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source: tags/arb-6.0/EDIT4/ED4_edit_string.cxx

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Last change on this file was 11126, checked in by westram, 12 years ago
reintegrates 'redev' into 'trunk': fixed key-bindings (mark, fold, …) improved several -commands (move, rotate, spread, length, width) fixed #68 adds: log:branches/dev@7912,7914,7938,7942:7943 log:branches/redev@11088:11119,11122:11125
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 44.4 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
11	#include <aw_awar.hxx>
12	#include <aw_msg.hxx>
13	#include <aw_root.hxx>
14	#include <aw_question.hxx>
15	#include <aw_advice.hxx>
16	#include <cctype>
17
18	#define SAFE_EDITING // undef this to remove sequence test code
19
20	int ED4_Edit_String::nrepeat = 0; // # of times command should be repeated
21	int ED4_Edit_String::nrepeat_zero_requested = 0; // nrepeat should be set to zero
22	int ED4_Edit_String::nrepeat_is_already_set = 0; // nrepeat was zero (and was set to 1)
23
24	unsigned char *ED4_is_align_character = NULL;
25
26	void ED4_init_is_align_character(GB_CSTR gap_chars) {
27	static unsigned char array[256];
28	memset(array, 0, 256);
29	for (int p = 0; gap_chars[p]; ++p) {
30	array[(unsigned char)(gap_chars[p])] = 1;
31	}
32	ED4_is_align_character = array;
33	}
34
35	GB_ERROR ED4_Edit_String::insert(char *text, long position, int direction, int removeAtNextGap) {
36	long i;
37	int text_len = strlen(text);
38	if (text_len == 0) return 0;
39
40	int rest_len;
41
42	if (direction>=0) {
43	rest_len = seq_len-position;
44	}
45	else {
46	rest_len = position;
47	}
48
49	if (rest_len<=0 \|\| text_len>rest_len) {
50	return GBS_global_string("You can't insert text after the end of the sequence!");
51	}
52
53	if (removeAtNextGap) {
54	int nextGap = get_next_gap(position, direction);
55	if (nextGap==-1) {
56	goto no_gaps;
57	}
58
59	int afterGap = nextGap+direction;
60
61	if (afterGap>=0 && afterGap<seq_len) { // in sequence
62	if (seq[afterGap]!=seq[nextGap]) { // gap type changed -> warn to avoid overwrite of '?'
63	return GBS_global_string("Only one gap %s text => insert aborted", direction>=0 ? "after" : "before");
64	}
65	}
66
67	rest_len = (afterGap-position)*direction;
68	}
69
70	if (direction>=0) {
71	if (text_len + position >= seq_len) {
72	return GBS_global_string("You cannot insert that many characters after cursor!");
73	}
74
75	for (i = rest_len-text_len; i<rest_len; i++) {
76	if (!ADPP_IS_ALIGN_CHARACTER(seq[position+i])) {
77	goto no_gaps;
78	}
79	}
80
81	for (i = position+rest_len-text_len-1; i>=position; i--) {
82	seq[i+text_len] = seq[i];
83	}
84
85	for (i = 0; i<text_len; i++) {
86	seq[position+i] = text[i];
87	}
88	}
89	else {
90	if (position - text_len < 0) {
91	return GBS_global_string("You cannot insert that many characters before cursor!");
92	}
93
94	for (i = 0; i<text_len; i++) {
95	if (i<0 \|\| !ADPP_IS_ALIGN_CHARACTER(seq[i])) {
96	goto no_gaps;
97	}
98	}
99	for (i = 0; i<position-text_len; i++) {
100	seq[i] = seq[i+text_len];
101	}
102
103	for (i = 0; i<text_len; i++) {
104	seq[position-i-1] = text[i];
105	}
106	}
107
108	return 0;
109
110	no_gaps :
111	return GBS_global_string("There are no/not enough gaps at %s of sequence => can't insert characters%s",
112	direction >= 0 ? "end" : "start",
113	direction >= 0 ? "\nMaybe your sequences are not formatted?" : "");
114	}
115
116	GB_ERROR ED4_Edit_String::remove(int len, long position, int direction, int insertAtNextGap) {
117
118	int rest_len; // bases between cursor-position and the directed sequence end
119
120	if (direction>=0) { // forward
121	if ((len + position) >= seq_len) len = (int)(seq_len-position);
122	rest_len = seq_len-position;
123	}
124	else { // backward
125	position--;
126	if (len>position) len = position;
127	rest_len = position;
128	}
129
130	if ((position >= seq_len) \|\| (len == 0) \|\| (seq_len - len < 0)) {
131	return GBS_global_string("Illegal delete position/length");
132	}
133
134	if (insertAtNextGap) {
135	int nextGap = get_next_gap(position+len*direction, direction);
136
137	if (nextGap!=-1) {
138	rest_len = (nextGap-position)*direction;
139	}
140	}
141
142	int new_len = rest_len-len; // no of bases that will be copied
143	int i;
144
145	if (direction>=0) {
146	for (i=0; i<new_len; i++) {
147	seq[position+i] = seq[position+len+i];
148	}
149	for (; i<rest_len; i++) {
150	seq[position+i] = '.';
151	}
152	}
153	else {
154	for (i=0; i<new_len; i++) {
155	seq[position-i] = seq[position-len-i];
156	}
157	for (; i<rest_len; i++) {
158	seq[position-i] = '.';
159	}
160	}
161
162	e4_assert(seq[seq_len]=='\0');
163
164	return 0;
165	}
166
167	GB_ERROR ED4_Edit_String::replace(char *text, long position, int direction) {
168	int text_len = strlen(text);
169	int i;
170	if (direction>=0) {
171
172	if ((position + text_len > seq_len) \|\| (position > seq_len)) {
173	return GBS_global_string("Replace after end of sequence !");
174	}
175	for (i = 0; i < text_len; i ++) {
176	seq[i+position] = text[i];
177	}
178	}
179	else {
180	if ((position - text_len < 0) \|\| (position > seq_len)) {
181	return GBS_global_string("Replace before start of sequence !");
182	}
183	for (i = 0; i < text_len; i ++) {
184	seq[position - i - 1] = text[i];
185	}
186	}
187	return 0;
188	}
189
190	GB_ERROR ED4_Edit_String::swap_gaps(long position, char ch) {
191	long i;
192	for (i = position; i < seq_len; i++) {
193	if (!ADPP_IS_ALIGN_CHARACTER(seq[i])) break;
194	seq[i] = ch;
195	}
196	for (i = position; i >= 0; i--) {
197	if (!ADPP_IS_ALIGN_CHARACTER(seq[i])) break;
198	seq[i] = ch;
199	}
200	return 0;
201	}
202
203
204	GB_ERROR ED4_Edit_String::moveBase(long source_position, long dest_position, unsigned char gap_to_use)
205	{
206	e4_assert(source_position!=dest_position);
207	#ifdef SAFE_EDITING
208	if (!legal_seqpos(dest_position) \|\| !legal_seqpos(source_position)) {
209	return "Position out of sequence";
210	}
211	#endif
212
213	int direction = dest_position<source_position ? -1 : 1;
214	int base = seq[source_position];
215	e4_assert(!ADPP_IS_ALIGN_CHARACTER(base));
216	seq[source_position] = gap_to_use;
217
218	long p = source_position+direction;
219	while (p!=dest_position) {
220	#ifdef SAFE_EDITING
221	if (!ADPP_IS_ALIGN_CHARACTER(seq[p])) {
222	e4_assert(0);
223	return "Internal error: Tried to change base order in moveBase()";
224	}
225	#endif
226	e4_assert(ADPP_IS_ALIGN_CHARACTER(seq[p]));
227	seq[p] = gap_to_use;
228	p += direction;
229	}
230
231	seq[dest_position] = base;
232	return 0;
233	}
234
235	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)
236	// shifts bases from source_pos-last_source to dest_pos
237	// last_dest is set to the position after the last dest_pos (direction<0 ? pos. right of bases : pos. left of bases)
238	{
239	GB_ERROR err = 0;
240
241	if (direction<0) {
242	e4_assert(dest_pos<source_pos);
243	e4_assert(source_pos<=last_source);
244	while (1) {
245	err = moveBase(source_pos, dest_pos, gap_to_use);
246	if (err \|\| source_pos>=last_source) break;
247	source_pos++;
248	dest_pos++;
249	while (!ADPP_IS_ALIGN_CHARACTER(seq[dest_pos])) {
250	dest_pos++;
251	}
252	}
253	}
254	else {
255	e4_assert(source_pos<dest_pos);
256	e4_assert(last_source<=source_pos);
257	while (1) {
258	err = moveBase(source_pos, dest_pos, gap_to_use);
259	if (err \|\| source_pos<=last_source) break;
260	source_pos--;
261	dest_pos--;
262	while (!ADPP_IS_ALIGN_CHARACTER(seq[dest_pos])) {
263	dest_pos--;
264	}
265	}
266	}
267
268	if (last_dest) {
269	*last_dest = dest_pos;
270	}
271
272	return err;
273	}
274
275	long ED4_Edit_String::get_next_base(long position, int direction) {
276	long pos;
277	if (direction < 0) position--;
278	for (pos = position; pos>=0 && pos < seq_len; pos += direction) {
279	if (!ADPP_IS_ALIGN_CHARACTER(seq[pos])) break;
280	}
281
282	return pos<0 \|\| pos>=seq_len ? -1 : pos;
283	}
284	long ED4_Edit_String::get_next_gap(long position, int direction) {
285	long pos;
286	if (direction < 0) position--;
287	for (pos = position; pos >= 0 && pos < seq_len; pos += direction) {
288	if (ADPP_IS_ALIGN_CHARACTER(seq[pos])) break;
289	}
290
291	return pos<0 \|\| pos>=seq_len ? -1 : pos;
292	}
293	long ED4_Edit_String::get_next_visible_base(long position, int direction)
294	{
295	long pos;
296	if (direction < 0) position--;
297	for (pos = position; pos>=0 && pos < seq_len; pos += direction) {
298	if (!ADPP_IS_ALIGN_CHARACTER(seq[pos]) && remap->is_shown(pos)) {
299	break;
300	}
301	}
302
303	return pos<0 \|\| pos>=seq_len ? -1 : pos;
304	}
305	long ED4_Edit_String::get_next_visible_gap(long position, int direction) {
306	long pos;
307	if (direction < 0) position--;
308	for (pos = position; pos >= 0 && pos < seq_len; pos += direction) {
309	if (ADPP_IS_ALIGN_CHARACTER(seq[pos]) && remap->is_shown(pos)) {
310	break;
311	}
312	}
313
314	return pos<0 \|\| pos>=seq_len ? -1 : pos;
315	}
316	long ED4_Edit_String::get_next_visible_pos(long position, int direction)
317	{
318	long pos;
319	if (direction < 0) position--;
320	for (pos = position; pos >= 0 && pos < seq_len; pos += direction) {
321	if (remap->is_shown(pos)) {
322	break;
323	}
324	}
325	return pos<0 \|\| pos>=seq_len ? -1 : pos;
326	}
327
328	extern AlignDataAccess dataAccess_4_aligner;
329
330	unsigned char ED4_Edit_String::get_gap_type(long pos, int direction)
331	{
332	pos += direction;
333	if (!legal_seqpos(pos)) return '.';
334	char gap = seq[pos];
335	if (ADPP_IS_ALIGN_CHARACTER(gap)) return gap;
336	return '-';
337	}
338
339	static GB_ERROR toggle_cursor_group_folding() {
340	GB_ERROR error = NULL;
341	ED4_cursor& cursor = current_cursor();
342	if (cursor.owner_of_cursor) {
343	ED4_terminal *cursor_term = cursor.owner_of_cursor;
344
345	if (cursor_term->is_in_folded_group()) {
346	// cursor not visible -> unfold group which hides cursor
347	cursor_term->setCursorTo(&cursor, cursor.get_sequence_pos(), true, ED4_JUMP_KEEP_POSITION);
348	}
349	else {
350	ED4_base *group = cursor.owner_of_cursor->get_parent(ED4_L_GROUP);
351	if (group) {
352	ED4_group_manager *group_man = group->to_group_manager();
353	ED4_bracket_terminal *bracket_term = group_man->get_defined_level(ED4_L_BRACKET)->to_bracket_terminal();
354
355	if (group_man->dynamic_prop & ED4_P_IS_FOLDED) {
356	bracket_term->unfold();
357	}
358	else {
359	ED4_species_manager *consensus_man = group_man->get_multi_species_manager()->get_consensus_manager();
360	if (consensus_man) consensus_man->setCursorTo(&cursor, cursor.get_sequence_pos(), true, ED4_JUMP_KEEP_POSITION);
361
362	bracket_term->fold();
363	}
364	}
365	}
366	}
367	return error;
368	}
369
370	static void toggle_mark_of_specData(GBDATA *gb_data) {
371	// toggle mark of species owning data 'gb_data'
372	GB_transaction ta(gb_data);
373	GBDATA *gb_species = GB_get_grandfather(gb_data);
374	if (gb_species) GB_write_flag(gb_species, !GB_read_flag(gb_species));
375	}
376
377	GB_ERROR ED4_Edit_String::command(AW_key_mod keymod, AW_key_code keycode, char key, int direction, ED4_EDITMODI mode, bool is_consensus,
378	long &seq_pos, bool &changed_flag, ED4_CursorJumpType& cursor_jump, bool &cannot_handle, bool &write_fault, GBDATA* gb_data, bool is_sequence)
379	{
380	changed_flag = 0;
381	write_fault = 0;
382	if (keymod+keycode+key==0) return 0;
383
384	e4_assert(nrepeat>0);
385
386	long old_seq_pos = seq_pos;
387	int screen_len = remap->sequence_to_screen(seq_len);
388	int cursorpos = remap->sequence_to_screen(seq_pos);
389
390	char str[2];
391	str[0] = key;
392	str[1] = 0;
393
394	direction = direction>0 ? 1 : -1;
395
396	if ((cursorpos > screen_len) \|\| (cursorpos < 0)) {
397	if (cursorpos<MAXSEQUENCECHARACTERLENGTH && cursorpos>=0) {
398	char *seq2 = new char[MAXSEQUENCECHARACTERLENGTH+1];
399
400	memcpy(seq2, seq, seq_len);
401	memset(seq2+seq_len, '.', MAXSEQUENCECHARACTERLENGTH-seq_len);
402	seq_len = MAXSEQUENCECHARACTERLENGTH;
403	seq2[seq_len] = 0;
404
405	delete seq;
406	seq = seq2;
407
408	changed_flag = 1;
409	}
410	else {
411	return GBS_global_string("Cursor out of sequence at screen_pos #%i!", cursorpos);
412	}
413	}
414
415	GB_ERROR ad_err = 0;
416	long h;
417	bool reinterpret_key = true;
418
419	while (reinterpret_key) {
420	reinterpret_key = false;
421
422	switch (keycode) {
423	case AW_KEY_HOME: {
424	int new_seq_pos = get_next_visible_base(0, 1);
425	if (new_seq_pos>=0) seq_pos = new_seq_pos==seq_pos ? 0 : new_seq_pos;
426	else seq_pos = 0;
427	break;
428	}
429	case AW_KEY_END: {
430	int new_seq_pos = get_next_visible_base(seq_len, -1);
431	if (new_seq_pos>=0) {
432	int new_gap_pos = get_next_visible_gap(new_seq_pos, 1);
433	if (new_gap_pos >= 0) {
434	seq_pos = new_gap_pos==seq_pos ? seq_len : new_gap_pos;
435	}
436	else {
437	seq_pos = seq_len;
438	}
439	}
440	else {
441	seq_pos = seq_len;
442	}
443	break;
444	}
445	case AW_KEY_LEFT:
446	case AW_KEY_RIGHT: {
447	direction = keycode==AW_KEY_RIGHT ? 1 : -1;
448
449	// no key modifier -> just move cursor
450
451	int n = nrepeat;
452
453	if (keymod == AW_KEYMODE_NONE) {
454	while (n--) {
455	do {
456	seq_pos += direction;
457	}
458	while (legal_curpos(seq_pos) && !remap->is_shown(seq_pos));
459	}
460	break;
461	}
462
463	if (mode==AD_NOWRITE) { write_fault = 1; break; }
464
465	int jump_or_fetch = 0; // 1=jump selected 2=fetch selected (for repeat only)
466	int push_or_pull = 0; // 1=push selected 2=pull selected (for repeat only)
467
468	// ------------------
469	// loop over nrepeat:
470
471	while (!ad_err && n-->0 && legal_curpos(seq_pos)) {
472	cursorpos = remap->sequence_to_screen(seq_pos);
473
474	int adjacent_scr_pos = cursorpos - (direction<0); // screen position next to the cursor
475	if (adjacent_scr_pos<0 \|\| size_t(adjacent_scr_pos)>remap->get_max_screen_pos()) {
476	ad_err = GBS_global_string("Action beyond end of screen!");
477	break;
478	}
479
480	int adjacent_seq_pos = remap->screen_to_sequence(adjacent_scr_pos); // _visible_ sequence position next to the cursor
481	int real_adjacent_seq_pos = seq_pos - (direction<0); // sequence position next to cursor (not necessarily visible)
482
483	if (adjacent_seq_pos<0 \|\| adjacent_seq_pos>=seq_len) {
484	ad_err = GBS_global_string("Action beyond end of sequence!");
485	break;
486	}
487
488	// Ctrl+Cursor = move cursor to next end of word (or to end of next word)
489
490	if (keymod & AW_KEYMODE_CONTROL) {
491	if (adjacent_scr_pos>=0) {
492	long pos = adjacent_seq_pos;
493
494	if (ED4_ROOT->aw_root->awar(ED4_AWAR_FAST_CURSOR_JUMP)->read_int()) { // should cursor jump over next group?
495	if (ADPP_IS_ALIGN_CHARACTER(seq[pos])) {
496	pos = get_next_visible_base(pos, direction);
497	if (pos>=0) pos = get_next_visible_gap(pos, direction);
498	}
499	else {
500	pos = get_next_visible_gap(pos, direction);
501	}
502
503	seq_pos = (pos>=0
504	? (direction<0 ? pos+1 : pos)
505	: (direction<0 ? 0 : seq_len-1));
506	}
507	else {
508	if (ADPP_IS_ALIGN_CHARACTER(seq[pos])) { seq_pos = get_next_visible_base(pos, direction); }
509	else { seq_pos = get_next_visible_gap(pos, direction); }
510
511	if (direction<0) { seq_pos = seq_pos==-1 ? 0 : seq_pos+1; }
512	else { seq_pos = seq_pos==-1 ? seq_len : seq_pos; }
513	}
514	}
515	continue;
516	}
517
518	// ALT/META+Cursor = jump & fetch
519
520	if (keymod & (AW_KEYMODE_ALT)) {
521	if (is_consensus) { cannot_handle = 1; return 0; }
522
523	if (ADPP_IS_ALIGN_CHARACTER(seq[adjacent_seq_pos])) { // there's a _gap_ next to the cursor -> let's fetch
524	if (jump_or_fetch!=1) {
525	jump_or_fetch = 2;
526	long source_pos = get_next_base(adjacent_seq_pos, direction); // position of base to fetch
527	if (source_pos==-1) { // there is nothing to fetch
528	n = 0;
529	}
530	else {
531	ad_err = moveBase(source_pos, adjacent_seq_pos, get_gap_type(source_pos, direction));
532	seq_pos = adjacent_seq_pos + (direction>0);
533	}
534	}
535	else {
536	n = 0;
537	}
538	}
539	else { // there's a _base_ next to the cursor -> let it jump
540	if (jump_or_fetch!=2) {
541	jump_or_fetch = 1;
542	int next_gap = adjacent_seq_pos - direction;
543
544	if (ADPP_IS_ALIGN_CHARACTER(seq[next_gap])) {
545	int dest_pos = get_next_base(next_gap, -direction);
546
547	if (dest_pos<0) {
548	dest_pos = direction>0 ? 0 : seq_len-1;
549	}
550	else {
551	dest_pos += direction;
552	}
553
554	if (ADPP_IS_ALIGN_CHARACTER(seq[dest_pos])) {
555	ad_err = moveBase(adjacent_seq_pos, dest_pos, get_gap_type(adjacent_seq_pos, direction));
556	if (!ad_err) {
557	seq_pos = get_next_base(seq_pos, direction)+(direction<0);
558	if (seq_pos==-1) {
559	seq_pos = direction<0 ? 0 : seq_len;
560	}
561	}
562	}
563	else {
564	e4_assert(0);
565	}
566	}
567	else {
568	ad_err = GBS_global_string("You can only jump single bases.");
569	}
570	}
571	else {
572	n = 0;
573	}
574	}
575
576	if (!ad_err) {
577	changed_flag = 1;
578	}
579
580	continue;
581	}
582
583	// Shift+Cursor = push/pull character
584
585	if (is_consensus) { cannot_handle = 1; return 0; };
586
587	if (ADPP_IS_ALIGN_CHARACTER(seq[real_adjacent_seq_pos])) { // pull
588	long dest_pos = real_adjacent_seq_pos;
589	long source_pos = real_adjacent_seq_pos-direction;
590
591	if (!ADPP_IS_ALIGN_CHARACTER(seq[source_pos]) && push_or_pull!=1) {
592	push_or_pull = 2;
593
594	long next_gap = get_next_gap(source_pos, -direction);
595	long last_source = next_gap>=0 ? next_gap : (direction>0 ? 0 : seq_len-1);
596
597	if (ADPP_IS_ALIGN_CHARACTER(seq[last_source])) {
598	last_source = get_next_base(last_source, direction);
599	}
600
601	ad_err = shiftBases(source_pos, last_source, dest_pos, direction, 0,
602	is_sequence ? get_gap_type(last_source, -direction) : '.');
603
604	if (!ad_err) {
605	seq_pos = dest_pos + (direction>0);
606	changed_flag = 1;
607	}
608	}
609	else {
610	n = 0;
611	}
612	}
613	else { // push
614	long next_gap = get_next_gap(adjacent_seq_pos, direction);
615
616	if (next_gap>=0 && push_or_pull!=2) {
617	push_or_pull = 1;
618	long dest_pos = next_gap;
619	long source_pos = get_next_base(next_gap, -direction);
620	long last_source = adjacent_seq_pos;
621
622	e4_assert(source_pos>=0);
623	ad_err = shiftBases(source_pos, last_source, dest_pos, direction, &dest_pos,
624	is_sequence ? get_gap_type(last_source, -direction) : '.');
625
626	if (!ad_err) {
627	seq_pos = dest_pos + (direction<0);
628	changed_flag = 1;
629	}
630	}
631	else {
632	n = 0;
633	}
634	}
635	}
636	break;
637	}
638
639	case AW_KEY_BACKSPACE:
640	h = seq_pos;
641
642	if (direction>0) {
643	seq_pos -= nrepeat;
644	}
645	else {
646	seq_pos += nrepeat;
647	}
648	if (seq_pos <0 \|\| seq_pos >= seq_len) {
649	seq_pos = h;
650	break;
651	}
652	// fall-through
653
654	case AW_KEY_DELETE:
655	h = seq_pos;
656
657	if (is_consensus) { cannot_handle = 1; return 0; };
658	if (keymod) { return 0; }
659
660	if (mode==AD_NOWRITE) { write_fault = 1; break; }
661
662	switch (mode) {
663	case AD_ALIGN:
664	{
665	int len;
666	int offset;
667
668	ad_err = 0;
669	if (direction>=0) offset = 0;
670	else offset = -nrepeat;
671
672	for (len = nrepeat-1; len>=0; len--) {
673	if (!ADPP_IS_ALIGN_CHARACTER(seq[h+offset+len])) {
674	ad_err = GBS_global_string("You cannot remove bases in align mode");
675	break;
676	}
677	}
678	if (ad_err) break;
679	}
680	case AD_REPLACE:
681	case AD_INSERT:
682	ad_err = remove(nrepeat, h, direction, !is_sequence);
683	if (!ad_err) {
684	changed_flag = 1;
685	}
686	break;
687	default:
688	break;
689	}
690
691	break;
692
693	case AW_KEY_RETURN:
694	ad_err = toggle_cursor_group_folding();
695	break;
696
697	case AW_KEY_ASCII: {
698
699	// keyboard layout:
700	//
701	// - CTRL-A Align ok
702	// - CTRL-E Toggle edit/align ok
703	// - CTRL-I Toggle insert/replace ok
704	// - CTRL-J Jump opposite helix position ok
705	// - CTRL-L Refresh ok
706	// - CTRL-M Invert mark ok
707	// - CTRL-R set aligner reference species ok
708	// - CTRL-S Repeat last search ok
709	// - CTRL-U Undo @@@ crashes!!!
710
711
712	if (key >0 && key<=26) { // CTRL-Keys
713	switch (key+'A'-1) {
714	case 'R': { // CTRL-R = set aligner reference species
715	if (is_consensus) { cannot_handle = 1; return 0; };
716
717	FastAligner_set_reference_species(0, (AW_CL)ED4_ROOT->aw_root);
718	break;
719	}
720	case 'A': { // CTRL-A = Start Fast-Aligner
721	AW_window *aw_tmp = current_aww();
722	if (is_consensus) { cannot_handle = 1; return 0; };
723	if (mode==AD_NOWRITE) { write_fault = 1; return 0; }
724
725	int old_refresh = dataAccess_4_aligner.do_refresh;
726	dataAccess_4_aligner.do_refresh = 0;
727
728	ED4_init_aligner_data_access(&dataAccess_4_aligner);
729
730	FastAligner_set_align_current(ED4_ROOT->aw_root, ED4_ROOT->props_db);
731	AW_clock_cursor(ED4_ROOT->aw_root);
732	GB_commit_transaction(dataAccess_4_aligner.gb_main);
733
734	FastAligner_start(aw_tmp, (AW_CL)&dataAccess_4_aligner);
735
736	GB_begin_transaction(dataAccess_4_aligner.gb_main);
737	AW_normal_cursor(ED4_ROOT->aw_root);
738	dataAccess_4_aligner.do_refresh = old_refresh;
739
740	int basesLeftOf = 0;
741	int pos;
742
743	for (pos=0; pos < seq_pos && pos<seq_len; pos++) { // count # of bases left of cursorpos
744	if (!ADPP_IS_ALIGN_CHARACTER(seq[pos])) {
745	basesLeftOf++;
746	}
747	}
748
749	char *aligned_seq = GB_read_string(gb_data); // read new sequence
750	ad_err = GB_write_string(gb_data, seq); // restore old sequence
751
752	freeset(seq, aligned_seq); // set new sequence
753	changed_flag = 1; // and mark changed
754
755	{
756	int basesLeftOf2 = 0;
757	int lastCorrectPos = -1;
758	for (pos=0; pos<seq_pos && pos<seq_len; pos++) { // count # of bases left of cursorpos
759	if (!ADPP_IS_ALIGN_CHARACTER(seq[pos])) {
760	basesLeftOf2++;
761	if (basesLeftOf2 == basesLeftOf) lastCorrectPos = pos;
762	}
763	}
764
765	if (basesLeftOf != basesLeftOf2) { // old cursor-position has different basepos
766	if (lastCorrectPos != -1) { // already seen position with same basepos
767	seq_len = lastCorrectPos+1;
768	}
769	else {
770	for (; pos<seq_len; pos++) {
771	if (!ADPP_IS_ALIGN_CHARACTER(seq[pos])) {
772	basesLeftOf2++;
773	if (basesLeftOf2 == basesLeftOf) {
774	seq_pos = pos+1;
775	break; // stop after first matching position
776	}
777	}
778	}
779	}
780	}
781	}
782	break;
783	}
784	case 'E': { // CTRL-E = Toggle Edit/Align-Mode
785	ED4_ROOT->aw_root->awar(AWAR_EDIT_MODE)->toggle_toggle();
786	break;
787	}
788	case 'I': { // CTRL-I = Toggle Insert/Replace-Mode
789	ED4_ROOT->aw_root->awar(AWAR_INSERT_MODE)->toggle_toggle();
790	break;
791	}
792	case 'J': { // CTRL-J = Jump to opposite helix position
793	AW_helix *helix = ED4_ROOT->helix;
794
795	if (!helix->has_entries()) ad_err = strdup("Got no helix information");
796	else if (helix->pairtype(seq_pos) != HELIX_NONE) {
797	seq_pos = helix->opposite_position(seq_pos);
798	cursor_jump = ED4_JUMP_KEEP_POSITION;
799	}
800	else ad_err = strdup("Not at helix position");
801	break;
802	}
803	case 'K': { // Ctrl-K = Compression on/off
804	static int last_mode;
805	int current_mode = (ED4_remap_mode)ED4_ROOT->aw_root->awar(ED4_AWAR_COMPRESS_SEQUENCE_GAPS)->read_int();
806	int next_mode = last_mode;
807
808	if (current_mode==0) { // if not compressed
809	if (last_mode==0) next_mode = 2; // force compress
810	}
811	else { // if compressed
812	next_mode = 0; // force uncompressed
813	}
814
815	ED4_ROOT->aw_root->awar(ED4_AWAR_COMPRESS_SEQUENCE_GAPS)->write_int(next_mode);
816
817	last_mode = current_mode;
818	break;
819	}
820	case 'L': { // CTRL-L = Refresh
821	ED4_request_full_refresh();
822	ED4_request_relayout();
823	cursor_jump = ED4_JUMP_CENTERED;
824	break;
825	}
826	case 'M': // CTRL-M = Invert mark(s)
827	if (is_consensus) { cannot_handle = 1; return 0; }
828	toggle_mark_of_specData(gb_data);
829	break;
830
831	case 'S': { // CTRL-S = Repeat last search
832	ad_err = ED4_repeat_last_search(current_ed4w());
833	seq_pos = current_cursor().get_sequence_pos();
834	cursor_jump = ED4_JUMP_KEEP_POSITION;
835	break;
836	}
837	case 'U': {
838	// ad_err = GB_undo(gb_main, GB_UNDO_UNDO); // @@@ stuerzt ab - wahrscheinlich weil Transaktion offen ist
839	break;
840	}
841	case 'O': { // for ALT-left
842	keycode = AW_KEY_LEFT;
843	keymod = AW_KEYMODE_ALT;
844	reinterpret_key = true;
845	break;
846	}
847	case 'P': { // for ALT-right
848	keycode = AW_KEY_RIGHT;
849	keymod = AW_KEYMODE_ALT;
850	reinterpret_key = true;
851	break;
852	}
853	}
854	}
855	else { // normal characters
856	if (is_consensus) { cannot_handle = 1; return 0; }
857	if (mode==AD_NOWRITE) { write_fault = 1; break; }
858
859	if (key == ' ') {
860	if (is_sequence) {
861	long left = seq_pos>0 ? seq_pos-1 : 0;
862	int l = seq[left];
863	int r = seq[seq_pos];
864
865	char gapchar_at_pos = ADPP_IS_ALIGN_CHARACTER(l) ? l : (ADPP_IS_ALIGN_CHARACTER(r) ? r : 0);
866
867	switch (keymod) {
868	case AW_KEYMODE_NONE:
869	key = gapchar_at_pos ? gapchar_at_pos : '-'; // insert (same) gap
870	break;
871
872	case AW_KEYMODE_CONTROL:
873	if (gapchar_at_pos) key = gapchar_at_pos == '-' ? '.' : '-'; // toggle gaptype
874	break;
875
876	default: break;
877	}
878	}
879	str[0] = key;
880	}
881
882	if (ADPP_IS_ALIGN_CHARACTER(key) && keymod == AW_KEYMODE_CONTROL) { // gap-type change works in all modes
883	// gap type functions ('.' <-> '-')
884
885	long left = seq_pos>0 ? seq_pos-1 : 0;
886	int l = seq[left];
887	int r = seq[seq_pos];
888
889	if (ADPP_IS_ALIGN_CHARACTER(l) && l!=key) { ad_err = swap_gaps(left, key); changed_flag = 1; }
890	else if (ADPP_IS_ALIGN_CHARACTER(r) && r!=key) { ad_err = swap_gaps(seq_pos, key); changed_flag = 1; }
891	}
892	else {
893	switch (mode) {
894	case AD_ALIGN: {
895	if (ADPP_IS_ALIGN_CHARACTER(key)) {
896	if (keymod == AW_KEYMODE_NONE) {
897	if (!ad_err) {
898	char nstr = (char )GB_calloc(1, nrepeat+1);
899	int i;
900
901	for (i = 0; i< nrepeat; i++) nstr[i] = key;
902	ad_err = insert(nstr, seq_pos, direction, 0);
903	if (!ad_err) seq_pos = get_next_visible_pos(seq_pos+(direction>=0 ? nrepeat : 0), direction);
904	delete nstr;
905	}
906	changed_flag = 1;
907	}
908	}
909	else { // check typed bases against sequence
910	while (nrepeat && !ad_err) {
911	nrepeat--;
912	seq_pos = get_next_visible_base(seq_pos, direction);
913	if (seq_pos<0 \|\| seq_pos>=seq_len) {
914	ad_err = GBS_global_string("End of sequence reached");
915	}
916	else if (seq[seq_pos]!=key) {
917	ad_err = GBS_global_string("Base '%c' at %li does not match '%c'", seq[seq_pos], seq_pos, key);
918	}
919	else {
920	seq_pos = get_next_visible_pos(seq_pos, direction)+1;
921	ad_err = 0;
922	}
923	if (ad_err) {
924	ed4_beep();
925	}
926	}
927	}
928	break;
929	}
930	case AD_REPLACE: {
931	while (nrepeat && !ad_err) {
932	nrepeat--;
933	if (direction>0) {
934	ad_err = replace(str, seq_pos, 1);
935
936	if (!ad_err) {
937	seq_pos++;
938	changed_flag = 1;
939	}
940	}
941	else {
942	int left_pos = get_next_visible_pos(seq_pos, -1);
943
944	if (left_pos>=0) ad_err = replace(str, left_pos+1, -1);
945	else ad_err = "End of sequence";
946
947	if (!ad_err) {
948	seq_pos = left_pos;
949	changed_flag = 1;
950	}
951	}
952	}
953	break;
954	}
955	case AD_INSERT: {
956	while (nrepeat && !ad_err) {
957	nrepeat--;
958	if (direction>0) {
959	ad_err = insert(str, seq_pos, 1, !is_sequence);
960
961	if (!ad_err) {
962	seq_pos++;
963	changed_flag = 1;
964	}
965	}
966	else {
967	int left_pos = get_next_visible_pos(seq_pos, -1);
968
969	if (left_pos>=0) {
970	ad_err = insert(str, left_pos+1, -1, !is_sequence);
971	}
972	else {
973	ad_err = "End of sequence";
974	}
975
976	if (!ad_err) {
977	seq_pos = left_pos;
978	changed_flag = 1;
979	}
980	}
981	}
982	break;
983	}
984	default: {
985	break;
986	}
987	}
988	}
989
990	}
991	break;
992	}
993	default: {
994	break;
995	}
996
997	}
998	}
999
1000	if (ad_err) seq_pos = old_seq_pos;
1001	seq_pos = seq_pos<0 ? 0 : (seq_pos>seq_len ? seq_len : seq_pos); // ensure legal position
1002
1003	return ad_err;
1004	}
1005
1006	ED4_Edit_String::ED4_Edit_String()
1007	{
1008	memset((char )this, 0, sizeof(this));
1009	remap = ED4_ROOT->root_group_man->remap();
1010	}
1011
1012	ED4_Edit_String::~ED4_Edit_String()
1013	{
1014	free(old_seq);
1015	}
1016
1017	GB_ERROR ED4_Edit_String::edit(ED4_work_info *info) {
1018	e4_assert(info->working_terminal != 0);
1019
1020	if (!info->rightward) { // 5'<-3'
1021	info->char_position++;
1022	}
1023
1024	info->out_seq_position = remap->screen_to_sequence(info->char_position);
1025	info->refresh_needed = false;
1026	info->cursor_jump = ED4_JUMP_KEEP_VISIBLE;
1027	info->cannot_handle = false;
1028	old_seq = 0;
1029
1030	if (info->string) {
1031	seq = info->string;
1032	seq_len = strlen(seq);
1033	}
1034	else {
1035	e4_assert(info->gb_data);
1036	int seq_len_int;
1037	seq = info->working_terminal->resolve_pointer_to_string_copy(&seq_len_int);
1038	seq_len = seq_len_int;
1039	}
1040
1041	int map_key;
1042	if (info->event.keymodifier == AW_KEYMODE_NONE) {
1043	map_key = ED4_ROOT->edk->map_key(info->event.character);
1044	if (map_key != info->event.character) { // remapped
1045	if (info->event.character == ' ') { // space
1046	AW_advice("You have keymapped the space-key!\n"
1047	"The new functionality assigned to space-key is not available when\n"
1048	"key-mapping is enabled.\n",
1049	AW_ADVICE_TOGGLE_AND_HELP, "Obsolete default keymapping", "nekey_map.hlp");
1050	}
1051	}
1052	}
1053	else {
1054	map_key = info->event.character;
1055	}
1056	GB_ERROR err = 0;
1057
1058	nrepeat_zero_requested = 1;
1059	if (!nrepeat) {
1060	nrepeat_is_already_set = 1;
1061	nrepeat = 1;
1062	}
1063
1064	if (info->event.keycode==AW_KEY_ASCII &&
1065	isdigit(map_key) &&
1066	ED4_ROOT->aw_root->awar(ED4_AWAR_DIGITS_AS_REPEAT)->read_int()) { // handle digits for repeated commands
1067
1068	if (nrepeat_is_already_set) { nrepeat = 0; }
1069	nrepeat_zero_requested = 0;
1070
1071	for (int r=0; r<info->repeat_count; r++) {
1072	nrepeat = nrepeat * 10 + (map_key - '0');
1073	if (nrepeat>10000) {
1074	nrepeat = 10000;
1075	}
1076	else if (nrepeat<0) {
1077	nrepeat = 0;
1078	}
1079	}
1080	#ifdef DEBUG
1081	if (nrepeat>1) {
1082	printf("nrepeat=%i\n", nrepeat);
1083	}
1084	#endif
1085	}
1086	else if (info->event.keymodifier==AW_KEYMODE_NONE && info->event.keycode==AW_KEY_NONE) {
1087	nrepeat_zero_requested = 0;
1088	}
1089	else {
1090	nrepeat += info->repeat_count-1;
1091
1092	#ifdef DEBUG
1093	if (nrepeat>1) {
1094	printf("nrepeat is %i\n", nrepeat);
1095	}
1096	#endif
1097
1098	int is_remapped_sequence = !info->is_sequence && ED4_ROOT->aw_root->awar(ED4_AWAR_COMPRESS_SEQUENCE_TYPE)->read_int()!=ED4_RM_NONE;
1099	if (info->mode==AD_NOWRITE_IF_COMPRESSED) {
1100	if (is_remapped_sequence) {
1101	info->mode = AD_NOWRITE;
1102	}
1103	else {
1104	info->mode = AD_INSERT;
1105	}
1106	}
1107
1108	bool write_fault = 0;
1109
1110	err = command(info->event.keymodifier,
1111	info->event.keycode,
1112	map_key,
1113	info->rightward,
1114	info->mode,
1115	(int)(info->string!=0),
1116	info->out_seq_position,
1117	info->refresh_needed,
1118	info->cursor_jump,
1119	info->cannot_handle,
1120	write_fault,
1121	info->gb_data,
1122	info->is_sequence);
1123
1124	e4_assert(!(err && info->cannot_handle));
1125
1126	if (write_fault) {
1127	e4_assert(info->mode==AD_NOWRITE);
1128	aw_message(is_remapped_sequence
1129	? "Check 'Show all gaps' when editing remarks"
1130	: "This terminal is write-protected!");
1131	}
1132	}
1133
1134	if (!err) {
1135	if (info->gb_data) {
1136	if (info->refresh_needed) {
1137	e4_assert(info->working_terminal->get_species_pointer() == info->gb_data);
1138
1139	int old_seq_len_int;
1140	old_seq = info->working_terminal->resolve_pointer_to_string_copy(&old_seq_len_int);
1141	old_seq_len = old_seq_len_int;
1142
1143	err = info->working_terminal->write_sequence(seq, seq_len);
1144	if (err) {
1145	info->out_seq_position = remap->screen_to_sequence(info->char_position); // correct cursor_pos if protection error occurred
1146	}
1147	}
1148	freenull(seq);
1149	}
1150	}
1151
1152	if (!info->rightward) {
1153	info->char_position = remap->sequence_to_screen_PLAIN(info->out_seq_position);
1154	e4_assert(info->char_position >= 0);
1155	info->char_position--;
1156	info->out_seq_position = remap->screen_to_sequence(info->char_position);
1157	}
1158
1159	return err;
1160	}
1161
1162	void ED4_Edit_String::finish_edit()
1163	{
1164	nrepeat_is_already_set = 0;
1165	if (nrepeat_zero_requested) {
1166	nrepeat_zero_requested = 0;
1167	nrepeat = 0;
1168	}
1169	}
1170
1171	void ED4_Edit_String::init_edit() {
1172	freenull(old_seq);
1173	seq_len = 0;
1174	seq = 0;
1175	gbd = 0;
1176	old_seq_len = 0;
1177	remap = ED4_ROOT->root_group_man->remap();
1178	}
1179

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