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fast_aligner.cxx

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Last change on this file was 19206, checked in by westram, 2 years ago
reintegrates 'ali' into 'trunk' adds: log:branches/ali@19183:19205
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 136.2 KB

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1	// =============================================================== //
2	// //
3	// File : fast_aligner.cxx //
4	// Purpose : A fast aligner (not a multiple aligner!) //
5	// //
6	// Coded by Ralf Westram (coder@reallysoft.de) in 1998 //
7	// Institute of Microbiology (Technical University Munich) //
8	// http://www.arb-home.de/ //
9	// //
10	// =============================================================== //
11
12
13	#include "fast_aligner.hxx"
14	#include "ClustalV.hxx"
15	#include "seq_search.hxx"
16
17	#include <island_hopping.h>
18
19	#include <awtc_next_neighbours.hxx>
20	#include <awt_sel_boxes.hxx>
21
22	#include <aw_awars.hxx>
23	#include <aw_root.hxx>
24	#include <aw_question.hxx>
25
26	#include <arbdbt.h>
27	#include <ad_cb.h>
28
29	#include <arb_defs.h>
30	#include <arb_progress.h>
31	#include <RangeList.h>
32
33	#include <cctype>
34	#include <cmath>
35	#include <climits>
36
37	#include <list>
38	#include <awt_config_manager.hxx>
39	#include <rootAsWin.h>
40
41	// --------------------------------------------------------------------------------
42
43	#if defined(DEBUG)
44	// #define TRACE_CLUSTAL_DATA
45	// #define TRACE_ISLANDHOPPER_DATA
46	// #define TRACE_COMPRESSED_ALIGNMENT
47	// #define TRACE_RELATIVES
48	#endif // DEBUG
49
50	// --------------------------------------------------------------------------------
51
52	enum FA_report {
53	FA_NO_REPORT, // no report
54	FA_TEMP_REPORT, // report to temporary entries
55	FA_REPORT, // report to resident entries
56	};
57
58	enum FA_range {
59	FA_WHOLE_SEQUENCE, // align whole sequence
60	FA_AROUND_CURSOR, // align xxx positions around current cursor position
61	FA_SELECTED_RANGE, // align selected range
62	FA_SAI_MULTI_RANGE, // align versus multi range define by SAI
63	};
64
65	enum FA_turn {
66	FA_TURN_NEVER, // never try to turn sequence
67	FA_TURN_INTERACTIVE, // try to turn, but query user
68	FA_TURN_ALWAYS, // turn if score is better
69	};
70
71	enum FA_reference {
72	FA_REF_EXPLICIT, // reference sequence explicitly specified
73	FA_REF_CONSENSUS, // use group consensus as reference
74	FA_REF_RELATIVES, // search next relatives by PT server
75	};
76
77	enum FA_alignTarget {
78	FA_CURRENT, // align current species
79	FA_MARKED, // align all marked species
80	FA_SELECTED, // align selected species (= range)
81	};
82
83	enum FA_errorAction {
84	FA_NO_ACTION, // do nothing
85	FA_MARK_FAILED, // mark failed species (unmark rest)
86	FA_MARK_ALIGNED, // mark aligned species (unmark rest)
87	};
88
89	struct AlignParams {
90	FA_report report;
91	bool showGapsMessages; // display messages about missing gaps in master?
92	PosRange range; // range to be aligned
93	};
94
95	struct SearchRelativeParams : virtual Noncopyable {
96	FamilyFinder *ff;
97	char *pt_server_alignment; // alignment used in pt_server (may differ from 'alignment')
98	int maxRelatives; // max # of relatives to use
99
100	SearchRelativeParams(FamilyFinder ff_, const char pt_server_alignment_, int maxRelatives_)
101	: ff(ff_),
102	pt_server_alignment(strdup(pt_server_alignment_)),
103	maxRelatives(maxRelatives_)
104	{}
105
106	~SearchRelativeParams() {
107	free(pt_server_alignment);
108	delete(ff);
109	}
110
111	FamilyFinder *getFamilyFinder() { return ff; }
112	};
113
114	// --------------------------------------------------------------------------------
115
116	#define GAP_CHAR '-'
117	#define QUALITY_NAME "ASC_ALIGNER_CLIENT_SCORE"
118	#define INSERTS_NAME "AMI_ALIGNER_MASTER_INSERTS"
119
120	#define FA_AWAR_ROOT "faligner/"
121	#define FA_AWAR_TO_ALIGN FA_AWAR_ROOT "what"
122	#define FA_AWAR_REFERENCE FA_AWAR_ROOT "against"
123	#define FA_AWAR_REFERENCE_NAME FA_AWAR_ROOT "sagainst"
124	#define FA_AWAR_RANGE FA_AWAR_ROOT "range"
125	#define FA_AWAR_PROTECTION FA_AWAR_ROOT "protection"
126	#define FA_AWAR_AROUND FA_AWAR_ROOT "around"
127	#define FA_AWAR_MIRROR FA_AWAR_ROOT "mirror"
128	#define FA_AWAR_REPORT FA_AWAR_ROOT "report"
129	#define FA_AWAR_SHOW_GAPS_MESSAGES FA_AWAR_ROOT "show_gaps"
130	#define FA_AWAR_CONTINUE_ON_ERROR FA_AWAR_ROOT "continue_on_error"
131	#define FA_AWAR_ACTION_ON_ERROR FA_AWAR_ROOT "action_on_error"
132	#define FA_AWAR_USE_SECONDARY FA_AWAR_ROOT "use_secondary"
133	#define FA_AWAR_NEXT_RELATIVES FA_AWAR_ROOT "next_relatives"
134	#define FA_AWAR_RELATIVE_RANGE FA_AWAR_ROOT "relrange"
135	#define FA_AWAR_PT_SERVER_ALIGNMENT "tmp/" FA_AWAR_ROOT "relative_ali"
136	#define FA_AWAR_SAI_RANGE_NAME FA_AWAR_ROOT "sai/sainame"
137	#define FA_AWAR_SAI_RANGE_CHARS FA_AWAR_ROOT "sai/chars"
138
139	#define FA_AWAR_ISLAND_HOPPING_ROOT "island_hopping/"
140	#define FA_AWAR_USE_ISLAND_HOPPING FA_AWAR_ISLAND_HOPPING_ROOT "use"
141	#define FA_AWAR_ESTIMATE_BASE_FREQ FA_AWAR_ISLAND_HOPPING_ROOT "estimate_base_freq"
142	#define FA_AWAR_BASE_FREQ_A FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_a"
143	#define FA_AWAR_BASE_FREQ_C FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_c"
144	#define FA_AWAR_BASE_FREQ_G FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_g"
145	#define FA_AWAR_BASE_FREQ_T FA_AWAR_ISLAND_HOPPING_ROOT "base_freq_t"
146	#define FA_AWAR_SUBST_PARA_AC FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ac"
147	#define FA_AWAR_SUBST_PARA_AG FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ag"
148	#define FA_AWAR_SUBST_PARA_AT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_at"
149	#define FA_AWAR_SUBST_PARA_CG FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_cg"
150	#define FA_AWAR_SUBST_PARA_CT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_ct"
151	#define FA_AWAR_SUBST_PARA_GT FA_AWAR_ISLAND_HOPPING_ROOT "subst_para_gt"
152	#define FA_AWAR_EXPECTED_DISTANCE FA_AWAR_ISLAND_HOPPING_ROOT "expected_dist"
153	#define FA_AWAR_STRUCTURE_SUPPLEMENT FA_AWAR_ISLAND_HOPPING_ROOT "struct_suppl"
154	#define FA_AWAR_THRESHOLD FA_AWAR_ISLAND_HOPPING_ROOT "threshold"
155	#define FA_AWAR_GAP_A FA_AWAR_ISLAND_HOPPING_ROOT "gapa"
156	#define FA_AWAR_GAP_B FA_AWAR_ISLAND_HOPPING_ROOT "gapb"
157	#define FA_AWAR_GAP_C FA_AWAR_ISLAND_HOPPING_ROOT "gapc"
158
159	// --------------------------------------------------------------------------------
160
161	static IslandHopping *island_hopper = NULp; // NULp -> use fast aligner; else use island hopper
162
163	static GB_alignment_type global_alignmentType = GB_AT_UNKNOWN; // type of actually aligned sequence
164
165	static int currentSequenceNumber; // used for counter
166	static int overallSequenceNumber;
167
168	// --------------------------------------------------------------------------------
169
170	inline ARB_ERROR species_not_found(GB_CSTR species_name) {
171	return GBS_global_string("No species '%s' found!", species_name);
172	}
173
174	static ARB_ERROR reverseComplement(GBDATA *gb_species, GB_CSTR ali, int max_protection) {
175	GBDATA *gbd = GBT_find_sequence(gb_species, ali);
176	ARB_ERROR error = NULp;
177
178	if (!gbd) {
179	error = GBS_global_string("No 'data' found for species '%s'", GBT_get_name_or_description(gb_species));
180	}
181	else {
182	int my_protection = GB_read_security_write(gbd);
183
184	if (my_protection<=max_protection) { // ok
185	char *seq = GB_read_string(gbd);
186	int length = GB_read_string_count(gbd);
187	GBDATA *gb_main = GB_get_root(gb_species);
188
189	GB_alignment_type ali_type = GBT_get_alignment_type(gb_main, ali);
190	fa_assert(ali_type != GB_AT_UNKNOWN);
191
192	char T_or_U;
193	error = GBT_determine_T_or_U(ali_type, &T_or_U, "reverse-complement");
194	if (!error) {
195	GBT_reverseComplementNucSequence(seq, length, T_or_U);
196	error = GB_write_string(gbd, seq);
197	}
198	}
199	else { // protection error
200	error = GBS_global_string("Cannot reverse-complement species '%s' because of protection level", GBT_get_name_or_description(gb_species));
201	}
202
203	}
204
205	return error;
206	}
207
208	static void build_reverse_complement(AW_window aw, const AlignDataAccess data_access) {
209	GBDATA *gb_main = data_access->gb_main;
210
211	GB_push_transaction(gb_main);
212
213	AW_root *root = aw->get_root();
214	FA_alignTarget revComplWhat = static_cast<FA_alignTarget>(root->awar(FA_AWAR_TO_ALIGN)->read_int());
215	GB_CSTR alignment = data_access->alignment_name.c_str();
216	ARB_ERROR error = NULp;
217	int max_protection = root->awar(FA_AWAR_PROTECTION)->read_int();
218
219	switch (revComplWhat) {
220	case FA_CURRENT: { // current species
221	GB_CSTR species_name = root->awar(AWAR_SPECIES_NAME)->read_string();
222	GBDATA *gb_species = GBT_find_species(gb_main, species_name);
223	if (!gb_species) error = species_not_found(species_name);
224	if (!error) error = reverseComplement(gb_species, alignment, max_protection);
225	break;
226	}
227	case FA_MARKED: { // marked species
228	GBDATA *gb_species = GBT_first_marked_species(gb_main);
229
230	if (!gb_species) {
231	error = "There is no marked species";
232	}
233	while (gb_species) {
234	error = reverseComplement(gb_species, alignment, max_protection);
235	if (error) break;
236	gb_species = GBT_next_marked_species(gb_species);
237	}
238	break;
239	}
240	case FA_SELECTED: { // selected species (editor selection!)
241
242	Aligner_get_first_selected_species get_first_selected_species = data_access->get_first_selected_species;
243	Aligner_get_next_selected_species get_next_selected_species = data_access->get_next_selected_species;
244
245	int count = 0;
246	GBDATA *gb_species = get_first_selected_species(&count);
247
248	if (!gb_species) {
249	error = "There is no selected species!";
250	}
251	while (gb_species) {
252	error = reverseComplement(gb_species, alignment, max_protection);
253	if (error) break;
254	gb_species = get_next_selected_species();
255	}
256	break;
257	}
258	default: {
259	fa_assert(0);
260	break;
261	}
262	}
263
264	GB_end_transaction_show_error(gb_main, error, aw_message);
265	}
266
267	// --------------------------------------------------------------------------------
268
269	class AliChange { // describes a local alignment change
270	const CompactedSubSequence& Old;
271	const CompactedSubSequence& New;
272
273	public:
274	AliChange(const CompactedSubSequence& old_, const CompactedSubSequence& new_)
275	: Old(old_), New(new_)
276	{
277	fa_assert(Old.may_refer_to_same_part_as(New));
278	}
279
280	int follow(ExplicitRange& range) const {
281	ExplicitRange compressed(Old.compPosition(range.start()),
282	Old.compPosition(range.end()));
283
284	int exp_start = New.expdPosition(compressed.start());
285	int exp_end = New.expdPosition(compressed.end());
286
287	int gaps_before = New.no_of_gaps_before(compressed.start());
288	int gaps_after = New.no_of_gaps_after(compressed.end());
289
290	fa_assert(gaps_before >= 0);
291	fa_assert(gaps_after >= 0);
292
293	range = ExplicitRange(exp_start-gaps_before, exp_end+gaps_after);
294
295	return compressed.size(); // number of bases
296	}
297	};
298
299	class LooseBases {
300	typedef std::list<ExplicitRange> Ranges;
301
302	Ranges ranges;
303
304	public:
305
306	bool is_empty() const { return ranges.empty(); }
307	void clear() { ranges.clear(); }
308
309	void memorize(ExplicitRange range) {
310	ranges.push_front(range);
311	}
312	ExplicitRange recall() {
313	ExplicitRange range = ranges.front();
314	ranges.pop_front();
315	return range;
316	}
317	int follow_ali_change(const AliChange& change) {
318	// transform positions according to changed alignment (oldSequence -> newSequence)
319	// returns the number of bases contained in 'this'
320	int basecount = 0;
321	if (!is_empty()) {
322	for (Ranges::iterator r = ranges.begin(); r != ranges.end(); ++r) {
323	basecount += change.follow(*r);
324	}
325	}
326	return basecount;
327	}
328	void append(LooseBases& loose) { ranges.splice(ranges.end(), loose.ranges); }
329	int follow_ali_change_and_append(LooseBases& loose, const AliChange& change) {
330	// returns the number of loose bases (added from 'loose')
331	int basecount = loose.follow_ali_change(change);
332	append(loose);
333	return basecount;
334	}
335	};
336
337	static LooseBases unaligned_bases; // if fast_align cannot align (no master bases) -> stores positions here
338
339
340	static const char read_name(GBDATA gbd) {
341	if (!gbd) return "GROUP-CONSENSUS";
342	const char *name = GBT_get_name(gbd);
343	return name ? name : "<unnamed-species>";
344	}
345
346	inline int relatedBases(char base1, char base2) {
347	return baseMatch(base1, base2)==1;
348	}
349
350	inline char alignQuality(char slave, char master) {
351	fa_assert(slave);
352	fa_assert(master);
353
354	char result = '#';
355	if (slave==master) result = '-'; // equal
356	else if (slave==GAP_CHAR) result = '+'; // inserted gap
357	else if (master==GAP_CHAR) result = '+'; // no gap in master
358	else if (relatedBases(slave, master)) result = '~'; // mutation (related bases)
359
360	return result; // mutation (non-related bases)
361	}
362
363	// -------------------------
364	// Debugging stuff
365
366	#ifdef DEBUG
367	static char lstr(const char s, int len) {
368	static int alloc;
369	static char *buffer;
370
371	if (alloc<(len+1)) {
372	if (alloc) free(buffer);
373	ARB_alloc(buffer, alloc=len+100);
374	}
375
376	memcpy(buffer, s, len);
377	buffer[len] = 0;
378
379	return buffer;
380	}
381
382	#define BUFLEN 120
383
384	inline char compareChar(char base1, char base2) {
385	return base1==base2 ? '=' : (relatedBases(base1, base2) ? 'x' : 'X');
386	}
387
388	#if defined(TRACE_COMPRESSED_ALIGNMENT)
389
390	static void dump_n_compare_one(const char seq1, const char seq2, long len, long offset) {
391	fa_assert(len<=BUFLEN);
392	char compare[BUFLEN+1];
393
394	for (long l=0; l<len; l++) {
395	compare[l] = (is_ali_gap(seq1[l]) && is_ali_gap(seq2[l])) ? ' ' : compareChar(seq1[l], seq2[l]);
396	}
397
398	compare[len] = 0;
399
400	printf(" %li '%s'\n", offset, lstr(seq1, len));
401	printf(" %li '%s'\n", offset, lstr(seq2, len));
402	printf(" %li '%s'\n", offset, compare);
403	}
404
405	inline void dump_rest(const char *seq, long len, int idx, long offset) {
406	printf(" Rest von Sequenz %i:\n", idx);
407	while (len>BUFLEN) {
408	printf(" %li '%s'\n", offset, lstr(seq, BUFLEN));
409	seq += BUFLEN;
410	len -= BUFLEN;
411	offset += BUFLEN;
412	}
413
414	fa_assert(len>0);
415	printf(" '%s'\n", lstr(seq, len));
416	}
417
418	static void dump_n_compare(const char text, const char seq1, long len1, const char *seq2, long len2) {
419	long offset = 0;
420
421	printf(" Comparing %s:\n", text);
422
423	while (len1>0 && len2>0) {
424	long done = 0;
425
426	if (len1>=BUFLEN && len2>=BUFLEN) {
427	dump_n_compare_one(seq1, seq2, done=BUFLEN, offset);
428	}
429	else {
430	long min = len1<len2 ? len1 : len2;
431	dump_n_compare_one(seq1, seq2, done=min, offset);
432	}
433
434	seq1 += done;
435	seq2 += done;
436	len1 -= done;
437	len2 -= done;
438	offset += done;
439	}
440
441	if (len1>0) dump_rest(seq1, len1, 1, offset);
442	if (len2>0) dump_rest(seq2, len2, 2, offset);
443	printf(" -------------------\n");
444	}
445
446	static void dump_n_compare(const char *text, const CompactedSubSequence& seq1, const CompactedSubSequence& seq2) {
447	dump_n_compare(text, seq1.text(), seq1.length(), seq2.text(), seq2.length());
448	}
449	#endif // TRACE_COMPRESSED_ALIGNMENT
450
451	#undef BUFLEN
452
453	inline void dumpSeq(const char *seq, long len, long pos) {
454	printf("'%s' ", lstr(seq, len));
455	printf("(Pos=%li,Len=%li)", pos, len);
456	}
457
458	#define dump() \
459	do { \
460	double sig = partSignificance(sequence().length(), slaveSequence.length(), bestLength); \
461	\
462	printf(" Score = %li (Significance=%f)\n" \
463	" Master = ", bestScore, sig); \
464	dumpSeq(bestMasterLeft.text(), bestLength, bestMasterLeft.leftOf()); \
465	printf("\n" \
466	" Slave = "); \
467	dumpSeq(bestSlaveLeft.text(), bestLength, bestSlaveLeft.leftOf()); \
468	printf("\n"); \
469	} while (0)
470
471	#endif //DEBUG
472
473
474	// ------------------------------------------------
475	// INLINE-functions used in fast_align():
476
477	inline double log3(double d) {
478	return log(d)/log(3.0);
479	}
480	inline double partSignificance(long seq1len, long seq2len, long partlen) {
481	// returns log3 of significance of the part
482	// usage: partSignificance(...) < log3(maxAllowedSignificance)
483	return log3((seq1len-partlen)*(seq2len-partlen)) - partlen;
484	}
485
486	inline ARB_ERROR bufferTooSmall() {
487	return "Cannot align - reserved buffer is to small";
488	}
489
490	inline long insertsToNextBase(AlignBuffer *alignBuffer, const SequencePosition& master) {
491	int inserts;
492	int nextBase;
493
494	if (master.rightOf()>0) {
495	nextBase = master.expdPosition();
496	}
497	else {
498	nextBase = master.sequence().expdPosition(master.sequence().length());
499	}
500	inserts = nextBase-alignBuffer->offset();
501
502	return inserts;
503	}
504
505	inline void insertBase(AlignBuffer *alignBuffer,
506	SequencePosition& master, SequencePosition& slave,
507	FastAlignReport *report)
508	{
509	char slaveBase = *slave.text();
510	char masterBase = *master.text();
511
512	alignBuffer->set(slaveBase, alignQuality(slaveBase, masterBase));
513	report->count_aligned_base(slaveBase!=masterBase);
514	++slave;
515	++master;
516	}
517
518	inline void insertSlaveBases(AlignBuffer *alignBuffer,
519	SequencePosition& slave,
520	int length,
521	FastAlignReport *report)
522	{
523	alignBuffer->copy(slave.text(), alignQuality(*slave.text(), GAP_CHAR), length);
524	report->count_unaligned_base(length);
525	slave += length;
526	}
527
528	inline void insertGap(AlignBuffer *alignBuffer,
529	SequencePosition& master,
530	FastAlignReport *report)
531	{
532	char masterBase = *master.text();
533
534	alignBuffer->set(GAP_CHAR, alignQuality(GAP_CHAR, masterBase));
535	report->count_aligned_base(masterBase!=GAP_CHAR);
536	++master;
537	}
538
539	static ARB_ERROR insertClustalValigned(AlignBuffer *alignBuffer,
540	SequencePosition& master,
541	SequencePosition& slave,
542	const char masterAlignment, const char slaveAlignment, long alignmentLength,
543	FastAlignReport *report)
544	{
545	// inserts bases of 'slave' to 'alignBuffer' according to alignment in 'masterAlignment' and 'slaveAlignment'
546	#define ACID '*' // contents of 'masterAlignment' and 'slaveAlignment'
547	#define GAP '-'
548
549	int pos;
550	int baseAtLeft = 0; // TRUE -> last position in alignBuffer contains a base
551
552	for (pos=0; pos<alignmentLength; pos++) {
553	long insert = insertsToNextBase(alignBuffer, master); // in expanded seq
554
555	if (masterAlignment[pos]==ACID) {
556	if (insert>0) {
557	if (insert>alignBuffer->free()) return bufferTooSmall();
558	alignBuffer->set(GAP_CHAR, alignQuality(GAP_CHAR, GAP_CHAR), insert);
559	fa_assert(insertsToNextBase(alignBuffer, master)==0);
560	insert = 0;
561	}
562
563	if (!alignBuffer->free()) return bufferTooSmall();
564	if (slaveAlignment[pos]==ACID) {
565	insertBase(alignBuffer, master, slave, report);
566	baseAtLeft = 1;
567	}
568	else {
569	insertGap(alignBuffer, master, report);
570	baseAtLeft = 0;
571	}
572	}
573	else {
574	int slave_bases;
575
576	fa_assert(masterAlignment[pos]==GAP);
577	for (slave_bases=1; pos+slave_bases<alignmentLength && masterAlignment[pos+slave_bases]==GAP; slave_bases++) {
578	; // count gaps in master (= # of slave bases to insert)
579	}
580	if (!baseAtLeft && insert>slave_bases) {
581	int ins_gaps = insert-slave_bases;
582
583	fa_assert(alignBuffer->free()>=ins_gaps);
584	alignBuffer->set(GAP_CHAR, alignQuality(GAP_CHAR, GAP_CHAR), ins_gaps);
585	insert -= ins_gaps;
586	}
587
588	if (insert<slave_bases) { // master has less gaps than slave bases to insert
589	report->memorize_insertion(master.expdPosition(), slave_bases-insert);
590	}
591	else if (insert>slave_bases) { // master has more gaps than slave bases to insert
592	fa_assert(baseAtLeft);
593	}
594
595	unaligned_bases.memorize(ExplicitRange(slave.expdPosition(), // memorize base positions without counterpart in master
596	slave.expdPosition(slave_bases-1)));
597
598	if (slave_bases>alignBuffer->free()) return bufferTooSmall();
599	insertSlaveBases(alignBuffer, slave, slave_bases, report);
600	pos += slave_bases-1; // -1 compensates for()-increment
601	baseAtLeft = 1;
602	}
603	}
604
605	return NULp;
606
607	#undef GAP
608	#undef ACID
609	}
610
611	static ARB_ERROR insertAligned(AlignBuffer *alignBuffer,
612	SequencePosition& master, SequencePosition& slave, long partLength,
613	FastAlignReport *report)
614	{
615	// insert bases of 'slave' to 'alignBuffer' according to 'master'
616	if (partLength) {
617	long insert = insertsToNextBase(alignBuffer, master);
618
619	fa_assert(partLength>=0);
620
621	if (insert<0) { // insert gaps into master
622	long min_insert = insert;
623
624	report->memorize_insertion(master.expdPosition(), -insert);
625
626	while (insert<0 && partLength) {
627	if (insert<min_insert) min_insert = insert;
628	if (!alignBuffer->free()) {
629	return bufferTooSmall();
630	}
631	insertBase(alignBuffer, master, slave, report);
632	partLength--;
633	insert = insertsToNextBase(alignBuffer, master);
634	}
635
636	fa_assert(partLength>=0);
637	if (partLength==0) { // all inserted
638	return NULp;
639	}
640	}
641
642	fa_assert(insert>=0);
643
644	if (insert>0) { // insert gaps into slave
645	if (insert>alignBuffer->free()) return bufferTooSmall();
646	alignBuffer->set(GAP_CHAR, alignQuality(GAP_CHAR, GAP_CHAR), insert);
647	fa_assert(insertsToNextBase(alignBuffer, master)==0);
648	}
649
650	fa_assert(partLength>=0);
651
652	while (partLength--) {
653	insert = insertsToNextBase(alignBuffer, master);
654
655	fa_assert(insert>=0);
656	if (insert>0) {
657	if (insert>=alignBuffer->free()) return bufferTooSmall();
658	alignBuffer->set(GAP_CHAR, alignQuality(GAP_CHAR, GAP_CHAR), insert);
659	}
660	else {
661	if (!alignBuffer->free()) {
662	return bufferTooSmall();
663	}
664	}
665
666	insertBase(alignBuffer, master, slave, report);
667	}
668	}
669
670	return NULp;
671	}
672
673	static ARB_ERROR cannot_fast_align(const CompactedSubSequence& master, long moffset, long mlength,
674	const CompactedSubSequence& slaveSequence, long soffset, long slength,
675	int max_seq_length,
676	AlignBuffer *alignBuffer,
677	FastAlignReport *report)
678	{
679	const char *mtext = master.text(moffset);
680	const char *stext = slaveSequence.text(soffset);
681	ARB_ERROR error = NULp;
682
683	if (slength) {
684	if (mlength) { // if slave- and master-sequences contain bases, we call the slow aligner
685	#ifdef TRACE_CLUSTAL_DATA
686	printf("ClustalV-Align:\n");
687	printf(" mseq = '%s'\n", lstr(mtext, mlength));
688	printf(" sseq = '%s'\n", lstr(stext, slength));
689	#endif // TRACE_CLUSTAL_DATA
690
691	int is_dna = -1;
692
693	switch (global_alignmentType) {
694	case GB_AT_RNA:
695	case GB_AT_DNA: is_dna = 1; break;
696	case GB_AT_AA: is_dna = 0; break;
697	default: error = "Unknown alignment type - aligner aborted"; break;
698	}
699
700	const char maligned, saligned;
701	int len;
702	if (!error) {
703	int score; // unused
704	error = ClustalV_align(is_dna,
705	1,
706	mtext, mlength, stext, slength,
707	master.gapsBefore(moffset),
708	max_seq_length,
709	maligned, saligned, len, score);
710	}
711
712	if (!error) {
713	#ifdef TRACE_CLUSTAL_DATA
714	printf("ClustalV returns:\n");
715	printf(" maligned = '%s'\n", lstr(maligned, len));
716	printf(" saligned = '%s'\n", lstr(saligned, len));
717	#endif // TRACE_CLUSTAL_DATA
718
719	SequencePosition masterPos(master, moffset);
720	SequencePosition slavePos(slaveSequence, soffset);
721
722	error = insertClustalValigned(alignBuffer, masterPos, slavePos, maligned, saligned, len, report);
723
724	#if (defined(DEBUG) && 0)
725
726	SequencePosition master2(master->sequence(), moffset);
727	SequencePosition slave2(slaveSequence, soffset);
728	char *cmp = new char[len];
729
730	for (int l=0; l<len; l++) {
731	int gaps = 0;
732
733	if (maligned[l]=='*') {
734	maligned[l] = *master2.text();
735	++master2;
736	}
737	else {
738	gaps++;
739	}
740
741	if (saligned[l]=='*') {
742	saligned[l] = *slave2.text();
743	++slave2;
744	}
745	else {
746	gaps++;
747	}
748
749	cmp[l] = gaps \|\| maligned[l]==saligned[l] ? '=' : 'X';
750	}
751
752	printf(" master = '%s'\n", lstr(maligned, len));
753	printf(" slave = '%s'\n", lstr(saligned, len));
754	printf(" '%s'\n", lstr(cmp, len));
755
756	delete [] cmp;
757	#endif
758	}
759	}
760	else { // master is empty here, so we just copy in the slave bases
761	if (slength<=alignBuffer->free()) {
762	unaligned_bases.memorize(ExplicitRange(slaveSequence.expdPosition(soffset),
763	slaveSequence.expdPosition(soffset+slength-1)));
764
765	alignBuffer->copy(slaveSequence.text(soffset), '?', slength); // '?' means not aligned (just inserted)
766	// corrected by at alignBuffer->correctUnalignedPositions()
767	report->count_unaligned_base(slength);
768	}
769	else {
770	error = bufferTooSmall();
771	}
772	}
773	}
774
775	return error;
776	}
777
778	// ------------------------------------
779	// #define's for fast_align()
780
781	#define TEST_BETTER_SCORE() \
782	do { \
783	if (score>bestScore) { \
784	bestScore = score; \
785	bestLength = masterRight.text() - masterLeft.text(); \
786	bestMasterLeft = masterLeft; \
787	bestSlaveLeft = slaveLeft; \
788	} \
789	} while (0)
790
791	#define CAN_SCORE_LEFT() (masterLeft.leftOf() && slaveLeft.leftOf())
792	#define CAN_SCORE_RIGHT() (masterRight.rightOf() && slaveRight.rightOf())
793
794	#define SCORE_LEFT() \
795	do { \
796	score += (--masterLeft).text()==(--slaveLeft).text() ? match : mismatch; \
797	TEST_BETTER_SCORE(); \
798	} while (0)
799
800	#define SCORE_RIGHT() \
801	do { \
802	score += (++masterRight).text()==(++slaveRight).text() ? match : mismatch; \
803	TEST_BETTER_SCORE(); \
804	} while (0)
805
806
807	ARB_ERROR FastSearchSequence::fast_align(const CompactedSubSequence& slaveSequence,
808	AlignBuffer *alignBuffer,
809	int max_seq_length,
810	int match, int mismatch,
811	FastAlignReport *report) const
812	{
813	// aligns 'slaveSequence' to 'this'
814	//
815	// returns
816	// NULp -> all ok -> 'alignBuffer' contains aligned sequence
817	// or error -> failure -> no results
818
819	ARB_ERROR error = NULp;
820	int aligned = 0;
821
822	// set the following #if to zero to test ClustalV-Aligner (not fast_aligner)
823	#if 1
824
825	static double lowSignificance;
826	static int lowSignificanceInitialized;
827
828	if (!lowSignificanceInitialized) {
829	lowSignificance = log3(0.01);
830	lowSignificanceInitialized = 1;
831	}
832
833	SequencePosition slave(slaveSequence);
834	long bestScore=0;
835	SequencePosition bestMasterLeft(sequence());
836	SequencePosition bestSlaveLeft(slaveSequence);
837	long bestLength=0;
838
839	while (slave.rightOf()>=3) { // with all triples of slaveSequence
840	FastSearchOccurrence occurrence(*this, slave.text()); // "search" first
841	SequencePosition rightmostSlave = slave;
842
843	while (occurrence.found()) { // with all occurrences of the triple
844	long score = match*3;
845	SequencePosition masterLeft(occurrence.sequence(), occurrence.offset());
846	SequencePosition masterRight(occurrence.sequence(), occurrence.offset()+3);
847	SequencePosition slaveLeft(slave);
848	SequencePosition slaveRight(slave, 3);
849
850	while (score>0) {
851	if (CAN_SCORE_LEFT()) {
852	SCORE_LEFT();
853	}
854	else {
855	while (score>0 && CAN_SCORE_RIGHT()) {
856	SCORE_RIGHT();
857	}
858	break;
859	}
860
861	if (CAN_SCORE_RIGHT()) {
862	SCORE_RIGHT();
863	}
864	else {
865	while (score>0 && CAN_SCORE_LEFT()) {
866	SCORE_LEFT();
867	}
868	break;
869	}
870	}
871
872	occurrence.gotoNext(); // "search" next
873
874	if (rightmostSlave<slaveRight) {
875	rightmostSlave = slaveRight;
876	rightmostSlave -= 3;
877	}
878	}
879
880	if (rightmostSlave>slave) slave = rightmostSlave;
881	else ++slave;
882	}
883
884	if (bestLength) {
885	double sig = partSignificance(sequence().length(), slaveSequence.length(), bestLength);
886
887	if (sig<lowSignificance) {
888	long masterLeftOf = bestMasterLeft.leftOf();
889	long masterRightStart = masterLeftOf+bestLength;
890	long masterRightOf = bestMasterLeft.rightOf()-bestLength;
891	long slaveLeftOf = bestSlaveLeft.leftOf();
892	long slaveRightStart = slaveLeftOf+bestLength;
893	long slaveRightOf = bestSlaveLeft.rightOf()-bestLength;
894
895	#define MIN_ALIGNMENT_RANGE 4
896
897	if (!error) {
898	if (masterLeftOf >= MIN_ALIGNMENT_RANGE && slaveLeftOf >= MIN_ALIGNMENT_RANGE) {
899	CompactedSubSequence leftCompactedMaster(sequence(), 0, masterLeftOf);
900	FastSearchSequence leftMaster(leftCompactedMaster);
901
902	error = leftMaster.fast_align(CompactedSubSequence(slaveSequence, 0, slaveLeftOf),
903	alignBuffer, max_seq_length, match, mismatch, report);
904	}
905	else if (slaveLeftOf>0) {
906	error = cannot_fast_align(sequence(), 0, masterLeftOf,
907	slaveSequence, 0, slaveLeftOf,
908	max_seq_length, alignBuffer, report);
909	}
910
911	aligned = 1;
912	}
913
914	// align part of slave sequence according to master sequence:
915
916	if (!error) {
917	#if (defined(DEBUG) && 0)
918	long offset = alignBuffer->offset();
919	long used;
920	#endif
921	error = insertAligned(alignBuffer, bestMasterLeft, bestSlaveLeft, bestLength, report);
922	#if (defined(DEBUG) && 0)
923	used = alignBuffer->offset()-offset;
924	printf("aligned '%s' (len=%li, address=%li)\n", lstr(alignBuffer->text()+offset, used), used, long(alignBuffer));
925	#endif
926	aligned = 1;
927	}
928
929	if (!error) {
930	if (masterRightOf >= MIN_ALIGNMENT_RANGE && slaveRightOf >= MIN_ALIGNMENT_RANGE) {
931	CompactedSubSequence rightCompactedMaster(sequence(), masterRightStart, masterRightOf);
932	FastSearchSequence rightMaster(rightCompactedMaster);
933
934	error = rightMaster.fast_align(CompactedSubSequence(slaveSequence, slaveRightStart, slaveRightOf),
935	alignBuffer,
936	max_seq_length, match, mismatch, report);
937	}
938	else if (slaveRightOf>0) {
939	error = cannot_fast_align(sequence(), masterRightStart, masterRightOf,
940	slaveSequence, slaveRightStart, slaveRightOf,
941	max_seq_length, alignBuffer, report);
942	}
943
944	aligned = 1;
945	}
946
947	}
948	}
949
950	#endif
951
952	if (!aligned && !error) {
953	error = cannot_fast_align(sequence(), 0, sequence().length(),
954	slaveSequence, 0, slaveSequence.length(),
955	max_seq_length, alignBuffer, report);
956	}
957
958	return error;
959	}
960
961	#undef dump
962	#undef TEST_BETTER_SCORE
963	#undef CAN_SCORE_LEFT
964	#undef CAN_SCORE_RIGHT
965	#undef SCORE_LEFT
966	#undef SCORE_RIGHT
967
968	inline long calcSequenceChecksum(const char *data, long length) {
969	return GB_checksum(data, length, 1, GAP_CHARS);
970	}
971
972	static CompactedSubSequence readCompactedSequence(GBDATA gb_species,
973	const char *ali,
974	ARB_ERROR *errorPtr,
975	char **dataPtr, // if dataPtr is specified, it will be set to the WHOLE uncompacted sequence
976	long *seqChksum, // may be NULp (of part of sequence)
977	PosRange range) // if !range.is_whole() -> return only part of the sequence
978	{
979	ARB_ERROR error = NULp;
980	GBDATA *gbd;
981	CompactedSubSequence *seq = NULp;
982
983	gbd = GBT_find_sequence(gb_species, ali); // get sequence
984
985	if (gbd) {
986	long length = GB_read_string_count(gbd);
987	char *data = GB_read_string(gbd);
988	long partLength;
989	char *partData;
990
991	if (dataPtr) { // make a copy of the whole uncompacted sequence (returned to caller)
992	*dataPtr = data;
993	}
994
995	int firstColumn = range.start();
996	if (range.is_part()) { // take only part of sequence
997	int lastColumn = range.end();
998
999	fa_assert(firstColumn>=0);
1000	fa_assert(firstColumn<=lastColumn);
1001
1002	// include all surrounding gaps (@@@ this might cause problems with partial alignment)
1003	while (firstColumn>0 && is_ali_gap(data[firstColumn-1])) {
1004	firstColumn--;
1005	}
1006	if (lastColumn!=-1) {
1007	while (lastColumn<(length-1) && is_ali_gap(data[lastColumn+1])) lastColumn++;
1008	fa_assert(lastColumn<length);
1009	}
1010
1011	partData = data+firstColumn;
1012	int slen = length-firstColumn;
1013
1014	fa_assert(slen>=0);
1015	fa_assert((size_t)slen==strlen(partData));
1016
1017	if (lastColumn==-1) { // take all till end of sequence
1018	partLength = slen;
1019	}
1020	else {
1021	partLength = lastColumn-firstColumn+1;
1022	if (partLength>slen) partLength = slen; // cut rest, if we have any
1023	}
1024	}
1025	else {
1026	partLength = length;
1027	partData = data;
1028	}
1029
1030	if (!error) {
1031	if (seqChksum) {
1032	*seqChksum = calcSequenceChecksum(partData, partLength);
1033	}
1034
1035	seq = new CompactedSubSequence(partData, partLength, GBT_get_name_or_description(gb_species), firstColumn);
1036	}
1037
1038	if (!dataPtr) { // free sequence only if user has not requested to get it
1039	free(data);
1040	}
1041	}
1042	else {
1043	error = GBS_global_string("No 'data' found for species '%s'", GBT_get_name_or_description(gb_species));
1044	if (dataPtr) *dataPtr = NULp; // (user must not care to free data if we fail)
1045	}
1046
1047	fa_assert(errorPtr);
1048	*errorPtr = error;
1049
1050	return seq;
1051	}
1052
1053	static ARB_ERROR writeStringToAlignment(GBDATA *gb_species, GB_CSTR alignment, GB_CSTR data_name, GB_CSTR str, bool temporary) {
1054	GBDATA *gb_ali = GB_search(gb_species, alignment, GB_DB);
1055	ARB_ERROR error = NULp;
1056	GBDATA *gb_name = GB_search(gb_ali, data_name, GB_STRING);
1057
1058	if (gb_name) {
1059	fa_assert(GB_is_ancestor_of(gb_ali, gb_name));
1060	error = GB_write_string(gb_name, str);
1061	if (temporary && !error) error = GB_set_temporary(gb_name);
1062	}
1063	else {
1064	error = GBS_global_string("Cannot create entry '%s' for '%s'", data_name, GBT_get_name_or_description(gb_species));
1065	}
1066
1067	return error;
1068	}
1069
1070	// --------------------------------------------------------------------------------
1071
1072	static ARB_ERROR alignCompactedTo(CompactedSubSequence *toAlignSequence,
1073	const FastSearchSequence *alignTo,
1074	int max_seq_length,
1075	GB_CSTR alignment,
1076	long toAlignChksum,
1077	GBDATA *gb_toAlign,
1078	GBDATA *gb_alignTo, // may be NULp
1079	const AlignParams& ali_params)
1080	{
1081	// if only part of the sequence should be aligned, then this functions already gets only the part
1082	// (i.o.w.: toAlignSequence, alignTo and toAlignChksum refer to the partial sequence)
1083	AlignBuffer alignBuffer(max_seq_length);
1084	if (ali_params.range.start()>0) {
1085	alignBuffer.set(GAP_CHAR, alignQuality(GAP_CHAR, GAP_CHAR), ali_params.range.start());
1086	}
1087
1088	const char *master_name = read_name(gb_alignTo);
1089
1090	FastAlignReport report(master_name, ali_params.showGapsMessages);
1091
1092	{
1093	static GBDATA *last_gb_toAlign = NULp;
1094	if (gb_toAlign!=last_gb_toAlign) {
1095	last_gb_toAlign = gb_toAlign;
1096	currentSequenceNumber++;
1097	}
1098	}
1099
1100	#ifdef TRACE_COMPRESSED_ALIGNMENT
1101	printf("alignCompactedTo(): master='%s' ", master_name);
1102	printf("slave='%s'\n", toAlignSequence->name());
1103	#endif // TRACE_COMPRESSED_ALIGNMENT
1104
1105	ARB_ERROR error = GB_pop_transaction(gb_toAlign);
1106	if (!error) {
1107	if (island_hopper) {
1108	error = island_hopper->do_align();
1109	if (!error) {
1110	fa_assert(island_hopper->was_aligned());
1111
1112	#ifdef TRACE_ISLANDHOPPER_DATA
1113	printf("Island-Hopper returns:\n");
1114	printf("maligned = '%s'\n", lstr(island_hopper->get_result_ref(), island_hopper->get_result_length()));
1115	printf("saligned = '%s'\n", lstr(island_hopper->get_result(), island_hopper->get_result_length()));
1116	#endif // TRACE_ISLANDHOPPER_DATA
1117
1118	SequencePosition masterPos(alignTo->sequence(), 0);
1119	SequencePosition slavePos(*toAlignSequence, 0);
1120
1121	error = insertClustalValigned(&alignBuffer, masterPos, slavePos, island_hopper->get_result_ref(), island_hopper->get_result(), island_hopper->get_result_length(), &report);
1122	}
1123	}
1124	else {
1125	error = alignTo->fast_align(*toAlignSequence, &alignBuffer, max_seq_length, 2, -10, &report); // <- here we align
1126	}
1127	}
1128
1129	if (!error) {
1130	alignBuffer.correctUnalignedPositions();
1131	if (alignBuffer.free()) {
1132	alignBuffer.set('-', alignQuality(GAP_CHAR, GAP_CHAR), alignBuffer.free()); // rest of alignBuffer is set to '-'
1133	}
1134	alignBuffer.restoreDots(*toAlignSequence);
1135	}
1136
1137	#ifdef TRACE_COMPRESSED_ALIGNMENT
1138	if (!error) {
1139	CompactedSubSequence alignedSlave(alignBuffer.text(), alignBuffer.length(), toAlignSequence->name());
1140	dump_n_compare("reference vs. aligned:", alignTo->sequence(), alignedSlave);
1141	}
1142	#endif // TRACE_COMPRESSED_ALIGNMENT
1143
1144	{
1145	GB_ERROR err = GB_push_transaction(gb_toAlign);
1146	if (!error) error = err;
1147	}
1148
1149	if (!error) {
1150	if (calcSequenceChecksum(alignBuffer.text(), alignBuffer.length())!=toAlignChksum) { // sequence-chksum changed
1151	error = "Internal aligner error (sequence checksum changed) -- aborted";
1152
1153	#ifdef TRACE_COMPRESSED_ALIGNMENT
1154	CompactedSubSequence alignedSlave(alignBuffer.text(), alignBuffer.length(), toAlignSequence->name());
1155	dump_n_compare("Old Slave vs. new Slave", *toAlignSequence, alignedSlave);
1156	#endif // TRACE_COMPRESSED_ALIGNMENT
1157	}
1158	else {
1159	{
1160	GB_topSecurityLevel unsecured(gb_toAlign);
1161	GBDATA *gbd = GBT_add_data(gb_toAlign, alignment, "data", GB_STRING);
1162
1163	if (!gbd) {
1164	error = "Can't find/create sequence data";
1165	}
1166	else {
1167	if (ali_params.range.is_part()) { // we aligned just a part of the sequence
1168	char *buffer = GB_read_string(gbd); // so we read old sequence data
1169	long len = GB_read_string_count(gbd);
1170	if (!buffer) error = GB_await_error();
1171	else {
1172	int lenToCopy = ali_params.range.size();
1173	long wholeChksum = calcSequenceChecksum(buffer, len);
1174
1175	memcpy(buffer+ali_params.range.start(), alignBuffer.text()+ali_params.range.start(), lenToCopy); // copy in the aligned part
1176	// @@@ genau um 1 position zu niedrig
1177
1178	if (calcSequenceChecksum(buffer, len) != wholeChksum) {
1179	error = "Internal aligner error (sequence checksum changed) -- aborted";
1180	# ifdef TRACE_COMPRESSED_ALIGNMENT
1181	char *buffer_org = GB_read_string(gbd);
1182	dump_n_compare("Old seq vs. new seq (slave)", buffer_org, len, buffer, len);
1183	free(buffer_org);
1184	# endif // TRACE_COMPRESSED_ALIGNMENT
1185	}
1186	else {
1187	GB_write_string(gbd, "");
1188	error = GB_write_string(gbd, buffer);
1189	}
1190	}
1191
1192	free(buffer);
1193	}
1194	else {
1195	alignBuffer.setDotsAtEOSequence();
1196	error = GB_write_string(gbd, alignBuffer.text()); // aligned all -> write all
1197	}
1198	}
1199	}
1200
1201	if (!error && ali_params.report != FA_NO_REPORT) {
1202	// create temp-entry for slave containing alignment quality:
1203
1204	error = writeStringToAlignment(gb_toAlign, alignment, QUALITY_NAME, alignBuffer.quality(), ali_params.report==FA_TEMP_REPORT);
1205	if (!error) {
1206	// create temp-entry for master containing insert dots:
1207
1208	int buflen = max_seq_length*2;
1209	char *buffer = ARB_alloc<char>(buflen+1);
1210	char *afterLast = buffer;
1211
1212	if (!buffer) {
1213	error = "out of memory";
1214	}
1215	else {
1216	memset(buffer, '-', buflen);
1217	buffer[buflen] = 0;
1218
1219	const FastAlignInsertion *inserts = report.insertion();
1220	while (inserts) {
1221	memset(buffer+inserts->offset(), '>', inserts->gaps());
1222	afterLast = buffer+inserts->offset()+inserts->gaps();
1223	inserts = inserts->next();
1224	}
1225
1226	*afterLast = 0;
1227	if (gb_alignTo) {
1228	error = writeStringToAlignment(gb_alignTo, alignment, INSERTS_NAME, buffer, ali_params.report==FA_TEMP_REPORT);
1229	}
1230	}
1231	}
1232	}
1233	}
1234	}
1235	return error;
1236	}
1237
1238	ARB_ERROR FastAligner_delete_temp_entries(GBDATA gb_species, const char alignment) {
1239	fa_assert(gb_species);
1240	fa_assert(alignment);
1241
1242	GBDATA *gb_ali = GB_search(gb_species, alignment, GB_FIND);
1243	ARB_ERROR error = NULp;
1244
1245	if (gb_ali) {
1246	GBDATA *gb_name = GB_search(gb_ali, QUALITY_NAME, GB_FIND);
1247	if (gb_name) {
1248	error = GB_delete(gb_name);
1249	#if defined(DEBUG)
1250	printf("deleted '%s' of '%s' (gb_name=%p)\n", QUALITY_NAME, GBT_get_name_or_description(gb_species), gb_name);
1251	#endif
1252	}
1253
1254	if (!error) {
1255	gb_name = GB_search(gb_ali, INSERTS_NAME, GB_FIND);
1256	if (gb_name) {
1257	error = GB_delete(gb_name);
1258	#if defined(DEBUG)
1259	printf("deleted '%s' of '%s' (gb_name=%p)\n", INSERTS_NAME, GBT_get_name_or_description(gb_species), gb_name);
1260	#endif
1261	}
1262	}
1263	}
1264
1265	return error;
1266	}
1267
1268	static ARB_ERROR align_error(ARB_ERROR olderr, GBDATA gb_toAlign, GBDATA gb_alignTo) {
1269	// used by alignTo() and alignToNextRelative() to transform errors coming from subroutines
1270	// can be used by higher functions
1271
1272	const char *name_toAlign = read_name(gb_toAlign);
1273	const char *name_alignTo = read_name(gb_alignTo);
1274
1275	fa_assert(olderr);
1276
1277	return GBS_global_string("Error while aligning '%s' to '%s':\n%s",
1278	name_toAlign, name_alignTo, olderr.deliver());
1279	}
1280
1281	static ARB_ERROR alignTo(GBDATA *gb_toAlign,
1282	GB_CSTR alignment,
1283	const FastSearchSequence *alignTo,
1284	GBDATA *gb_alignTo, // may be NULp
1285	int max_seq_length,
1286	const AlignParams& ali_params)
1287	{
1288	ARB_ERROR error = NULp;
1289	long chksum = -1;
1290
1291	CompactedSubSequence *toAlignSequence = readCompactedSequence(gb_toAlign, alignment, &error, NULp, &chksum, ali_params.range);
1292
1293	if (island_hopper) {
1294	GBDATA *gb_seq = GBT_find_sequence(gb_toAlign, alignment); // get sequence
1295	if (gb_seq) {
1296	long length = GB_read_string_count(gb_seq);
1297	const char *data = GB_read_char_pntr(gb_seq);
1298
1299	island_hopper->set_toAlign_sequence(data);
1300	island_hopper->set_alignment_length(length);
1301	}
1302	}
1303
1304
1305
1306	if (!error) {
1307	error = alignCompactedTo(toAlignSequence, alignTo, max_seq_length, alignment, chksum, gb_toAlign, gb_alignTo, ali_params);
1308	if (error) error = align_error(error, gb_toAlign, gb_alignTo);
1309	delete toAlignSequence;
1310	}
1311
1312	return error;
1313	}
1314
1315	static ARB_ERROR alignToGroupConsensus(GBDATA *gb_toAlign,
1316	GB_CSTR alignment,
1317	Aligner_get_consensus_func get_consensus,
1318	int max_seq_length,
1319	const AlignParams& ali_params)
1320	{
1321	ARB_ERROR error = NULp;
1322	char *consensus = get_consensus(read_name(gb_toAlign), ali_params.range);
1323	size_t cons_len = strlen(consensus);
1324
1325	fa_assert(cons_len);
1326
1327	for (size_t i = 0; i<cons_len; ++i) { // translate consensus to be accepted by aligner
1328	switch (consensus[i]) {
1329	case '=': consensus[i] = '-'; break;
1330	default: break;
1331	}
1332	}
1333
1334	CompactedSubSequence compacted(consensus, cons_len, "group consensus", ali_params.range.start());
1335
1336	{
1337	FastSearchSequence fast(compacted);
1338	error = alignTo(gb_toAlign, alignment, &fast, NULp, max_seq_length, ali_params);
1339	}
1340
1341	free(consensus);
1342
1343	return error;
1344	}
1345
1346	static void appendNameAndUsedBasePositions(char *toString, GBDATA gb_species, int usedBasePositions) {
1347	// if usedBasePositions == -1 -> unknown;
1348
1349	char *currInfo;
1350	if (usedBasePositions<0) {
1351	currInfo = strdup(GBT_get_name_or_description(gb_species));
1352	}
1353	else {
1354	fa_assert(usedBasePositions>0); // otherwise it should NOT be announced here!
1355	currInfo = GBS_global_string_copy("%s:%i", GBT_get_name_or_description(gb_species), usedBasePositions);
1356	}
1357
1358	char *newString = NULp;
1359	if (*toString) {
1360	newString = GBS_global_string_copy("%s, %s", *toString, currInfo);
1361	}
1362	else {
1363	newString = currInfo;
1364	currInfo = NULp; // don't free
1365	}
1366
1367	freeset(*toString, newString);
1368	free(currInfo);
1369	}
1370
1371	inline int min(int i, int j) { return i<j ? i : j; }
1372
1373	static ARB_ERROR alignToNextRelative(SearchRelativeParams& relSearch,
1374	int max_seq_length,
1375	FA_turn turnAllowed,
1376	GB_CSTR alignment,
1377	GBDATA *gb_toAlign,
1378	const AlignParams& ali_params)
1379	{
1380	CompactedSubSequence *toAlignSequence = NULp;
1381	bool use_different_pt_server_alignment = 0 != strcmp(relSearch.pt_server_alignment, alignment);
1382
1383	ARB_ERROR error;
1384	long chksum;
1385	int relativesToTest = relSearch.maxRelatives*2; // get more relatives from pt-server (needed when use_different_pt_server_alignment == true)
1386	char *nearestRelative = new char[relativesToTest+1];
1387	int next_relatives;
1388	int i;
1389	GBDATA *gb_main = GB_get_root(gb_toAlign);
1390
1391	if (use_different_pt_server_alignment) {
1392	turnAllowed = FA_TURN_NEVER; // makes no sense if we're using a different alignment for the pt_server
1393	}
1394
1395	for (next_relatives=0; next_relatives<relativesToTest; next_relatives++) {
1396	nearestRelative[next_relatives] = NULp;
1397	}
1398	next_relatives = 0;
1399
1400	bool restart = true;
1401	while (restart) {
1402	restart = false;
1403
1404	char *findRelsBySeq = NULp;
1405	if (use_different_pt_server_alignment) {
1406	toAlignSequence = readCompactedSequence(gb_toAlign, alignment, &error, NULp, &chksum, ali_params.range);
1407
1408	GBDATA *gbd = GBT_find_sequence(gb_toAlign, relSearch.pt_server_alignment); // use a different alignment for next relative search
1409	if (!gbd) {
1410	error = GBS_global_string("Species '%s' has no data in alignment '%s'", GBT_get_name_or_description(gb_toAlign), relSearch.pt_server_alignment);
1411	}
1412	else {
1413	findRelsBySeq = GB_read_string(gbd);
1414	}
1415	}
1416	else {
1417	toAlignSequence = readCompactedSequence(gb_toAlign, alignment, &error, &findRelsBySeq, &chksum, ali_params.range);
1418	}
1419
1420	if (error) {
1421	delete toAlignSequence;
1422	return error; // @@@ leaks ?
1423	}
1424
1425	while (next_relatives) {
1426	next_relatives--;
1427	freenull(nearestRelative[next_relatives]);
1428	}
1429
1430	{
1431	// find relatives
1432	FamilyFinder *familyFinder = relSearch.getFamilyFinder();
1433	const PosRange& range = familyFinder->get_TargetRange();
1434
1435	if (range.is_part()) {
1436	range.copy_corresponding_part(findRelsBySeq, findRelsBySeq, strlen(findRelsBySeq));
1437	turnAllowed = FA_TURN_NEVER; // makes no sense if we're using partial relative search
1438	}
1439
1440	error = familyFinder->searchFamily(findRelsBySeq, FF_FORWARD, relativesToTest+1, 0); // @@@ make min_score configurable
1441
1442	// @@@ case where no relative found (due to min score) handle how ? abort ? warn ?
1443
1444	double bestScore = 0;
1445	if (!error) {
1446	#if defined(DEBUG)
1447	double lastScore = -1;
1448	#if defined(TRACE_RELATIVES)
1449	fprintf(stderr, "List of relatives used for '%s':\n", GBT_get_name_or_description(gb_toAlign));
1450	#endif // TRACE_RELATIVES
1451	#endif // DEBUG
1452	for (const FamilyList *fl = familyFinder->getFamilyList(); fl; fl=fl->next) {
1453	if (strcmp(toAlignSequence->name(), fl->name)!=0) {
1454	if (GBT_find_species(gb_main, fl->name)) { // @@@
1455	double thisScore = familyFinder->uses_rel_matches() ? fl->rel_matches : fl->matches;
1456	#if defined(DEBUG)
1457	// check whether family list is sorted correctly
1458	fa_assert(lastScore < 0 \|\| lastScore >= thisScore);
1459	lastScore = thisScore;
1460	#if defined(TRACE_RELATIVES)
1461	fprintf(stderr, "- %s (%5.2f)\n", fl->name, thisScore);
1462	#endif // TRACE_RELATIVES
1463	#endif // DEBUG
1464	if (thisScore>=bestScore) bestScore = thisScore;
1465	if (next_relatives<(relativesToTest+1)) {
1466	nearestRelative[next_relatives] = strdup(fl->name);
1467	next_relatives++;
1468	}
1469	}
1470	}
1471	}
1472	}
1473
1474	if (!error && turnAllowed != FA_TURN_NEVER) { // test if mirrored sequence has better relatives
1475	char *mirroredSequence = strdup(findRelsBySeq);
1476	long length = strlen(mirroredSequence);
1477	double bestMirroredScore = 0;
1478
1479	char T_or_U;
1480	error = GBT_determine_T_or_U(global_alignmentType, &T_or_U, "reverse-complement");
1481	if (!error) {
1482	GBT_reverseComplementNucSequence(mirroredSequence, length, T_or_U);
1483	error = familyFinder->searchFamily(mirroredSequence, FF_FORWARD, relativesToTest+1, 0); // @@@ make min_score configurable
1484	}
1485	if (!error) {
1486	#if defined(DEBUG)
1487	double lastScore = -1;
1488	#if defined(TRACE_RELATIVES)
1489	fprintf(stderr, "List of relatives used for '%s' (turned seq):\n", GBT_get_name_or_description(gb_toAlign));
1490	#endif // TRACE_RELATIVES
1491	#endif // DEBUG
1492	for (const FamilyList *fl = familyFinder->getFamilyList(); fl; fl = fl->next) {
1493	double thisScore = familyFinder->uses_rel_matches() ? fl->rel_matches : fl->matches;
1494	#if defined(DEBUG)
1495	// check whether family list is sorted correctly
1496	fa_assert(lastScore < 0 \|\| lastScore >= thisScore);
1497	lastScore = thisScore;
1498	#if defined(TRACE_RELATIVES)
1499	fprintf(stderr, "- %s (%5.2f)\n", fl->name, thisScore);
1500	#endif // TRACE_RELATIVES
1501	#endif // DEBUG
1502	if (thisScore >= bestMirroredScore) {
1503	if (strcmp(toAlignSequence->name(), fl->name)!=0) {
1504	if (GBT_find_species(gb_main, fl->name)) bestMirroredScore = thisScore; // @@@
1505	}
1506	}
1507	}
1508	}
1509
1510	int turnIt = 0;
1511	if (bestMirroredScore>bestScore) {
1512	if (turnAllowed==FA_TURN_INTERACTIVE) {
1513	const char *message;
1514	if (familyFinder->uses_rel_matches()) {
1515	message = GBS_global_string("'%s' seems to be the other way round (score: %.1f%%, score if turned: %.1f%%)",
1516	toAlignSequence->name(), bestScore100, bestMirroredScore100);
1517	}
1518	else {
1519	message = GBS_global_string("'%s' seems to be the other way round (score: %li, score if turned: %li)",
1520	toAlignSequence->name(), long(bestScore+.5), long(bestMirroredScore+.5));
1521	}
1522	turnIt = aw_question("fastali_turn_sequence", message, "Turn sequence,Leave sequence alone")==0;
1523	}
1524	else {
1525	fa_assert(turnAllowed == FA_TURN_ALWAYS);
1526	turnIt = 1;
1527	#if defined(TRACE_RELATIVES)
1528	fprintf(stderr, "Using turned sequence!\n");
1529	#endif // TRACE_RELATIVES
1530	}
1531	}
1532
1533	if (turnIt) { // write mirrored sequence
1534	GBDATA *gbd = GBT_find_sequence(gb_toAlign, alignment);
1535	GB_topSecurityLevel unsecured(gbd);
1536	error = GB_write_string(gbd, mirroredSequence);
1537	if (!error) {
1538	delete toAlignSequence;
1539	restart = true; // continue while loop
1540	}
1541	}
1542
1543	free(mirroredSequence);
1544	}
1545	}
1546	free(findRelsBySeq);
1547	}
1548
1549	if (!error) {
1550	if (!next_relatives) {
1551	char warning[200];
1552	sprintf(warning, "No relative found for '%s'", toAlignSequence->name());
1553	aw_message(warning);
1554	}
1555	else {
1556	// assuming relatives are sorted! (nearest to farthest)
1557
1558	// get data pointers
1559	typedef GBDATA *GBDATAP;
1560	GBDATAP *gb_reference = new GBDATAP[relSearch.maxRelatives];
1561
1562	{
1563	for (i=0; i<relSearch.maxRelatives && i<next_relatives; i++) {
1564	GBDATA *gb_species = GBT_find_species(gb_main, nearestRelative[i]);
1565	if (!gb_species) { // pt-server seems not up to date!
1566	error = species_not_found(nearestRelative[i]);
1567	break;
1568	}
1569
1570	GBDATA *gb_sequence = GBT_find_sequence(gb_species, alignment);
1571	if (gb_sequence) { // if relative has sequence data in the current alignment ..
1572	gb_reference[i] = gb_species;
1573	}
1574	else { // remove this relative
1575	free(nearestRelative[i]);
1576	for (int j = i+1; j<next_relatives; ++j) {
1577	nearestRelative[j-1] = nearestRelative[j];
1578	}
1579	next_relatives--;
1580	nearestRelative[next_relatives] = NULp;
1581	i--; // redo same index
1582	}
1583	}
1584
1585	// delete superfluous relatives
1586	for (; i<next_relatives; ++i) freenull(nearestRelative[i]);
1587
1588	if (next_relatives>relSearch.maxRelatives) {
1589	next_relatives = relSearch.maxRelatives;
1590	}
1591	}
1592
1593	// align
1594
1595	if (!error) {
1596	CompactedSubSequence *alignToSequence = readCompactedSequence(gb_reference[0], alignment, &error, NULp, NULp, ali_params.range);
1597	fa_assert(alignToSequence);
1598
1599	if (island_hopper) {
1600	GBDATA *gb_ref = GBT_find_sequence(gb_reference[0], alignment); // get reference sequence
1601	GBDATA *gb_align = GBT_find_sequence(gb_toAlign, alignment); // get sequence to align
1602
1603	if (gb_ref && gb_align) {
1604	long length_ref = GB_read_string_count(gb_ref);
1605	const char *data;
1606
1607	data = GB_read_char_pntr(gb_ref);
1608	island_hopper->set_ref_sequence(data);
1609
1610	data = GB_read_char_pntr(gb_align);
1611	island_hopper->set_toAlign_sequence(data);
1612
1613	island_hopper->set_alignment_length(length_ref);
1614	}
1615	}
1616
1617	{
1618	FastSearchSequence referenceFastSeq(*alignToSequence);
1619
1620	error = alignCompactedTo(toAlignSequence, &referenceFastSeq,
1621	max_seq_length, alignment, chksum,
1622	gb_toAlign, gb_reference[0], ali_params);
1623	}
1624
1625	if (error) {
1626	error = align_error(error, gb_toAlign, gb_reference[0]);
1627	}
1628	else {
1629	char *used_relatives = NULp;
1630
1631	if (unaligned_bases.is_empty()) {
1632	appendNameAndUsedBasePositions(&used_relatives, gb_reference[0], -1);
1633	}
1634	else {
1635	if (island_hopper) {
1636	appendNameAndUsedBasePositions(&used_relatives, gb_reference[0], -1);
1637	if (next_relatives>1) error = "Island hopping uses only one relative";
1638	}
1639	else {
1640	LooseBases loose;
1641	LooseBases loose_for_next_relative;
1642
1643	int unaligned_positions;
1644	{
1645	CompactedSubSequence *alignedSequence = readCompactedSequence(gb_toAlign, alignment, &error, NULp, NULp, ali_params.range);
1646
1647	unaligned_positions = loose.follow_ali_change_and_append(unaligned_bases, AliChange(toAlignSequence, alignedSequence));
1648	// now loose holds the unaligned (and recalculated) parts from last relative
1649	delete alignedSequence;
1650	}
1651
1652	if (!error) {
1653	int toalign_positions = toAlignSequence->length();
1654	if (unaligned_positions<toalign_positions) {
1655	appendNameAndUsedBasePositions(&used_relatives, gb_reference[0], toalign_positions-unaligned_positions);
1656	}
1657	}
1658
1659	for (i=1; i<next_relatives && !error; i++) {
1660	loose.append(loose_for_next_relative);
1661	int unaligned_positions_for_next = 0;
1662
1663	while (!loose.is_empty() && !error) {
1664	ExplicitRange partRange(intersection(loose.recall(), ali_params.range));
1665	CompactedSubSequence *alignToPart = readCompactedSequence(gb_reference[i], alignment, &error, NULp, NULp, partRange);
1666
1667	if (!error) {
1668	long part_chksum;
1669	CompactedSubSequence *toAlignPart = readCompactedSequence(gb_toAlign, alignment, &error, NULp, &part_chksum, partRange);
1670
1671	fa_assert(contradicted(error, toAlignPart));
1672
1673	if (!error) {
1674	AlignParams loose_ali_params = { ali_params.report, ali_params.showGapsMessages, partRange };
1675
1676	FastSearchSequence referenceFastSeq(*alignToPart);
1677	error = alignCompactedTo(toAlignPart, &referenceFastSeq,
1678	max_seq_length, alignment, part_chksum,
1679	gb_toAlign, gb_reference[i], loose_ali_params);
1680	if (!error) {
1681	CompactedSubSequence *alignedPart = readCompactedSequence(gb_toAlign, alignment, &error, NULp, NULp, partRange);
1682	if (!error) {
1683	unaligned_positions_for_next += loose_for_next_relative.follow_ali_change_and_append(unaligned_bases, AliChange(toAlignPart, alignedPart));
1684	}
1685	delete alignedPart;
1686	}
1687	}
1688	delete toAlignPart;
1689	}
1690	delete alignToPart;
1691	}
1692
1693	if (!error) {
1694	fa_assert(unaligned_positions_for_next <= unaligned_positions); // means: number of unaligned positions has increased by use of relative
1695	if (unaligned_positions_for_next<unaligned_positions) {
1696	appendNameAndUsedBasePositions(&used_relatives, gb_reference[i], unaligned_positions-unaligned_positions_for_next);
1697	unaligned_positions = unaligned_positions_for_next;
1698	}
1699	}
1700	}
1701	}
1702	}
1703
1704	if (!error) { // write used relatives to db-field
1705	error = GBT_write_string(gb_toAlign, "used_rels", used_relatives);
1706	}
1707	free(used_relatives);
1708	}
1709
1710	delete alignToSequence;
1711	}
1712
1713	delete [] gb_reference;
1714	}
1715	}
1716
1717	delete toAlignSequence;
1718
1719	for (i=0; i<next_relatives; i++) freenull(nearestRelative[i]);
1720	delete [] nearestRelative;
1721
1722	return error;
1723	}
1724
1725	// ------------------------
1726	// AlignmentReference
1727
1728	class AlignmentReference : virtual Noncopyable {
1729	GB_CSTR alignment;
1730	int max_seq_length;
1731	const AlignParams& ali_params;
1732
1733	public:
1734	AlignmentReference(GB_CSTR alignment_,
1735	int max_seq_length_,
1736	const AlignParams& ali_params_)
1737	: alignment(alignment_),
1738	max_seq_length(max_seq_length_),
1739	ali_params(ali_params_)
1740	{}
1741	virtual ~AlignmentReference() {}
1742
1743	virtual ARB_ERROR align_to(GBDATA *gb_toalign) const = 0;
1744
1745	GB_CSTR get_alignment() const { return alignment; }
1746	int get_max_seq_length() const { return max_seq_length; }
1747	const AlignParams& get_ali_params() const { return ali_params; }
1748	};
1749
1750
1751	// @@@ make alignTo a member of ExplicitReference (or of AlignmentReference)
1752	// @@@ let alignToGroupConsensus and alignToNextRelative use ExplicitReference
1753
1754
1755	class ExplicitReference: public AlignmentReference { // derived from a Noncopyable
1756	const FastSearchSequence *targetSequence;
1757	GBDATA *gb_alignTo;
1758
1759	public:
1760	ExplicitReference(GB_CSTR alignment_,
1761	const FastSearchSequence *targetSequence_,
1762	GBDATA *gb_alignTo_,
1763	int max_seq_length_,
1764	const AlignParams& ali_params_)
1765	: AlignmentReference(alignment_, max_seq_length_, ali_params_),
1766	targetSequence(targetSequence_),
1767	gb_alignTo(gb_alignTo_)
1768	{}
1769
1770	ARB_ERROR align_to(GBDATA *gb_toalign) const OVERRIDE {
1771	return alignTo(gb_toalign, get_alignment(), targetSequence, gb_alignTo, get_max_seq_length(), get_ali_params());
1772	}
1773	};
1774
1775	// @@@ make alignToGroupConsensus a member of ConsensusReference
1776
1777	class ConsensusReference: public AlignmentReference {
1778	Aligner_get_consensus_func get_consensus;
1779
1780	public:
1781	ConsensusReference(GB_CSTR alignment_,
1782	Aligner_get_consensus_func get_consensus_,
1783	int max_seq_length_,
1784	const AlignParams& ali_params_)
1785	: AlignmentReference(alignment_, max_seq_length_, ali_params_),
1786	get_consensus(get_consensus_)
1787	{}
1788
1789	ARB_ERROR align_to(GBDATA *gb_toalign) const OVERRIDE {
1790	return alignToGroupConsensus(gb_toalign, get_alignment(), get_consensus, get_max_seq_length(), get_ali_params());
1791	}
1792	};
1793
1794	// @@@ make alignToNextRelative a member of SearchRelativesReference
1795
1796	class SearchRelativesReference: public AlignmentReference {
1797	SearchRelativeParams& relSearch;
1798	FA_turn turnAllowed;
1799
1800	public:
1801	SearchRelativesReference(SearchRelativeParams& relSearch_,
1802	int max_seq_length_,
1803	FA_turn turnAllowed_,
1804	GB_CSTR alignment_,
1805	const AlignParams& ali_params_)
1806	: AlignmentReference(alignment_, max_seq_length_, ali_params_),
1807	relSearch(relSearch_),
1808	turnAllowed(turnAllowed_)
1809	{}
1810
1811	ARB_ERROR align_to(GBDATA *gb_toalign) const OVERRIDE {
1812	return alignToNextRelative(relSearch, get_max_seq_length(), turnAllowed, get_alignment(), gb_toalign, get_ali_params());
1813	}
1814	};
1815
1816
1817	// ----------------
1818	// Aligner
1819
1820	class Aligner : virtual Noncopyable {
1821	GBDATA *gb_main;
1822
1823	// define alignment target(s):
1824	FA_alignTarget alignWhat;
1825	GB_CSTR alignment; // name of alignment to use
1826	GB_CSTR toalign; // name of species to align (used if alignWhat == FA_CURRENT)
1827	Aligner_get_first_selected_species get_first_selected_species; // used if alignWhat == FA_SELECTED
1828	Aligner_get_next_selected_species get_next_selected_species; // --- "" ---
1829
1830	// define reference sequence(s):
1831	GB_CSTR reference; // name of reference species
1832	Aligner_get_consensus_func get_consensus; // function to get consensus seq
1833	SearchRelativeParams& relSearch; // params to search for relatives
1834
1835	// general params:
1836	FA_turn turnAllowed;
1837	const AlignParams& ali_params;
1838	int maxProtection; // protection level
1839
1840	// -------------------- new members
1841	int wasNotAllowedToAlign; // number of failures caused by wrong protection
1842	int err_count; // count errors
1843	bool continue_on_error; /* true -> run single alignments in separate transactions.
1844	* If one target fails, continue with rest.
1845	* false -> run all in one transaction
1846	* One fails -> all fail!
1847	*/
1848	FA_errorAction error_action;
1849
1850	typedef std::list<GBDATA*> GBDATAlist;
1851	GBDATAlist species_to_mark; // species that will be marked after aligning
1852
1853	ARB_ERROR alignToReference(GBDATA *gb_toalign, const AlignmentReference& ref);
1854	ARB_ERROR alignTargetsToReference(const AlignmentReference& ref, GBDATA *gb_species_data);
1855
1856	ARB_ERROR alignToExplicitReference(GBDATA *gb_species_data, int max_seq_length);
1857	ARB_ERROR alignToConsensus(GBDATA *gb_species_data, int max_seq_length);
1858	ARB_ERROR alignToRelatives(GBDATA *gb_species_data, int max_seq_length);
1859
1860	void triggerAction(GBDATA *gb_species, bool has_been_aligned) {
1861	bool mark = false;
1862	switch (error_action) {
1863	case FA_MARK_FAILED: mark = !has_been_aligned; break;
1864	case FA_MARK_ALIGNED: mark = has_been_aligned; break;
1865	case FA_NO_ACTION: mark = false; break;
1866	}
1867	if (mark) species_to_mark.push_back(gb_species);
1868	}
1869
1870	public:
1871
1872	// @@@ pass AlignmentReference from caller (replacing reference parameters)
1873
1874	Aligner(GBDATA *gb_main_,
1875
1876	// define alignment target(s):
1877	FA_alignTarget alignWhat_,
1878	GB_CSTR alignment_, // name of alignment to use
1879	GB_CSTR toalign_, // name of species to align (used if alignWhat == FA_CURRENT)
1880	Aligner_get_first_selected_species get_first_selected_species_, // used if alignWhat == FA_SELECTED
1881	Aligner_get_next_selected_species get_next_selected_species_, // --- "" ---
1882
1883	// define reference sequence(s):
1884	GB_CSTR reference_, // name of reference species
1885	Aligner_get_consensus_func get_consensus_, // function to get consensus seq
1886	SearchRelativeParams& relSearch_, // params to search for relatives
1887
1888	// general params:
1889	FA_turn turnAllowed_,
1890	const AlignParams& ali_params_,
1891	int maxProtection_, // protection level
1892	bool continue_on_error_,
1893	FA_errorAction error_action_)
1894	: gb_main(gb_main_),
1895	alignWhat(alignWhat_),
1896	alignment(alignment_),
1897	toalign(toalign_),
1898	get_first_selected_species(get_first_selected_species_),
1899	get_next_selected_species(get_next_selected_species_),
1900	reference(reference_),
1901	get_consensus(get_consensus_),
1902	relSearch(relSearch_),
1903	turnAllowed(turnAllowed_),
1904	ali_params(ali_params_),
1905	maxProtection(maxProtection_),
1906	wasNotAllowedToAlign(0),
1907	err_count(0),
1908	continue_on_error(continue_on_error_),
1909	error_action(continue_on_error ? error_action_ : FA_NO_ACTION)
1910	{
1911	gb_assert(alignment);
1912	}
1913
1914	ARB_ERROR run();
1915	};
1916
1917	ARB_ERROR Aligner::alignToReference(GBDATA *gb_toalign, const AlignmentReference& ref) {
1918	int myProtection;
1919	ARB_ERROR error;
1920	{
1921	GBDATA *gb_seq = GBT_find_sequence(gb_toalign, alignment);
1922	// if sequence not found (e.g. wrong alignment) => assume protection is low + let align_to() fail below
1923	myProtection = gb_seq ? GB_read_security_write(gb_seq) : 0;
1924	}
1925
1926	if (myProtection<=maxProtection) {
1927	// Depending on 'continue_on_error' we either
1928	// * stop aligning if an error occurs or
1929	// * run the alignment of each species in its own transaction, ignore but report errors and
1930	// optionally mark aligned or failed species.
1931
1932	if (continue_on_error) {
1933	fa_assert(GB_get_transaction_level(gb_main) == 1);
1934	error = GB_end_transaction(gb_main, error); // end global transaction
1935	}
1936
1937	if (!error) {
1938	error = GB_push_transaction(gb_main);
1939	if (!error) error = ref.align_to(gb_toalign);
1940	error = GB_end_transaction(gb_main, error);
1941
1942	if (error) err_count++;
1943	triggerAction(gb_toalign, !error);
1944	}
1945
1946	if (continue_on_error) {
1947	if (error) {
1948	GB_warning(error.deliver());
1949	error = NULp;
1950	}
1951	error = GB_begin_transaction(gb_main); // re-open global transaction
1952	}
1953	}
1954	else {
1955	wasNotAllowedToAlign++;
1956	triggerAction(gb_toalign, false);
1957	}
1958
1959	return error;
1960	}
1961
1962	ARB_ERROR Aligner::alignTargetsToReference(const AlignmentReference& ref, GBDATA *gb_species_data) {
1963	ARB_ERROR error;
1964
1965	fa_assert(GB_get_transaction_level(gb_main) == 1);
1966
1967	switch (alignWhat) {
1968	case FA_CURRENT: { // align one sequence
1969	fa_assert(toalign);
1970
1971	GBDATA *gb_toalign = GBT_find_species_rel_species_data(gb_species_data, toalign);
1972	if (!gb_toalign) {
1973	error = species_not_found(toalign);
1974	}
1975	else {
1976	currentSequenceNumber = overallSequenceNumber = 1;
1977	error = alignToReference(gb_toalign, ref);
1978	}
1979	break;
1980	}
1981	case FA_MARKED: { // align all marked sequences
1982	int count = GBT_count_marked_species(gb_main);
1983	GBDATA *gb_species = GBT_first_marked_species_rel_species_data(gb_species_data);
1984
1985	arb_progress progress("Aligning marked species", long(count));
1986	progress.auto_subtitles("Species");
1987
1988	currentSequenceNumber = 1;
1989	overallSequenceNumber = count;
1990
1991	while (gb_species && !error) {
1992	error = alignToReference(gb_species, ref);
1993	progress.inc_and_check_user_abort(error);
1994	gb_species = GBT_next_marked_species(gb_species);
1995	}
1996	break;
1997	}
1998	case FA_SELECTED: { // align all selected species
1999	int count;
2000	GBDATA *gb_species = get_first_selected_species(&count);
2001
2002
2003	currentSequenceNumber = 1;
2004	overallSequenceNumber = count;
2005
2006	if (!gb_species) {
2007	aw_message("There is no selected species!");
2008	}
2009	else {
2010	arb_progress progress("Aligning selected species", long(count));
2011	progress.auto_subtitles("Species");
2012
2013	while (gb_species && !error) {
2014	error = alignToReference(gb_species, ref);
2015	progress.inc_and_check_user_abort(error);
2016	gb_species = get_next_selected_species();
2017	}
2018	}
2019	break;
2020	}
2021	}
2022
2023	fa_assert(GB_get_transaction_level(gb_main) == 1);
2024	return error;
2025	}
2026
2027	ARB_ERROR Aligner::alignToExplicitReference(GBDATA *gb_species_data, int max_seq_length) {
2028	ARB_ERROR error;
2029	GBDATA *gb_reference = GBT_find_species_rel_species_data(gb_species_data, reference);
2030
2031	if (!gb_reference) {
2032	error = species_not_found(reference);
2033	}
2034	else {
2035	long referenceChksum;
2036	CompactedSubSequence *referenceSeq = readCompactedSequence(gb_reference, alignment, &error, NULp, &referenceChksum, ali_params.range);
2037
2038	if (island_hopper) {
2039	// @@@ setting island_hopper reference has to be done in called function (seems that it is NOT done for alignToConsensus and alignToRelatives). First get tests in place!
2040
2041	GBDATA *gb_seq = GBT_find_sequence(gb_reference, alignment); // get sequence
2042	if (gb_seq) {
2043	long length = GB_read_string_count(gb_seq);
2044	const char *data = GB_read_char_pntr(gb_seq);
2045
2046	island_hopper->set_ref_sequence(data);
2047	island_hopper->set_alignment_length(length);
2048	}
2049	}
2050
2051
2052	if (!error) {
2053	// @@@ do not pass FastSearchSequence to ExplicitReference, instead pass sequence and length (ExplicitReference shall create it itself)
2054
2055	FastSearchSequence referenceFastSeq(*referenceSeq);
2056	ExplicitReference target(alignment, &referenceFastSeq, gb_reference, max_seq_length, ali_params);
2057
2058	error = alignTargetsToReference(target, gb_species_data);
2059	}
2060	delete referenceSeq;
2061	}
2062	return error;
2063	}
2064
2065	ARB_ERROR Aligner::alignToConsensus(GBDATA *gb_species_data, int max_seq_length) {
2066	return alignTargetsToReference(ConsensusReference(alignment, get_consensus, max_seq_length, ali_params),
2067	gb_species_data);
2068	}
2069
2070	ARB_ERROR Aligner::alignToRelatives(GBDATA *gb_species_data, int max_seq_length) {
2071	return alignTargetsToReference(SearchRelativesReference(relSearch, max_seq_length, turnAllowed, alignment, ali_params),
2072	gb_species_data);
2073	}
2074
2075	ARB_ERROR Aligner::run() {
2076	fa_assert(GB_get_transaction_level(gb_main) == 0); // no open transaction allowed here!
2077	ARB_ERROR error = GB_push_transaction(gb_main);
2078
2079	// if neither 'reference' nor 'get_consensus' are specified -> use next relative for (each) sequence:
2080	bool search_by_pt_server = !reference && !get_consensus;
2081
2082	err_count = 0;
2083	wasNotAllowedToAlign = 0; // incremented for every sequence which has higher protection level (and was not aligned)
2084	species_to_mark.clear();
2085
2086	fa_assert(!reference \|\| !get_consensus); // can't do both modes
2087
2088	if (turnAllowed != FA_TURN_NEVER) {
2089	if ((ali_params.range.is_part()) \|\| !search_by_pt_server) {
2090	// if not selected 'Range/Whole sequence' or not selected 'Reference/Auto search..'
2091	turnAllowed = FA_TURN_NEVER; // then disable mirroring for the current call
2092	}
2093	}
2094
2095	if (!error) {
2096	global_alignmentType = GBT_get_alignment_type(gb_main, alignment);
2097	fa_assert(global_alignmentType != GB_AT_UNKNOWN);
2098
2099	if (search_by_pt_server) {
2100	GB_alignment_type pt_server_alignmentType = GBT_get_alignment_type(gb_main, relSearch.pt_server_alignment);
2101	if (pt_server_alignmentType == GB_AT_UNKNOWN) {
2102	error = GB_append_exportedError("failed to detect type of alignment to use for ptserver-search");
2103	}
2104	else if (pt_server_alignmentType != GB_AT_RNA && pt_server_alignmentType != GB_AT_DNA) {
2105	error = "pt_servers only support RNA/DNA sequences.\n"
2106	"In the aligner window you may specify a RNA/DNA alignment \n"
2107	"and use a pt_server build on that alignment.";
2108	}
2109	}
2110	}
2111
2112	if (!error) {
2113	GBDATA *gb_species_data = GBT_get_species_data(gb_main);
2114	int max_seq_length = GBT_get_alignment_len(gb_main, alignment);
2115	fa_assert(max_seq_length>0);
2116
2117	if (reference) error = alignToExplicitReference(gb_species_data, max_seq_length);
2118	else if (get_consensus) error = alignToConsensus(gb_species_data, max_seq_length);
2119	else error = alignToRelatives(gb_species_data, max_seq_length);
2120	}
2121
2122	ClustalV_exit();
2123	unaligned_bases.clear();
2124
2125	error = GB_end_transaction(gb_main, error); // close global transaction
2126
2127	if (wasNotAllowedToAlign>0) {
2128	const char *mess = GBS_global_string("%i species were not aligned (because of protection level)", wasNotAllowedToAlign);
2129	aw_message(mess);
2130	}
2131
2132	if (err_count) {
2133	aw_message_if(error);
2134	error = GBS_global_string("Aligner produced %i error%c", err_count, err_count==1 ? '\0' : 's');
2135	}
2136
2137	if (error_action != FA_NO_ACTION) {
2138	fa_assert(continue_on_error);
2139
2140	GB_transaction ta(gb_main);
2141	GBT_mark_all(gb_main, 0);
2142	for (GBDATAlist::iterator sp = species_to_mark.begin(); sp != species_to_mark.end(); ++sp) {
2143	GB_write_flag(*sp, 1);
2144	}
2145
2146	const char *whatsMarked = (error_action == FA_MARK_ALIGNED) ? "aligned" : "failed";
2147	size_t markCount = species_to_mark.size();
2148	if (markCount>0) {
2149	const char *msg = GBS_global_string("%zu %s species %s been marked",
2150	markCount,
2151	whatsMarked,
2152	(markCount == 1) ? "has" : "have");
2153	aw_message(msg);
2154	}
2155	}
2156
2157	return error;
2158	}
2159
2160	void FastAligner_start(AW_window aw, const AlignDataAccess data_access) {
2161	AW_root *root = aw->get_root();
2162	char *reference = NULp; // align against next relatives
2163	char *toalign = NULp; // align marked species
2164	ARB_ERROR error = NULp;
2165	int get_consensus = 0;
2166	int pt_server_id = -1;
2167
2168	Aligner_get_first_selected_species get_first_selected_species = NULp;
2169	Aligner_get_next_selected_species get_next_selected_species = NULp;
2170
2171	fa_assert(!island_hopper);
2172	if (root->awar(FA_AWAR_USE_ISLAND_HOPPING)->read_int()) {
2173	island_hopper = new IslandHopping;
2174	if (root->awar(FA_AWAR_USE_SECONDARY)->read_int()) {
2175	char *helix_string = data_access->getHelixString();
2176	if (helix_string) {
2177	island_hopper->set_helix(helix_string);
2178	free(helix_string);
2179	}
2180	else {
2181	error = "Warning: No HELIX found. Can't use secondary structure";
2182	}
2183	}
2184
2185	if (!error) {
2186	island_hopper->set_parameters(root->awar(FA_AWAR_ESTIMATE_BASE_FREQ)->read_int(),
2187	root->awar(FA_AWAR_BASE_FREQ_T)->read_float(),
2188	root->awar(FA_AWAR_BASE_FREQ_C)->read_float(),
2189	root->awar(FA_AWAR_BASE_FREQ_A)->read_float(),
2190	root->awar(FA_AWAR_BASE_FREQ_C)->read_float(),
2191	root->awar(FA_AWAR_SUBST_PARA_CT)->read_float(),
2192	root->awar(FA_AWAR_SUBST_PARA_AT)->read_float(),
2193	root->awar(FA_AWAR_SUBST_PARA_GT)->read_float(),
2194	root->awar(FA_AWAR_SUBST_PARA_AC)->read_float(),
2195	root->awar(FA_AWAR_SUBST_PARA_CG)->read_float(),
2196	root->awar(FA_AWAR_SUBST_PARA_AG)->read_float(),
2197	root->awar(FA_AWAR_EXPECTED_DISTANCE)->read_float(),
2198	root->awar(FA_AWAR_STRUCTURE_SUPPLEMENT)->read_float(),
2199	root->awar(FA_AWAR_GAP_A)->read_float(),
2200	root->awar(FA_AWAR_GAP_B)->read_float(),
2201	root->awar(FA_AWAR_GAP_C)->read_float(),
2202	root->awar(FA_AWAR_THRESHOLD)->read_float()
2203	);
2204	}
2205	}
2206
2207	FA_alignTarget alignWhat = static_cast<FA_alignTarget>(root->awar(FA_AWAR_TO_ALIGN)->read_int());
2208	if (!error) {
2209	switch (alignWhat) {
2210	case FA_CURRENT: { // align current species
2211	toalign = root->awar(AWAR_SPECIES_NAME)->read_string();
2212	break;
2213	}
2214	case FA_MARKED: { // align marked species
2215	break;
2216	}
2217	case FA_SELECTED: { // align selected species
2218	get_first_selected_species = data_access->get_first_selected_species;
2219	get_next_selected_species = data_access->get_next_selected_species;
2220	break;
2221	}
2222	default: {
2223	fa_assert(0);
2224	break;
2225	}
2226	}
2227
2228	switch (static_cast<FA_reference>(root->awar(FA_AWAR_REFERENCE)->read_int())) {
2229	case FA_REF_EXPLICIT: // align against specified species
2230	reference = root->awar(FA_AWAR_REFERENCE_NAME)->read_string();
2231	break;
2232
2233	case FA_REF_CONSENSUS: // align against group consensus
2234	if (data_access->get_group_consensus) {
2235	get_consensus = 1;
2236	}
2237	else {
2238	error = "Can't get group consensus here.";
2239	}
2240	break;
2241
2242	case FA_REF_RELATIVES: // align against species searched via pt_server
2243	pt_server_id = root->awar(AWAR_PT_SERVER)->read_int();
2244	if (pt_server_id<0) {
2245	error = "No pt_server selected";
2246	}
2247	break;
2248
2249	default: fa_assert(0);
2250	break;
2251	}
2252	}
2253
2254	RangeList ranges;
2255	bool autoRestrictRange4nextRelSearch = true;
2256
2257	if (!error) {
2258	switch (static_cast<FA_range>(root->awar(FA_AWAR_RANGE)->read_int())) {
2259	case FA_WHOLE_SEQUENCE:
2260	autoRestrictRange4nextRelSearch = false;
2261	ranges.add(PosRange::whole());
2262	break;
2263
2264	case FA_AROUND_CURSOR: {
2265	int curpos = root->awar(AWAR_CURSOR_POSITION_LOCAL)->read_int();
2266	int size = root->awar(FA_AWAR_AROUND)->read_int();
2267
2268	ranges.add(PosRange(curpos-size, curpos+size));
2269	break;
2270	}
2271	case FA_SELECTED_RANGE: {
2272	PosRange range;
2273	if (!data_access->get_selected_range(range)) {
2274	error = "There is no selected species!";
2275	}
2276	else {
2277	ranges.add(range);
2278	}
2279	break;
2280	}
2281
2282	case FA_SAI_MULTI_RANGE: {
2283	GB_transaction ta(data_access->gb_main);
2284
2285	char *sai_name = root->awar(FA_AWAR_SAI_RANGE_NAME)->read_string();
2286	char *aliuse = GBT_get_default_alignment(data_access->gb_main);
2287	fa_assert(aliuse);
2288
2289	GBDATA *gb_sai = GBT_expect_SAI(data_access->gb_main, sai_name);
2290	if (!gb_sai) error = GB_await_error();
2291	else {
2292	GBDATA *gb_data = GBT_find_sequence(gb_sai, aliuse);
2293	if (!gb_data) {
2294	error = GB_have_error()
2295	? GB_await_error()
2296	: GBS_global_string("SAI '%s' has no data in alignment '%s'", sai_name, aliuse);
2297	}
2298	else {
2299	char *sai_data = GB_read_string(gb_data); // @@@ NOT_ALL_SAI_HAVE_DATA
2300	char *set_bits = root->awar(FA_AWAR_SAI_RANGE_CHARS)->read_string();
2301
2302	ranges = build_RangeList_from_string(sai_data, set_bits, false);
2303
2304	free(set_bits);
2305	free(sai_data);
2306	}
2307	}
2308	free(aliuse);
2309	free(sai_name);
2310	break;
2311	}
2312	}
2313	}
2314
2315	if (!error) {
2316	const char *alignment_name = data_access->alignment_name.c_str();
2317	for (RangeList::iterator r = ranges.begin(); r != ranges.end() && !error; ++r) {
2318	PosRange range = *r;
2319
2320	GBDATA *gb_main = data_access->gb_main;
2321	long alignment_length;
2322	{
2323	GB_transaction ta(gb_main);
2324	alignment_length = GBT_get_alignment_len(gb_main, alignment_name);
2325	fa_assert(alignment_length>0);
2326	}
2327
2328	char *pt_server_alignment = root->awar(FA_AWAR_PT_SERVER_ALIGNMENT)->read_string();
2329	PosRange relRange = PosRange::whole(); // unrestricted!
2330
2331	if (autoRestrictRange4nextRelSearch) {
2332	AW_awar *awar_relrange = root->awar(FA_AWAR_RELATIVE_RANGE);
2333	const char *relrange = awar_relrange->read_char_pntr();
2334	if (relrange[0]) {
2335	int region_plus = atoi(relrange);
2336
2337	fa_assert(range.is_part());
2338
2339	relRange = PosRange(range.start()-region_plus, range.end()+region_plus); // restricted
2340	awar_relrange->write_as_string(GBS_global_string("%i", region_plus)); // set awar to detected value (avoid misbehavior when it contains ' ' or similar)
2341	}
2342	}
2343
2344	if (island_hopper) {
2345	island_hopper->set_range(ExplicitRange(range, alignment_length));
2346	range = PosRange::whole();
2347	}
2348
2349	SearchRelativeParams relSearch(new PT_FamilyFinder(gb_main,
2350	pt_server_id,
2351	root->awar(AWAR_NN_OLIGO_LEN)->read_int(),
2352	root->awar(AWAR_NN_MISMATCHES)->read_int(),
2353	root->awar(AWAR_NN_FAST_MODE)->read_int(),
2354	root->awar(AWAR_NN_REL_MATCHES)->read_int(),
2355	RSS_BOTH_MIN), // old scaling as b4 [8520] @@@ make configurable
2356	pt_server_alignment,
2357	root->awar(FA_AWAR_NEXT_RELATIVES)->read_int());
2358
2359	relSearch.getFamilyFinder()->restrict_2_region(relRange);
2360
2361	struct AlignParams ali_params = {
2362	static_cast<FA_report>(root->awar(FA_AWAR_REPORT)->read_int()),
2363	bool(root->awar(FA_AWAR_SHOW_GAPS_MESSAGES)->read_int()),
2364	range
2365	};
2366
2367	{
2368	arb_progress progress("FastAligner");
2369	progress.allow_title_reuse();
2370
2371	int cont_on_error = root->awar(FA_AWAR_CONTINUE_ON_ERROR)->read_int();
2372
2373	Aligner aligner(gb_main,
2374	alignWhat,
2375	alignment_name,
2376	toalign,
2377	get_first_selected_species,
2378	get_next_selected_species,
2379
2380	reference,
2381	get_consensus ? data_access->get_group_consensus : NULp,
2382	relSearch,
2383
2384	static_cast<FA_turn>(root->awar(FA_AWAR_MIRROR)->read_int()),
2385	ali_params,
2386	root->awar(FA_AWAR_PROTECTION)->read_int(),
2387	cont_on_error,
2388	(FA_errorAction)root->awar(FA_AWAR_ACTION_ON_ERROR)->read_int());
2389	error = aligner.run();
2390
2391	if (error && cont_on_error) {
2392	aw_message_if(error);
2393	error = NULp;
2394	}
2395	}
2396
2397	free(pt_server_alignment);
2398	}
2399	}
2400
2401	if (island_hopper) {
2402	delete island_hopper;
2403	island_hopper = NULp;
2404	}
2405
2406	if (toalign) free(toalign);
2407	aw_message_if(error);
2408	if (data_access->do_refresh) data_access->refresh_display();
2409	}
2410
2411	static void nullcb() { }
2412
2413	void FastAligner_create_variables(AW_root *root, AW_default db1) {
2414	root->awar_string(FA_AWAR_REFERENCE_NAME, "", db1);
2415
2416	root->awar_int(FA_AWAR_TO_ALIGN, FA_CURRENT, db1);
2417	root->awar_int(FA_AWAR_REFERENCE, FA_REF_EXPLICIT, db1);
2418	root->awar_int(FA_AWAR_RANGE, FA_WHOLE_SEQUENCE, db1);
2419
2420	AW_awar *ali_protect = root->awar_int(FA_AWAR_PROTECTION, 0, db1);
2421	if (ARB_in_novice_mode(root)) {
2422	ali_protect->write_int(0); // reset protection for noobs
2423	}
2424
2425	root->awar_int(FA_AWAR_AROUND, 25, db1);
2426	root->awar_int(FA_AWAR_MIRROR, FA_TURN_INTERACTIVE, db1);
2427	root->awar_int(FA_AWAR_REPORT, FA_NO_REPORT, db1);
2428	root->awar_int(FA_AWAR_SHOW_GAPS_MESSAGES, 1, db1);
2429	root->awar_int(FA_AWAR_CONTINUE_ON_ERROR, 1, db1);
2430	root->awar_int(FA_AWAR_ACTION_ON_ERROR, FA_NO_ACTION, db1);
2431	root->awar_int(FA_AWAR_USE_SECONDARY, 0, db1);
2432	root->awar_int(AWAR_PT_SERVER, 0, db1);
2433	root->awar_int(FA_AWAR_NEXT_RELATIVES, 1, db1)->set_minmax(1, 100);
2434
2435	root->awar_string(FA_AWAR_RELATIVE_RANGE, "", db1);
2436	root->awar_string(FA_AWAR_PT_SERVER_ALIGNMENT, root->awar(AWAR_DEFAULT_ALIGNMENT)->read_char_pntr(), db1);
2437
2438	root->awar_string(FA_AWAR_SAI_RANGE_NAME, "", db1);
2439	root->awar_string(FA_AWAR_SAI_RANGE_CHARS, "x1", db1);
2440
2441	// island hopping:
2442
2443	root->awar_int(FA_AWAR_USE_ISLAND_HOPPING, 0, db1);
2444
2445	root->awar_int(FA_AWAR_ESTIMATE_BASE_FREQ, 1, db1);
2446
2447	root->awar_float(FA_AWAR_BASE_FREQ_A, 0.25, db1);
2448	root->awar_float(FA_AWAR_BASE_FREQ_C, 0.25, db1);
2449	root->awar_float(FA_AWAR_BASE_FREQ_G, 0.25, db1);
2450	root->awar_float(FA_AWAR_BASE_FREQ_T, 0.25, db1);
2451
2452	root->awar_float(FA_AWAR_SUBST_PARA_AC, 1.0, db1);
2453	root->awar_float(FA_AWAR_SUBST_PARA_AG, 4.0, db1);
2454	root->awar_float(FA_AWAR_SUBST_PARA_AT, 1.0, db1);
2455	root->awar_float(FA_AWAR_SUBST_PARA_CG, 1.0, db1);
2456	root->awar_float(FA_AWAR_SUBST_PARA_CT, 4.0, db1);
2457	root->awar_float(FA_AWAR_SUBST_PARA_GT, 1.0, db1);
2458
2459	root->awar_float(FA_AWAR_EXPECTED_DISTANCE, 0.3, db1);
2460	root->awar_float(FA_AWAR_STRUCTURE_SUPPLEMENT, 0.5, db1);
2461	root->awar_float(FA_AWAR_THRESHOLD, 0.005, db1);
2462
2463	root->awar_float(FA_AWAR_GAP_A, 8.0, db1);
2464	root->awar_float(FA_AWAR_GAP_B, 4.0, db1);
2465	root->awar_float(FA_AWAR_GAP_C, 7.0, db1);
2466
2467	AWTC_create_common_next_neighbour_vars(root, makeRootCallback(nullcb));
2468	}
2469
2470	void FastAligner_set_align_current(AW_root *root, AW_default db1) {
2471	root->awar_int(FA_AWAR_TO_ALIGN, FA_CURRENT, db1);
2472	}
2473
2474	void FastAligner_set_reference_species(AW_root *root) {
2475	// sets the aligner reference species to current species
2476	char *specName = root->awar(AWAR_SPECIES_NAME)->read_string();
2477	root->awar(FA_AWAR_REFERENCE_NAME)->write_string(specName);
2478	free(specName);
2479	}
2480
2481	static AW_window create_island_hopping_window(AW_root root) {
2482	AW_window_simple *aws = new AW_window_simple;
2483
2484	aws->init(root, "ISLAND_HOPPING_PARA", "Parameters for Island Hopping");
2485	aws->load_xfig("faligner/islandhopping.fig");
2486
2487	aws->at("close");
2488	aws->callback(AW_POPDOWN);
2489	aws->create_button("CLOSE", "CLOSE", "O");
2490
2491	aws->at("help");
2492	aws->callback(makeHelpCallback("islandhopping.hlp"));
2493	aws->create_button("HELP", "HELP");
2494
2495	aws->at("use_secondary");
2496	aws->label("Use secondary structure (only for re-align)");
2497	aws->create_toggle(FA_AWAR_USE_SECONDARY);
2498
2499	aws->at("freq");
2500	aws->create_toggle_field(FA_AWAR_ESTIMATE_BASE_FREQ, "Base freq.");
2501	aws->insert_default_toggle("Estimate", "E", 1);
2502	aws->insert_toggle("Define here: ", "D", 0);
2503	aws->update_toggle_field();
2504
2505	aws->at("freq_a"); aws->label("A:"); aws->create_input_field(FA_AWAR_BASE_FREQ_A, 4);
2506	aws->at("freq_c"); aws->label("C:"); aws->create_input_field(FA_AWAR_BASE_FREQ_C, 4);
2507	aws->at("freq_g"); aws->label("G:"); aws->create_input_field(FA_AWAR_BASE_FREQ_G, 4);
2508	aws->at("freq_t"); aws->label("T:"); aws->create_input_field(FA_AWAR_BASE_FREQ_T, 4);
2509
2510	int xpos[4], ypos[4];
2511	{
2512	aws->button_length(1);
2513
2514	int dummy;
2515	aws->at("h_a"); aws->get_at_position(&xpos[0], &dummy); aws->create_button(NULp, "A");
2516	aws->at("h_c"); aws->get_at_position(&xpos[1], &dummy); aws->create_button(NULp, "C");
2517	aws->at("h_g"); aws->get_at_position(&xpos[2], &dummy); aws->create_button(NULp, "G");
2518	aws->at("h_t"); aws->get_at_position(&xpos[3], &dummy); aws->create_button(NULp, "T");
2519
2520	aws->at("v_a"); aws->get_at_position(&dummy, &ypos[0]); aws->create_button(NULp, "A");
2521	aws->at("v_c"); aws->get_at_position(&dummy, &ypos[1]); aws->create_button(NULp, "C");
2522	aws->at("v_g"); aws->get_at_position(&dummy, &ypos[2]); aws->create_button(NULp, "G");
2523	aws->at("v_t"); aws->get_at_position(&dummy, &ypos[3]); aws->create_button(NULp, "T");
2524	}
2525
2526	aws->at("subst"); aws->create_button(NULp, "Substitution rate parameters:");
2527
2528	#define XOFF -25
2529	#define YOFF 0
2530
2531	aws->at(xpos[1]+XOFF, ypos[0]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_AC, 4);
2532	aws->at(xpos[2]+XOFF, ypos[0]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_AG, 4);
2533	aws->at(xpos[3]+XOFF, ypos[0]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_AT, 4);
2534	aws->at(xpos[2]+XOFF, ypos[1]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_CG, 4);
2535	aws->at(xpos[3]+XOFF, ypos[1]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_CT, 4);
2536	aws->at(xpos[3]+XOFF, ypos[2]+YOFF); aws->create_input_field(FA_AWAR_SUBST_PARA_GT, 4);
2537
2538	#undef XOFF
2539	#undef YOFF
2540
2541	aws->label_length(22);
2542
2543	aws->at("dist");
2544	aws->label("Expected distance");
2545	aws->create_input_field(FA_AWAR_EXPECTED_DISTANCE, 5);
2546
2547	aws->at("supp");
2548	aws->label("Structure supplement");
2549	aws->create_input_field(FA_AWAR_STRUCTURE_SUPPLEMENT, 5);
2550
2551	aws->at("thres");
2552	aws->label("Threshold");
2553	aws->create_input_field(FA_AWAR_THRESHOLD, 5);
2554
2555	aws->label_length(10);
2556
2557	aws->at("gapA");
2558	aws->label("Gap A");
2559	aws->create_input_field(FA_AWAR_GAP_A, 5);
2560
2561	aws->at("gapB");
2562	aws->label("Gap B");
2563	aws->create_input_field(FA_AWAR_GAP_B, 5);
2564
2565	aws->at("gapC");
2566	aws->label("Gap C");
2567	aws->create_input_field(FA_AWAR_GAP_C, 5);
2568
2569	return aws;
2570	}
2571
2572	static AW_window create_family_settings_window(AW_root root) {
2573	static AW_window_simple *aws = NULp;
2574
2575	if (!aws) {
2576	aws = new AW_window_simple;
2577
2578	aws->init(root, "FAMILY_PARAMS", "Family search parameters");
2579	aws->load_xfig("faligner/family_settings.fig");
2580
2581	aws->at("close");
2582	aws->callback(AW_POPDOWN);
2583	aws->create_button("CLOSE", "CLOSE", "O");
2584
2585	aws->at("help");
2586	aws->callback(makeHelpCallback("next_neighbours_common.hlp"));
2587	aws->create_button("HELP", "HELP");
2588
2589	aws->auto_space(5, 5);
2590	AWTC_create_common_next_neighbour_fields(aws, 200);
2591	}
2592
2593	return aws;
2594	}
2595
2596	static AWT_config_mapping_def aligner_config_mapping[] = {
2597	{ FA_AWAR_USE_ISLAND_HOPPING, "island" },
2598	{ FA_AWAR_TO_ALIGN, "target" },
2599	{ FA_AWAR_REFERENCE, "ref" },
2600	{ FA_AWAR_REFERENCE_NAME, "refname" },
2601	{ FA_AWAR_RELATIVE_RANGE, "relrange" },
2602	{ FA_AWAR_NEXT_RELATIVES, "relatives" },
2603	{ FA_AWAR_PT_SERVER_ALIGNMENT, "ptali" },
2604
2605	// relative-search specific parameters from subwindow (create_family_settings_window)
2606	// same as ../DB_UI/ui_species.cxx@RELATIVES_CONFIG
2607	{ AWAR_NN_OLIGO_LEN, "oligolen" },
2608	{ AWAR_NN_MISMATCHES, "mismatches" },
2609	{ AWAR_NN_FAST_MODE, "fastmode" },
2610	{ AWAR_NN_REL_MATCHES, "relmatches" },
2611	{ AWAR_NN_REL_SCALING, "relscaling" },
2612
2613	// island-hopping parameters (create_island_hopping_window)
2614	{ FA_AWAR_USE_SECONDARY, "use2nd" },
2615	{ FA_AWAR_ESTIMATE_BASE_FREQ, "estbasefreq" },
2616	{ FA_AWAR_BASE_FREQ_A, "freq_a" },
2617	{ FA_AWAR_BASE_FREQ_C, "freq_c" },
2618	{ FA_AWAR_BASE_FREQ_G, "freq_g" },
2619	{ FA_AWAR_BASE_FREQ_T, "freq_t" },
2620	{ FA_AWAR_SUBST_PARA_AC, "subst_ac" },
2621	{ FA_AWAR_SUBST_PARA_AG, "subst_ag" },
2622	{ FA_AWAR_SUBST_PARA_AT, "subst_at" },
2623	{ FA_AWAR_SUBST_PARA_CG, "subst_cg" },
2624	{ FA_AWAR_SUBST_PARA_CT, "subst_ct" },
2625	{ FA_AWAR_SUBST_PARA_GT, "subst_gt" },
2626	{ FA_AWAR_EXPECTED_DISTANCE, "distance" },
2627	{ FA_AWAR_STRUCTURE_SUPPLEMENT, "supplement" },
2628	{ FA_AWAR_THRESHOLD, "threshold" },
2629	{ FA_AWAR_GAP_A, "gap_a" },
2630	{ FA_AWAR_GAP_B, "gap_b" },
2631	{ FA_AWAR_GAP_C, "gap_c" },
2632
2633	{ NULp, NULp }
2634	};
2635
2636	AW_window FastAligner_create_window(AW_root root, const AlignDataAccess *data_access) {
2637	AW_window_simple *aws = new AW_window_simple;
2638
2639	aws->init(root, "INTEGRATED_ALIGNERS", INTEGRATED_ALIGNERS_TITLE);
2640	aws->load_xfig("faligner/faligner.fig");
2641
2642	aws->label_length(10);
2643	aws->button_length(10);
2644
2645	aws->at("close");
2646	aws->callback(AW_POPDOWN);
2647	aws->create_button("CLOSE", "CLOSE", "O");
2648
2649	aws->at("help");
2650	aws->callback(makeHelpCallback("faligner.hlp"));
2651	aws->create_button("HELP", "HELP");
2652
2653	aws->at("aligner");
2654	aws->create_toggle_field(FA_AWAR_USE_ISLAND_HOPPING, "Aligner");
2655	aws->insert_default_toggle("Fast aligner", "F", 0);
2656	aws->sens_mask(AWM_EXP);
2657	aws->insert_toggle ("Island Hopping", "I", 1);
2658	aws->sens_mask(AWM_ALL);
2659	aws->update_toggle_field();
2660
2661	aws->button_length(12);
2662	aws->at("island_para");
2663	aws->callback(create_island_hopping_window);
2664	aws->sens_mask(AWM_EXP);
2665	aws->create_button("island_para", "Parameters", "");
2666	aws->sens_mask(AWM_ALL);
2667
2668	aws->button_length(10);
2669
2670	aws->at("rev_compl");
2671	aws->callback(makeWindowCallback(build_reverse_complement, data_access));
2672	aws->create_button("reverse_complement", "Turn now!", "");
2673
2674	aws->at("what");
2675	aws->create_toggle_field(FA_AWAR_TO_ALIGN, "Align what?");
2676	aws->insert_toggle ("Current Species:", "A", FA_CURRENT);
2677	aws->insert_default_toggle("Marked Species", "M", FA_MARKED);
2678	aws->insert_toggle ("Selected Species", "S", FA_SELECTED);
2679	aws->update_toggle_field();
2680
2681	aws->at("swhat");
2682	aws->create_input_field(AWAR_SPECIES_NAME, 2);
2683
2684	aws->at("against");
2685	aws->create_toggle_field(FA_AWAR_REFERENCE, "Reference");
2686	aws->insert_toggle ("Species by name:", "S", FA_REF_EXPLICIT);
2687	aws->insert_toggle ("Group consensus", "K", FA_REF_CONSENSUS);
2688	aws->insert_default_toggle("Auto search by pt_server:", "A", FA_REF_RELATIVES);
2689	aws->update_toggle_field();
2690
2691	aws->at("sagainst");
2692	aws->create_input_field(FA_AWAR_REFERENCE_NAME, 2);
2693
2694	aws->at("copy");
2695	aws->callback(RootAsWindowCallback::simple(FastAligner_set_reference_species));
2696	aws->create_button("Copy", "Copy", "");
2697
2698	aws->label_length(0);
2699	aws->at("pt_server");
2700	awt_create_PTSERVER_selection_button(aws, AWAR_PT_SERVER);
2701
2702	aws->label_length(23);
2703	aws->at("relrange");
2704	aws->label("Data from range only, plus");
2705	aws->create_input_field(FA_AWAR_RELATIVE_RANGE, 3);
2706
2707	aws->at("relatives");
2708	aws->label("Number of relatives to use");
2709	aws->create_input_field(FA_AWAR_NEXT_RELATIVES, 3);
2710
2711	aws->label_length(9);
2712	aws->at("use_ali");
2713	aws->label("Alignment");
2714	aws->create_input_field(FA_AWAR_PT_SERVER_ALIGNMENT, 12);
2715
2716	aws->at("relSett");
2717	aws->callback(create_family_settings_window);
2718	aws->create_autosize_button("Settings", "More settings", "");
2719
2720	// Range
2721
2722	aws->label_length(10);
2723	aws->at("range");
2724	aws->create_toggle_field(FA_AWAR_RANGE, "Range");
2725	aws->insert_default_toggle("Whole sequence", "", FA_WHOLE_SEQUENCE);
2726	aws->insert_toggle ("Positions around cursor: ", "", FA_AROUND_CURSOR);
2727	aws->insert_toggle ("Selected range", "", FA_SELECTED_RANGE);
2728	aws->insert_toggle ("Multi-Range by SAI", "", FA_SAI_MULTI_RANGE);
2729	aws->update_toggle_field();
2730
2731	aws->at("around");
2732	aws->create_input_field(FA_AWAR_AROUND, 2);
2733
2734	aws->at("sai");
2735	awt_create_SAI_selection_button(data_access->gb_main, aws, FA_AWAR_SAI_RANGE_NAME);
2736
2737	aws->at("rchars");
2738	aws->create_input_field(FA_AWAR_SAI_RANGE_CHARS, 2);
2739
2740	// Protection
2741
2742	aws->at("protection");
2743	aws->label("Protection");
2744	aws->create_option_menu(FA_AWAR_PROTECTION);
2745	aws->insert_default_option("0", NULp, 0);
2746	aws->insert_option ("1", NULp, 1);
2747	aws->insert_option ("2", NULp, 2);
2748	aws->insert_option ("3", NULp, 3);
2749	aws->insert_option ("4", NULp, 4);
2750	aws->insert_option ("5", NULp, 5);
2751	aws->insert_option ("6", NULp, 6);
2752	aws->update_option_menu();
2753
2754	// MirrorCheck
2755
2756	aws->at("mirror");
2757	aws->label("Turn check");
2758	aws->create_option_menu(FA_AWAR_MIRROR);
2759	aws->insert_option ("Never turn sequence", "", FA_TURN_NEVER);
2760	aws->insert_default_option("User acknowledgment ", "", FA_TURN_INTERACTIVE);
2761	aws->insert_option ("Automatically turn sequence", "", FA_TURN_ALWAYS);
2762	aws->update_option_menu();
2763
2764	// Report
2765
2766	aws->at("insert");
2767	aws->label("Report");
2768	aws->create_option_menu(FA_AWAR_REPORT);
2769	aws->insert_option ("No report", "", FA_NO_REPORT);
2770	aws->sens_mask(AWM_EXP);
2771	aws->insert_default_option("Report to temporary entries", "", FA_TEMP_REPORT);
2772	aws->insert_option ("Report to resident entries", "", FA_REPORT);
2773	aws->sens_mask(AWM_ALL);
2774	aws->update_option_menu();
2775
2776	aws->at("gaps");
2777	aws->create_toggle(FA_AWAR_SHOW_GAPS_MESSAGES);
2778
2779	aws->at("continue");
2780	aws->create_toggle(FA_AWAR_CONTINUE_ON_ERROR);
2781
2782	aws->at("on_failure");
2783	aws->label("On failure");
2784	aws->create_option_menu(FA_AWAR_ACTION_ON_ERROR);
2785	aws->insert_default_option("do nothing", "", FA_NO_ACTION);
2786	aws->insert_option ("mark failed", "", FA_MARK_FAILED);
2787	aws->insert_option ("mark aligned", "", FA_MARK_ALIGNED);
2788	aws->update_option_menu();
2789
2790	aws->at("align");
2791	aws->callback(makeWindowCallback(FastAligner_start, data_access));
2792	aws->highlight();
2793	aws->create_button("GO", "GO", "G");
2794
2795	aws->at("config");
2796	AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, "aligner", aligner_config_mapping);
2797
2798	return aws;
2799	}
2800
2801	// --------------------------------------------------------------------------------
2802
2803	#ifdef UNIT_TESTS
2804
2805	#include <test_unit.h>
2806
2807	// ---------------------
2808	// OligoCounter
2809
2810	#include <map>
2811	#include <string>
2812
2813	using std::map;
2814	using std::string;
2815
2816	typedef map<string, size_t> OligoCount;
2817
2818	class OligoCounter {
2819	size_t oligo_len;
2820	size_t datasize;
2821
2822	mutable OligoCount occurrence;
2823
2824	static string removeGaps(const char *seq) {
2825	size_t len = strlen(seq);
2826	string nogaps;
2827	nogaps.reserve(len);
2828
2829	for (size_t p = 0; p<len; ++p) {
2830	char c = seq[p];
2831	if (!is_gap(c)) nogaps.append(1, c);
2832	}
2833	return nogaps;
2834	}
2835
2836	void count_oligos(const string& seq) {
2837	occurrence.clear();
2838	size_t max_pos = seq.length()-oligo_len;
2839	for (size_t p = 0; p <= max_pos; ++p) {
2840	string oligo(seq, p, oligo_len);
2841	occurrence[oligo]++;
2842	}
2843	}
2844
2845	public:
2846	OligoCounter()
2847	: oligo_len(0),
2848	datasize(0)
2849	{}
2850	OligoCounter(const char *seq, size_t oligo_len_)
2851	: oligo_len(oligo_len_)
2852	{
2853	string seq_nogaps = removeGaps(seq);
2854	datasize = seq_nogaps.length();
2855	count_oligos(seq_nogaps);
2856	}
2857
2858	size_t oligo_count(const char *oligo) {
2859	fa_assert(strlen(oligo) == oligo_len);
2860	return occurrence[oligo];
2861	}
2862
2863	size_t similarity_score(const OligoCounter& other) const {
2864	size_t score = 0;
2865	if (oligo_len == other.oligo_len) {
2866	for (OligoCount::const_iterator o = occurrence.begin(); o != occurrence.end(); ++o) {
2867	const string& oligo = o->first;
2868	size_t count = o->second;
2869
2870	score += min(count, other.occurrence[oligo]);
2871	}
2872	}
2873	return score;
2874	}
2875
2876	size_t getDataSize() const { return datasize; }
2877	};
2878
2879	void TEST_OligoCounter() {
2880	OligoCounter oc1("CCAGGT", 3);
2881	OligoCounter oc2("GGTCCA", 3);
2882	OligoCounter oc2_gaps("..GGT--CCA..", 3);
2883	OligoCounter oc3("AGGTCC", 3);
2884	OligoCounter oc4("AGGTCCAGG", 3);
2885
2886	TEST_EXPECT_EQUAL(oc1.oligo_count("CCA"), 1);
2887	TEST_EXPECT_ZERO(oc1.oligo_count("CCG"));
2888	TEST_EXPECT_EQUAL(oc4.oligo_count("AGG"), 2);
2889
2890	int sc1_2 = oc1.similarity_score(oc2);
2891	int sc2_1 = oc2.similarity_score(oc1);
2892	TEST_EXPECT_EQUAL(sc1_2, sc2_1);
2893
2894	int sc1_2gaps = oc1.similarity_score(oc2_gaps);
2895	TEST_EXPECT_EQUAL(sc1_2, sc1_2gaps);
2896
2897	int sc1_3 = oc1.similarity_score(oc3);
2898	int sc2_3 = oc2.similarity_score(oc3);
2899	int sc3_4 = oc3.similarity_score(oc4);
2900
2901	TEST_EXPECT_EQUAL(sc1_2, 2); // common oligos (CCA GGT)
2902	TEST_EXPECT_EQUAL(sc1_3, 2); // common oligos (AGG GGT)
2903	TEST_EXPECT_EQUAL(sc2_3, 3); // common oligos (GGT GTC TCC)
2904
2905	TEST_EXPECT_EQUAL(sc3_4, 4);
2906	}
2907
2908	// -------------------------
2909	// FakeFamilyFinder
2910
2911	class FakeFamilyFinder: public FamilyFinder { // derived from a Noncopyable
2912	// used by unit tests to detect next relatives instead of asking the pt-server
2913
2914	GBDATA *gb_main;
2915	string ali_name;
2916	map<string, OligoCounter> oligos_counted; // key = species name
2917	PosRange counted_for_range;
2918	size_t oligo_len;
2919
2920	public:
2921	FakeFamilyFinder(GBDATA *gb_main_, string ali_name_, bool rel_matches_, size_t oligo_len_)
2922	: FamilyFinder(rel_matches_, RSS_BOTH_MIN),
2923	gb_main(gb_main_),
2924	ali_name(ali_name_),
2925	counted_for_range(PosRange::whole()),
2926	oligo_len(oligo_len_)
2927	{}
2928
2929	GB_ERROR searchFamily(const char *sequence, FF_complement compl_mode, int max_results, double min_score) OVERRIDE {
2930	// 'sequence' has to contain full sequence or part corresponding to 'range'
2931
2932	TEST_EXPECT_EQUAL(compl_mode, FF_FORWARD); // not fit for other modes
2933
2934	delete_family_list();
2935
2936	OligoCounter seq_oligo_count(sequence, oligo_len);
2937
2938	if (range != counted_for_range) {
2939	oligos_counted.clear(); // forget results for different range
2940	counted_for_range = range;
2941	}
2942
2943	char *buffer = NULp;
2944	int buffersize = 0;
2945
2946	bool partial_match = range.is_part();
2947
2948	GB_transaction ta(gb_main);
2949	int results = 0;
2950
2951	for (GBDATA *gb_species = GBT_first_species(gb_main);
2952	gb_species && results<max_results;
2953	gb_species = GBT_next_species(gb_species))
2954	{
2955	string name = GBT_get_name_or_description(gb_species);
2956	if (oligos_counted.find(name) == oligos_counted.end()) {
2957	GBDATA *gb_data = GBT_find_sequence(gb_species, ali_name.c_str());
2958	const char *spec_seq = GB_read_char_pntr(gb_data);
2959
2960	if (partial_match) {
2961	int spec_seq_len = GB_read_count(gb_data);
2962	int range_len = ExplicitRange(range, spec_seq_len).size();
2963
2964	if (buffersize<range_len) {
2965	delete [] buffer;
2966	buffersize = range_len;
2967	buffer = new char[buffersize+1];
2968	}
2969
2970	range.copy_corresponding_part(buffer, spec_seq, spec_seq_len);
2971	oligos_counted[name] = OligoCounter(buffer, oligo_len);
2972	}
2973	else {
2974	oligos_counted[name] = OligoCounter(spec_seq, oligo_len);
2975	}
2976	}
2977
2978	const OligoCounter& spec_oligo_count = oligos_counted[name];
2979	size_t score = seq_oligo_count.similarity_score(spec_oligo_count);
2980
2981	if (score>=min_score) {
2982	FamilyList *newMember = new FamilyList;
2983
2984	newMember->name = strdup(name.c_str());
2985	newMember->matches = score;
2986	newMember->rel_matches = score/spec_oligo_count.getDataSize();
2987	newMember->next = NULp;
2988
2989	family_list = newMember->insertSortedBy_matches(family_list);
2990	results++;
2991	}
2992	}
2993
2994	delete [] buffer;
2995
2996	return NULp;
2997	}
2998	};
2999
3000	// ----------------------------
3001	// test_alignment_data
3002
3003	#include <arb_unit_test.h>
3004
3005	static const char *test_aliname = "ali_test";
3006
3007	static const char get_aligned_data_of(GBDATA gb_main, const char *species_name) {
3008	GB_transaction ta(gb_main);
3009	ARB_ERROR error;
3010	const char *data = NULp;
3011
3012	GBDATA *gb_species = GBT_find_species(gb_main, species_name);
3013	if (!gb_species) error = GB_await_error();
3014	else {
3015	GBDATA *gb_data = GBT_find_sequence(gb_species, test_aliname);
3016	if (!gb_data) error = GB_await_error();
3017	else {
3018	data = GB_read_char_pntr(gb_data);
3019	if (!data) error = GB_await_error();
3020	}
3021	}
3022
3023	TEST_EXPECT_NULL(error.deliver());
3024
3025	return data;
3026	}
3027
3028	static const char get_used_rels_for(GBDATA gb_main, const char *species_name) {
3029	GB_transaction ta(gb_main);
3030	const char *result = NULp;
3031	GBDATA *gb_species = GBT_find_species(gb_main, species_name);
3032	if (!gb_species) result = GBS_global_string("<No such species '%s'>", species_name);
3033	else {
3034	GBDATA *gb_used_rels = GB_search(gb_species, "used_rels", GB_FIND);
3035	if (!gb_used_rels) result = "<No such field 'used_rels'>";
3036	else result = GB_read_char_pntr(gb_used_rels);
3037	}
3038	return result;
3039	}
3040
3041	static GB_ERROR forget_used_relatives(GBDATA *gb_main) {
3042	GB_ERROR error = NULp;
3043	GB_transaction ta(gb_main);
3044	for (GBDATA *gb_species = GBT_first_species(gb_main);
3045	gb_species && !error;
3046	gb_species = GBT_next_species(gb_species))
3047	{
3048	GBDATA *gb_used_rels = GB_search(gb_species, "used_rels", GB_FIND);
3049	if (gb_used_rels) {
3050	error = GB_delete(gb_used_rels);
3051	}
3052	}
3053	return error;
3054	}
3055
3056
3057	#define ALIGNED_DATA_OF(name) get_aligned_data_of(gb_main, name)
3058	#define USED_RELS_FOR(name) get_used_rels_for(gb_main, name)
3059
3060	// ----------------------------------------
3061
3062	static GBDATA *selection_fake_gb_main = NULp;
3063	static GBDATA *selection_fake_gb_last = NULp;
3064
3065	static GBDATA fake_first_selected(int count) {
3066	selection_fake_gb_last = NULp;
3067	*count = 2; // we fake two species as selected ("c1" and "c2")
3068	return GBT_find_species(selection_fake_gb_main, "c1");
3069	}
3070	static GBDATA *fake_next_selected() {
3071	if (!selection_fake_gb_last) {
3072	selection_fake_gb_last = GBT_find_species(selection_fake_gb_main, "c2");
3073	}
3074	else {
3075	selection_fake_gb_last = NULp;
3076	}
3077	return selection_fake_gb_last;
3078	}
3079
3080	static char fake_get_consensus(const char, PosRange range) {
3081	const char *data = get_aligned_data_of(selection_fake_gb_main, "s1");
3082	if (range.is_whole()) return strdup(data);
3083	return ARB_strpartdup(data+range.start(), data+range.end());
3084	}
3085
3086	static void test_install_fakes(GBDATA *gb_main) {
3087	selection_fake_gb_main = gb_main;
3088	}
3089
3090
3091	// ----------------------------------------
3092
3093	static AlignParams test_ali_params = {
3094	FA_NO_REPORT,
3095	false, // showGapsMessages
3096	PosRange::whole()
3097	};
3098
3099	static AlignParams test_ali_params_partial = {
3100	FA_NO_REPORT,
3101	false, // showGapsMessages
3102	PosRange(25, 60)
3103	};
3104
3105	// ----------------------------------------
3106
3107	static struct arb_unit_test::test_alignment_data TestAlignmentData_TargetAndReferenceHandling[] = {
3108	{ 0, "s1", ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C..........." }, // reference
3109	{ 0, "s2", "AUCUCCUAAACCCAACCGUAGUUCGAAUUGAGGACUGUAACUC......................................................" }, // align single sequence (same data as reference)
3110	{ 1, "m1", "UAGAGGAUUUGGGUUGGCAUCAAGCUUAACUCCUGACAUUGAG......................................................" }, // align marked sequences.. (complement of reference)
3111	{ 1, "m2", "...UCCUAAACCAACCCGUAGUUCGAAUUGAGGACUGUAA........................................................." },
3112	{ 1, "m3", "AUC---UAAACCAACCCGUAGUUCGAAUUGAGGACUG---CUC......................................................" },
3113	{ 0, "c1", "AUCUCCUAAACCCAACC--------AAUUGAGGACUGUAACUC......................................................" }, // align selected sequences..
3114	{ 0, "c2", "AUCUCCU------AACCGUAGUUCCCCGAA------ACUGUAACUC..................................................." },
3115	{ 0, "r1", "GAGUUACAGUCCUCAAUUCGGGGAACUACGGUUGGGUUUAGGAGAU..................................................." }, // align by faked pt_server
3116	};
3117
3118	void TEST_Aligner_TargetAndReferenceHandling() {
3119	// performs some alignments to check logic of target and reference handling
3120
3121	GB_shell shell;
3122	ARB_ERROR error;
3123	GBDATA *gb_main = TEST_CREATE_DB(error, test_aliname, TestAlignmentData_TargetAndReferenceHandling, false);
3124
3125	TEST_EXPECT_NULL(error.deliver());
3126
3127	SearchRelativeParams search_relative_params(new FakeFamilyFinder(gb_main, test_aliname, false, 8),
3128	test_aliname,
3129	2);
3130
3131	test_install_fakes(gb_main);
3132	arb_suppress_progress silence;
3133
3134	// bool cont_on_err = true;
3135	bool cont_on_err = false;
3136
3137	TEST_EXPECT_EQUAL(GBT_count_marked_species(gb_main), 3); // we got 3 marked species
3138	{
3139	Aligner aligner(gb_main,
3140	FA_CURRENT,
3141	test_aliname,
3142	"s2", // toalign
3143	NULp, // get_first_selected_species
3144	NULp, // get_next_selected_species
3145	"s1", // reference species
3146	NULp, // get_consensus
3147	search_relative_params, // relative search
3148	FA_TURN_ALWAYS,
3149	test_ali_params,
3150	0,
3151	cont_on_err,
3152	FA_NO_ACTION);
3153	error = aligner.run();
3154	TEST_EXPECT_NULL(error.deliver());
3155	}
3156	TEST_EXPECT_EQUAL(GBT_count_marked_species(gb_main), 3); // we still got 3 marked species
3157	{
3158	Aligner aligner(gb_main,
3159	FA_MARKED,
3160	test_aliname,
3161	NULp, // toalign
3162	NULp, // get_first_selected_species
3163	NULp, // get_next_selected_species
3164	"s1", // reference species
3165	NULp, // get_consensus
3166	search_relative_params, // relative search
3167	FA_TURN_ALWAYS,
3168	test_ali_params,
3169	0,
3170	cont_on_err,
3171	FA_MARK_FAILED);
3172	error = aligner.run();
3173	TEST_EXPECT_NULL(error.deliver());
3174
3175	TEST_EXPECT(!cont_on_err \|\| GBT_count_marked_species(gb_main) == 0); // FA_MARK_FAILED (none failed -> none marked)
3176	}
3177	{
3178	Aligner aligner(gb_main,
3179	FA_SELECTED,
3180	test_aliname,
3181	NULp, // toalign
3182	fake_first_selected, // get_first_selected_species
3183	fake_next_selected, // get_next_selected_species
3184	NULp, // reference species
3185	fake_get_consensus, // get_consensus
3186	search_relative_params, // relative search
3187	FA_TURN_ALWAYS,
3188	test_ali_params,
3189	0,
3190	cont_on_err,
3191	FA_MARK_ALIGNED);
3192	error = aligner.run();
3193	TEST_EXPECT_NULL(error.deliver());
3194
3195	TEST_EXPECT(!cont_on_err \|\| GBT_count_marked_species(gb_main) == 2); // FA_MARK_ALIGNED (2 selected were aligned)
3196	}
3197	{
3198	Aligner aligner(gb_main,
3199	FA_CURRENT,
3200	test_aliname,
3201	"r1", // toalign
3202	NULp, // get_first_selected_species
3203	NULp, // get_next_selected_species
3204	NULp, // reference species
3205	NULp, // get_consensus
3206	search_relative_params, // relative search
3207	FA_TURN_ALWAYS,
3208	test_ali_params,
3209	0,
3210	cont_on_err,
3211	FA_MARK_ALIGNED);
3212
3213	error = aligner.run();
3214	TEST_EXPECT_NULL(error.deliver());
3215
3216	TEST_EXPECT(!cont_on_err \|\| GBT_count_marked_species(gb_main) == 1);
3217	}
3218
3219	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("s2"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C...........");
3220
3221	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m1"), ".......UAG--AGG-A------U-U-UGGGU-UG-G-C-A-U-CAA-GCU--------UAA-C-UCCUG-AC--A-UUGAG...............");
3222	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m2"), "..............U-C------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA................");
3223	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m3"), ".........A--U----------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-G----CU-C...........");
3224
3225	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-------------------AA-U-UGAGG-AC--U-GUAA-CU-C...........");
3226	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c2"), ".........A--UCU-C------C-U-AA---------C-C-G-UAG-UUC------------C-CCGAA-AC--U-GUAA-CU-C...........");
3227
3228	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("r1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUCCCC-----GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // here sequence shall be turned!
3229
3230
3231	TEST_EXPECT_EQUAL(USED_RELS_FOR("r1"), "s2:43, s1:1");
3232
3233	// ----------------------------------------------
3234	// now align all others vs next relative
3235
3236	search_relative_params.maxRelatives = 5;
3237	TEST_EXPECT_NO_ERROR(forget_used_relatives(gb_main));
3238
3239	int species_count = ARRAY_ELEMS(TestAlignmentData_TargetAndReferenceHandling);
3240	for (int sp = 0; sp<species_count; ++sp) {
3241	const char *name = TestAlignmentData_TargetAndReferenceHandling[sp].name;
3242	if (strcmp(name, "r1") != 0) { // skip "r1" (already done above)
3243	Aligner aligner(gb_main,
3244	FA_CURRENT,
3245	test_aliname,
3246	name, // toalign
3247	NULp, // get_first_selected_species
3248	NULp, // get_next_selected_species
3249	NULp, // reference species
3250	NULp, // get_consensus
3251	search_relative_params, // relative search
3252	FA_TURN_ALWAYS,
3253	test_ali_params,
3254	0,
3255	cont_on_err,
3256	FA_MARK_ALIGNED);
3257
3258	error = aligner.run();
3259	TEST_EXPECT_NULL(error.deliver());
3260
3261	TEST_EXPECT(!cont_on_err \|\| GBT_count_marked_species(gb_main) == 1);
3262	}
3263	}
3264
3265	TEST_EXPECT_EQUAL(USED_RELS_FOR("s1"), "s2");
3266	TEST_EXPECT_EQUAL(USED_RELS_FOR("s2"), "s1"); // same as done manually
3267	TEST_EXPECT_EQUAL(USED_RELS_FOR("m1"), "r1:42");
3268	TEST_EXPECT_EQUAL(USED_RELS_FOR("m2"), "m3");
3269	TEST_EXPECT_EQUAL(USED_RELS_FOR("m3"), "m2");
3270	TEST_EXPECT_EQUAL(USED_RELS_FOR("c1"), "r1");
3271	TEST_EXPECT_EQUAL(USED_RELS_FOR("c2"), "r1");
3272
3273	// range aligned below (see test_ali_params_partial)
3274	// "-------------------------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX------------------------------------"
3275	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("s1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // 1st aligning of 's1'
3276	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("s2"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above (again aligned vs 's1')
3277
3278	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m1"), ".........U--AGA-G------G---AUUUG-GG-U-U-G-G-CAU-CAAGCU-----UAA-C-UCCUG-AC--A-UUGAG---------------"); // changed; @@@ bug: no dots at end
3279
3280	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m2"), ".........U--C----------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-G----UA-A..........."); // changed (1st align vs 's1', this align vs 'm3')
3281	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m3"), ".........A--U----------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-G----CU-C..........."); // same_as_above (1st align vs 's1', this align vs 'm2')
3282	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-------------------AA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above
3283	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c2"), ".........A--UCU-C------C-U--------A-A-C-C-G-UAG-UUCCCC-----GA--------A-AC--U-GUAA-CU-C..........."); // changed
3284
3285	// --------------------------------------
3286	// test partial relative search
3287
3288	search_relative_params.getFamilyFinder()->restrict_2_region(test_ali_params_partial.range);
3289	TEST_EXPECT_NO_ERROR(forget_used_relatives(gb_main));
3290
3291	for (int sp = 0; sp<species_count; ++sp) {
3292	const char *name = TestAlignmentData_TargetAndReferenceHandling[sp].name;
3293	Aligner aligner(gb_main,
3294	FA_CURRENT,
3295	test_aliname,
3296	name, // toalign
3297	NULp, // get_first_selected_species
3298	NULp, // get_next_selected_species
3299	NULp, // reference species
3300	NULp, // get_consensus
3301	search_relative_params, // relative search
3302	FA_TURN_NEVER,
3303	test_ali_params_partial,
3304	0,
3305	cont_on_err,
3306	FA_MARK_ALIGNED);
3307
3308	error = aligner.run();
3309	TEST_EXPECT_NULL(error.deliver());
3310
3311	TEST_EXPECT(!cont_on_err \|\| GBT_count_marked_species(gb_main) == 1);
3312	}
3313
3314	TEST_EXPECT_EQUAL(USED_RELS_FOR("s1"), "s2");
3315	TEST_EXPECT_EQUAL(USED_RELS_FOR("s2"), "s1");
3316	TEST_EXPECT_EQUAL(USED_RELS_FOR("m1"), "r1"); // (not really differs)
3317	TEST_EXPECT_EQUAL(USED_RELS_FOR("m2"), "m3");
3318	TEST_EXPECT_EQUAL(USED_RELS_FOR("m3"), "m2");
3319	TEST_EXPECT_EQUAL(USED_RELS_FOR("c1"), "r1");
3320	TEST_EXPECT_EQUAL(USED_RELS_FOR("c2"), "r1");
3321	TEST_EXPECT_EQUAL(USED_RELS_FOR("r1"), "s2:20, c2:3");
3322
3323	// aligned range (see test_ali_params_partial)
3324	// "-------------------------XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX------------------------------------"
3325	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("s1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above
3326	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("s2"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above
3327
3328	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m1"), ".........U--AGA-G------G-A-UU-UG-GG-U-U-G-G-CAU-CAAGCU-----UAA-C-UCCUG-AC--A-UUGAG---------------"); // changed
3329	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m2"), ".........U--C----------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-G----UA-A..........."); // same_as_above
3330	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("m3"), ".........A--U----------C-U-AAACC-AA-C-C-C-G-UAG-UUC--------GAA-U-UGAGG-AC--U-G----CU-C..........."); // same_as_above
3331
3332	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-------------------AA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above
3333	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("c2"), ".........A--UCU-C------C---------UA-A-C-C-G-UAG-UUCCCC-----GA--------A-AC--U-GUAA-CU-C..........."); // changed
3334
3335	TEST_EXPECT_EQUAL(ALIGNED_DATA_OF("r1"), ".........A--UCU-C------C-U-AAACC-CA-A-C-C-G-UAG-UUCCCC-----GAA-U-UGAGG-AC--U-GUAA-CU-C..........."); // same_as_above
3336
3337	GB_close(gb_main);
3338	}
3339
3340	// ----------------------------------------
3341
3342	static struct arb_unit_test::test_alignment_data TestAlignmentData_checksumError[] = {
3343	{ 0, "MtnK1722", "...G-GGC-C-G............CCC-GG--------CAAUGGGGGCGGCCCGGCGGAC----GG--C-UCAGU-A---AAG-UCGUAACAA-GG-UAG-CCGU-AGGGGAA-CCUG-CGGC-UGGAUCACCUCC....." }, // gets aligned
3344	{ 0, "MhnFormi", "...A-CGA-U-C------------CUUCGG--------GGUCG-U-GG-C-GU-A--C------GG--C-UCAGU-A---AAG-UCGUAACAA-GG-UAG-CCGU-AGGGGAA-CCUG-CGGC-UGGAUCACCUCCU...." }, // 1st relative
3345	{ 0, "MhnT1916", "...A-CGA-A-C------------CUU-GU--------GUUCG-U-GG-C-GA-A--C------GG--C-UCAGU-A---AAG-UCGUAACAA-GG-UAG-CCGU-AGGGGAA-CCUG-CGGC-UGGAUCACCUCCU...." }, // next relative
3346	{ 0, "MthVanni", "...U-GGU-U-U------------C-------------GGCCA-U-GG-C-GG-A--C------GG--C-UCAUU-A---AAG-UCGUAACAA-GG-UAG-CCGU-AGGGGAA-CCUG-CGGC-UGGAUCACCUCC....." }, // next relative
3347	{ 0, "ThcCeler", "...G-GGG-C-G...CC-U---U--------GC--G--CGCAC-C-GG-C-GG-A--C------GG--C-UCAGU-A---AAG-UCGUAACAA-GG-UAG-CCGU-AGGGGAA-CCUA-CGGC-UCGAUCACCUCCU...." }, // next relative
3348	};
3349
3350	void TEST_SLOW_Aligner_checksumError() {
3351	// @@@ SLOW cause this often gets terminated in nightly builds
3352	// no idea why. normally it runs a few ms
3353
3354	// this produces an internal aligner error
3355
3356	GB_shell shell;
3357	ARB_ERROR error;
3358	GBDATA *gb_main = TEST_CREATE_DB(error, test_aliname, TestAlignmentData_checksumError, false);
3359
3360	SearchRelativeParams search_relative_params(new FakeFamilyFinder(gb_main, test_aliname, false, 8),
3361	test_aliname,
3362	10); // use up to 10 relatives
3363
3364	test_install_fakes(gb_main);
3365	arb_suppress_progress silence;
3366
3367	bool cont_on_err = true;
3368	if (!error) {
3369	Aligner aligner(gb_main,
3370	FA_CURRENT,
3371	test_aliname,
3372	"MtnK1722", // toalign
3373	NULp, // get_first_selected_species
3374	NULp, // get_next_selected_species
3375	NULp, // reference species
3376	NULp, // get_consensus
3377	search_relative_params, // relative search
3378	FA_TURN_ALWAYS,
3379	test_ali_params,
3380	0,
3381	cont_on_err,
3382	FA_MARK_ALIGNED);
3383
3384	error = aligner.run();
3385	}
3386	{
3387	GB_ERROR err = error.deliver();
3388	TEST_EXPECT_NULL__BROKEN(err, "Aligner produced 1 error");
3389	}
3390	TEST_EXPECT_EQUAL__BROKEN(USED_RELS_FOR("MtnK1722"), "???", "<No such field 'used_rels'>"); // subsequent failure
3391
3392	GB_close(gb_main);
3393	}
3394
3395	static const char *asstr(LooseBases& ub) {
3396	LooseBases tmp;
3397	while (!ub.is_empty()) tmp.memorize(ub.recall());
3398
3399	const char *result = "";
3400	while (!tmp.is_empty()) {
3401	ExplicitRange r = tmp.recall();
3402	result = GBS_global_string("%s %i/%i", result, r.start(), r.end());
3403	ub.memorize(r);
3404	}
3405	return result;
3406	}
3407
3408	void TEST_BASIC_UnalignedBases() {
3409	LooseBases ub;
3410	TEST_EXPECT(ub.is_empty());
3411	TEST_EXPECT_EQUAL(asstr(ub), "");
3412
3413	// test add+remove
3414	ub.memorize(ExplicitRange(5, 7));
3415	TEST_REJECT(ub.is_empty());
3416	TEST_EXPECT_EQUAL(asstr(ub), " 5/7");
3417
3418	TEST_EXPECT(ub.recall() == ExplicitRange(5, 7));
3419	TEST_EXPECT(ub.is_empty());
3420
3421	ub.memorize(ExplicitRange(2, 4));
3422	TEST_EXPECT_EQUAL(asstr(ub), " 2/4");
3423
3424	ub.memorize(ExplicitRange(4, 9));
3425	TEST_EXPECT_EQUAL(asstr(ub), " 2/4 4/9");
3426
3427	ub.memorize(ExplicitRange(8, 10));
3428	ub.memorize(ExplicitRange(11, 14));
3429	ub.memorize(ExplicitRange(12, 17));
3430	TEST_EXPECT_EQUAL(asstr(ub), " 2/4 4/9 8/10 11/14 12/17");
3431	TEST_EXPECT_EQUAL(asstr(ub), " 2/4 4/9 8/10 11/14 12/17"); // check asstr has no side-effect
3432
3433	{
3434	LooseBases toaddNrecalc;
3435
3436	CompactedSubSequence Old("ACGTACGT", 8, "name1");
3437	CompactedSubSequence New("--A-C--G-T--A-C-G-T", 19, "name2");
3438	// ---------------------- 0123456789012345678
3439
3440	toaddNrecalc.memorize(ExplicitRange(1, 7));
3441	toaddNrecalc.memorize(ExplicitRange(3, 5));
3442	TEST_EXPECT_EQUAL(asstr(toaddNrecalc), " 1/7 3/5");
3443
3444	ub.follow_ali_change_and_append(toaddNrecalc, AliChange(Old, New));
3445
3446	TEST_EXPECT_EQUAL(asstr(ub), " 3/18 8/15 2/4 4/9 8/10 11/14 12/17");
3447	TEST_EXPECT(toaddNrecalc.is_empty());
3448
3449	LooseBases selfRecalc;
3450	selfRecalc.follow_ali_change_and_append(ub, AliChange(New, New));
3451	TEST_EXPECT_EQUAL__BROKEN(asstr(selfRecalc),
3452	" 3/18 8/15 0/6 3/11 8/11 10/15 10/17", // wanted behavior?
3453	" 3/18 8/17 0/6 3/11 8/13 10/15 10/18"); // doc wrong behavior @@@ "8/17", "8/13", "10/18" are wrong
3454
3455	ub.follow_ali_change_and_append(selfRecalc, AliChange(New, Old));
3456	TEST_EXPECT_EQUAL__BROKEN(asstr(ub),
3457	" 1/7 3/5 0/1 1/3 3/3 4/5 4/6", // wanted behavior? (from wanted behavior above)
3458	" 1/7 3/7 0/2 1/4 3/5 4/6 4/7"); // document wrong behavior
3459	TEST_EXPECT_EQUAL__BROKEN(asstr(ub),
3460	" 1/7 3/6 0/1 1/3 3/4 4/5 4/7", // wanted behavior? (from wrong result above)
3461	" 1/7 3/7 0/2 1/4 3/5 4/6 4/7"); // document wrong behavior
3462	}
3463	}
3464
3465
3466	#endif // UNIT_TESTS
3467
3468

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source: trunk/SL/FAST_ALIGNER/fast_aligner.cxx

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