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chartable.cxx

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Last change on this file was 17651, checked in by westram, 6 years ago
reintegrates 'cleanup' into 'trunk' adds: log:branches/cleanup@17627:17650
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 44.3 KB

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1	// ================================================================= //
2	// //
3	// File : chartable.cxx //
4	// Purpose : count characters of multiple sequences //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// ================================================================= //
10
11	#include "chartable.h"
12
13	#include <arb_msg.h>
14	#include <arb_mem.h>
15	#include <iupac.h>
16	#include <arb_defs.h>
17	#include <smartptr.h>
18
19	#include <cctype>
20
21	#define CONSENSUS_AWAR_SOURCE CAS_INTERNAL // not awar-constructable here
22	#include <consensus.h>
23
24	using namespace chartable;
25
26	// ------------------------
27	// SepBaseFreq
28
29	#ifdef DEBUG
30	// # define COUNT_BASES_TABLE_SIZE
31	#endif
32
33	#ifdef COUNT_BASES_TABLE_SIZE
34	static long bases_table_size = 0L;
35	#endif
36
37	void SepBaseFreq::init(int length) {
38	if (length) {
39	if (no_of_bases.shortTable) {
40	delete no_of_bases.shortTable;
41	no_of_bases.shortTable = NULp;
42	#ifdef COUNT_BASES_TABLE_SIZE
43	bases_table_size -= (no_of_entries+1)*table_entry_size;
44	#endif
45	}
46
47	no_of_entries = length;
48	int new_size = (no_of_entries+1)*table_entry_size;
49	no_of_bases.shortTable = (unsigned char*)new char[new_size];
50	memset(no_of_bases.shortTable, 0, new_size);
51	#ifdef COUNT_BASES_TABLE_SIZE
52	bases_table_size += new_size;
53	printf("bases_table_size = %li\n", bases_table_size);
54	#endif
55	}
56	}
57
58	void SepBaseFreq::expand_table_entry_size() { // converts short table into long table
59	ct_assert(table_entry_size==SHORT_TABLE_ELEM_SIZE);
60
61	int *new_table = new int[no_of_entries+1];
62	int i;
63
64	for (i=0; i<=no_of_entries; i++) { // LOOP_VECTORIZED[!<5.0]
65	new_table[i] = no_of_bases.shortTable[i];
66	}
67	delete [] no_of_bases.shortTable;
68
69	#ifdef COUNT_BASES_TABLE_SIZE
70	bases_table_size += (no_of_entries+1)*(LONG_TABLE_ELEM_SIZE-SHORT_TABLE_ELEM_SIZE);
71	printf("bases_table_size = %li\n", bases_table_size);
72	#endif
73
74	no_of_bases.longTable = new_table;
75	table_entry_size = LONG_TABLE_ELEM_SIZE;
76	}
77
78	#define INVALID_TABLE_OPERATION() GBK_terminatef("SepBaseFreq: invalid operation at %i", __LINE__)
79
80	void SepBaseFreq::add(const SepBaseFreq& other, int start, int end) {
81	ct_assert(no_of_entries==other.no_of_entries);
82	ct_assert(start>=0);
83	ct_assert(end<no_of_entries);
84	ct_assert(start<=end);
85
86	int i;
87	if (table_entry_size==SHORT_TABLE_ELEM_SIZE) {
88	if (other.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
89	for (i=start; i<=end; i++) {
90	set_elem_short(i, get_elem_short(i)+other.get_elem_short(i));
91	}
92	}
93	else {
94	INVALID_TABLE_OPERATION(); // cannot add long to short
95	}
96	}
97	else {
98	if (other.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
99	for (i=start; i<=end; i++) { // LOOP_VECTORIZED[!>=620<7]
100	set_elem_long(i, get_elem_long(i)+other.get_elem_short(i));
101	}
102	}
103	else {
104	for (i=start; i<=end; i++) { // LOOP_VECTORIZED[!>=620<7]
105	set_elem_long(i, get_elem_long(i)+other.get_elem_long(i));
106	}
107	}
108	}
109	}
110	void SepBaseFreq::sub(const SepBaseFreq& other, int start, int end) {
111	ct_assert(no_of_entries==other.no_of_entries);
112	ct_assert(start>=0);
113	ct_assert(end<no_of_entries);
114	ct_assert(start<=end);
115
116	int i;
117	if (table_entry_size==SHORT_TABLE_ELEM_SIZE) {
118	if (other.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
119	for (i=start; i<=end; i++) {
120	set_elem_short(i, get_elem_short(i)-other.get_elem_short(i));
121	}
122	}
123	else {
124	INVALID_TABLE_OPERATION(); // cannot sub long from short
125	}
126	}
127	else {
128	if (other.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
129	for (i=start; i<=end; i++) { // LOOP_VECTORIZED[!>=620<7]
130	set_elem_long(i, get_elem_long(i)-other.get_elem_short(i));
131	}
132	}
133	else {
134	for (i=start; i<=end; i++) { // LOOP_VECTORIZED[!>=620<7]
135	set_elem_long(i, get_elem_long(i)-other.get_elem_long(i));
136	}
137	}
138	}
139	}
140	void SepBaseFreq::sub_and_add(const SepBaseFreq& Sub, const SepBaseFreq& Add, PosRange range) {
141	ct_assert(no_of_entries==Sub.no_of_entries);
142	ct_assert(no_of_entries==Add.no_of_entries);
143
144	int start = range.start();
145	int end = range.end();
146
147	ct_assert(start>=0);
148	ct_assert(end<no_of_entries);
149	ct_assert(start<=end);
150
151	int i;
152	if (table_entry_size==SHORT_TABLE_ELEM_SIZE) {
153	if (Sub.table_entry_size==SHORT_TABLE_ELEM_SIZE &&
154	Add.table_entry_size==SHORT_TABLE_ELEM_SIZE)
155	{
156	for (i=start; i<=end; i++) {
157	set_elem_short(i, get_elem_short(i)-Sub.get_elem_short(i)+Add.get_elem_short(i));
158	}
159	}
160	else {
161	INVALID_TABLE_OPERATION(); // cannot add or sub long to/from short
162	}
163	}
164	else {
165	if (Sub.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
166	if (Add.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
167	for (i=start; i<=end; i++) { // LOOP_VECTORIZED[!>=620<7]
168	set_elem_long(i, get_elem_long(i)-Sub.get_elem_short(i)+Add.get_elem_short(i));
169	}
170	}
171	else {
172	for (i=start; i<=end; i++) { // LOOP_VECTORIZED[!>=620<7]
173	set_elem_long(i, get_elem_long(i)-Sub.get_elem_short(i)+Add.get_elem_long(i));
174	}
175	}
176	}
177	else {
178	if (Add.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
179	for (i=start; i<=end; i++) { // LOOP_VECTORIZED[!>=620<7]
180	set_elem_long(i, get_elem_long(i)-Sub.get_elem_long(i)+Add.get_elem_short(i));
181	}
182	}
183	else {
184	for (i=start; i<=end; i++) { // LOOP_VECTORIZED[!>=620<7]
185	set_elem_long(i, get_elem_long(i)-Sub.get_elem_long(i)+Add.get_elem_long(i));
186	}
187	}
188	}
189	}
190	}
191
192	int SepBaseFreq::firstDifference(const SepBaseFreq& other, int start, int end, int *firstDifferentPos) const {
193	int i;
194	int result = 0;
195
196	if (table_entry_size==SHORT_TABLE_ELEM_SIZE) {
197	if (other.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
198	for (i=start; i<=end; i++) {
199	if (get_elem_short(i)!=other.get_elem_short(i)) {
200	*firstDifferentPos = i;
201	result = 1;
202	break;
203	}
204	}
205	}
206	else {
207	for (i=start; i<=end; i++) {
208	if (get_elem_short(i)!=other.get_elem_long(i)) {
209	*firstDifferentPos = i;
210	result = 1;
211	break;
212	}
213	}
214	}
215	}
216	else {
217	if (other.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
218	for (i=start; i<=end; i++) {
219	if (get_elem_long(i)!=other.get_elem_short(i)) {
220	*firstDifferentPos = i;
221	result = 1;
222	break;
223	}
224	}
225	}
226	else {
227	for (i=start; i<=end; i++) {
228	if (get_elem_long(i)!=other.get_elem_long(i)) {
229	*firstDifferentPos = i;
230	result = 1;
231	break;
232	}
233	}
234	}
235	}
236
237	return result;
238	}
239	int SepBaseFreq::lastDifference(const SepBaseFreq& other, int start, int end, int *lastDifferentPos) const {
240	int i;
241	int result = 0;
242
243	if (table_entry_size==SHORT_TABLE_ELEM_SIZE) {
244	if (other.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
245	for (i=end; i>=start; i--) {
246	if (get_elem_short(i)!=other.get_elem_short(i)) {
247	*lastDifferentPos = i;
248	result = 1;
249	break;
250	}
251	}
252	}
253	else {
254	for (i=end; i>=start; i--) {
255	if (get_elem_short(i)!=other.get_elem_long(i)) {
256	*lastDifferentPos = i;
257	result = 1;
258	break;
259	}
260	}
261	}
262	}
263	else {
264	if (other.table_entry_size==SHORT_TABLE_ELEM_SIZE) {
265	for (i=end; i>=start; i--) {
266	if (get_elem_long(i)!=other.get_elem_short(i)) {
267	*lastDifferentPos = i;
268	result = 1;
269	break;
270	}
271	}
272	}
273	else {
274	for (i=end; i>=start; i--) {
275	if (get_elem_long(i)!=other.get_elem_long(i)) {
276	*lastDifferentPos = i;
277	result = 1;
278	break;
279	}
280	}
281	}
282	}
283
284	return result;
285	}
286
287
288	SepBaseFreq::SepBaseFreq(int maxseqlength)
289	: table_entry_size(SHORT_TABLE_ELEM_SIZE),
290	no_of_entries(0)
291	{
292	no_of_bases.shortTable = NULp;
293	if (maxseqlength) init(maxseqlength);
294	}
295
296	SepBaseFreq::~SepBaseFreq() {
297	delete [] no_of_bases.shortTable;
298	#ifdef COUNT_BASES_TABLE_SIZE
299	bases_table_size -= (no_of_entries+1)*table_entry_size;
300	printf("bases_table_size = %li\n", bases_table_size);
301	#endif
302	}
303
304	void SepBaseFreq::change_table_length(int new_length, int default_entry) {
305	if (new_length!=no_of_entries) {
306	int min_length = new_length<no_of_entries ? new_length : no_of_entries;
307	int growth = new_length-no_of_entries;
308
309	if (table_entry_size==SHORT_TABLE_ELEM_SIZE) {
310	unsigned char *new_table = new unsigned char[new_length+1];
311
312	ct_assert(default_entry>=0 && default_entry<256);
313
314	memcpy(new_table, no_of_bases.shortTable, min_lengthsizeof(new_table));
315	new_table[new_length] = no_of_bases.shortTable[no_of_entries];
316	if (growth>0) {
317	for (int e=no_of_entries; e<new_length; ++e) new_table[e] = default_entry;
318	}
319
320	delete [] no_of_bases.shortTable;
321	no_of_bases.shortTable = new_table;
322	}
323	else {
324	int *new_table = new int[new_length+1];
325
326	memcpy(new_table, no_of_bases.longTable, min_lengthsizeof(new_table));
327	new_table[new_length] = no_of_bases.longTable[no_of_entries];
328	if (growth>0) {
329	for (int e=no_of_entries; e<new_length; ++e) { // LOOP_VECTORIZED
330	new_table[e] = default_entry;
331	}
332	}
333
334	delete [] no_of_bases.longTable;
335	no_of_bases.longTable = new_table;
336	}
337
338	#ifdef COUNT_BASES_TABLE_SIZE
339	bases_table_size += growth*table_entry_size;
340	printf("bases_table_size = %li\n", bases_table_size);
341	#endif
342	no_of_entries = new_length;
343	}
344	}
345
346	#if defined(TEST_CHAR_TABLE_INTEGRITY) \|\| defined(ASSERTION_USED)
347
348	int SepBaseFreq::empty() const {
349	int i;
350
351	if (table_entry_size==SHORT_TABLE_ELEM_SIZE) {
352	for (i=0; i<no_of_entries; i++) {
353	if (get_elem_short(i)) {
354	return 0;
355	}
356	}
357	}
358	else {
359	for (i=0; i<no_of_entries; i++) {
360	if (get_elem_long(i)) {
361	return 0;
362	}
363	}
364	}
365
366	return 1;
367	}
368	#endif // ASSERTION_USED
369
370	char *BaseFrequencies::build_consensus_string(PosRange r, const ConsensusBuildParams& cbp) const {
371	ExplicitRange range(r, size());
372
373	long entries = range.size();
374	char *new_buf = ARB_alloc<char>(entries+1);
375
376	build_consensus_string_to(new_buf, range, cbp);
377	new_buf[entries] = 0;
378
379	return new_buf;
380	}
381
382	#if defined(DEBUG)
383	// #define DEBUG_CONSENSUS
384	#endif
385
386	void BaseFrequencies::build_consensus_string_to(char *consensus_string, ExplicitRange range, const ConsensusBuildParams& BK) const {
387	// 'consensus_string' has to be a buffer of size 'range.size()+1'
388	// Note : Always check that consensus behavior is identical to that used in CON_evaluatestatistic()
389
390	ct_assert(consensus_string);
391	ct_assert(range.end()<size());
392
393	#define PERCENT(part, all) ((100*(part))/(all))
394	#define MAX_BASES_TABLES 41 // 25
395
396	ct_assert(used_bases_tables<=MAX_BASES_TABLES); // this is correct for DNA/RNA -> build_consensus_string() must be corrected for AMI/PRO
397
398	const int left_idx = range.start();
399	const int right_idx = range.end();
400
401	#if defined(DEBUG_CONSENSUS)
402	#define DUMPINT(var) do { if (dumpcol) fprintf(stderr, "%s=%i ", #var, var); } while(0)
403	#else
404	#define DUMPINT(var)
405	#endif
406
407	if (sequenceUnits) {
408	for (int i=left_idx; i<=right_idx; i++) {
409	#if defined(DEBUG_CONSENSUS)
410	int column = i+1;
411	bool dumpcol = (column == 21);
412	DUMPINT(column);
413	#endif
414
415	const int o = i-left_idx; // output offset
416
417	int bases = 0; // count of all bases together
418	int base[MAX_BASES_TABLES]; // count of specific base
419	int max_base = -1; // maximum count of specific base
420	int max_base_idx = -1; // index of this base
421
422	for (int j=0; j<used_bases_tables; j++) {
423	base[j] = linear_table(j)[i];
424	if (!isGap(index_to_upperChar(j))) {
425	bases += base[j];
426	if (base[j]>max_base) { // search for most used base
427	max_base = base[j];
428	max_base_idx = j;
429	}
430	}
431	}
432
433	int gaps = sequenceUnits-bases; // count of gaps
434
435	DUMPINT(sequenceUnits);
436	DUMPINT(gaps);
437	DUMPINT(bases);
438
439	// What to do with gaps?
440
441	if (gaps == sequenceUnits) {
442	consensus_string[o] = '=';
443	}
444	else if (BK.countgaps && PERCENT(gaps, sequenceUnits) >= BK.gapbound) {
445	DUMPINT(PERCENT(gaps,sequenceUnits));
446	DUMPINT(BK.gapbound);
447	consensus_string[o] = '-';
448	}
449	else {
450	char kchar = 0; // character for consensus
451	int kcount = 0; // count this character
452
453	if (BK.group) { // simplify using IUPAC
454	if (ali_type == GB_AT_RNA \|\| ali_type == GB_AT_DNA) {
455	int no_of_bases = 0; // count of different bases used to create iupac
456	char used_bases[MAX_BASES_TABLES+1]; // string containing those bases
457
458	for (int j=0; j<used_bases_tables; j++) {
459	int bchar = index_to_upperChar(j);
460
461	if (!isGap(bchar)) {
462	if (base[j]>0 && PERCENT(base[j],bases) >= BK.considbound) {
463	#if defined(DEBUG_CONSENSUS)
464	if (!kcount) DUMPINT(BK.considbound);
465	#endif
466	used_bases[no_of_bases++] = index_to_upperChar(j);
467	kcount += base[j];
468
469	DUMPINT(base[j]);
470	DUMPINT(PERCENT(base[j],bases));
471	DUMPINT(kcount);
472	}
473	}
474	}
475	used_bases[no_of_bases] = 0;
476	kchar = iupac::encode(used_bases, ali_type);
477	}
478	else {
479	ct_assert(ali_type == GB_AT_AA);
480
481	const int amino_groups = iupac::AA_GROUP_COUNT;
482	int group_count[amino_groups];
483
484	for (int j=0; j<amino_groups; j++) {
485	group_count[j] = 0;
486	}
487	for (int j=0; j<used_bases_tables; j++) {
488	unsigned char bchar = index_to_upperChar(j);
489
490	if (!isGap(bchar)) {
491	group_count[iupac::get_amino_group_for(bchar)] += base[j];
492	}
493	}
494
495	int bestGroup = 0;
496	for (int j=0; j<amino_groups; j++) {
497	if (group_count[j]>kcount) {
498	bestGroup = j;
499	kcount = group_count[j];
500	}
501	}
502
503	ct_assert(kcount>0);
504	if (PERCENT(kcount, bases) >= BK.considbound) {
505	kchar = iupac::get_amino_consensus_char(iupac::Amino_Group(bestGroup));
506	}
507	else {
508	kchar = 'X';
509	kcount = bases;
510	}
511	}
512	}
513	if (!kcount) { // IUPAC grouping is either off OR didnt consider any bases
514	ct_assert(max_base); // expect at least one base to occur
515	ct_assert(max_base_idx >= 0);
516
517	kchar = index_to_upperChar(max_base_idx);
518	kcount = max_base;
519	}
520
521	ct_assert(kchar);
522	ct_assert(kcount);
523	ct_assert(kcount<=bases);
524
525	// show as upper or lower case ?
526	int percent = PERCENT(kcount, BK.countgaps ? sequenceUnits : bases);
527	DUMPINT(percent);
528	DUMPINT(BK.upper);
529	DUMPINT(BK.lower);
530	if (percent>=BK.upper) {
531	consensus_string[o] = kchar;
532	}
533	else if (percent>=BK.lower) {
534	consensus_string[o] = tolower(kchar);
535	}
536	else {
537	consensus_string[o] = '.';
538	}
539	}
540	ct_assert(consensus_string[o]);
541
542	#if defined(DEBUG_CONSENSUS)
543	if (dumpcol) fprintf(stderr, "result='%c'\n", consensus_string[o]);
544	#endif
545	}
546	}
547	else {
548	memset(consensus_string, '?', right_idx-left_idx+1);
549	}
550	#undef PERCENT
551	}
552
553	// -----------------------
554	// BaseFrequencies
555
556	bool BaseFrequencies::initialized = false;
557	Ambiguity BaseFrequencies::ambiguity_table[MAX_AMBIGUITY_CODES];
558	uint8_t BaseFrequencies::unitsPerSequence = 1;
559	unsigned char BaseFrequencies::char_to_index_tab[MAXCHARTABLE];
560	bool BaseFrequencies::is_gap[MAXCHARTABLE];
561	unsigned char BaseFrequencies::upper_index_chars[MAX_USED_BASES_TABLES];
562	int BaseFrequencies::used_bases_tables = 0;
563	GB_alignment_type BaseFrequencies::ali_type = GB_AT_RNA;
564
565	inline void BaseFrequencies::set_char_to_index(unsigned char c, int index) {
566	ct_assert(index>=0 && index<used_bases_tables);
567	char_to_index_tab[upper_index_chars[index] = toupper(c)] = index;
568	char_to_index_tab[tolower(c)] = index;
569	}
570
571	void BaseFrequencies::expand_tables() {
572	int i;
573	for (i=0; i<used_bases_tables; i++) {
574	linear_table(i).expand_table_entry_size();
575	}
576	}
577
578	static const char *getAAgroupDefinition() {
579	using namespace iupac;
580	static SmartCharPtr aadef;
581
582	if (aadef.isNull()) {
583	char buffer[2*26+1];
584	int off = 0;
585	for (int c = 'A'; c<='Z'; ++c) {
586	switch (get_amino_group_for(c)) {
587	case AA_GROUP_NONE: break; // cannot add: would add invalid characters -> add 'X' manually below.
588	case AA_GROUP_ILLEGAL: ct_assert(0); break;
589	default:
590	buffer[off++] = c;
591	buffer[off++] = ',';
592	break;
593	}
594	}
595	buffer[off] = 'X';
596	buffer[off+1] = 0;
597
598	aadef = strdup(buffer);
599	}
600
601	return &*aadef;
602	}
603
604	void BaseFrequencies::setup(const char *gap_chars, GB_alignment_type ali_type_) {
605	const char *groups = NULp;
606	const char *ambiguous = NULp;
607
608	ali_type = ali_type_;
609
610	switch (ali_type) {
611	case GB_AT_RNA:
612	groups = "A,C,G,TU,"; // Note: terminal ',' defines a group for unknown characters
613	ambiguous = "MRWSYKVHDBN";
614	unitsPerSequence = 12;
615	break;
616
617	case GB_AT_DNA:
618	groups = "A,C,G,UT,";
619	ambiguous = "MRWSYKVHDBN";
620	unitsPerSequence = 12;
621	break;
622
623	case GB_AT_AA:
624	groups = getAAgroupDefinition();
625	unitsPerSequence = 1;
626	break;
627
628	default:
629	ct_assert(0);
630	break;
631	}
632
633	ct_assert(groups);
634	#if defined(ASSERTION_USED)
635	if (ali_type == GB_AT_AA) {
636	ct_assert(!ambiguous);
637	// ct_assert(strlen(ambiguous) <= MAX_AMBIGUITY_CODES); // @@@ later
638	}
639	else {
640	ct_assert(strlen(ambiguous) == MAX_AMBIGUITY_CODES);
641	}
642	#endif
643
644	for (int i = 0; i<MAXCHARTABLE; ++i) is_gap[i] = false;
645
646	int gapcharcount = 0;
647	char *unique_gap_chars = strdup(gap_chars);
648	for (int i = 0; gap_chars[i]; ++i) {
649	if (!is_gap[safeCharIndex(gap_chars[i])]) { // ignore duplicate occurrences in 'gap_chars'
650	is_gap[safeCharIndex(gap_chars[i])] = true;
651	unique_gap_chars[gapcharcount++] = gap_chars[i];
652	}
653	}
654
655	used_bases_tables = gapcharcount;
656
657	for (int i=0; groups[i]; i++) {
658	if (groups[i]==',') {
659	used_bases_tables++;
660	}
661	}
662
663	ct_assert(used_bases_tables<=MAX_USED_BASES_TABLES);
664
665	int idx = 0;
666	unsigned char init_val = used_bases_tables-1; // map all unknown stuff to last table
667	memset(char_to_index_tab, init_val, MAXCHARTABLEsizeof(char_to_index_tab));
668
669	for (int i=0; groups[i]; i++) {
670	if (groups[i]==',') {
671	idx++;
672	}
673	else {
674	ct_assert(isupper(groups[i]));
675	set_char_to_index(groups[i], idx);
676	}
677	}
678
679	const char *align_string_ptr = unique_gap_chars;
680	while (1) {
681	char c = *align_string_ptr++;
682	if (!c) break;
683	set_char_to_index(c, idx++);
684	}
685
686	if (ambiguous) {
687	ct_assert(ali_type == GB_AT_DNA \|\| ali_type == GB_AT_RNA); // @@@ amino ambiguities not impl
688
689	const uint8_t indices2increment[MAX_TARGET_INDICES+1] = { 0, 0, 6, 4, 3 };
690	for (int i = 0; ambiguous[i]; ++i) {
691	const char *contained = iupac::decode(ambiguous[i], ali_type, false);
692
693	Ambiguity& amb = ambiguity_table[i];
694
695	amb.indices = strlen(contained);
696	ct_assert(amb.indices>=2 && amb.indices<=MAX_TARGET_INDICES);
697	amb.increment = indices2increment[amb.indices];
698
699	for (int j = 0; j<amb.indices; ++j) {
700	int cidx = char_to_index_tab[safeCharIndex(contained[j])];
701	ct_assert(cidx<MAX_INDEX_TABLES); // has to be non-ambiguous
702	amb.index[j] = cidx;
703	}
704
705	char_to_index_tab[toupper(ambiguous[i])] =
706	char_to_index_tab[tolower(ambiguous[i])] = i+MAX_INDEX_TABLES;
707	}
708	}
709
710	free(unique_gap_chars);
711	ct_assert(idx==used_bases_tables);
712	initialized = true;
713	}
714
715	BaseFrequencies::BaseFrequencies(int maxseqlength)
716	: ignore(0)
717	{
718	ct_assert(initialized);
719
720	bases_table = new SepBaseFreqPtr[used_bases_tables];
721
722	for (int i=0; i<used_bases_tables; i++) {
723	bases_table[i] = new SepBaseFreq(maxseqlength);
724	}
725
726	sequenceUnits = 0;
727	}
728
729	void BaseFrequencies::init(int maxseqlength) {
730	int i;
731	for (i=0; i<used_bases_tables; i++) {
732	linear_table(i).init(maxseqlength);
733	}
734
735	sequenceUnits = 0;
736	}
737
738	void BaseFrequencies::bases_and_gaps_at(int column, int bases, int gaps) const {
739	int b = 0;
740	int g = 0;
741
742	for (int i=0; i<used_bases_tables; i++) {
743	char c = upper_index_chars[i];
744
745	if (isGap(c)) {
746	g += table(c)[column];
747	}
748	else {
749	b += table(c)[column];
750	}
751	}
752
753	if (bases) {
754	*bases = b/unitsPerSequence;
755	ct_assert((b%unitsPerSequence) == 0); // could happen if an ambiguous code contains a gap
756	}
757	if (gaps) {
758	*gaps = g/unitsPerSequence;
759	ct_assert((g%unitsPerSequence) == 0); // could happen if an ambiguous code contains a gap
760	}
761	}
762
763	double BaseFrequencies::max_frequency_at(int column, bool ignore_gaps) const {
764	int gaps = 0;
765	int minus = 0;
766	int maxb = 0;
767
768	for (int i=0; i<used_bases_tables; i++) {
769	char c = upper_index_chars[i];
770
771	if (isGap(c)) {
772	if (c == '-') {
773	minus += table(c)[column];
774	}
775	else {
776	gaps += table(c)[column];
777	}
778	}
779	else {
780	maxb = std::max(maxb, table(c)[column]);
781	}
782	}
783
784	if (ignore_gaps) {
785	gaps += minus;
786	}
787	else {
788	maxb = std::max(maxb, minus);
789	}
790
791	double mfreq;
792	if (sequenceUnits>gaps) {
793	mfreq = maxb/double(sequenceUnits-gaps);
794	}
795	else { // only gaps (but no '-')
796	ct_assert(sequenceUnits == gaps);
797	mfreq = 0.0;
798	}
799
800	#if defined(ASSERTION_USED)
801	if (mfreq != 0.0) {
802	if (ali_type != GB_AT_AA) {
803	ct_assert(mfreq>=0.2); // wrong for amino acids
804	}
805	ct_assert(mfreq<=1.0);
806	}
807	#endif
808
809	return mfreq;
810	}
811
812	BaseFrequencies::~BaseFrequencies() {
813	int i;
814	for (i=0; i<used_bases_tables; i++) {
815	delete bases_table[i];
816	}
817
818	delete [] bases_table;
819	}
820
821	const PosRange *BaseFrequencies::changed_range(const BaseFrequencies& other) const {
822	int i;
823	int Size = size();
824	int start = Size-1;
825	int end = 0;
826
827	ct_assert(Size==other.size());
828	for (i=0; i<used_bases_tables; i++) {
829	if (linear_table(i).firstDifference(other.linear_table(i), 0, start, &start)) {
830	if (end<start) {
831	end = start;
832	}
833	linear_table(i).lastDifference(other.linear_table(i), end+1, Size-1, &end);
834
835	for (; i<used_bases_tables; i++) {
836	linear_table(i).firstDifference(other.linear_table(i), 0, start-1, &start);
837	if (end<start) {
838	end = start;
839	}
840	linear_table(i).lastDifference(other.linear_table(i), end+1, Size-1, &end);
841	}
842
843	ct_assert(start<=end);
844
845	static PosRange range;
846	range = PosRange(start, end);
847
848	return &range;
849	}
850	}
851	return NULp;
852	}
853	void BaseFrequencies::add(const BaseFrequencies& other) {
854	if (other.ignore) return;
855	if (other.size()==0) return;
856	prepare_to_add_elements(other.added_sequences());
857	add(other, 0, other.size()-1);
858	}
859	void BaseFrequencies::add(const BaseFrequencies& other, int start, int end) {
860	if (other.ignore) return;
861
862	test();
863	other.test();
864
865	ct_assert(start<=end);
866
867	int i;
868	for (i=0; i<used_bases_tables; i++) {
869	linear_table(i).add(other.linear_table(i), start, end);
870	}
871
872	sequenceUnits += other.sequenceUnits;
873
874	test();
875	}
876
877	void BaseFrequencies::sub(const BaseFrequencies& other) {
878	if (other.ignore) return;
879	sub(other, 0, other.size()-1);
880	}
881
882	void BaseFrequencies::sub(const BaseFrequencies& other, int start, int end) {
883	if (other.ignore) return;
884
885	test();
886	other.test();
887	ct_assert(start<=end);
888
889	int i;
890	for (i=0; i<used_bases_tables; i++) {
891	linear_table(i).sub(other.linear_table(i), start, end);
892	}
893
894	sequenceUnits -= other.sequenceUnits;
895
896	test();
897	}
898
899	void BaseFrequencies::sub_and_add(const BaseFrequencies& Sub, const BaseFrequencies& Add, PosRange range) {
900	test();
901	Sub.test();
902	Add.test();
903
904	ct_assert(!Sub.ignore && !Add.ignore);
905	ct_assert(range.is_part());
906
907	int i;
908	for (i=0; i<used_bases_tables; i++) {
909	linear_table(i).sub_and_add(Sub.linear_table(i), Add.linear_table(i), range);
910	}
911
912	test();
913	}
914
915	const PosRange BaseFrequencies::changed_range(const char string1, const char *string2, int min_len) {
916	const unsigned long range1 = (const unsigned long )string1;
917	const unsigned long range2 = (const unsigned long )string2;
918	const int step = sizeof(*range1);
919
920	int l = min_len/step;
921	int r = min_len%step;
922	int i;
923	int j;
924	int k;
925
926	int start = -1, end = -1;
927
928	for (i=0; i<l; i++) { // search wordwise (it's faster)
929	if (range1[i] != range2[i]) {
930	k = i*step;
931	for (j=0; j<step; j++) {
932	if (string1[k+j] != string2[k+j]) {
933	start = end = k+j;
934	break;
935	}
936	}
937
938	break;
939	}
940	}
941
942	k = l*step;
943	if (i==l) { // no difference found in word -> look at rest
944	for (j=0; j<r; j++) {
945	if (string1[k+j] != string2[k+j]) {
946	start = end = k+j;
947	break;
948	}
949	}
950
951	if (j==r) { // the strings are equal
952	return NULp;
953	}
954	}
955
956	ct_assert(start != -1 && end != -1);
957
958	for (j=r-1; j>=0; j--) { // search rest backwards
959	if (string1[k+j] != string2[k+j]) {
960	end = k+j;
961	break;
962	}
963	}
964
965	if (j==-1) { // not found in rest -> search words backwards
966	int m = start/step;
967	for (i=l-1; i>=m; i--) {
968	if (range1[i] != range2[i]) {
969	k = i*step;
970	for (j=step-1; j>=0; j--) {
971	if (string1[k+j] != string2[k+j]) {
972	end = k+j;
973	break;
974	}
975	}
976	break;
977	}
978	}
979	}
980
981	ct_assert(start<=end);
982
983	static PosRange range;
984	range = PosRange(start, end);
985
986	return &range;
987	}
988
989	#define INC_DEC(incdec) do { \
990	int idx = char_to_index_tab[c]; \
991	if (idx<MAX_INDEX_TABLES) { \
992	table(c).incdec(offset, unitsPerSequence); \
993	} \
994	else { \
995	Ambiguity& amb = ambiguity_table[idx-MAX_INDEX_TABLES]; \
996	for (int i = 0; i<amb.indices; ++i) { \
997	linear_table(amb.index[i]).incdec(offset, amb.increment); \
998	} \
999	} \
1000	} while(0)
1001
1002	void BaseFrequencies::incr_short(unsigned char c, int offset) {
1003	INC_DEC(inc_short);
1004	}
1005
1006	void BaseFrequencies::decr_short(unsigned char c, int offset) {
1007	INC_DEC(dec_short);
1008	}
1009
1010	void BaseFrequencies::incr_long(unsigned char c, int offset) {
1011	INC_DEC(inc_long);
1012	}
1013
1014	void BaseFrequencies::decr_long(unsigned char c, int offset) {
1015	INC_DEC(dec_long);
1016	}
1017
1018	#undef INC_DEC
1019
1020	void BaseFrequencies::add(const char *scan_string, int len) {
1021	test();
1022
1023	prepare_to_add_elements(1);
1024
1025	int i;
1026	int sz = size();
1027
1028	if (get_table_entry_size()==SHORT_TABLE_ELEM_SIZE) {
1029	for (i=0; i<len; i++) {
1030	unsigned char c = scan_string[i];
1031	if (!c) break;
1032	incr_short(c, i);
1033	}
1034	SepBaseFreq& t = table('.');
1035	for (; i<sz; i++) {
1036	t.inc_short(i, unitsPerSequence);
1037	}
1038	}
1039	else {
1040	for (i=0; i<len; i++) {
1041	unsigned char c = scan_string[i];
1042	if (!c) break;
1043	incr_long(c, i);
1044	}
1045	SepBaseFreq& t = table('.');
1046	for (; i<sz; i++) { // LOOP_VECTORIZED[!>=620<7]
1047	t.inc_long(i, unitsPerSequence);
1048	}
1049	}
1050
1051	sequenceUnits += unitsPerSequence;
1052
1053	test();
1054	}
1055
1056	void BaseFrequencies::sub(const char *scan_string, int len) {
1057	test();
1058
1059	int i;
1060	int sz = size();
1061
1062	if (get_table_entry_size()==SHORT_TABLE_ELEM_SIZE) {
1063	for (i=0; i<len; i++) {
1064	unsigned char c = scan_string[i];
1065	if (!c) break;
1066	decr_short(c, i);
1067	}
1068	SepBaseFreq& t = table('.');
1069	for (; i<sz; i++) {
1070	t.dec_short(i, unitsPerSequence);
1071	}
1072	}
1073	else {
1074	for (i=0; i<len; i++) {
1075	unsigned char c = scan_string[i];
1076	if (!c) break;
1077	decr_long(c, i);
1078	}
1079	SepBaseFreq& t = table('.');
1080	for (; i<sz; i++) { // LOOP_VECTORIZED[!>=620<7]
1081	t.dec_long(i, unitsPerSequence);
1082	}
1083	}
1084
1085	sequenceUnits -= unitsPerSequence;
1086
1087	test();
1088	}
1089
1090	void BaseFrequencies::sub_and_add(const char old_string, const char new_string, PosRange range) {
1091	test();
1092	int start = range.start();
1093	int end = range.end();
1094	ct_assert(start<=end);
1095
1096	if (get_table_entry_size()==SHORT_TABLE_ELEM_SIZE) {
1097	for (int i=start; i<=end; i++) {
1098	unsigned char o = old_string[i];
1099	unsigned char n = new_string[i];
1100
1101	ct_assert(o && n); // passed string have to be defined in range
1102
1103	if (o!=n) {
1104	decr_short(o, i);
1105	incr_short(n, i);
1106	}
1107	}
1108	}
1109	else {
1110	for (int i=start; i<=end; i++) {
1111	unsigned char o = old_string[i];
1112	unsigned char n = new_string[i];
1113
1114	ct_assert(o && n); // passed string have to be defined in range
1115
1116	if (o!=n) {
1117	decr_long(o, i);
1118	incr_long(n, i);
1119	}
1120	}
1121	}
1122
1123	test();
1124	}
1125
1126	void BaseFrequencies::change_table_length(int new_length) {
1127	for (int c=0; c<used_bases_tables; c++) {
1128	linear_table(c).change_table_length(new_length, 0);
1129	}
1130	test();
1131	}
1132
1133	// --------------
1134	// tests:
1135
1136	#if defined(TEST_CHAR_TABLE_INTEGRITY) \|\| defined(ASSERTION_USED)
1137
1138	bool BaseFrequencies::empty() const {
1139	int i;
1140	for (i=0; i<used_bases_tables; i++) {
1141	if (!linear_table(i).empty()) {
1142	return false;
1143	}
1144	}
1145	return true;
1146	}
1147
1148	bool BaseFrequencies::ok() const {
1149	if (empty()) return true;
1150	if (is_ignored()) return true;
1151
1152	if (sequenceUnits<0) {
1153	fprintf(stderr, "Negative # of sequences (%i) in BaseFrequencies\n", added_sequences());
1154	return false;
1155	}
1156
1157	const int table_size = size();
1158	for (int i=0; i<table_size; i++) {
1159	int bases, gaps;
1160	bases_and_gaps_at(i, &bases, &gaps);
1161
1162	if (!bases && !gaps) { // this occurs after insert column
1163	for (int j=i+1; j<table_size; j++) { // test if we find any bases till end of table !!!
1164
1165	bases_and_gaps_at(j, &bases, NULp);
1166	if (bases) { // bases found -> empty position was illegal
1167	fprintf(stderr, "Zero in BaseFrequencies at column %i\n", i);
1168	return false;
1169	}
1170	}
1171	break;
1172	}
1173	else {
1174	if ((bases+gaps)!=added_sequences()) {
1175	fprintf(stderr, "bases+gaps should be equal to # of sequences at column %i (bases=%i, gaps=%i, added_sequences=%i)\n",
1176	i, bases, gaps, added_sequences());
1177	return false;
1178	}
1179	}
1180	}
1181
1182	return true;
1183	}
1184
1185	#endif // TEST_CHAR_TABLE_INTEGRITY \|\| ASSERTION_USED
1186
1187	#if defined(TEST_CHAR_TABLE_INTEGRITY)
1188
1189	void BaseFrequencies::test() const {
1190
1191	if (!ok()) {
1192	GBK_terminate("BaseFrequencies::test() failed");
1193	}
1194	}
1195
1196	#endif // TEST_CHAR_TABLE_INTEGRITY
1197
1198
1199	// --------------------------------------------------------------------------------
1200
1201	#ifdef UNIT_TESTS
1202	#ifndef TEST_UNIT_H
1203	#include <test_unit.h>
1204	#endif
1205	#include <arbdb.h>
1206
1207	#define SETUP(gapChars,alitype) BaseFrequencies::setup(gapChars,alitype)
1208
1209	void TEST_char_table() {
1210	for (int useAminoAcids = 0; useAminoAcids<=1; ++useAminoAcids) {
1211	const char *alphabeth = useAminoAcids ? "ABCDEFGHIJKLMNPQRSTVWXYZ-" : "ACGTN-";
1212	const int alphabeth_size = strlen(alphabeth);
1213
1214	TEST_EXPECT_EQUAL(alphabeth_size, (useAminoAcids ? 23 : 4)+2); // "+2" is for gap and N/X
1215
1216	const int SEQLEN = 30;
1217	char seq[SEQLEN+1];
1218
1219	const char *gapChars = ".-"; // @@@ doesnt make any difference which gaps are used - why?
1220	// const char *gapChars = "-";
1221	// const char *gapChars = ".";
1222	// const char *gapChars = "A"; // makes me fail
1223	SETUP(gapChars, useAminoAcids ? GB_AT_AA : GB_AT_RNA);
1224
1225	if (useAminoAcids) {
1226	// document used amino acid group definition:
1227	TEST_EXPECT_EQUAL(getAAgroupDefinition(), "A,B,C,D,E,F,G,H,I,J,K,L,M,N,P,Q,R,S,T,V,W,Y,Z,X");
1228	}
1229
1230	ConsensusBuildParams BK;
1231	// BK.lower = 70; BK.upper = 95; BK.gapbound = 60; // defaults from awars
1232	BK.lower = 40; BK.upper = 70; BK.gapbound = 40;
1233
1234	const int LOOPS = 5;
1235	GB_random_seed(100);
1236
1237	int seed[LOOPS];
1238	for (int loop = 0; loop<5; ++loop) {
1239	seed[loop] = GB_random(INT_MAX);
1240	}
1241
1242	for (int loop = 0; loop<5; ++loop) {
1243	GB_random_seed(seed[loop]);
1244
1245	BaseFrequencies tab(SEQLEN);
1246
1247	// build some seq
1248	for (int c = 0; c<SEQLEN; ++c) {
1249	seq[c] = alphabeth[GB_random(alphabeth_size)];
1250	}
1251	seq[SEQLEN] = 0;
1252
1253	TEST_EXPECT_EQUAL(strlen(seq), size_t(SEQLEN));
1254
1255	const int add_count = 300;
1256	char *added_seqs[add_count];
1257
1258	const char *s1; // length = SEQLEN
1259	const char *s2;
1260	if (useAminoAcids) {
1261	s1 = "ABCDEFGHIJKLMNPQRSTVWXYZabcdef";
1262	s2 = "ghijklmnpqrstvwxyzABCDEFGHIJKL";
1263	}
1264	else { // rna
1265	s1 = "ACGTACGTAcgtacgtaCGTACGTACGTAC"; // @@@ insert gaps! -> adapt changed results
1266	s2 = "MRWSYKVHDBNmrwsykvhdbnSYKVHDBN"; // use ambiguities
1267	}
1268
1269	// add seq multiple times
1270	for (int a = 0; a<add_count; ++a) {
1271	tab.add(seq, SEQLEN);
1272	added_seqs[a] = strdup(seq);
1273
1274	// modify 1 character in seq:
1275	int sidx = GB_random(SEQLEN);
1276	int aidx = GB_random(alphabeth_size);
1277	seq[sidx] = alphabeth[aidx];
1278
1279	if (a == 16) { // with 15 sequences in tab
1280	// test sub_and_add (short table version)
1281	char *consensus = tab.build_consensus_string(BK);
1282
1283	tab.add(s1, SEQLEN);
1284	PosRange r(0, SEQLEN-1);
1285	tab.sub_and_add(s1, s2, r);
1286	tab.sub_and_add(s2, consensus, r);
1287	tab.sub(consensus, SEQLEN);
1288
1289	char *consensus2 = tab.build_consensus_string(BK);
1290	TEST_EXPECT_EQUAL(consensus, consensus2);
1291
1292	free(consensus2);
1293	free(consensus);
1294	}
1295	}
1296
1297	// build consensi (just check regression)
1298	// Note: semantic tests for consensus are in ../../NTREE/AP_consensus.cxx@TEST_nucleotide_consensus_and_maxFrequency
1299	{
1300	char *consensus = tab.build_consensus_string(BK);
1301	if (useAminoAcids) {
1302	switch (seed[loop]) {
1303	case 1080710223: TEST_EXPECT_EQUAL(consensus, "a.i.dXi.haai.hifdi.d.adXaa..dX"); break;
1304	case 290469779: TEST_EXPECT_EQUAL(consensus, ".......I.D.A......-f..iXi...dX"); break;
1305	case 346019116: TEST_EXPECT_EQUAL(consensus, "if.a-hd.hd..a.di-ddf.i..aXIaI."); break;
1306	case 1708473987: TEST_EXPECT_EQUAL(consensus, "aia..df...haDaadd.d.fha.ii.X.."); break;
1307	case 2080862653: TEST_EXPECT_EQUAL(consensus, "a.ia.id...a.aah.had......i..d."); break;
1308	default: TEST_EXPECTATION(all().of(that(consensus).is_equal_to("undef"), that(seed[loop]).is_equal_to(-1))); // default case is unwanted (logs data -> want one case above for each pair)
1309	}
1310	}
1311	else {
1312	switch (seed[loop]) {
1313	case 1080710223: TEST_EXPECT_EQUAL(consensus, "W.gKyc.sR.urSkGcy.kuy......RY-"); break;
1314	case 290469779: TEST_EXPECT_EQUAL(consensus, ".u-SW.Mgcu.uw-uu..-mmb.sgcRuY."); break;
1315	case 346019116: TEST_EXPECT_EQUAL(consensus, "y-m.-Suy.c.-u.-g-y.cWgr.cyGrgY"); break;
1316	case 1708473987: TEST_EXPECT_EQUAL(consensus, ".K.Kc--.cakyw.uW..a-.guuggwH-a"); break;
1317	case 2080862653: TEST_EXPECT_EQUAL(consensus, ".sgaR..--.uu.cMuuycsk-u.cu.Wc."); break;
1318	default: TEST_EXPECTATION(all().of(that(consensus).is_equal_to("undef"), that(seed[loop]).is_equal_to(-1))); // default case is unwanted (logs data -> want one case above for each pair)
1319	}
1320	}
1321
1322	// test sub_and_add()
1323
1324	tab.add(s1, SEQLEN);
1325	PosRange r(0, SEQLEN-1);
1326	tab.sub_and_add(s1, s2, r);
1327	tab.sub_and_add(s2, consensus, r);
1328	tab.sub(consensus, SEQLEN);
1329
1330	char *consensus2 = tab.build_consensus_string(BK);
1331	TEST_EXPECT_EQUAL(consensus, consensus2);
1332
1333	free(consensus2);
1334	free(consensus);
1335	}
1336
1337	for (int a = 0; a<add_count; a++) {
1338	tab.sub(added_seqs[a], SEQLEN);
1339	freenull(added_seqs[a]);
1340	}
1341	{
1342	char *consensus = tab.build_consensus_string(BK);
1343	TEST_EXPECT_EQUAL(consensus, "??????????????????????????????"); // check tab is empty
1344	free(consensus);
1345	}
1346	}
1347	}
1348	}
1349
1350	void TEST_SepBaseFreq() {
1351	const int LEN = 20;
1352	const int OFF1 = 6;
1353	const int OFF2 = 7; // adjacent to OFF1
1354
1355	SepBaseFreq short1(LEN), short2(LEN);
1356	for (int i = 0; i<100; ++i) short1.inc_short(OFF1, 1);
1357	for (int i = 0; i<70; ++i) short1.inc_short(OFF2, 1);
1358	for (int i = 0; i<150; ++i) short2.inc_short(OFF1, 1);
1359	for (int i = 0; i<80; ++i) short2.inc_short(OFF2, 1);
1360
1361	SepBaseFreq long1(LEN), long2(LEN);
1362	long1.expand_table_entry_size();
1363	long2.expand_table_entry_size();
1364	for (int i = 0; i<2000; ++i) long1.inc_long(OFF1, 1);
1365	for (int i = 0; i<2500; ++i) long2.inc_long(OFF1, 1);
1366
1367	SepBaseFreq shortsum(LEN);
1368	shortsum.add(short1, 0, LEN-1); TEST_EXPECT_EQUAL(shortsum[OFF1], 100); TEST_EXPECT_EQUAL(shortsum[OFF2], 70);
1369	shortsum.add(short2, 0, LEN-1); TEST_EXPECT_EQUAL(shortsum[OFF1], 250); TEST_EXPECT_EQUAL(shortsum[OFF2], 150);
1370	shortsum.sub(short1, 0, LEN-1); TEST_EXPECT_EQUAL(shortsum[OFF1], 150); TEST_EXPECT_EQUAL(shortsum[OFF2], 80);
1371
1372	shortsum.sub_and_add(short1, short2, PosRange(0, LEN-1)); TEST_EXPECT_EQUAL(shortsum[OFF1], 200); TEST_EXPECT_EQUAL(shortsum[OFF2], 90);
1373
1374	// shortsum.add(long1, 0, LEN-1); // invalid operation -> terminate
1375
1376	SepBaseFreq longsum(LEN);
1377	longsum.expand_table_entry_size();
1378	longsum.add(long1, 0, LEN-1); TEST_EXPECT_EQUAL(longsum[OFF1], 2000);
1379	longsum.add(long2, 0, LEN-1); TEST_EXPECT_EQUAL(longsum[OFF1], 4500);
1380	longsum.sub(long1, 0, LEN-1); TEST_EXPECT_EQUAL(longsum[OFF1], 2500);
1381	longsum.add(short1, 0, LEN-1); TEST_EXPECT_EQUAL(longsum[OFF1], 2600);
1382	longsum.sub(short2, 0, LEN-1); TEST_EXPECT_EQUAL(longsum[OFF1], 2450);
1383
1384	longsum.sub_and_add(long1, long2, PosRange(0, LEN-1)); TEST_EXPECT_EQUAL(longsum[OFF1], 2950);
1385	longsum.sub_and_add(short1, short2, PosRange(0, LEN-1)); TEST_EXPECT_EQUAL(longsum[OFF1], 3000);
1386	longsum.sub_and_add(long1, short2, PosRange(0, LEN-1)); TEST_EXPECT_EQUAL(longsum[OFF1], 1150);
1387	longsum.sub_and_add(short1, long2, PosRange(0, LEN-1)); TEST_EXPECT_EQUAL(longsum[OFF1], 3550);
1388
1389	int pos = -1;
1390	TEST_EXPECT_EQUAL(short1.firstDifference(short2, 0, LEN-1, &pos), 1); TEST_EXPECT_EQUAL(pos, OFF1);
1391	TEST_EXPECT_EQUAL(short1.lastDifference (short2, 0, LEN-1, &pos), 1); TEST_EXPECT_EQUAL(pos, OFF2);
1392	TEST_EXPECT_EQUAL(short1.firstDifference(long1, 0, LEN-1, &pos), 1); TEST_EXPECT_EQUAL(pos, OFF1);
1393	TEST_EXPECT_EQUAL(short1.lastDifference (long1, 0, LEN-1, &pos), 1); TEST_EXPECT_EQUAL(pos, OFF2);
1394	TEST_EXPECT_EQUAL(long2.firstDifference (short2, 0, LEN-1, &pos), 1); TEST_EXPECT_EQUAL(pos, OFF1);
1395	TEST_EXPECT_EQUAL(long2.lastDifference (short2, 0, LEN-1, &pos), 1); TEST_EXPECT_EQUAL(pos, OFF2);
1396	TEST_EXPECT_EQUAL(long2.firstDifference (long1, 0, LEN-1, &pos), 1); TEST_EXPECT_EQUAL(pos, OFF1);
1397	TEST_EXPECT_EQUAL(long2.lastDifference (long1, 0, LEN-1, &pos), 1); TEST_EXPECT_EQUAL(pos, OFF1);
1398	}
1399
1400	#endif // UNIT_TESTS
1401
1402	// --------------------------------------------------------------------------------
1403
1404
1405

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source: branches/stable/SL/CONSENSUS/chartable.cxx

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