604	}
1605
1606	void ED4_clear_stored_curpos(AW_window * /* aww /, AW_CL / cd1 /, AW_CL / cd2 */)
1607	{
1608	CursorPos::clear();
1609	}
1610
1611	/* --------------------------------------------------------------------------------
1612	Other stuff
1613	-------------------------------------------------------------------------------- */
1614
1615	void ED4_helix_jump_opposite(AW_window aww, AW_CL / cd1 /, AW_CL / cd2 */) {
1616	GB_transaction dummy(GLOBAL_gb_main);
1617	ED4_LocalWinContext uses(aww);
1618	ED4_cursor *cursor = &current_cursor();
1619
1620	if (!cursor->owner_of_cursor) {
1621	aw_message("First you have to place the cursor.");
1622	return;
1623	}
1624
1625	int seq_pos = cursor->get_sequence_pos();
1626	AW_helix *helix = ED4_ROOT->helix;
1627	BI_PAIR_TYPE pairType = helix->pairtype(seq_pos);
1628
1629	if (pairType != HELIX_NONE) {
1630	int pairing_pos = helix->opposite_position(seq_pos);
1631	cursor->jump_sequence_pos(pairing_pos, ED4_JUMP_KEEP_POSITION);
1632	}
1633	else {
1634	aw_message("Not at helix position");
1635	}
1636	}
1637
1638	void ED4_change_cursor(AW_window aww, AW_CL / cd1 /, AW_CL / cd2 */) {
1639	ED4_LocalWinContext uses(aww);
1640	ED4_cursor *cursor = &current_cursor();
1641	ED4_CursorType typ = cursor->getType();
1642
1643	cursor->changeType((ED4_CursorType)((typ+1)%ED4_CURSOR_TYPES));
1644	}
1645
1646	// --------------------------------------------------------------------------------
1647
1648	#ifdef UNIT_TESTS
1649	#include <test_unit.h>
1650	#include <test_helpers.h>
1651
1652	struct test_absrel {
1653	bool torel;
1654	test_absrel(bool r) : torel(r) {}
1655	virtual ~test_absrel() {}
1656
1657	virtual int a2r(int a) const = 0;
1658	virtual int r2a(int r) const = 0;
1659
1660	virtual int abs_size() const = 0;
1661	virtual int rel_size() const = 0;
1662
1663	int gen(int i) const { return torel ? a2r(i) : r2a(i); }
1664	int get_size() const { return torel ? abs_size()+1 : rel_size(); }
1665
1666	char *genResult() const;
1667	};
1668
1669	struct membind {
1670	const test_absrel& me;
1671	membind(const test_absrel& ta) : me(ta) {}
1672	int operator()(int i) const { return me.gen(i); }
1673	};
1674
1675	char *test_absrel::genResult() const {
1676	return collectIntFunResults(membind(*this), 0, get_size()-1, 3, 1, 1);
1677	}
1678
1679	struct test_ecoli : public test_absrel {
1680	BI_ecoli_ref& eref;
1681	test_ecoli(BI_ecoli_ref& b, bool to_rel) : test_absrel(to_rel), eref(b) {}
1682	int a2r(int a) const OVERRIDE { return eref.abs_2_rel(a); }
1683	int r2a(int r) const OVERRIDE { return eref.rel_2_abs(r); }
1684	int abs_size() const OVERRIDE { return eref.abs_count(); }
1685	int rel_size() const OVERRIDE { return eref.base_count(); }
1686	};
1687
1688	struct test_basepos : public test_absrel {
1689	BasePosition& bpos;
1690	test_basepos(BasePosition& bpos_, bool to_rel)
1691	: test_absrel(to_rel), bpos(bpos_) {}
1692	int a2r(int a) const OVERRIDE { return bpos.abs_2_rel(a); }
1693	int r2a(int r) const OVERRIDE { return bpos.rel_2_abs(r); }
1694	int abs_size() const OVERRIDE { return bpos.abs_count(); }
1695	int rel_size() const OVERRIDE { return bpos.base_count(); }
1696	};
1697
1698	#define TEST_ABSREL_EQUALS(tester,expected) do { \
1699	char *res = tester.genResult(); \
1700	TEST_EXPECT_EQUAL(res,expected); \
1701	free(res); \
1702	} while(0)
1703
1704	#define TEST_ECOLIREF_EQUALS(data,alen,a2r,r2a) do { \
1705	BI_ecoli_ref eref; \
1706	eref.init(data,alen); \
1707	TEST_ABSREL_EQUALS(test_ecoli(eref, true), a2r); \
1708	TEST_ABSREL_EQUALS(test_ecoli(eref, false), r2a); \
1709	} while(0)
1710
1711
1712	#define TEST_BASE_POS_EQUALS(data,a2r,r2a) do { \
1713	{ \
1714	BasePosition bpos(data, strlen(data), CharPredicate(is_gap)); \
1715	TEST_ABSREL_EQUALS(test_basepos(bpos, true), a2r); \
1716	TEST_ABSREL_EQUALS(test_basepos(bpos, false), r2a); \
1717	} \
1718	} while(0)
1719
1720	void TEST_BI_ecoli_ref() {
1721	TEST_ECOLIREF_EQUALS("-.AC-G-T-.", 10,
1722	" [0] 0 0 0 1 2 2 3 3 4 4 4 [4]", // abs -> rel
1723	" [0] 2 3 5 7 [7]"); // rel -> abs
1724
1725	TEST_ECOLIREF_EQUALS("-", 1, " [0] 0 0 [0]", " [0] [0]");
1726	TEST_ECOLIREF_EQUALS("--A", 1, " [0] 0 0 [0]", " [0] [0]"); // part of sequence
1727	TEST_ECOLIREF_EQUALS("--", 2, " [0] 0 0 0 [0]", " [0] [0]");
1728	TEST_ECOLIREF_EQUALS("---", 3, " [0] 0 0 0 0 [0]", " [0] [0]");
1729
1730	TEST_ECOLIREF_EQUALS("A", 1, " [0] 0 1 [1]", " [0] 0 [0]");
1731	TEST_ECOLIREF_EQUALS("A", 2, " [0] 0 1 1 [1]", " [0] 0 [0]");
1732
1733	TEST_ECOLIREF_EQUALS("A-", 2, " [0] 0 1 1 [1]", " [0] 0 [0]");
1734	TEST_ECOLIREF_EQUALS("-A", 2, " [0] 0 0 1 [1]", " [0] 1 [1]");
1735
1736	TEST_ECOLIREF_EQUALS("A", 3, " [0] 0 1 1 1 [1]", " [0] 0 [0]"); // more than sequence
1737	TEST_ECOLIREF_EQUALS("A--", 3, " [0] 0 1 1 1 [1]", " [0] 0 [0]");
1738	TEST_ECOLIREF_EQUALS("-A-", 3, " [0] 0 0 1 1 [1]", " [0] 1 [1]");
1739	TEST_ECOLIREF_EQUALS("--A", 3, " [0] 0 0 0 1 [1]", " [0] 2 [2]");
1740	}
1741
1742	void TEST_base_position() {
1743	ED4_init_is_align_character("-"); // count '.' as base
1744
1745	TEST_BASE_POS_EQUALS("-.AC-G-T-.",
1746	" [0] 0 0 1 2 3 3 4 4 5 5 6 [6]", // abs -> rel
1747	" [0] 1 2 3 5 7 9 [9]"); // rel -> abs
1748
1749	// ------------------------------
1750	ED4_init_is_align_character(".-");
1751
1752	TEST_BASE_POS_EQUALS("-.AC-G-T-.",
1753	" [0] 0 0 0 1 2 2 3 3 4 4 4 [4]", // abs -> rel
1754	" [0] 2 3 5 7 [7]"); // rel -> abs
1755
1756	TEST_BASE_POS_EQUALS("-", " [0] 0 0 [0]", " [0] [0]");
1757	TEST_BASE_POS_EQUALS("--", " [0] 0 0 0 [0]", " [0] [0]");
1758	TEST_BASE_POS_EQUALS("---", " [0] 0 0 0 0 [0]", " [0] [0]");
1759
1760	TEST_BASE_POS_EQUALS("A", " [0] 0 1 [1]", " [0] 0 [0]");
1761
1762	TEST_BASE_POS_EQUALS("A-", " [0] 0 1 1 [1]", " [0] 0 [0]");
1763	TEST_BASE_POS_EQUALS("-A", " [0] 0 0 1 [1]", " [0] 1 [1]");
1764
1765	TEST_BASE_POS_EQUALS("A--", " [0] 0 1 1 1 [1]", " [0] 0 [0]");
1766	TEST_BASE_POS_EQUALS("-A-", " [0] 0 0 1 1 [1]", " [0] 1 [1]");
1767	TEST_BASE_POS_EQUALS("--A", " [0] 0 0 0 1 [1]", " [0] 2 [2]");
1768	}
1769
1770	#endif // UNIT_TESTS
1771
1772

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