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source: tags/ms_r16q2/EDIT4/ED4_edit_string.cxx

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Last change on this file was 14476, checked in by westram, 7 years ago
`AlignDataAccess`: use factory function (ensures proper initialization; was missing for SINA interface); removed global use callback to get helix-string (only used in island_hopping; optional) store alignment-name add proper ctor, copy-ctor and op= island_hopping store helix-string as copy
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 44.7 KB

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1	#include <arbdbt.h>
2	#include <AW_helix.hxx>
3
4	#include <fast_aligner.hxx>
5	#include <awt_map_key.hxx>
6
7	#include "ed4_edit_string.hxx"
8	#include "ed4_class.hxx"
9	#include "ed4_awars.hxx"
10	#include "ed4_seq_colors.hxx"
11
12	#include <aw_awar.hxx>
13	#include <aw_msg.hxx>
14	#include <aw_root.hxx>
15	#include <aw_question.hxx>
16	#include <aw_advice.hxx>
17	#include <cctype>
18
19	#define SAFE_EDITING // undef this to remove sequence test code
20
21	int ED4_Edit_String::nrepeat = 0; // # of times command should be repeated
22	int ED4_Edit_String::nrepeat_zero_requested = 0; // nrepeat should be set to zero
23	int ED4_Edit_String::nrepeat_is_already_set = 0; // nrepeat was zero (and was set to 1)
24
25	GB_ERROR ED4_Edit_String::insert(char *text, long position, int direction, int removeAtNextGap) {
26	long i;
27	int text_len = strlen(text);
28	if (text_len == 0) return 0;
29
30	int rest_len;
31
32	if (direction>=0) {
33	rest_len = seq_len-position;
34	}
35	else {
36	rest_len = position;
37	}
38
39	if (rest_len<=0 \|\| text_len>rest_len) {
40	return GBS_global_string("You can't insert text after the end of the sequence!");
41	}
42
43	if (removeAtNextGap) {
44	int nextGap = get_next_gap(position, direction);
45	if (nextGap==-1) {
46	goto no_gaps;
47	}
48
49	int afterGap = nextGap+direction;
50
51	if (afterGap>=0 && afterGap<seq_len) { // in sequence
52	if (seq[afterGap]!=seq[nextGap]) { // gap type changed -> warn to avoid overwrite of '?'
53	return GBS_global_string("Only one gap %s text => insert aborted", direction>=0 ? "after" : "before");
54	}
55	}
56
57	rest_len = (afterGap-position)*direction;
58	}
59
60	if (direction>=0) {
61	if (text_len + position >= seq_len) {
62	return GBS_global_string("You cannot insert that many characters after cursor!");
63	}
64
65	for (i = rest_len-text_len; i<rest_len; i++) {
66	if (!ED4_is_gap_character(seq[position+i])) {
67	goto no_gaps;
68	}
69	}
70
71	for (i = position+rest_len-text_len-1; i>=position; i--) {
72	seq[i+text_len] = seq[i];
73	}
74
75	for (i = 0; i<text_len; i++) {
76	seq[position+i] = text[i];
77	}
78	}
79	else {
80	if (position - text_len < 0) {
81	return GBS_global_string("You cannot insert that many characters before cursor!");
82	}
83
84	for (i = 0; i<text_len; i++) {
85	if (i<0 \|\| !ED4_is_gap_character(seq[i])) {
86	goto no_gaps;
87	}
88	}
89	for (i = 0; i<position-text_len; i++) {
90	seq[i] = seq[i+text_len];
91	}
92
93	for (i = 0; i<text_len; i++) {
94	seq[position-i-1] = text[i];
95	}
96	}
97
98	return 0;
99
100	no_gaps :
101	return GBS_global_string("There are no/not enough gaps at %s of sequence => can't insert characters%s",
102	direction >= 0 ? "end" : "start",
103	direction >= 0 ? "\nMaybe your sequences are not formatted?" : "");
104	}
105
106	GB_ERROR ED4_Edit_String::remove(int len, long position, int direction, int insertAtNextGap) {
107
108	int rest_len; // bases between cursor-position and the directed sequence end
109
110	if (direction>=0) { // forward
111	if ((len + position) >= seq_len) len = (int)(seq_len-position);
112	rest_len = seq_len-position;
113	}
114	else { // backward
115	position--;
116	if (len>position) len = position;
117	rest_len = position;
118	}
119
120	if ((position >= seq_len) \|\| (len == 0) \|\| (seq_len - len < 0)) {
121	return GBS_global_string("Illegal delete position/length");
122	}
123
124	if (insertAtNextGap) {
125	int nextGap = get_next_gap(position+len*direction, direction);
126
127	if (nextGap!=-1) {
128	rest_len = (nextGap-position)*direction;
129	}
130	}
131
132	int new_len = rest_len-len; // no of bases that will be copied
133	int i;
134
135	if (direction>=0) {
136	for (i=0; i<new_len; i++) {
137	seq[position+i] = seq[position+len+i];
138	}
139	for (; i<rest_len; i++) {
140	seq[position+i] = '.';
141	}
142	}
143	else {
144	for (i=0; i<new_len; i++) {
145	seq[position-i] = seq[position-len-i];
146	}
147	for (; i<rest_len; i++) {
148	seq[position-i] = '.';
149	}
150	}
151
152	e4_assert(seq[seq_len]=='\0');
153
154	return 0;
155	}
156
157	GB_ERROR ED4_Edit_String::replace(char *text, long position, int direction) {
158	int text_len = strlen(text);
159	int i;
160	if (direction>=0) {
161
162	if ((position + text_len > seq_len) \|\| (position > seq_len)) {
163	return GBS_global_string("Replace after end of sequence !");
164	}
165	for (i = 0; i < text_len; i ++) {
166	seq[i+position] = text[i];
167	}
168	}
169	else {
170	if ((position - text_len < 0) \|\| (position > seq_len)) {
171	return GBS_global_string("Replace before start of sequence !");
172	}
173	for (i = 0; i < text_len; i ++) {
174	seq[position - i - 1] = text[i];
175	}
176	}
177	return 0;
178	}
179
180	GB_ERROR ED4_Edit_String::swap_gaps(long position, char ch) {
181	long i;
182	for (i = position; i < seq_len; i++) {
183	if (!ED4_is_gap_character(seq[i])) break;
184	seq[i] = ch;
185	}
186	for (i = position; i >= 0; i--) {
187	if (!ED4_is_gap_character(seq[i])) break;
188	seq[i] = ch;
189	}
190	return 0;
191	}
192
193
194	GB_ERROR ED4_Edit_String::moveBase(long source_position, long dest_position, unsigned char gap_to_use)
195	{
196	e4_assert(source_position!=dest_position);
197	#ifdef SAFE_EDITING
198	if (!legal_seqpos(dest_position) \|\| !legal_seqpos(source_position)) {
199	return "Position out of sequence";
200	}
201	#endif
202
203	int direction = dest_position<source_position ? -1 : 1;
204	int base = seq[source_position];
205	e4_assert(!ED4_is_gap_character(base));
206	seq[source_position] = gap_to_use;
207
208	long p = source_position+direction;
209	while (p!=dest_position) {
210	#ifdef SAFE_EDITING
211	if (!ED4_is_gap_character(seq[p])) {
212	e4_assert(0);
213	return "Internal error: Tried to change base order in moveBase()";
214	}
215	#endif
216	e4_assert(ED4_is_gap_character(seq[p]));
217	seq[p] = gap_to_use;
218	p += direction;
219	}
220
221	seq[dest_position] = base;
222	return 0;
223	}
224
225	GB_ERROR ED4_Edit_String::shiftBases(long source_pos, long last_source, long dest_pos, int direction, long *last_dest, unsigned char gap_to_use)
226	// shifts bases from source_pos-last_source to dest_pos
227	// last_dest is set to the position after the last dest_pos (direction<0 ? pos. right of bases : pos. left of bases)
228	{
229	GB_ERROR err = 0;
230
231	if (direction<0) {
232	e4_assert(dest_pos<source_pos);
233	e4_assert(source_pos<=last_source);
234	while (1) {
235	err = moveBase(source_pos, dest_pos, gap_to_use);
236	if (err \|\| source_pos>=last_source) break;
237	source_pos++;
238	dest_pos++;
239	while (!ED4_is_gap_character(seq[dest_pos])) {
240	dest_pos++;
241	}
242	}
243	}
244	else {
245	e4_assert(source_pos<dest_pos);
246	e4_assert(last_source<=source_pos);
247	while (1) {
248	err = moveBase(source_pos, dest_pos, gap_to_use);
249	if (err \|\| source_pos<=last_source) break;
250	source_pos--;
251	dest_pos--;
252	while (!ED4_is_gap_character(seq[dest_pos])) {
253	dest_pos--;
254	}
255	}
256	}
257
258	if (last_dest) {
259	*last_dest = dest_pos;
260	}
261
262	return err;
263	}
264
265	long ED4_Edit_String::get_next_base(long position, int direction) {
266	long pos;
267	if (direction < 0) position--;
268	for (pos = position; pos>=0 && pos < seq_len; pos += direction) {
269	if (!ED4_is_gap_character(seq[pos])) break;
270	}
271
272	return pos<0 \|\| pos>=seq_len ? -1 : pos;
273	}
274	long ED4_Edit_String::get_next_gap(long position, int direction) {
275	long pos;
276	if (direction < 0) position--;
277	for (pos = position; pos >= 0 && pos < seq_len; pos += direction) {
278	if (ED4_is_gap_character(seq[pos])) break;
279	}
280
281	return pos<0 \|\| pos>=seq_len ? -1 : pos;
282	}
283	long ED4_Edit_String::get_next_visible_base(long position, int direction)
284	{
285	long pos;
286	if (direction < 0) position--;
287	for (pos = position; pos>=0 && pos < seq_len; pos += direction) {
288	if (!ED4_is_gap_character(seq[pos]) && remap->is_shown(pos)) {
289	break;
290	}
291	}
292
293	return pos<0 \|\| pos>=seq_len ? -1 : pos;
294	}
295	long ED4_Edit_String::get_next_visible_gap(long position, int direction) {
296	long pos;
297	if (direction < 0) position--;
298	for (pos = position; pos >= 0 && pos < seq_len; pos += direction) {
299	if (ED4_is_gap_character(seq[pos]) && remap->is_shown(pos)) {
300	break;
301	}
302	}
303
304	return pos<0 \|\| pos>=seq_len ? -1 : pos;
305	}
306	long ED4_Edit_String::get_next_visible_pos(long position, int direction)
307	{
308	long pos;
309	if (direction < 0) position--;
310	for (pos = position; pos >= 0 && pos < seq_len; pos += direction) {
311	if (remap->is_shown(pos)) {
312	break;
313	}
314	}
315	return pos<0 \|\| pos>=seq_len ? -1 : pos;
316	}
317
318	unsigned char ED4_Edit_String::get_gap_type(long pos, int direction)
319	{
320	pos += direction;
321	if (!legal_seqpos(pos)) return '.';
322	char gap = seq[pos];
323	if (ED4_is_gap_character(gap)) return gap;
324	return '-';
325	}
326
327	static GB_ERROR toggle_cursor_group_folding() {
328	GB_ERROR error = NULL;
329	ED4_cursor& cursor = current_cursor();
330	if (cursor.owner_of_cursor) {
331	ED4_terminal *cursor_term = cursor.owner_of_cursor;
332
333	if (cursor_term->is_in_folded_group()) {
334	// cursor not visible -> unfold group which hides cursor
335	cursor_term->setCursorTo(&cursor, cursor.get_sequence_pos(), true, ED4_JUMP_KEEP_POSITION);
336	}
337	else {
338	ED4_base *group = cursor.owner_of_cursor->get_parent(ED4_L_GROUP);
339	if (group) {
340	ED4_group_manager *group_man = group->to_group_manager();
341	ED4_bracket_terminal *bracket_term = group_man->get_defined_level(ED4_L_BRACKET)->to_bracket_terminal();
342
343	if (group_man->dynamic_prop & ED4_P_IS_FOLDED) {
344	bracket_term->unfold();
345	}
346	else {
347	ED4_species_manager *consensus_man = group_man->get_multi_species_manager()->get_consensus_manager();
348	if (consensus_man) consensus_man->setCursorTo(&cursor, cursor.get_sequence_pos(), true, ED4_JUMP_KEEP_POSITION);
349
350	bracket_term->fold();
351	}
352	}
353	}
354	}
355	return error;
356	}
357
358	static void toggle_mark_of_specData(GBDATA *gb_data) {
359	// toggle mark of species owning data 'gb_data'
360	GB_transaction ta(gb_data);
361	GBDATA *gb_species = GB_get_grandfather(gb_data);
362	if (gb_species) GB_write_flag(gb_species, !GB_read_flag(gb_species));
363	}
364
365	GB_ERROR ED4_Edit_String::command(AW_key_mod keymod, AW_key_code keycode, char key, int direction, ED4_EDITMODE mode, bool is_consensus,
366	long &seq_pos, bool &changed_flag, ED4_CursorJumpType& cursor_jump, bool &cannot_handle, bool &write_fault, GBDATA* gb_data, bool is_sequence)
367	{
368	changed_flag = 0;
369	write_fault = 0;
370	if (keymod+keycode+key==0) return 0;
371
372	e4_assert(nrepeat>0);
373
374	long old_seq_pos = seq_pos;
375	int screen_len = remap->sequence_to_screen(seq_len);
376	int cursorpos = remap->sequence_to_screen(seq_pos);
377
378	char str[2];
379	str[0] = key;
380	str[1] = 0;
381
382	direction = direction>0 ? 1 : -1;
383
384	if ((cursorpos > screen_len) \|\| (cursorpos < 0)) {
385	if (cursorpos<MAXSEQUENCECHARACTERLENGTH && cursorpos>=0) {
386	char *seq2 = new char[MAXSEQUENCECHARACTERLENGTH+1];
387
388	memcpy(seq2, seq, seq_len);
389	memset(seq2+seq_len, '.', MAXSEQUENCECHARACTERLENGTH-seq_len);
390	seq_len = MAXSEQUENCECHARACTERLENGTH;
391	seq2[seq_len] = 0;
392
393	delete seq;
394	seq = seq2;
395
396	changed_flag = 1;
397	}
398	else {
399	return GBS_global_string("Cursor out of sequence at screen_pos #%i!", cursorpos);
400	}
401	}
402
403	GB_ERROR ad_err = 0;
404	long h;
405	bool reinterpret_key = true;
406
407	while (reinterpret_key) {
408	reinterpret_key = false;
409
410	switch (keycode) {
411	case AW_KEY_HOME: {
412	int new_seq_pos = get_next_visible_base(0, 1);
413	if (new_seq_pos>=0) seq_pos = new_seq_pos==seq_pos ? 0 : new_seq_pos;
414	else seq_pos = 0;
415	break;
416	}
417	case AW_KEY_END: {
418	int new_seq_pos = get_next_visible_base(seq_len, -1);
419	if (new_seq_pos>=0) {
420	int new_gap_pos = get_next_visible_gap(new_seq_pos, 1);
421	if (new_gap_pos >= 0) {
422	seq_pos = new_gap_pos==seq_pos ? seq_len : new_gap_pos;
423	}
424	else {
425	seq_pos = seq_len;
426	}
427	}
428	else {
429	seq_pos = seq_len;
430	}
431	break;
432	}
433	case AW_KEY_LEFT:
434	case AW_KEY_RIGHT: {
435	direction = keycode==AW_KEY_RIGHT ? 1 : -1;
436
437	// no key modifier -> just move cursor
438
439	int n = nrepeat;
440
441	if (keymod == AW_KEYMODE_NONE) {
442	while (n--) {
443	do {
444	seq_pos += direction;
445	}
446	while (legal_curpos(seq_pos) && !remap->is_shown(seq_pos));
447	}
448	break;
449	}
450
451	if (mode==AD_NOWRITE) { write_fault = 1; break; }
452
453	int jump_or_fetch = 0; // 1=jump selected 2=fetch selected (for repeat only)
454	int push_or_pull = 0; // 1=push selected 2=pull selected (for repeat only)
455
456	// ------------------
457	// loop over nrepeat:
458
459	while (!ad_err && n-->0 && legal_curpos(seq_pos)) {
460	cursorpos = remap->sequence_to_screen(seq_pos);
461
462	int adjacent_scr_pos = cursorpos - (direction<0); // screen position next to the cursor
463	if (adjacent_scr_pos<0 \|\| size_t(adjacent_scr_pos)>remap->get_max_screen_pos()) {
464	ad_err = GBS_global_string("Action beyond end of screen!");
465	break;
466	}
467
468	int adjacent_seq_pos = remap->screen_to_sequence(adjacent_scr_pos); // _visible_ sequence position next to the cursor
469	int real_adjacent_seq_pos = seq_pos - (direction<0); // sequence position next to cursor (not necessarily visible)
470
471	if (adjacent_seq_pos<0 \|\| adjacent_seq_pos>=seq_len) {
472	ad_err = GBS_global_string("Action beyond end of sequence!");
473	break;
474	}
475
476	// Ctrl+Cursor = move cursor to next end of word (or to end of next word)
477
478	if (keymod & AW_KEYMODE_CONTROL) {
479	if (adjacent_scr_pos>=0) {
480	long pos = adjacent_seq_pos;
481
482	if (ED4_ROOT->aw_root->awar(ED4_AWAR_FAST_CURSOR_JUMP)->read_int()) { // should cursor jump over next group?
483	if (ED4_is_gap_character(seq[pos])) {
484	pos = get_next_visible_base(pos, direction);
485	if (pos>=0) pos = get_next_visible_gap(pos, direction);
486	}
487	else {
488	pos = get_next_visible_gap(pos, direction);
489	}
490
491	seq_pos = (pos>=0
492	? (direction<0 ? pos+1 : pos)
493	: (direction<0 ? 0 : seq_len-1));
494	}
495	else {
496	if (ED4_is_gap_character(seq[pos])) { seq_pos = get_next_visible_base(pos, direction); }
497	else { seq_pos = get_next_visible_gap(pos, direction); }
498
499	if (direction<0) { seq_pos = seq_pos==-1 ? 0 : seq_pos+1; }
500	else { seq_pos = seq_pos==-1 ? seq_len : seq_pos; }
501	}
502	}
503	continue;
504	}
505
506	// ALT/META+Cursor = jump & fetch
507
508	if (keymod & (AW_KEYMODE_ALT)) {
509	if (is_consensus) { cannot_handle = 1; return 0; }
510
511	if (ED4_is_gap_character(seq[adjacent_seq_pos])) { // there's a _gap_ next to the cursor -> let's fetch
512	if (jump_or_fetch!=1) {
513	jump_or_fetch = 2;
514	long source_pos = get_next_base(adjacent_seq_pos, direction); // position of base to fetch
515	if (source_pos==-1) { // there is nothing to fetch
516	n = 0;
517	}
518	else {
519	ad_err = moveBase(source_pos, adjacent_seq_pos, get_gap_type(source_pos, direction));
520	seq_pos = adjacent_seq_pos + (direction>0);
521	}
522	}
523	else {
524	n = 0;
525	}
526	}
527	else { // there's a _base_ next to the cursor -> let it jump
528	if (jump_or_fetch!=2) {
529	jump_or_fetch = 1;
530	int next_gap = adjacent_seq_pos - direction;
531
532	if (ED4_is_gap_character(seq[next_gap])) {
533	int dest_pos = get_next_base(next_gap, -direction);
534
535	if (dest_pos<0) {
536	dest_pos = direction>0 ? 0 : seq_len-1;
537	}
538	else {
539	dest_pos += direction;
540	}
541
542	if (ED4_is_gap_character(seq[dest_pos])) {
543	ad_err = moveBase(adjacent_seq_pos, dest_pos, get_gap_type(adjacent_seq_pos, direction));
544	if (!ad_err) {
545	seq_pos = get_next_base(seq_pos, direction)+(direction<0);
546	if (seq_pos==-1) {
547	seq_pos = direction<0 ? 0 : seq_len;
548	}
549	}
550	}
551	else {
552	e4_assert(0);
553	}
554	}
555	else {
556	ad_err = GBS_global_string("You can only jump single bases.");
557	}
558	}
559	else {
560	n = 0;
561	}
562	}
563
564	if (!ad_err) {
565	changed_flag = 1;
566	}
567
568	continue;
569	}
570
571	// Shift+Cursor = push/pull character
572
573	if (is_consensus) { cannot_handle = 1; return 0; };
574
575	if (ED4_is_gap_character(seq[real_adjacent_seq_pos])) { // pull
576	long dest_pos = real_adjacent_seq_pos;
577	long source_pos = real_adjacent_seq_pos-direction;
578
579	if (!ED4_is_gap_character(seq[source_pos]) && push_or_pull!=1) {
580	push_or_pull = 2;
581
582	long next_gap = get_next_gap(source_pos, -direction);
583	long last_source = next_gap>=0 ? next_gap : (direction>0 ? 0 : seq_len-1);
584
585	if (ED4_is_gap_character(seq[last_source])) {
586	last_source = get_next_base(last_source, direction);
587	}
588
589	ad_err = shiftBases(source_pos, last_source, dest_pos, direction, 0,
590	is_sequence ? get_gap_type(last_source, -direction) : '.');
591
592	if (!ad_err) {
593	seq_pos = dest_pos + (direction>0);
594	changed_flag = 1;
595	}
596	}
597	else {
598	n = 0;
599	}
600	}
601	else { // push
602	long next_gap = get_next_gap(adjacent_seq_pos, direction);
603
604	if (next_gap>=0 && push_or_pull!=2) {
605	push_or_pull = 1;
606	long dest_pos = next_gap;
607	long source_pos = get_next_base(next_gap, -direction);
608	long last_source = adjacent_seq_pos;
609
610	e4_assert(source_pos>=0);
611	ad_err = shiftBases(source_pos, last_source, dest_pos, direction, &dest_pos,
612	is_sequence ? get_gap_type(last_source, -direction) : '.');
613
614	if (!ad_err) {
615	seq_pos = dest_pos + (direction<0);
616	changed_flag = 1;
617	}
618	}
619	else {
620	n = 0;
621	}
622	}
623	}
624	break;
625	}
626
627	case AW_KEY_BACKSPACE:
628	h = seq_pos;
629
630	if (direction>0) {
631	seq_pos -= nrepeat;
632	}
633	else {
634	seq_pos += nrepeat;
635	}
636	if (seq_pos <0 \|\| seq_pos >= seq_len) {
637	seq_pos = h;
638	break;
639	}
640	// fall-through
641
642	case AW_KEY_DELETE:
643	h = seq_pos;
644
645	if (is_consensus) { cannot_handle = 1; return 0; };
646	if (keymod) { return 0; }
647
648	if (mode==AD_NOWRITE) { write_fault = 1; break; }
649
650	switch (mode) {
651	case AD_ALIGN:
652	{
653	int len;
654	int offset;
655
656	ad_err = 0;
657	if (direction>=0) offset = 0;
658	else offset = -nrepeat;
659
660	for (len = nrepeat-1; len>=0; len--) {
661	if (!ED4_is_gap_character(seq[h+offset+len])) {
662	ad_err = GBS_global_string("You cannot remove bases in align mode");
663	break;
664	}
665	}
666	if (ad_err) break;
667	}
668	case AD_REPLACE:
669	case AD_INSERT:
670	ad_err = remove(nrepeat, h, direction, !is_sequence);
671	if (!ad_err) {
672	changed_flag = 1;
673	}
674	break;
675	default:
676	break;
677	}
678
679	break;
680
681	case AW_KEY_RETURN:
682	ad_err = toggle_cursor_group_folding();
683	break;
684
685	case AW_KEY_ASCII: {
686
687	// keyboard layout:
688	//
689	// - CTRL-A Align ok
690	// - CTRL-D Toggle view differences ok
691	// - CTRL-E Toggle edit/align ok
692	// - CTRL-I Toggle insert/replace ok
693	// - CTRL-J Jump opposite helix position ok
694	// - CTRL-K Toggle compression on/off ok
695	// - CTRL-L Refresh ok
696	// - CTRL-M Invert mark ok
697	// - CTRL-O = ALT-LEFT ok
698	// - CTRL-P = ALT-RIGHT ok
699	// - CTRL-R Set aligner OR viewDiff reference species ok
700	// - CTRL-S Repeat last search ok
701	// - CTRL-U Undo @@@ crashes! disabled atm!
702
703
704	if (key >0 && key<=26) { // CTRL-Keys
705	switch (key+'A'-1) {
706	case 'A': { // CTRL-A = Start Fast-Aligner
707	AW_window *aw_tmp = current_aww();
708	if (is_consensus) { cannot_handle = 1; return 0; };
709	if (mode==AD_NOWRITE) { write_fault = 1; return 0; }
710
711	AlignDataAccess localDataAccess(*ED4_get_aligner_data_access()); // use local modified copy
712	localDataAccess.do_refresh = false;
713
714	FastAligner_set_align_current(ED4_ROOT->aw_root, ED4_ROOT->props_db);
715	AW_clock_cursor(ED4_ROOT->aw_root);
716	GB_commit_transaction(localDataAccess.gb_main);
717
718	FastAligner_start(aw_tmp, &localDataAccess);
719
720	GB_begin_transaction(localDataAccess.gb_main);
721	AW_normal_cursor(ED4_ROOT->aw_root);
722
723	int basesLeftOf = 0;
724	int pos;
725
726	for (pos=0; pos < seq_pos && pos<seq_len; pos++) { // count # of bases left of cursorpos
727	if (!ED4_is_gap_character(seq[pos])) {
728	basesLeftOf++;
729	}
730	}
731
732	char *aligned_seq = GB_read_string(gb_data); // read new sequence
733	ad_err = GB_write_string(gb_data, seq); // restore old sequence
734
735	freeset(seq, aligned_seq); // set new sequence
736	changed_flag = 1; // and mark changed
737
738	{
739	int basesLeftOf2 = 0;
740	int lastCorrectPos = -1;
741	for (pos=0; pos<seq_pos && pos<seq_len; pos++) { // count # of bases left of cursorpos
742	if (!ED4_is_gap_character(seq[pos])) {
743	basesLeftOf2++;
744	if (basesLeftOf2 == basesLeftOf) lastCorrectPos = pos;
745	}
746	}
747
748	if (basesLeftOf != basesLeftOf2) { // old cursor-position has different basepos
749	if (lastCorrectPos != -1) { // already seen position with same basepos
750	seq_len = lastCorrectPos+1;
751	}
752	else {
753	for (; pos<seq_len; pos++) {
754	if (!ED4_is_gap_character(seq[pos])) {
755	basesLeftOf2++;
756	if (basesLeftOf2 == basesLeftOf) {
757	seq_pos = pos+1;
758	break; // stop after first matching position
759	}
760	}
761	}
762	}
763	}
764	}
765	break;
766	}
767	case 'R': { // CTRL-R = set aligner reference species OR set reference for diff-mode
768	ED4_reference *ref = ED4_ROOT->reference;
769	if (ref->is_set()) { // if "view differences" is active = > set new reference
770	ED4_viewDifferences_setNewReference();
771	}
772	else { // otherwise set aligner reference
773	if (is_consensus) { cannot_handle = 1; return 0; };
774	FastAligner_set_reference_species(ED4_ROOT->aw_root);
775	}
776	break;
777	}
778	case 'D': { // CTRL-D = Toggle view differences
779	ED4_toggle_viewDifferences(ED4_ROOT->aw_root);
780	break;
781	}
782	case 'E': { // CTRL-E = Toggle Edit/Align-Mode
783	ED4_ROOT->aw_root->awar(AWAR_EDIT_MODE)->toggle_toggle();
784	break;
785	}
786	case 'I': { // CTRL-I = Toggle Insert/Replace-Mode
787	ED4_ROOT->aw_root->awar(AWAR_INSERT_MODE)->toggle_toggle();
788	break;
789	}
790	case 'J': { // CTRL-J = Jump to opposite helix position
791	AW_helix *helix = ED4_ROOT->helix;
792
793	if (!helix->has_entries()) ad_err = strdup("Got no helix information");
794	else if (helix->pairtype(seq_pos) != HELIX_NONE) {
795	seq_pos = helix->opposite_position(seq_pos);
796	cursor_jump = ED4_JUMP_KEEP_POSITION;
797	}
798	else ad_err = strdup("Not at helix position");
799	break;
800	}
801	case 'K': { // Ctrl-K = Compression on/off
802	static int last_mode;
803	int current_mode = (ED4_remap_mode)ED4_ROOT->aw_root->awar(ED4_AWAR_COMPRESS_SEQUENCE_GAPS)->read_int();
804	int next_mode = last_mode;
805
806	if (current_mode==0) { // if not compressed
807	if (last_mode==0) next_mode = 2; // force compress
808	}
809	else { // if compressed
810	next_mode = 0; // force uncompressed
811	}
812
813	ED4_ROOT->aw_root->awar(ED4_AWAR_COMPRESS_SEQUENCE_GAPS)->write_int(next_mode);
814
815	last_mode = current_mode;
816	break;
817	}
818	case 'L': { // CTRL-L = Refresh
819	ED4_request_full_refresh();
820	ED4_request_relayout();
821	cursor_jump = ED4_JUMP_CENTERED;
822	break;
823	}
824	case 'M': { // CTRL-M = Invert mark(s)
825	if (is_consensus) { cannot_handle = 1; return 0; }
826	toggle_mark_of_specData(gb_data);
827	break;
828	}
829	case 'O': { // for ALT-left
830	keycode = AW_KEY_LEFT;
831	keymod = AW_KEYMODE_ALT;
832	reinterpret_key = true;
833	break;
834	}
835	case 'P': { // for ALT-right
836	keycode = AW_KEY_RIGHT;
837	keymod = AW_KEYMODE_ALT;
838	reinterpret_key = true;
839	break;
840	}
841	case 'S': { // CTRL-S = Repeat last search
842	ad_err = ED4_repeat_last_search(current_ed4w());
843	seq_pos = current_cursor().get_sequence_pos();
844	cursor_jump = ED4_JUMP_KEEP_POSITION;
845	break;
846	}
847	case 'U': {
848	// ad_err = GB_undo(gb_main, GB_UNDO_UNDO); // @@@ stuerzt ab - wahrscheinlich weil Transaktion offen ist
849	break;
850	}
851	}
852	}
853	else { // normal characters
854	if (is_consensus) { cannot_handle = 1; return 0; }
855	if (mode==AD_NOWRITE) { write_fault = 1; break; }
856
857	if (key == ' ') {
858	if (is_sequence) {
859	long left = seq_pos>0 ? seq_pos-1 : 0;
860	int l = seq[left];
861	int r = seq[seq_pos];
862
863	char gapchar_at_pos = ED4_is_gap_character(l) ? l : (ED4_is_gap_character(r) ? r : 0);
864
865	switch (keymod) {
866	case AW_KEYMODE_NONE:
867	key = gapchar_at_pos ? gapchar_at_pos : '-'; // insert (same) gap
868	break;
869
870	case AW_KEYMODE_CONTROL:
871	if (gapchar_at_pos) key = gapchar_at_pos == '-' ? '.' : '-'; // toggle gaptype
872	break;
873
874	default: break;
875	}
876	}
877	str[0] = key;
878	}
879
880	if (ED4_is_gap_character(key) && keymod == AW_KEYMODE_CONTROL) { // gap-type change works in all modes
881	// gap type functions ('.' <-> '-')
882
883	long left = seq_pos>0 ? seq_pos-1 : 0;
884	int l = seq[left];
885	int r = seq[seq_pos];
886
887	if (ED4_is_gap_character(l) && l!=key) { ad_err = swap_gaps(left, key); changed_flag = 1; }
888	else if (ED4_is_gap_character(r) && r!=key) { ad_err = swap_gaps(seq_pos, key); changed_flag = 1; }
889	}
890	else {
891	switch (mode) {
892	case AD_ALIGN: {
893	if (ED4_is_gap_character(key)) {
894	if (keymod == AW_KEYMODE_NONE) {
895	if (!ad_err) {
896	char nstr = (char )GB_calloc(1, nrepeat+1);
897	int i;
898
899	for (i = 0; i< nrepeat; i++) nstr[i] = key;
900	ad_err = insert(nstr, seq_pos, direction, 0);
901	if (!ad_err) seq_pos = get_next_visible_pos(seq_pos+(direction>=0 ? nrepeat : 0), direction);
902	delete nstr;
903	}
904	changed_flag = 1;
905	}
906	}
907	else { // check typed bases against sequence
908	while (nrepeat && !ad_err) {
909	nrepeat--;
910	seq_pos = get_next_visible_base(seq_pos, direction);
911	if (seq_pos<0 \|\| seq_pos>=seq_len) {
912	ad_err = GBS_global_string("End of sequence reached");
913	}
914	else if (seq[seq_pos]!=key) {
915	ad_err = GBS_global_string("Base '%c' at %li does not match '%c'", seq[seq_pos], seq_pos, key);
916	}
917	else {
918	seq_pos = get_next_visible_pos(seq_pos, direction)+1;
919	ad_err = 0;
920	}
921	if (ad_err) {
922	ed4_beep();
923	}
924	}
925	}
926	break;
927	}
928	case AD_REPLACE: {
929	while (nrepeat && !ad_err) {
930	nrepeat--;
931	if (direction>0) {
932	ad_err = replace(str, seq_pos, 1);
933
934	if (!ad_err) {
935	seq_pos++;
936	changed_flag = 1;
937	}
938	}
939	else {
940	int left_pos = get_next_visible_pos(seq_pos, -1);
941
942	if (left_pos>=0) ad_err = replace(str, left_pos+1, -1);
943	else ad_err = "End of sequence";
944
945	if (!ad_err) {
946	seq_pos = left_pos;
947	changed_flag = 1;
948	}
949	}
950	}
951	break;
952	}
953	case AD_INSERT: {
954	while (nrepeat && !ad_err) {
955	nrepeat--;
956	if (direction>0) {
957	ad_err = insert(str, seq_pos, 1, !is_sequence);
958
959	if (!ad_err) {
960	seq_pos++;
961	changed_flag = 1;
962	}
963	}
964	else {
965	int left_pos = get_next_visible_pos(seq_pos, -1);
966
967	if (left_pos>=0) {
968	ad_err = insert(str, left_pos+1, -1, !is_sequence);
969	}
970	else {
971	ad_err = "End of sequence";
972	}
973
974	if (!ad_err) {
975	seq_pos = left_pos;
976	changed_flag = 1;
977	}
978	}
979	}
980	break;
981	}
982	default: {
983	break;
984	}
985	}
986	}
987
988	}
989	break;
990	}
991	default: {
992	break;
993	}
994
995	}
996	}
997
998	if (ad_err) seq_pos = old_seq_pos;
999	seq_pos = seq_pos<0 ? 0 : (seq_pos>seq_len ? seq_len : seq_pos); // ensure legal position
1000
1001	return ad_err;
1002	}
1003
1004	ED4_Edit_String::ED4_Edit_String()
1005	{
1006	memset((char )this, 0, sizeof(this));
1007	remap = ED4_ROOT->root_group_man->remap();
1008	}
1009
1010	ED4_Edit_String::~ED4_Edit_String()
1011	{
1012	free(old_seq);
1013	}
1014
1015	GB_ERROR ED4_Edit_String::edit(ED4_work_info *info) {
1016	e4_assert(info->working_terminal != 0);
1017
1018	if (!info->rightward) { // 5'<-3'
1019	info->char_position++;
1020	}
1021
1022	info->out_seq_position = remap->screen_to_sequence(info->char_position);
1023	info->refresh_needed = false;
1024	info->cursor_jump = ED4_JUMP_KEEP_VISIBLE;
1025	info->cannot_handle = false;
1026	old_seq = 0;
1027
1028	if (info->string) {
1029	seq = info->string;
1030	seq_len = strlen(seq);
1031	}
1032	else {
1033	e4_assert(info->gb_data);
1034	int seq_len_int;
1035	seq = info->working_terminal->resolve_pointer_to_string_copy(&seq_len_int);
1036	seq_len = seq_len_int;
1037	}
1038
1039	int map_key;
1040	if (info->event.keymodifier == AW_KEYMODE_NONE) {
1041	map_key = ED4_ROOT->edk->map_key(info->event.character);
1042	if (map_key != info->event.character) { // remapped
1043	if (info->event.character == ' ') { // space
1044	AW_advice("You have keymapped the space-key!\n"
1045	"The new functionality assigned to space-key is not available when\n"
1046	"key-mapping is enabled.\n",
1047	AW_ADVICE_TOGGLE_AND_HELP, "Obsolete default keymapping", "nekey_map.hlp");
1048	}
1049	}
1050	}
1051	else {
1052	map_key = info->event.character;
1053	}
1054	GB_ERROR err = 0;
1055
1056	nrepeat_zero_requested = 1;
1057	if (!nrepeat) {
1058	nrepeat_is_already_set = 1;
1059	nrepeat = 1;
1060	}
1061
1062	if (info->event.keycode==AW_KEY_ASCII &&
1063	isdigit(map_key) &&
1064	ED4_ROOT->aw_root->awar(ED4_AWAR_DIGITS_AS_REPEAT)->read_int()) { // handle digits for repeated commands
1065
1066	if (nrepeat_is_already_set) { nrepeat = 0; }
1067	nrepeat_zero_requested = 0;
1068
1069	for (int r=0; r<info->repeat_count; r++) {
1070	nrepeat = nrepeat * 10 + (map_key - '0');
1071	if (nrepeat>10000) {
1072	nrepeat = 10000;
1073	}
1074	else if (nrepeat<0) {
1075	nrepeat = 0;
1076	}
1077	}
1078	#ifdef DEBUG
1079	if (nrepeat>1) {
1080	printf("nrepeat=%i\n", nrepeat);
1081	}
1082	#endif
1083	}
1084	else if (info->event.keymodifier==AW_KEYMODE_NONE && info->event.keycode==AW_KEY_NONE) {
1085	nrepeat_zero_requested = 0;
1086	}
1087	else {
1088	nrepeat += info->repeat_count-1;
1089
1090	#ifdef DEBUG
1091	if (nrepeat>1) {
1092	printf("nrepeat is %i\n", nrepeat);
1093	}
1094	#endif
1095
1096	int is_remapped_sequence = !info->is_sequence && ED4_ROOT->aw_root->awar(ED4_AWAR_COMPRESS_SEQUENCE_TYPE)->read_int()!=ED4_RM_NONE;
1097	if (info->mode==AD_NOWRITE_IF_COMPRESSED) {
1098	if (is_remapped_sequence) {
1099	info->mode = AD_NOWRITE;
1100	}
1101	else {
1102	info->mode = AD_INSERT;
1103	}
1104	}
1105
1106	bool write_fault = 0;
1107
1108	err = command(info->event.keymodifier,
1109	info->event.keycode,
1110	map_key,
1111	info->rightward,
1112	info->mode,
1113	(int)(info->string!=0),
1114	info->out_seq_position,
1115	info->refresh_needed,
1116	info->cursor_jump,
1117	info->cannot_handle,
1118	write_fault,
1119	info->gb_data,
1120	info->is_sequence);
1121
1122	e4_assert(!(err && info->cannot_handle));
1123
1124	if (write_fault) {
1125	e4_assert(info->mode==AD_NOWRITE);
1126	aw_message(is_remapped_sequence
1127	? "Check 'Show all gaps' when editing remarks"
1128	: "This terminal is write-protected!");
1129	}
1130	}
1131
1132	if (!err) {
1133	if (info->gb_data) {
1134	if (info->refresh_needed) {
1135	e4_assert(info->working_terminal->get_species_pointer() == info->gb_data);
1136
1137	int old_seq_len_int;
1138	old_seq = info->working_terminal->resolve_pointer_to_string_copy(&old_seq_len_int);
1139	old_seq_len = old_seq_len_int;
1140
1141	err = info->working_terminal->write_sequence(seq, seq_len);
1142	if (err) {
1143	info->out_seq_position = remap->screen_to_sequence(info->char_position); // correct cursor_pos if protection error occurred
1144	}
1145	}
1146	freenull(seq);
1147	}
1148	}
1149
1150	if (!info->rightward) {
1151	info->char_position = remap->sequence_to_screen_PLAIN(info->out_seq_position);
1152	e4_assert(info->char_position >= 0);
1153	info->char_position--;
1154	info->out_seq_position = remap->screen_to_sequence(info->char_position);
1155	}
1156
1157	return err;
1158	}
1159
1160	void ED4_Edit_String::finish_edit()
1161	{
1162	nrepeat_is_already_set = 0;
1163	if (nrepeat_zero_requested) {
1164	nrepeat_zero_requested = 0;
1165	nrepeat = 0;
1166	}
1167	}
1168
1169	void ED4_Edit_String::init_edit() {
1170	freenull(old_seq);
1171	seq_len = 0;
1172	seq = 0;
1173	gbd = 0;
1174	old_seq_len = 0;
1175	remap = ED4_ROOT->root_group_man->remap();
1176	}
1177

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