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arb_probe.cxx

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Last change on this file was 19365, checked in by westram, 16 months ago
string splitters: unittests for `GBT_split_string`: add tests for dropEmptyTokens. document special behavior for empty string. define enum `SplitMode`. use enum instead of bool param for GBT_splitNdestroy_string + GBT_split_string.
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 133.5 KB

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1	// =============================================================== //
2	// //
3	// File : arb_probe.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// =============================================================== //
10
11	#include <PT_com.h>
12	#include <arbdb.h>
13
14	#include <client.h>
15	#include <servercntrl.h>
16
17	#include <arb_defs.h>
18	#include <arb_strbuf.h>
19	#include <arb_diff.h>
20	#include <RegExpr.hxx>
21
22	#include <algorithm>
23	#include <string> // need to include before test_unit.h
24	#include <unistd.h>
25
26	struct apd_sequence {
27	apd_sequence *next;
28	const char *sequence;
29	};
30
31	struct Params {
32	int DESIGNCLIPOUTPUT;
33	int SERVERID;
34	const char *DESIGNNAMES;
35	int DESIGNPROBELEN;
36	int DESIGNMAXPROBELEN;
37	const char *DESIGNSEQUENCE;
38
39	int MINTEMP;
40	int MAXTEMP;
41	int MINGC;
42	int MAXGC;
43	int MAXBOND;
44	int MINPOS;
45	int MAXPOS;
46	int MISHIT;
47	int MINTARGETS;
48	const char *SEQUENCE;
49	int MISMATCHES;
50	int ACCEPTN;
51	int LIMITN;
52	int MAXRESULT;
53	int ALSO_REVCOMPL;
54	int WEIGHTED;
55
56	apd_sequence *sequence;
57
58	int ITERATE;
59	int ITERATE_AMOUNT;
60	int ITERATE_READABLE;
61	const char *ITERATE_SEPARATOR;
62	const char *ITERATE_TU;
63
64	const char *DUMP;
65	};
66
67
68	struct gl_struct {
69	aisc_com *link;
70	T_PT_MAIN com;
71	T_PT_LOCS locs;
72	int pd_design_id;
73
74	gl_struct()
75	: link(NULp),
76	pd_design_id(0)
77	{}
78
79	};
80
81	static Params P;
82	static gl_struct pd_gl;
83
84	static int init_local_com_struct() {
85	const char *user = GB_getenvUSER();
86
87	if (aisc_create(pd_gl.link, PT_MAIN, pd_gl.com,
88	MAIN_LOCS, PT_LOCS, pd_gl.locs,
89	LOCS_USER, user,
90	NULp)) {
91	return 1;
92	}
93
94	return 0;
95	}
96
97	class PTserverConnection {
98	static int count;
99	bool need_close;
100	public:
101	PTserverConnection(ARB_ERROR& error)
102	: need_close(false)
103	{
104	if (count) {
105	error = "Only 1 PTserverConnection allowed";
106	}
107	else {
108	++count;
109
110	GB_ERROR lookerr = NULp;
111	const char *servername = arb_look_and_start_ptserver(AISC_MAGIC_NUMBER, P.SERVERID, lookerr);
112	if (servername) {
113	GB_ERROR openerr = NULp;
114	pd_gl.link = aisc_open(servername, pd_gl.com, AISC_MAGIC_NUMBER, &openerr);
115	if (openerr) {
116	error = openerr;
117	}
118	else {
119	if (!pd_gl.link) {
120	error = "Cannot contact PT_SERVER [1]";
121	}
122	else if (init_local_com_struct()) {
123	error = "Cannot contact PT_SERVER [2]";
124	}
125	else {
126	need_close = true;
127	}
128	}
129	}
130	else {
131	error = lookerr;
132	}
133	}
134	}
135	~PTserverConnection() {
136	if (need_close) {
137	aisc_close(pd_gl.link, pd_gl.com);
138	pd_gl.link = NULp;
139	}
140	--count;
141	}
142	};
143	int PTserverConnection::count = 0;
144
145	static char *AP_dump_index_event(ARB_ERROR& error) {
146	PTserverConnection contact(error);
147
148	char *result = NULp;
149	if (!error) {
150	aisc_put(pd_gl.link, PT_MAIN, pd_gl.com,
151	MAIN_DUMP_NAME, P.DUMP,
152	NULp);
153
154	if (aisc_get(pd_gl.link, PT_MAIN, pd_gl.com,
155	MAIN_DUMP_INDEX, &result,
156	NULp)) {
157	error = "Connection to PT_SERVER lost (1)";
158	}
159	else {
160	result = ARB_strdup("ok");
161	}
162	}
163	return result;
164	}
165
166	static char *AP_probe_iterate_event(ARB_ERROR& error) {
167	PTserverConnection contact(error);
168
169	char *result = NULp;
170	if (!error) {
171	T_PT_PEP pep;
172	int length = P.ITERATE;
173
174	if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs,
175	LOCS_PROBE_FIND_CONFIG, PT_PEP, pep,
176	PEP_PLENGTH, (long)length,
177	PEP_RESTART, (long)1,
178	PEP_READABLE, (long)P.ITERATE_READABLE,
179	PEP_TU, (long)P.ITERATE_TU[0],
180	PEP_SEPARATOR, (long)P.ITERATE_SEPARATOR[0],
181	NULp))
182	{
183	error = "Connection to PT_SERVER lost (1)";
184	}
185
186	if (!error) {
187	int amount = P.ITERATE_AMOUNT;
188	int amount_per_call = AISC_MAX_STRING_LEN/(length+2);
189
190	GBS_strstruct out(50000);
191	bool first = true;
192
193	while (amount && !error) {
194	int this_amount = std::min(amount, amount_per_call);
195
196	aisc_put(pd_gl.link, PT_PEP, pep,
197	PEP_NUMGET, (long)this_amount,
198	PEP_FIND_PROBES, (long)0,
199	NULp);
200
201	char *pep_result = NULp;
202	if (aisc_get(pd_gl.link, PT_PEP, pep,
203	PEP_RESULT, &pep_result,
204	NULp)) {
205	error = "Connection to PT_SERVER lost (2)";
206	}
207
208	if (!error) {
209	if (pep_result[0]) {
210	if (first) first = false;
211	else out.put(P.ITERATE_SEPARATOR[0]);
212
213	out.cat(pep_result);
214	amount -= this_amount;
215	}
216	else {
217	amount = 0; // terminate loop
218	}
219	}
220	free(pep_result);
221	}
222
223	if (!error) {
224	result = out.release();
225	}
226	}
227	}
228
229	if (error) freenull(result);
230	return result;
231	}
232
233	static char *AP_probe_design_event(ARB_ERROR& error) {
234	PTserverConnection contact(error);
235
236	if (!error) {
237	bytestring bs;
238	bs.data = (char*)(P.DESIGNNAMES);
239	bs.size = strlen(bs.data)+1;
240
241	T_PT_PDC pdc;
242	if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs,
243	LOCS_PROBE_DESIGN_CONFIG, PT_PDC, pdc,
244	PDC_MIN_PROBELEN, (long)P.DESIGNPROBELEN,
245	PDC_MAX_PROBELEN, (long)P.DESIGNMAXPROBELEN,
246	PDC_MINTEMP, (double)P.MINTEMP,
247	PDC_MAXTEMP, (double)P.MAXTEMP,
248	PDC_MINGC, (double)P.MINGC/100.0,
249	PDC_MAXGC, (double)P.MAXGC/100.0,
250	PDC_MAXBOND, (double)P.MAXBOND,
251	PDC_MIN_ECOLIPOS, (long)P.MINPOS,
252	PDC_MAX_ECOLIPOS, (long)P.MAXPOS,
253	PDC_MISHIT, (long)P.MISHIT,
254	PDC_MINTARGETS, (double)P.MINTARGETS/100.0,
255	PDC_CLIPRESULT, (long)P.DESIGNCLIPOUTPUT,
256	NULp))
257	{
258	error = "Connection to PT_SERVER lost (1)";
259	}
260
261	if (!error) {
262	for (apd_sequence *s = P.sequence; s; ) {
263	apd_sequence *next = s->next;
264
265	bytestring bs_seq;
266	T_PT_SEQUENCE pts;
267
268	bs_seq.data = (char*)s->sequence;
269	bs_seq.size = strlen(bs_seq.data)+1;
270	aisc_create(pd_gl.link, PT_PDC, pdc,
271	PDC_SEQUENCE, PT_SEQUENCE, pts,
272	SEQUENCE_SEQUENCE, &bs_seq,
273	NULp);
274
275	delete s;
276	s = next;
277	}
278
279	aisc_put(pd_gl.link, PT_PDC, pdc,
280	PDC_NAMES, &bs,
281	PDC_GO, (long)0,
282	NULp);
283
284	{
285	char *locs_error = NULp;
286	if (aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs,
287	LOCS_ERROR, &locs_error,
288	NULp)) {
289	error = "Connection to PT_SERVER lost (2)";
290	}
291	else {
292	if (*locs_error) error = GBS_static_string(locs_error);
293	free(locs_error);
294	}
295	}
296
297	if (!error) {
298	T_PT_TPROBE tprobe;
299	aisc_get(pd_gl.link, PT_PDC, pdc,
300	PDC_TPROBE, tprobe.as_result_param(),
301	NULp);
302
303
304	GBS_strstruct outstr(1000);
305
306	if (tprobe.exists()) {
307	char *match_info = NULp;
308	aisc_get(pd_gl.link, PT_PDC, pdc,
309	PDC_INFO_HEADER, &match_info,
310	NULp);
311	outstr.cat(match_info);
312	outstr.put('\n');
313	free(match_info);
314	}
315
316
317	while (tprobe.exists()) {
318	char *match_info = NULp;
319	if (aisc_get(pd_gl.link, PT_TPROBE, tprobe,
320	TPROBE_NEXT, tprobe.as_result_param(),
321	TPROBE_INFO, &match_info,
322	NULp)) break;
323	outstr.cat(match_info);
324	outstr.put('\n');
325	free(match_info);
326	}
327
328	return outstr.release();
329	}
330	}
331	}
332	return NULp;
333	}
334
335	static char *AP_probe_match_event(ARB_ERROR& error) {
336	PTserverConnection contact(error);
337
338	if (!error &&
339	aisc_nput(pd_gl.link, PT_LOCS, pd_gl.locs,
340	LOCS_MATCH_ALSO_REVCOMP, (long)P.ALSO_REVCOMPL,
341	LOCS_COMPLEMENT_FIRST, (long)0, // (use sequence passed below as is. do not complement it.)
342	LOCS_MATCH_SORT_BY, (long)P.WEIGHTED,
343	LOCS_MATCH_MAX_MISMATCHES, (long)P.MISMATCHES,
344	LOCS_MATCH_N_ACCEPT, (long)P.ACCEPTN,
345	LOCS_MATCH_N_LIMIT, (long)P.LIMITN,
346	LOCS_MATCH_MAX_HITS, (long)P.MAXRESULT,
347	LOCS_SEARCHMATCH, P.SEQUENCE,
348	NULp)) {
349	error = "Connection to PT_SERVER lost (1)";
350	}
351
352	if (!error) {
353	bytestring bs;
354	bs.data = NULp;
355	{
356	char *locs_error = NULp;
357	T_PT_MATCHLIST match_list;
358	long match_list_cnt;
359
360	aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs,
361	LOCS_MATCH_LIST, match_list.as_result_param(),
362	LOCS_MATCH_LIST_CNT, &match_list_cnt,
363	LOCS_MATCH_STRING, &bs,
364	LOCS_ERROR, &locs_error,
365	NULp);
366	if (*locs_error) error = GBS_static_string(locs_error);
367	free(locs_error);
368	}
369
370	if (!error) return bs.data; // freed by caller
371	free(bs.data);
372	}
373	return NULp;
374	}
375
376	static int pargc;
377	static const char **pargv = NULp;
378	static bool showhelp;
379	static bool outOfRange;
380
381	static int getInt(const char param, int val, int min, int max, const char description) {
382	if (showhelp) {
383	printf(" %s=%i [%i .. ", param, val, min);
384	if (max != INT_MAX) printf("%i", max);
385	printf("] %s\n", description);
386	return 0;
387	}
388	int i;
389	const char *s = NULp;
390
391	arb_assert(min<=val && val<=max); // wrong default value
392
393	arb_assert(pargc >= 1); // otherwise s stays 0
394
395	for (i=1; i<pargc; i++) {
396	s = pargv[i];
397	if (*s == '-') s++;
398	if (!strncasecmp(s, param, strlen(param))) break;
399	}
400	if (i==pargc) return val;
401	s += strlen(param);
402	if (*s == '=') {
403	s++;
404	val = atoi(s);
405
406	if (val<min \|\| val>max) {
407	outOfRange = true;
408	printf("Parameter '%s=%s' is outside allowed range:\n", param, s);
409	showhelp = true;
410	getInt(param, val, min, max, description);
411	showhelp = false;
412	val = 0;
413	}
414	}
415
416	pargc--; // remove parameter
417	for (; i<pargc; i++) {
418	pargv[i] = pargv[i+1];
419	}
420
421	return val;
422	}
423
424	static const char getString(const char param, const char val, const char description) {
425	if (showhelp) {
426	if (!val) val = "";
427	printf(" %s=%s %s\n", param, val, description);
428	return NULp;
429	}
430	int i;
431	const char *s = NULp;
432
433	arb_assert(pargc >= 1); // otherwise s stays 0
434
435	for (i=1; i<pargc; i++) {
436	s = pargv[i];
437	if (*s == '-') s++;
438	if (!strncasecmp(s, param, strlen(param))) break;
439	}
440	if (i==pargc) return val;
441	s += strlen(param);
442	if (*s != '=') return val;
443	s++;
444	pargc--; // remove parameter
445	for (; i<pargc; i++) {
446	pargv[i] = pargv[i+1];
447	}
448	return s;
449	}
450
451	static bool parseCommandLine(int argc, const char * const * const argv) {
452	pargc = argc;
453
454	// copy argv (since parser will remove matched arguments)
455	free(pargv);
456	ARB_alloc(pargv, pargc);
457	for (int i=0; i<pargc; i++) pargv[i] = argv[i];
458
459	showhelp = (pargc <= 1);
460	outOfRange = false;
461
462	#ifdef UNIT_TESTS // UT_DIFF
463	const int minServerID = TEST_GENESERVER_ID;
464	#else // !UNIT_TESTS
465	const int minServerID = 0;
466	#endif
467
468	P.SERVERID = getInt("serverid", 0, minServerID, 100, "Server Id, look into $ARBHOME/lib/arb_tcp.dat");
469	#ifdef UNIT_TESTS // UT_DIFF
470	if (P.SERVERID<0) { arb_assert(P.SERVERID == TEST_SERVER_ID \|\| P.SERVERID == TEST_GENESERVER_ID); }
471	#endif
472
473	P.DESIGNCLIPOUTPUT = getInt("designmaxhits", 100, 10, 10000, "Maximum Number of Probe Design Suggestions");
474	P.DESIGNNAMES = getString("designnames", "", "List of short names separated by '#'");
475
476	P.sequence = NULp;
477	while ((P.DESIGNSEQUENCE = getString("designsequence", NULp, "Additional Sequences, will be added to the target group"))) {
478	apd_sequence *s = new apd_sequence;
479	s->next = P.sequence;
480	P.sequence = s;
481	s->sequence = P.DESIGNSEQUENCE;
482	P.DESIGNSEQUENCE = NULp;
483	}
484	P.DESIGNPROBELEN = getInt("designprobelength", 18, 2, 100, "(min.) length of probe");
485	P.DESIGNMAXPROBELEN = getInt("designmaxprobelength", -1, -1, 100, "max. length of probe (if specified)");
486	P.MINTEMP = getInt("designmintemp", 0, 0, 400, "Minimum melting temperature of probe");
487	P.MAXTEMP = getInt("designmaxtemp", 400, 0, 400, "Maximum melting temperature of probe");
488	P.MINGC = getInt("designmingc", 30, 0, 100, "Minimum gc content");
489	P.MAXGC = getInt("designmaxgc", 80, 0, 100, "Maximum gc content");
490	P.MAXBOND = getInt("designmaxbond", 0, 0, 10, "Not implemented");
491	P.MINPOS = getInt("designminpos", -1, -1, INT_MAX, "Minimum ecoli position (-1=none)");
492	P.MAXPOS = getInt("designmaxpos", -1, -1, INT_MAX, "Maximum ecoli position (-1=none)");
493	P.MISHIT = getInt("designmishit", 0, 0, 10000, "Number of allowed hits outside the selected group");
494	P.MINTARGETS = getInt("designmintargets", 50, 0, 100, "Minimum percentage of hits within the selected species");
495
496	P.SEQUENCE = getString("matchsequence", "agtagtagt", "The sequence to search for");
497
498	P.MISMATCHES = getInt("matchmismatches", 0, 0, INT_MAX, "Maximum Number of allowed mismatches");
499	P.ALSO_REVCOMPL = getInt("matchAlsoRevcomp", 0, 0, 1, "Also match reverse-complemented probe");
500	P.WEIGHTED = getInt("matchweighted", 0, 0, 1, "Use weighted mismatches");
501	P.ACCEPTN = getInt("matchacceptN", 1, 0, INT_MAX, "Amount of N-matches not counted as mismatch");
502	P.LIMITN = getInt("matchlimitN", 4, 0, INT_MAX, "Limit for N-matches. If reached N-matches are mismatches");
503	P.MAXRESULT = getInt("matchmaxresults", 1000000, 0, INT_MAX, "Max. number of matches reported (0=unlimited)");
504
505	P.ITERATE = getInt("iterate", 0, 0, 20, "Iterate over probes of given length");
506	P.ITERATE_AMOUNT = getInt("iterate_amount", 100, 1, INT_MAX, "Number of results per answer");
507	P.ITERATE_READABLE = getInt("iterate_readable", 1, 0, 1, "readable results");
508
509	P.ITERATE_TU = getString("iterate_tu", "T", "use T or U in readable result");
510	P.ITERATE_SEPARATOR = getString("iterate_separator", ";", "Number of results per answer");
511
512	P.DUMP = getString("dump", "", "dump ptserver index to file (may be huge!)");
513
514	if (pargc>1) {
515	printf("Unknown (or duplicate) parameter %s\n", pargv[1]);
516	return false;
517	}
518	if (outOfRange) {
519	puts("Not all parameters were inside allowed range\n");
520	return false;
521	}
522
523	return !showhelp;
524	}
525
526	// --------------------------------------------------------------------------------
527
528	#ifdef UNIT_TESTS
529	#ifndef TEST_UNIT_H
530	#include <test_unit.h>
531	#endif
532
533	void TEST_BASIC_parseCommandLine() {
534	{
535	const char *args[] = { NULp, "serverid=0"};
536	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
537
538	// test default values here
539	TEST_EXPECT_EQUAL(P.ACCEPTN, 1);
540	TEST_EXPECT_EQUAL(P.LIMITN, 4);
541	TEST_EXPECT_EQUAL(P.MISMATCHES, 0);
542	TEST_EXPECT_EQUAL(P.MAXRESULT, 1000000);
543	}
544
545	{
546	const char *args[] = {NULp, "serverid=4", "matchmismatches=2"};
547	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
548	TEST_EXPECT_EQUAL(P.SERVERID, 4);
549	TEST_EXPECT_EQUAL(P.MISMATCHES, 2);
550	TEST_EXPECT_EQUAL(args[1], "serverid=4"); // check array args was not modified
551	}
552
553	{
554	const char *args[] = { NULp, "matchacceptN=0", "matchlimitN=5"};
555	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
556	TEST_EXPECT_EQUAL(P.ACCEPTN, 0);
557	TEST_EXPECT_EQUAL(P.LIMITN, 5);
558	}
559
560	{
561	const char *args[] = { NULp, "matchmaxresults=100"};
562	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
563	TEST_EXPECT_EQUAL(P.MAXRESULT, 100);
564	}
565	}
566
567	#endif // UNIT_TESTS
568
569	// --------------------------------------------------------------------------------
570
571
572	static char *execute(ARB_ERROR& error) {
573	char *answer;
574	if (*P.DESIGNNAMES \|\| P.sequence) {
575	answer = AP_probe_design_event(error);
576	}
577	else if (P.ITERATE>0) {
578	answer = AP_probe_iterate_event(error);
579	}
580	else if (P.DUMP[0]) {
581	answer = AP_dump_index_event(error);
582	}
583	else {
584	answer = AP_probe_match_event(error);
585	}
586	pd_gl.locs.clear();
587	return answer;
588	}
589
590	int ARB_main(int argc, char *argv[]) {
591	bool ok = parseCommandLine(argc, argv);
592	if (ok) {
593	ARB_ERROR error;
594	char *answer = execute(error);
595
596	arb_assert(contradicted(answer, error));
597
598	if (!answer) {
599	fprintf(stderr,
600	"arb_probe: Failed to process your request\n"
601	" Reason: %s",
602	error.deliver());
603	ok = false;
604	}
605	else {
606	fputs(answer, stdout);
607	free(answer);
608	error.expect_no_error();
609	}
610	}
611	return ok ? EXIT_SUCCESS : EXIT_FAILURE;
612	}
613
614	// --------------------------------------------------------------------------------
615
616	#ifdef UNIT_TESTS
617	#ifndef TEST_UNIT_H
618	#include <test_unit.h>
619	#endif
620
621	static int test_setup(bool use_gene_ptserver) {
622	static bool setup[2] = { false, false };
623	if (!setup[use_gene_ptserver]) {
624	TEST_SETUP_GLOBAL_ENVIRONMENT(use_gene_ptserver ? "ptserver_gene" : "ptserver"); // first call will recreate the test pt-server
625	setup[use_gene_ptserver] = true;
626	}
627	return use_gene_ptserver ? TEST_GENESERVER_ID : TEST_SERVER_ID;
628	}
629
630	// ----------------------------------
631	// test probe design / match
632
633	#define TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv) \
634	int serverid = test_setup(use_gene_ptserver); \
635	TEST_EXPECT_EQUAL(true, parseCommandLine(fake_argc, fake_argv)); \
636	TEST_EXPECT((serverid == TEST_SERVER_ID)\|\|(serverid == TEST_GENESERVER_ID)); \
637	P.SERVERID = serverid; \
638	ARB_ERROR error; \
639	char *answer = execute(error)
640
641	#define TEST_ARB_PROBE__REPORTS_ERROR(fake_argc,fake_argv,expected_error) \
642	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
643	free(answer); \
644	TEST_EXPECT_ERROR_CONTAINS(error.deliver(), expected_error)
645
646	#define TEST_ARB_PROBE__REPORTS_ERROR__BROKEN(fake_argc,fake_argv,expected_error) \
647	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
648	free(answer); \
649	TEST_EXPECT_ANY_ERROR(error.preserve()); \
650	TEST_EXPECT_ERROR_CONTAINS__BROKEN(error.deliver(), expected_error)
651
652
653	#define TEST_RUN_ARB_PROBE(fake_argc,fake_argv) \
654	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
655	TEST_EXPECT_NO_ERROR(error.deliver())
656
657	#define TEST_ARB_PROBE(fake_argc,fake_argv,expected) do { \
658	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
659	TEST_EXPECT_EQUAL(answer, expected); \
660	free(answer); \
661	} while(0)
662
663	#define TEST_ARB_PROBE__BROKEN(fake_argc,fake_argv,expected) do { \
664	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
665	TEST_EXPECT_EQUAL__BROKEN(answer, expected); \
666	free(answer); \
667	} while(0)
668
669	#define TEST_ARB_PROBE_FILT(fake_argc,fake_argv,filter,expected) do { \
670	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
671	char *filtered = filter(answer); \
672	TEST_EXPECT_EQUAL(filtered, expected); \
673	free(filtered); \
674	free(answer); \
675	} while(0)
676
677	typedef const char *CCP;
678
679	void TEST_SLOW_match_geneprobe() {
680	// test here runs versus database ../UNIT_TESTER/run/TEST_gpt_src.arb
681
682	bool use_gene_ptserver = true;
683	{
684	const char *arguments[] = {
685	"prgnamefake",
686	"matchsequence=NNUCNN",
687	"matchacceptN=4",
688	"matchlimitN=5",
689	};
690	CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NNUCNN'\1"
691	"genome2\1" " genome2 gene3 0 4 2.6 2 1 0 .........-UU==GG-UUGAUC.\1"
692	"genome2\1" " genome2 joined1 0 4 2.6 2 1 0 .........-UU==GG-UUGAUCCUG\1"
693	"genome2\1" " genome2 gene1 0 4 2.6 2 2 0 ........A-UU==GG-U.\1"
694	"genome2\1" " genome2 intergene_19_65 0 4 2.7 31 12 0 GGUUACUGC-AU==GG-UGUUCGCCU\1"
695	"genome1\1" " genome1 intergene_17_65 0 4 2.7 31 14 0 GGUUACUGC-UA==GG-UGUUCGCCU\1"
696	"genome2\1" " genome2 intergene_19_65 0 4 2.7 38 19 0 GCAUUCGGU-GU==GC-CUAAGCACU\1"
697	"genome1\1" " genome1 intergene_17_65 0 4 2.7 38 21 0 GCUAUCGGU-GU==GC-CUAAGCCAU\1"
698	"genome2\1" " genome2 gene3 0 4 2.9 10 9 0 .UUUCGGUU-GA==..-\1"
699	"genome2\1" " genome2 intergene_19_65 0 4 3.1 56 37 0 AGCACUGCG-AG==AU-AUGUA.\1"
700	"genome1\1" " genome1 intergene_17_65 0 4 3.1 56 39 0 AGCCAUGCG-AG==AU-AUGUA.\1"
701	"genome1\1" " genome1 gene2 0 4 3.1 10 2 0 ........U-GA==CU-GC.\1"
702	"genome2\1" " genome2 gene2 0 4 3.1 10 4 0 ......GUU-GA==CU-GCCA.\1"
703	"genome1\1" " genome1 joined1 0 4 3.1 10 7 0 ...CUGGUU-GA==CU-GC.\1"
704	"genome2\1" " genome2 joined1 0 4 3.1 10 9 0 .UUUCGGUU-GA==CU-GCCA.\1";
705
706	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd);
707	}
708
709	{
710	const char *arguments[] = {
711	"prgnamefake",
712	"matchsequence=NGGUUN",
713	"matchacceptN=2",
714	"matchlimitN=3",
715	};
716	CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NGGUUN'\1"
717	"genome1\1" " genome1 gene3 0 2 1.3 5 2 0 ........C-U====G-A.\1"
718	"genome1\1" " genome1 joined1 0 2 1.3 5 2 0 ........C-U====G-AUCCUGC.\1"
719	"genome2\1" " genome2 gene3 0 2 1.4 5 4 0 ......UUU-C====G-AUC.\1"
720	"genome2\1" " genome2 joined1 0 2 1.4 5 4 0 ......UUU-C====G-AUCCUGCCA\1"
721	"genome2\1" " genome2 intergene_19_65 0 2 1.8 21 2 0 ........G-A====A-CUGCAUUCG\1"
722	"genome1\1" " genome1 intergene_17_65 0 2 1.8 21 4 0 ......CAG-A====A-CUGCUAUCG\1";
723
724	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd);
725	}
726
727	{
728	const char *arguments[] = {
729	"prgnamefake",
730	"matchsequence=UGAUCCU", // exists in data
731	};
732	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UGAUCCU'\1"
733	"genome1\1" " genome1 gene2 0 0 0.0 9 1 0 .........-=======-GC.\1"
734	"genome2\1" " genome2 gene2 0 0 0.0 9 3 0 .......GU-=======-GCCA.\1"
735	"genome1\1" " genome1 joined1 0 0 0.0 9 6 0 ....CUGGU-=======-GC.\1"
736	"genome2\1" " genome2 joined1 0 0 0.0 9 8 0 ..UUUCGGU-=======-GCCA.\1";
737
738	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hits in 'joined1' (of both genomes)]
739	}
740	{
741	const char *arguments[] = {
742	"prgnamefake",
743	"matchsequence=GAUCCU",
744	};
745	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'GAUCCU'\1"
746	"genome1\1" " genome1 gene2 0 0 0.0 10 2 0 ........U-======-GC.\1"
747	"genome2\1" " genome2 gene2 0 0 0.0 10 4 0 ......GUU-======-GCCA.\1"
748	"genome1\1" " genome1 joined1 0 0 0.0 10 7 0 ...CUGGUU-======-GC.\1"
749	"genome2\1" " genome2 joined1 0 0 0.0 10 9 0 .UUUCGGUU-======-GCCA.\1";
750
751	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports as much hits as previous test; expected cause probe is part of above probe]
752	}
753	{
754	const char *arguments[] = {
755	"prgnamefake",
756	"matchsequence=UUUCGG", // exists only in genome2
757	};
758	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUUCGG'\1"
759	"genome2\1" " genome2 gene3 0 0 0.0 2 1 0 .........-======-UUGAUC.\1"
760	"genome2\1" " genome2 joined1 0 0 0.0 2 1 0 .........-======-UUGAUCCUG\1"
761	"genome2\1" " genome2 gene1 0 0 0.0 2 2 0 ........A-======-U.\1";
762
763	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hit in genome2/gene1]
764	}
765	{
766	const char *arguments[] = {
767	"prgnamefake",
768	"matchsequence=AUCCUG",
769	};
770	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'AUCCUG'\1"
771	"genome1\1" " genome1 gene2 0 0 0.0 11 3 0 .......UG-======-C.\1"
772	"genome2\1" " genome2 gene2 0 0 0.0 11 5 0 .....GUUG-======-CCA.\1"
773	"genome1\1" " genome1 joined1 0 0 0.0 11 8 0 ..CUGGUUG-======-C.\1"
774	"genome2\1" " genome2 joined1 0 0 0.0 11 10 0 UUUCGGUUG-======-CCA.\1";
775
776	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hits in 'gene2' and 'joined1' of both genomes]
777	}
778	{
779	const char *arguments[] = {
780	"prgnamefake",
781	"matchsequence=UUGAUCCUGC",
782	};
783	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUGAUCCUGC'\1"
784	"genome2\1" " genome2 gene2 0 0 0.0 8 2 0 ........G-==========-CA.\1"
785	"genome1\1" " genome1 joined1 0 0 0.0 8 5 0 .....CUGG-==========-.\1"
786	"genome2\1" " genome2 joined1 0 0 0.0 8 7 0 ...UUUCGG-==========-CA.\1";
787
788	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hit in 'genome2/joined1']
789	}
790	}
791
792	__ATTR__REDUCED_OPTIMIZE void TEST_SLOW_match_probe() {
793	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
794
795	bool use_gene_ptserver = false;
796	{
797	const char *arguments[] = {
798	"prgnamefake",
799	"matchsequence=UAUCGGAGAGUUUGA",
800	};
801	CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UAUCGGAGAGUUUGA'\1"
802	"BcSSSS00\1" " BcSSSS00 0 0 0.0 3 2 0 .......UU-===============-UCAAGUCGA\1";
803
804	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
805	}
806
807	// ----------------------------------------------------------------------------
808	// match with old(=default) N-mismatch-behavior (accepting 1 N-match)
809
810	{
811	const char *arguments[] = {
812	"prgnamefake",
813	"matchsequence=CANCUCCUUUC", // contains 1 N
814	NULp // matchmismatches
815	};
816
817	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
818	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"; // only N-mismatch accepted
819
820	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
821	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
822	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
823	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
824	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
825	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
826	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
827	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
828	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
829	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1";
830
831	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
832	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
833	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
834	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
835	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
836	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
837	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
838	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
839	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
840	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
841	"AclPleur\1" " AclPleur 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
842	"PtVVVulg\1" " PtVVVulg 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
843	"DlcTolu2\1" " DlcTolu2 2 3 2.3 176 162 0 CGGCUGGAU-==C======NN-N.\1"
844	"FrhhPhil\1" " FrhhPhil 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
845	"HllHalod\1" " HllHalod 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
846	"CPPParap\1" " CPPParap 2 3 2.3 177 163 0 CGGNUGGAU-==C======..-\1";
847
848	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
849	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
850	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
851	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
852	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
853	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
854	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
855	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
856	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
857	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
858	"AclPleur\1" " AclPleur 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
859	"PtVVVulg\1" " PtVVVulg 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
860	"DlcTolu2\1" " DlcTolu2 2 3 2.3 176 162 0 CGGCUGGAU-==C======NN-N.\1"
861	"FrhhPhil\1" " FrhhPhil 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
862	"HllHalod\1" " HllHalod 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
863	"CPPParap\1" " CPPParap 2 3 2.3 177 163 0 CGGNUGGAU-==C======..-\1"
864	"VblVulni\1" " VblVulni 3 1 3.6 49 44 0 AGCACAGAG-a=A==uG====-UCGGGUGGC\1";
865
866	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
867	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
868	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
869	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
870	}
871
872	{
873	const char *arguments[] = {
874	"prgnamefake",
875	"matchsequence=UCACCUCCUUUC", // contains no N
876	NULp // matchmismatches
877	};
878
879	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
880	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
881	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
882	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
883	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
884	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
885	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
886	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
887	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1";
888
889	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
890	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
891	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
892	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
893	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
894	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
895	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
896	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
897	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
898	"AclPleur\1" " AclPleur 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
899	"PtVVVulg\1" " PtVVVulg 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
900	"DlcTolu2\1" " DlcTolu2 1 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
901	"FrhhPhil\1" " FrhhPhil 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
902	"HllHalod\1" " HllHalod 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
903	"CPPParap\1" " CPPParap 1 2 1.4 176 162 0 GCGGNUGGA-==========..-\1";
904
905	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
906	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
907	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
908	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
909	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
910	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
911	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
912	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
913	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
914	"AclPleur\1" " AclPleur 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
915	"PtVVVulg\1" " PtVVVulg 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
916	"DlcTolu2\1" " DlcTolu2 1 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
917	"FrhhPhil\1" " FrhhPhil 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
918	"HllHalod\1" " HllHalod 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
919	"CPPParap\1" " CPPParap 1 2 1.4 176 162 0 GCGGNUGGA-==========..-\1"
920	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C=========-U.\1"
921	"LgtLytic\1" " LgtLytic 2 3 2.1 175 161 0 GCGGCUGGA-=========N..-\1"
922	"PslFlave\1" " PslFlave 2 3 2.1 175 161 0 GCGGCUGGA-=========...-\1";
923
924	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
925	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
926	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
927	}
928
929	{
930	const char *arguments[] = {
931	"prgnamefake",
932	"matchsequence=UCACCUCCUUUC", // contains no N
933	NULp, // matchmismatches
934	"matchweighted=1", // use weighted mismatches
935	};
936
937	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
938	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
939	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
940	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
941	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
942	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
943	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
944	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
945	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1";
946
947	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
948	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
949	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
950	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
951	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
952	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
953	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
954	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
955	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
956	"DlcTolu2\1" " DlcTolu2 1 2 0.6 175 161 0 GCGGCUGGA-==========NN-N.\1"
957	"FrhhPhil\1" " FrhhPhil 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
958	"HllHalod\1" " HllHalod 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
959	"CPPParap\1" " CPPParap 1 2 0.6 176 162 0 GCGGNUGGA-==========..-\1"
960	"AclPleur\1" " AclPleur 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
961	"PtVVVulg\1" " PtVVVulg 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
962	"LgtLytic\1" " LgtLytic 2 3 1.3 175 161 0 GCGGCUGGA-=========N..-\1"
963	"PslFlave\1" " PslFlave 2 3 1.3 175 161 0 GCGGCUGGA-=========...-\1"
964	"ClfPerfr\1" " ClfPerfr 2 0 1.3 175 161 0 AAGAUUAAU-A=C=========-U.\1";
965
966	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
967	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
968	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
969	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
970	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
971	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
972	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
973	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
974	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
975	"DlcTolu2\1" " DlcTolu2 1 2 0.6 175 161 0 GCGGCUGGA-==========NN-N.\1"
976	"FrhhPhil\1" " FrhhPhil 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
977	"HllHalod\1" " HllHalod 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
978	"CPPParap\1" " CPPParap 1 2 0.6 176 162 0 GCGGNUGGA-==========..-\1"
979	"AclPleur\1" " AclPleur 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
980	"PtVVVulg\1" " PtVVVulg 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
981	"LgtLytic\1" " LgtLytic 2 3 1.3 175 161 0 GCGGCUGGA-=========N..-\1"
982	"PslFlave\1" " PslFlave 2 3 1.3 175 161 0 GCGGCUGGA-=========...-\1"
983	"ClfPerfr\1" " ClfPerfr 2 0 1.3 175 161 0 AAGAUUAAU-A=C=========-U.\1"
984	"AclPleur\1" " AclPleur 5 0 2.4 50 45 0 GAAGGGAGC-=ug=u=u====G-CCGACGAGU\1"
985	"PtVVVulg\1" " PtVVVulg 5 0 2.4 50 45 0 GGAGAAAGC-=ug=u=u===g=-UGACGAGCG\1";
986
987	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
988	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
989	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
990	}
991
992	// ----------------------------------------------
993	// do not accept any N-matches as match
994
995	{
996	const char *arguments[] = {
997	"prgnamefake",
998	"matchsequence=CANCUCCUUUC", // contains 1 N
999	NULp, // matchmismatches
1000	"matchacceptN=0",
1001	};
1002
1003	CCP expectd0 = ""; // nothing matches
1004
1005	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
1006	"BcSSSS00\1" " BcSSSS00 1 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1";
1007
1008	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
1009	"BcSSSS00\1" " BcSSSS00 1 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
1010	"ClfPerfr\1" " ClfPerfr 2 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
1011	"PbcAcet2\1" " PbcAcet2 2 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1012	"PbrPropi\1" " PbrPropi 2 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1013	"Stsssola\1" " Stsssola 2 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
1014	"DcdNodos\1" " DcdNodos 2 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
1015	"VbrFurni\1" " VbrFurni 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
1016	"VblVulni\1" " VblVulni 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
1017	"VbhChole\1" " VbhChole 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1";
1018
1019	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1020	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1021	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1022	}
1023	{
1024	const char *arguments[] = {
1025	"prgnamefake",
1026	"matchsequence=UUUCUUU", // contains no N
1027	NULp, // matchmismatches
1028	"matchacceptN=0",
1029	};
1030
1031	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1032	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1";
1033
1034	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1035	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1"
1036	"AclPleur\1" " AclPleur 1 0 0.6 50 45 0 GAAGGGAGC-==g====-CUUUGCCGA\1"
1037	"PtVVVulg\1" " PtVVVulg 1 0 0.6 50 45 0 GGAGAAAGC-==g====-CUUGCUGAC\1"
1038	"PtVVVulg\1" " PtVVVulg 1 0 0.6 54 49 0 AAAGCUUGC-======g-CUGACGAGC\1"
1039	"ClfPerfr\1" " ClfPerfr 1 0 1.1 49 44 0 GCGAUGAAG-====C==-CGGGAAACG\1";
1040
1041	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1042	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1"
1043	"AclPleur\1" " AclPleur 1 0 0.6 50 45 0 GAAGGGAGC-==g====-CUUUGCCGA\1"
1044	"PtVVVulg\1" " PtVVVulg 1 0 0.6 50 45 0 GGAGAAAGC-==g====-CUUGCUGAC\1"
1045	"PtVVVulg\1" " PtVVVulg 1 0 0.6 54 49 0 AAAGCUUGC-======g-CUGACGAGC\1"
1046	"ClfPerfr\1" " ClfPerfr 1 0 1.1 49 44 0 GCGAUGAAG-====C==-CGGGAAACG\1"
1047	"DlcTolu2\1" " DlcTolu2 2 0 1.2 47 42 0 AGAAAGGGA-==g===g-CAAUCCUGA\1"
1048	"ClnCorin\1" " ClnCorin 2 0 1.7 48 43 0 AGCGAUGAA-g===C==-CGGGAAUGG\1"
1049	"CPPParap\1" " CPPParap 2 0 1.7 48 43 0 AGCGAUGAA-g===C==-CGGGAACGG\1"
1050	"HllHalod\1" " HllHalod 2 0 1.7 49 44 0 GAUGGAAGC-==g===C-CAGGCGUCG\1"
1051	"DcdNodos\1" " DcdNodos 2 0 1.7 50 45 0 UUAUGUAGC-==g==A=-GUAACCUAG\1"
1052	"VbhChole\1" " VbhChole 2 0 1.7 55 50 0 GAGGAACUU-g===C==-GGGUGGCGA\1"
1053	"VbrFurni\1" " VbrFurni 2 0 1.7 62 57 0 UUCGGGGGA-===G==g-GGCGGCGAG\1"
1054	"VblVulni\1" " VblVulni 2 0 1.7 62 57 0 AGAAACUUG-=====Cg-GGUGGCGAG\1"
1055	"VbhChole\1" " VbhChole 2 0 1.7 62 57 0 AGGAACUUG-==C===g-GGUGGCGAG\1"
1056	"ClnCorin\1" " ClnCorin 2 0 2.2 49 44 0 GCGAUGAAG-==C===C-GGGAAUGGA\1"
1057	"CltBotul\1" " CltBotul 2 0 2.2 49 44 0 GCGAUGAAG-C=====C-GGAAGUGGA\1"
1058	"CPPParap\1" " CPPParap 2 0 2.2 49 44 0 GCGAUGAAG-==C===C-GGGAACGGA\1"
1059	"ClfPerfr\1" " ClfPerfr 2 0 2.2 50 45 0 CGAUGAAGU-==C===C-GGGAAACGG\1"
1060	"VblVulni\1" " VblVulni 2 0 2.2 52 47 0 ACAGAGAAA-C==G===-CUCGGGUGG\1"
1061	"BcSSSS00\1" " BcSSSS00 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-CU.\1"
1062	"ClfPerfr\1" " ClfPerfr 2 0 2.2 179 165 0 UUAAUACCC-C=C====-CU.\1"
1063	"PbcAcet2\1" " PbcAcet2 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-NN.\1"
1064	"PbrPropi\1" " PbrPropi 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-NN.\1"
1065	"Stsssola\1" " Stsssola 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1066	"DcdNodos\1" " DcdNodos 2 0 2.2 179 165 0 UUGGAUCAC-C=C====-.\1"
1067	"VbrFurni\1" " VbrFurni 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1068	"VblVulni\1" " VblVulni 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1069	"VbhChole\1" " VbhChole 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1070	"BcSSSS00\1" " BcSSSS00 2 2 1.4 183 169 0 AUCACCUCC-=====..-\1"
1071	"ClfPerfr\1" " ClfPerfr 2 2 1.4 183 169 0 UACCCCUCC-=====..-\1";
1072
1073	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1074	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1075	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1076	}
1077	{
1078	const char *arguments[] = {
1079	"prgnamefake",
1080	"matchsequence=UCACCUCCUUUC", // contains no N
1081	NULp, // matchmismatches
1082	"matchacceptN=0",
1083	};
1084
1085	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1086	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "";
1087
1088	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1089	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
1090	"PbcAcet2\1" " PbcAcet2 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1091	"PbrPropi\1" " PbrPropi 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1092	"Stsssola\1" " Stsssola 1 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
1093	"DcdNodos\1" " DcdNodos 1 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
1094	"VbrFurni\1" " VbrFurni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1095	"VblVulni\1" " VblVulni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1096	"VbhChole\1" " VbhChole 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1";
1097
1098	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1099	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
1100	"PbcAcet2\1" " PbcAcet2 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1101	"PbrPropi\1" " PbrPropi 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1102	"Stsssola\1" " Stsssola 1 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
1103	"DcdNodos\1" " DcdNodos 1 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
1104	"VbrFurni\1" " VbrFurni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1105	"VblVulni\1" " VblVulni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1106	"VbhChole\1" " VbhChole 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1107	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C=========-U.\1"
1108	"AclPleur\1" " AclPleur 2 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
1109	"PtVVVulg\1" " PtVVVulg 2 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
1110	"DlcTolu2\1" " DlcTolu2 2 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
1111	"FrhhPhil\1" " FrhhPhil 2 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
1112	"HllHalod\1" " HllHalod 2 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
1113	"CPPParap\1" " CPPParap 2 2 1.4 176 162 0 GCGGNUGGA-==========..-\1";
1114
1115	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1116	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1117	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1118	}
1119	{
1120	const char *arguments[] = {
1121	"prgnamefake",
1122	"matchsequence=UCACCUCCUUUCU", // contains no N
1123	NULp, // matchmismatches
1124	"matchacceptN=0",
1125	};
1126
1127	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1128	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1";
1129
1130	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1131	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1132	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1133	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1134	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1135	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1136	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1137	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1138	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1139	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1";
1140
1141	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1142	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1143	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1144	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1145	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1146	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1147	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1148	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1149	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1150	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1151	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1152	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1153	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1154	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1155	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1156	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1";
1157
1158	CCP expectd4 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1159	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1160	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1161	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1162	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1163	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1164	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1165	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1166	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1167	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1168	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1169	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1170	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1171	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1172	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1173	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1"
1174	"LgtLytic\1" " LgtLytic 4 4 2.8 175 161 0 GCGGCUGGA-=========N...-\1"
1175	"PslFlave\1" " PslFlave 4 4 2.8 175 161 0 GCGGCUGGA-=========....-\1";
1176
1177	CCP expectd5 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1178	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1179	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1180	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1181	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1182	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1183	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1184	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1185	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1186	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1187	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1188	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1189	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1190	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1191	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1192	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1"
1193	"LgtLytic\1" " LgtLytic 4 4 2.8 175 161 0 GCGGCUGGA-=========N...-\1"
1194	"PslFlave\1" " PslFlave 4 4 2.8 175 161 0 GCGGCUGGA-=========....-\1"
1195	"PtVVVulg\1" " PtVVVulg 5 0 2.6 50 45 0 GGAGAAAGC-=ug=u=u===g==-GACGAGCGG\1"
1196	"AclPleur\1" " AclPleur 5 0 3.5 46 41 0 ACGGGAAGG-gag=u=G======-UUGCCGACG\1"
1197	"PtVVVulg\1" " PtVVVulg 5 0 4.0 45 40 0 ...AGGAGA-Aag=u=G======-UGCUGACGA\1"
1198	"VblVulni\1" " VblVulni 5 0 4.3 48 43 0 CAGCACAGA-ga=a==uG=====-CGGGUGGCG\1";
1199
1200	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1201	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1202	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1203	arguments[2] = "matchmismatches=4"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd4);
1204	arguments[2] = "matchmismatches=5"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd5);
1205	}
1206
1207	// ----------------------------------
1208	// accept several N-matches
1209
1210	{
1211	const char *arguments[] = {
1212	"prgnamefake",
1213	"matchsequence=CANCUCCUUNC", // contains 2 N
1214	NULp, // matchmismatches
1215	"matchacceptN=2",
1216	"matchlimitN=4",
1217	};
1218
1219	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1220	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1";
1221
1222	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1223	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1"
1224	"ClfPerfr\1" " ClfPerfr 1 2 2.8 176 162 0 AGAUUAAUA-=CC======U=-U.\1"
1225	"DlcTolu2\1" " DlcTolu2 1 3 2.4 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1226	"FrhhPhil\1" " FrhhPhil 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1227	"HllHalod\1" " HllHalod 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1228	"CPPParap\1" " CPPParap 1 3 2.4 177 163 0 CGGNUGGAU-==C======..-\1"
1229	"PbcAcet2\1" " PbcAcet2 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1230	"PbrPropi\1" " PbrPropi 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1231	"Stsssola\1" " Stsssola 1 3 2.4 176 162 0 CGGCUGGAU-==C======U.-\1"
1232	"DcdNodos\1" " DcdNodos 1 3 2.4 176 162 0 CGGUUGGAU-==C======U.-\1"
1233	"VbrFurni\1" " VbrFurni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1234	"VblVulni\1" " VblVulni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1235	"VbhChole\1" " VbhChole 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1236	"AclPleur\1" " AclPleur 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1"
1237	"PtVVVulg\1" " PtVVVulg 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1";
1238
1239	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1240	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1"
1241	"ClfPerfr\1" " ClfPerfr 1 2 2.8 176 162 0 AGAUUAAUA-=CC======U=-U.\1"
1242	"DlcTolu2\1" " DlcTolu2 1 3 2.4 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1243	"FrhhPhil\1" " FrhhPhil 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1244	"HllHalod\1" " HllHalod 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1245	"CPPParap\1" " CPPParap 1 3 2.4 177 163 0 CGGNUGGAU-==C======..-\1"
1246	"PbcAcet2\1" " PbcAcet2 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1247	"PbrPropi\1" " PbrPropi 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1248	"Stsssola\1" " Stsssola 1 3 2.4 176 162 0 CGGCUGGAU-==C======U.-\1"
1249	"DcdNodos\1" " DcdNodos 1 3 2.4 176 162 0 CGGUUGGAU-==C======U.-\1"
1250	"VbrFurni\1" " VbrFurni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1251	"VblVulni\1" " VblVulni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1252	"VbhChole\1" " VbhChole 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1253	"AclPleur\1" " AclPleur 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1"
1254	"PtVVVulg\1" " PtVVVulg 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1";
1255
1256	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1257	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1258	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1259	}
1260
1261	{
1262	const char *arguments[] = {
1263	"prgnamefake",
1264	"matchsequence=GAGCGGUCAG", // similar to a region where dots occur in seqdata
1265	NULp, // matchmismatches
1266	"matchacceptN=0",
1267	"matchlimitN=4",
1268	};
1269
1270	CCP expectd0 = "";
1271
1272	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1273	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1";
1274
1275	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1276	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1"
1277	"Bl0LLL00\1" " Bl0LLL00 2 0 2.2 25 21 0 GAUCAAGUC-======A=C=-ACGGGAGCU\1";
1278
1279	// this probe-match is also tested with 'arb_probe_match'. see arb_test.cxx@TEST_arb_probe_match
1280	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1281	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1"
1282	"Bl0LLL00\1" " Bl0LLL00 2 0 2.2 25 21 0 GAUCAAGUC-======A=C=-ACGGGAGCU\1"
1283	"VbrFurni\1" " VbrFurni 3 0 2.4 68 60 0 GGAUUUGUU-=g====CG==-CGGCGGACG\1"
1284	"FrhhPhil\1" " FrhhPhil 3 0 2.8 82 70 0 ACGAGUGGC-=gA===C===-UUGGAAACG\1"
1285	"ClfPerfr\1" " ClfPerfr 3 0 3.2 86 74 0 CGGCGGGAC-=g==CU====-AACCUGCGG\1"
1286	"HllHalod\1" " HllHalod 3 0 3.6 25 21 0 GAUCAAGUC-======Aa=C-GAUGGAAGC\1"
1287	"DlcTolu2\1" " DlcTolu2 3 0 3.6 95 83 0 GGACUGCCC-==Aa==A===-CUAAUACCG\1"
1288	"FrhhPhil\1" " FrhhPhil 3 0 4.0 25 21 0 GAUCAAGUC-==A====a=C-AGGUCUUCG\1"
1289	"AclPleur\1" " AclPleur 3 0 4.0 29 24 0 GAUCAAGUC-==A====a=C-GGGAAGGGA\1"
1290	"ClnCorin\1" " ClnCorin 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUCCUUCG\1"
1291	"CltBotul\1" " CltBotul 3 0 4.1 25 21 0 .AUCAAGUC-=====A=G=A-GCUUCUUCG\1"
1292	"CPPParap\1" " CPPParap 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUCCUUCG\1"
1293	"ClfPerfr\1" " ClfPerfr 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUUCCUUC\1"
1294	"DlcTolu2\1" " DlcTolu2 3 0 4.1 157 143 0 GUAGCCGUU-===GAA====-CGGCUGGAU\1"
1295	"PslFlave\1" " PslFlave 3 3 2.4 25 21 0 GAUCAAGUC-=======...-<more>\1"
1296	"PtVVVulg\1" " PtVVVulg 3 3 2.4 29 24 0 GAUCAAGUC-=======...-<more>\1";
1297
1298	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1299	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1300	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1301	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1302	}
1303
1304	{
1305	const char *arguments[] = {
1306	"prgnamefake",
1307	"matchsequence=GAGCGGUCAGGAG", // as above, but continues behind '...'
1308	NULp, // matchmismatches
1309	"matchweighted=1", // use weighted mismatches
1310	};
1311
1312	CCP expectd2 = "";
1313	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAGGAG'\1"
1314	"ClnCorin\1" " ClnCorin 6 0 3.4 77 66 0 AUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1315	"CltBotul\1" " CltBotul 6 0 3.4 77 66 0 GUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1316	"CPPParap\1" " CPPParap 6 0 3.4 77 66 0 ACGGAUUAG-Cg====A=g==CC-UUCCGAAAG\1"
1317	"BcSSSS00\1" " BcSSSS00 3 0 3.4 25 21 0 GAUCAAGUC-======A===AU=-GGAGCUUGC\1";
1318
1319	CCP expectd4 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAGGAG'\1"
1320	"ClnCorin\1" " ClnCorin 6 0 3.4 77 66 0 AUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1321	"CltBotul\1" " CltBotul 6 0 3.4 77 66 0 GUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1322	"CPPParap\1" " CPPParap 6 0 3.4 77 66 0 ACGGAUUAG-Cg====A=g==CC-UUCCGAAAG\1"
1323	"BcSSSS00\1" " BcSSSS00 3 0 3.4 25 21 0 GAUCAAGUC-======A===AU=-GGAGCUUGC\1"
1324	"ClfPerfr\1" " ClfPerfr 6 0 3.9 121 108 0 AUCAUAAUG-C====A=ug==gU-GAAGUCGUA\1"
1325	"ClnCorin\1" " ClnCorin 6 0 3.9 122 109 0 CGCAUAAGA-C====A=ug==gU-GAAGUCGUA\1"
1326	"CltBotul\1" " CltBotul 6 0 3.9 122 109 0 CUCAUAAGA-C====A=ug==gU-GAAGUCGUA\1"
1327	"CPPParap\1" " CPPParap 6 0 3.9 122 109 0 GCAUAAGAU-C====A=ug==gU-AAGUCGUAA\1"
1328	"DcdNodos\1" " DcdNodos 6 0 4.2 77 66 0 GUAACCUAG-Ug====A=g=AC=-UAUGGAAAC\1"
1329	"PsAAAA00\1" " PsAAAA00 6 0 4.2 77 66 0 UGGAUUCAG-Cg====A=g=AC=-UCCGGAAAC\1"
1330	"PslFlave\1" " PslFlave 6 0 4.2 77 66 0 CUGAUUCAG-Cg====A=g=AC=-UUUCGAAAG\1"
1331	"FrhhPhil\1" " FrhhPhil 5 0 4.2 149 135 0 UAACAAUGG-U===C==ag===A-CCUGCGGCU\1"
1332	"AclPleur\1" " AclPleur 4 0 4.3 29 24 0 GAUCAAGUC-==A====a=C=g=-AAGGGAGCU\1"
1333	"PbcAcet2\1" " PbcAcet2 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1334	"PbrPropi\1" " PbrPropi 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1335	"Stsssola\1" " Stsssola 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1336	"LgtLytic\1" " LgtLytic 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1337	"PslFlave\1" " PslFlave 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1338	"HllHalod\1" " HllHalod 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1339	"VbrFurni\1" " VbrFurni 5 0 4.4 68 60 0 GGAUUUGUU-=g====CG==Cg=-CGGACGGAC\1"
1340	"AclPleur\1" " AclPleur 6 0 4.4 35 30 0 GUCGAACGG-U=A===ga===gA-GCUUGCUUU\1"
1341	"PslFlave\1" " PslFlave 6 6 4.4 25 21 0 GAUCAAGUC-=======......-<more>\1"
1342	"PtVVVulg\1" " PtVVVulg 6 6 4.4 29 24 0 GAUCAAGUC-=======......-<more>\1"
1343	"VbrFurni\1" " VbrFurni 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1"
1344	"VblVulni\1" " VblVulni 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1"
1345	"VbhChole\1" " VbhChole 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1";
1346
1347	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1348	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1349	arguments[2] = "matchmismatches=4"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd4);
1350	}
1351
1352	// --------------------------
1353	// truncate results
1354
1355	{
1356	const char *arguments[] = {
1357	"prgnamefake",
1358	"matchsequence=CANCNCNNUNC", // contains 5N
1359	NULp, // matchmismatches
1360	"matchacceptN=5",
1361	"matchlimitN=7",
1362	"matchmaxresults=5",
1363	};
1364
1365	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1366	"BcSSSS00\1" " BcSSSS00 0 5 4.2 176 162 0 CGGCUGGAU-==C=U=CU=U=-U.\1";
1367
1368	// many hits are truncated here:
1369	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1370	"DlcTolu2\1" " DlcTolu2 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU==N-N.\1"
1371	"FrhhPhil\1" " FrhhPhil 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU=..-\1"
1372	"HllHalod\1" " HllHalod 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU=..-\1"
1373	"CPPParap\1" " CPPParap 1 6 4.9 177 163 0 CGGNUGGAU-==C=U=CU=..-\1"
1374	"AclPleur\1" " AclPleur 1 6 5.0 176 162 0 CGGUUGGAU-==C=U=CU=A.-\1";
1375
1376	// many hits are truncated here:
1377	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1378	"HllHalod\1" " HllHalod 2 5 5.1 45 40 0 AAACGAUGG-a=G=UuGC=U=-CAGGCGUCG\1"
1379	"VblVulni\1" " VblVulni 2 5 5.4 49 44 0 AGCACAGAG-a=A=UuGU=U=-UCGGGUGGC\1"
1380	"VbrFurni\1" " VbrFurni 2 5 5.7 40 35 0 CGGCAGCGA-==A=AuUGAA=-CUUCGGGGG\1"
1381	"LgtLytic\1" " LgtLytic 2 5 6.2 101 89 0 GGGGAAACU-==AGCuAA=A=-CGCAUAAUC\1"
1382	"ClfPerfr\1" " ClfPerfr 2 5 6.5 172 158 0 AGGAAGAUU-a=UaC=CC=C=-UUUCU.\1";
1383
1384	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1385	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1386	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1387	}
1388
1389	// -------------------------------------------------------------
1390	// tests related to http://bugs.arb-home.de/ticket/410
1391	{
1392	const char *arguments[] = {
1393	"prgnamefake",
1394	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACC", // length=29
1395	NULp, // matchmismatches
1396	"matchacceptN=5",
1397	"matchlimitN=7",
1398	"matchmaxresults=10",
1399	};
1400
1401	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'ACGGACUCCGGGAAACCGGGGCUAAUACC'\1"
1402	"BcSSSS00\1" " BcSSSS00 0 0 0.0 84 72 0 UAGCGGCGG-=============================-GGAUGGUGA\1"
1403	"Bl0LLL00\1" " Bl0LLL00 0 0 0.0 84 72 0 CAGCGGCGG-=============================-GGAUGCUGA\1"
1404	"AclPleur\1" " AclPleur 4 0 4.6 84 72 0 GAGUGGCGG-=======a========u=UA=========-GCGUAAUCA\1"
1405	"PtVVVulg\1" " PtVVVulg 4 0 5.1 84 72 0 GAGCGGCGG-=======a=U======G=U==========-GCAUGACCA\1"
1406	"DsssDesu\1" " DsssDesu 5 0 5.3 84 72 0 GAGUGGCGC-========u=C====Gu==A=========-GGAUACAGA\1"
1407	"PsAAAA00\1" " PsAAAA00 5 0 5.3 84 72 0 CAGCGGCGG-======gu=C======G==C=========-GCAUACGCA\1";
1408
1409	arguments[2] = "matchmismatches=5"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1410	}
1411	{
1412	const char *arguments[] = {
1413	"prgnamefake",
1414	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA", // length=38
1415	NULp, // matchmismatches
1416	"matchacceptN=5",
1417	"matchlimitN=7",
1418	"matchmaxresults=100",
1419	};
1420
1421	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA'\1"
1422	"BcSSSS00\1" " BcSSSS00 0 0 0.0 84 72 0 UAGCGGCGG-======================================-UGAUUGGGG\1"
1423	"Bl0LLL00\1" " Bl0LLL00 1 0 1.5 84 72 0 CAGCGGCGG-==================================C===-UGAUUGGGG\1"
1424	"DsssDesu\1" " DsssDesu 8 0 9.4 84 72 0 GAGUGGCGC-========u=C====Gu==A=============ACA==-G.\1"
1425	"PtVVVulg\1" " PtVVVulg 8 0 10.7 84 72 0 GAGCGGCGG-=======a=U======G=U===========C===ACC=-UGACUGGGG\1"
1426	"AclPleur\1" " AclPleur 9 0 10.8 84 72 0 GAGUGGCGG-=======a========u=UA==========Cg=AA=C=-UGACUGGGG\1"
1427	"PsAAAA00\1" " PsAAAA00 10 0 11.9 84 72 0 CAGCGGCGG-======gu=C======G==C==========C==ACgC=-UGGUAACAA\1"
1428	"LgtLytic\1" " LgtLytic 10 0 12.8 84 72 0 GAGNGGCGA-=======uG=======uCAA==========C==AA=C=-UGACUGGGG\1"
1429	"VbrFurni\1" " VbrFurni 10 0 12.8 84 72 0 GAGCGGCGG-======CauU======GAU===========C===A=C=-UGACUGGGG\1"
1430	"VblVulni\1" " VblVulni 10 0 12.8 84 72 0 GAGCGGCGG-======CauU======GAU===========C===A=C=-UGACUGGGG\1"
1431	"Stsssola\1" " Stsssola 10 0 12.9 84 72 0 AAGUGGCGC-======gG=U======G=UC=============AACA=-UGAUUGGGG\1"
1432	"DlcTolu2\1" " DlcTolu2 10 0 13.4 84 72 0 GAGUGGCGC-=======G=CC====GGACA==============AA==-UAAUUGGGG\1"
1433	"PbcAcet2\1" " PbcAcet2 11 0 12.2 84 72 0 AAGUGGCGC-======A=uUC====GG==U=============AAg=g-UAACUGGGG\1"
1434	"HllHalod\1" " HllHalod 11 0 13.0 84 72 0 GAGCGGCGG-======CuG=======uCA===========C==ACgC=-UGACUGGGG\1"
1435	"PbrPropi\1" " PbrPropi 12 0 13.6 84 72 0 UAGUGGCGC-======A=uUC====Ga==U=========U===AAg=g-UGACUGGGG\1"
1436	"DcdNodos\1" " DcdNodos 12 0 14.4 84 72 0 UAGUGGCGG-======guaU======GUAC==========C==AAg==-UGACUGGGG\1"
1437	"VbhChole\1" " VbhChole 12 0 15.4 84 72 0 GAGCGGCGG-======CauU======GAU===========C==AACC=-UGACUGGGG\1";
1438
1439	arguments[2] = "matchmismatches=12"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1440	}
1441
1442
1443	// test expected errors
1444	{
1445	const char *arguments[] = {
1446	"prgnamefake",
1447	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA", // length = 38
1448	"matchmismatches=20",
1449	};
1450
1451	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, "Max. 19 mismatches are allowed for probes of length 38");
1452	}
1453	}
1454
1455	static char extract_locations(const char probe_design_result) {
1456	const char *Target = strstr(probe_design_result, "\nTarget");
1457	if (Target) {
1458	const char *designed = strchr(Target+7, '\n');
1459	if (designed) {
1460	++designed;
1461
1462	GBS_strstruct result(300);
1463	RegExpr reg_designed("^[A-Z]+"
1464	"[[:space:]]+[0-9]+"
1465	"[[:space:]]+([A-Z][=+-])" // subexpr #1 (loc+-=)
1466	"[[:space:]]*([0-9]+)", // subexpr #2 (abs or locrel)
1467	true);
1468
1469
1470	while (designed) {
1471	const char *eol = strchr(designed, '\n');
1472	const RegMatch *match = reg_designed.match(designed); if (!match) break;
1473
1474	match = reg_designed.subexpr_match(1); if (!match) break;
1475	std::string loc = match->extract(designed);
1476
1477	match = reg_designed.subexpr_match(2); if (!match) break;
1478	std::string pos = match->extract(designed);
1479
1480	result.cat(loc.c_str());
1481	result.cat(pos.c_str());
1482
1483	designed = eol ? eol+1 : NULp;
1484	}
1485	arb_assert(implicated(designed, !reg_designed.has_failed())); // assert RegExpr compiled
1486
1487	return result.release();
1488	}
1489	}
1490	return ARB_strdup("can't extract");
1491	}
1492
1493	inline const char next_line(const char this_line) {
1494	const char *lf = strchr(this_line, '\n');
1495	return (lf && lf[1] && strchr("ACGTU", lf[1])) ? lf+1 : NULp;
1496	}
1497	inline int count_hits(const char *design_result) {
1498	const char *target = strstr(design_result, "\nTarget");
1499	if (target) {
1500	const char *hit = next_line(target+1);
1501	int hits = 0;
1502
1503	while (hit) {
1504	++hits;
1505	hit = next_line(hit);
1506	}
1507	return hits;
1508	}
1509	return -1;
1510	}
1511
1512	void TEST_SLOW_design_probe() {
1513	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
1514
1515	bool use_gene_ptserver = false;
1516	{
1517	int hits_len_18;
1518	{
1519	const char *arguments[] = {
1520	"prgnamefake",
1521	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1522	"designmintargets=100",
1523	};
1524	const char *expected =
1525	"Probe design parameters:\n"
1526	"Length of probe 18\n"
1527	"Temperature [ 0.0 -400.0]\n"
1528	"GC-content [30.0 - 80.0]\n"
1529	"E.Coli position [any]\n"
1530	"Max. nongroup hits 0\n"
1531	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1532	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1533	"CGAAAGGAAGAUUAAUAC 18 A=94 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1534	"GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC \| - - - - - - - - - - - - - - - - - - - -\n"
1535	"UCAAGUCGAGCGAUGAAG 18 B=18 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA \| - - - - - - - - - - - - - - - 2 2 2 2 2\n"
1536	"AUCAAGUCGAGCGAUGAA 18 B- 1 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU \| - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n";
1537
1538	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1539	hits_len_18 = count_hits(expected);
1540	TEST_EXPECT_EQUAL(hits_len_18, 4);
1541
1542	// test extraction of positions:
1543	{
1544	char *positions = extract_locations(expected);
1545	TEST_EXPECT_EQUAL(positions, "A=94A+1B=18B-1");
1546	free(positions);
1547	}
1548	}
1549	// same as above with probelength 17
1550	int hits_len_17;
1551	{
1552	const char *arguments[] = {
1553	"prgnamefake",
1554	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1555	"designmintargets=100",
1556	"designprobelength=17",
1557	};
1558	const char *expected =
1559	"Probe design parameters:\n"
1560	"Length of probe 17\n"
1561	"Temperature [ 0.0 -400.0]\n"
1562	"GC-content [30.0 - 80.0]\n"
1563	"E.Coli position [any]\n"
1564	"Max. nongroup hits 0\n"
1565	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1566	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1567	"CAAGUCGAGCGAUGAAG 17 A=19 18 65 4 52.9 52.0 CUUCAUCGCUCGACUUG \| - - - - - - - - - - - - - - - - 2 2 2 2\n"
1568	"UCAAGUCGAGCGAUGAA 17 A- 1 17 49 4 47.1 50.0 UUCAUCGCUCGACUUGA \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1569	"AUCAAGUCGAGCGAUGA 17 A- 2 16 33 4 47.1 50.0 UCAUCGCUCGACUUGAU \| - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2 4\n";
1570
1571	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1572	hits_len_17 = count_hits(expected);
1573	TEST_EXPECT_EQUAL(hits_len_17, 3);
1574	}
1575	// same as above with probelength 16
1576	int hits_len_16;
1577	{
1578	const char *arguments[] = {
1579	"prgnamefake",
1580	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1581	"designmintargets=100",
1582	"designprobelength=16",
1583	};
1584	const char *expected =
1585	"Probe design parameters:\n"
1586	"Length of probe 16\n"
1587	"Temperature [ 0.0 -400.0]\n"
1588	"GC-content [30.0 - 80.0]\n"
1589	"E.Coli position [any]\n"
1590	"Max. nongroup hits 0\n"
1591	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1592	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1593	"CGAAAGGAAGAUUAAU 16 A=94 82 77 4 31.2 42.0 AUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1594	"AAGGAAGAUUAAUACC 16 A+ 3 85 77 4 31.2 42.0 GGUAUUAAUCUUCCUU \| - - - - - - - - - - - - - - - - - - - -\n"
1595	"AAGUCGAGCGAUGAAG 16 B=20 19 69 4 50.0 48.0 CUUCAUCGCUCGACUU \| - - - - - - - - - - - - - - - - - 2 2 2\n"
1596	"CAAGUCGAGCGAUGAA 16 B- 1 18 49 4 50.0 48.0 UUCAUCGCUCGACUUG \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1597	"UCAAGUCGAGCGAUGA 16 B- 2 17 37 4 50.0 48.0 UCAUCGCUCGACUUGA \| - - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2\n"
1598	"AUCAAGUCGAGCGAUG 16 B- 3 16 21 4 50.0 48.0 CAUCGCUCGACUUGAU \| - - - - - 2 2 2 2 2 2 2 2 2 2 2 2 9 9 9\n";
1599
1600	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1601	hits_len_16 = count_hits(expected);
1602	TEST_EXPECT_EQUAL(hits_len_16, 6);
1603	}
1604	// combine the 3 preceeding designs
1605	int combined_hits;
1606	{
1607	const char *arguments[] = {
1608	"prgnamefake",
1609	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1610	"designmintargets=100",
1611	"designprobelength=16",
1612	"designmaxprobelength=18",
1613	};
1614	const char *expected =
1615	"Probe design parameters:\n"
1616	"Length of probe 16-18\n"
1617	"Temperature [ 0.0 -400.0]\n"
1618	"GC-content [30.0 - 80.0]\n"
1619	"E.Coli position [any]\n"
1620	"Max. nongroup hits 0\n"
1621	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1622	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1623	"CGAAAGGAAGAUUAAU 16 A=94 82 77 4 31.2 42.0 AUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1624	"CGAAAGGAAGAUUAAUAC 18 A+ 0 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1625	"GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC \| - - - - - - - - - - - - - - - - - - - -\n"
1626	"AAGGAAGAUUAAUACC 16 A+ 3 85 77 4 31.2 42.0 GGUAUUAAUCUUCCUU \| - - - - - - - - - - - - - - - - - - - -\n"
1627	"AAGUCGAGCGAUGAAG 16 B=20 19 69 4 50.0 48.0 CUUCAUCGCUCGACUU \| - - - - - - - - - - - - - - - - - 2 2 2\n"
1628	"CAAGUCGAGCGAUGAAG 17 B- 1 18 65 4 52.9 52.0 CUUCAUCGCUCGACUUG \| - - - - - - - - - - - - - - - - 2 2 2 2\n"
1629	"UCAAGUCGAGCGAUGAAG 18 B- 2 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA \| - - - - - - - - - - - - - - - 2 2 2 2 2\n"
1630	"UCAAGUCGAGCGAUGAA 17 B- 2 17 49 4 47.1 50.0 UUCAUCGCUCGACUUGA \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1631	"CAAGUCGAGCGAUGAA 16 B- 1 18 49 4 50.0 48.0 UUCAUCGCUCGACUUG \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1632	"AUCAAGUCGAGCGAUGAA 18 B- 3 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU \| - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n"
1633	"UCAAGUCGAGCGAUGA 16 B- 2 17 37 4 50.0 48.0 UCAUCGCUCGACUUGA \| - - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2\n"
1634	"AUCAAGUCGAGCGAUGA 17 B- 3 16 33 4 47.1 50.0 UCAUCGCUCGACUUGAU \| - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2 4\n"
1635	"AUCAAGUCGAGCGAUG 16 B- 3 16 21 4 50.0 48.0 CAUCGCUCGACUUGAU \| - - - - - 2 2 2 2 2 2 2 2 2 2 2 2 9 9 9\n";
1636
1637	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1638	combined_hits = count_hits(expected);
1639	}
1640
1641	// check that combined design reports all probes reported by single designs:
1642	TEST_EXPECT_EQUAL(combined_hits, hits_len_16+hits_len_17+hits_len_18);
1643	}
1644	// test vs bug (fails with [8988] .. [9175])
1645	{
1646	const char *arguments[] = {
1647	"prgnamefake",
1648	"designnames=VbhChole#VblVulni",
1649	"designmintargets=50", // hit at least 1 of the 2 targets
1650	"designmingc=60", "designmaxgc=75", // specific GC range
1651	};
1652
1653	const char *expected =
1654	"Probe design parameters:\n"
1655	"Length of probe 18\n"
1656	"Temperature [ 0.0 -400.0]\n"
1657	"GC-content [60.0 - 75.0]\n"
1658	"E.Coli position [any]\n"
1659	"Max. nongroup hits 0 (lowest rejected nongroup hits: 1)\n"
1660	"Min. group hits 50%\n"
1661	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1662	"AGUCGAGCGGCAGCACAG 18 A=21 20 39 2 66.7 60.0 CUGUGCUGCCGCUCGACU \| - - - - - - - - - - - - - - - - - - - -\n"
1663	"GUCGAGCGGCAGCACAGA 18 A+ 1 21 39 2 66.7 60.0 UCUGUGCUGCCGCUCGAC \| - - - - - - - - - - - - - - - - - - - -\n"
1664	"UCGAGCGGCAGCACAGAG 18 A+ 2 21 39 2 66.7 60.0 CUCUGUGCUGCCGCUCGA \| - - - - - - - - - - - - - - - - - - - -\n"
1665	"AAGUCGAGCGGCAGCACA 18 A- 1 19 25 2 61.1 58.0 UGUGCUGCCGCUCGACUU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1666	"CGAGCGGCAGCACAGAGA 18 A+ 3 21 20 1 66.7 60.0 UCUCUGUGCUGCCGCUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1667	"CGAGCGGCAGCACAGAGG 18 A+ 3 21 20 1 72.2 62.0 CCUCUGUGCUGCCGCUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1668	"GAGCGGCAGCACAGAGAA 18 A+ 4 21 20 1 61.1 58.0 UUCUCUGUGCUGCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1669	"GAGCGGCAGCACAGAGGA 18 A+ 4 21 20 1 66.7 60.0 UCCUCUGUGCUGCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1670	"AGCGGCAGCACAGAGGAA 18 A+ 5 21 20 1 61.1 58.0 UUCCUCUGUGCUGCCGCU \| - - - - - - - - - - - - - - - - - - - -\n"
1671	"GCGGCAGCACAGAGAAAC 18 A+ 6 22 20 1 61.1 58.0 GUUUCUCUGUGCUGCCGC \| - - - - - - - - - - - - - - - - - - - -\n"
1672	"GCGGCAGCACAGAGGAAC 18 A+ 6 22 20 1 66.7 60.0 GUUCCUCUGUGCUGCCGC \| - - - - - - - - - - - - - - - - - - - -\n"
1673	"CGGCAGCACAGAGGAACU 18 A+ 7 23 20 1 61.1 58.0 AGUUCCUCUGUGCUGCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1674	"CUUGUUCCUUGGGUGGCG 18 B=52 47 20 1 61.1 58.0 CGCCACCCAAGGAACAAG \| - - - - - - - - - - - - - - - - - - - -\n"
1675	"CUUGUUUCUCGGGUGGCG 18 B+ 0 47 20 1 61.1 58.0 CGCCACCCGAGAAACAAG \| - - - - - - - - - - - - - - - - - - - -\n"
1676	"UGUUCCUUGGGUGGCGAG 18 B+ 2 49 20 1 61.1 58.0 CUCGCCACCCAAGGAACA \| - - - - - - - - - - - - - - - - - - - -\n"
1677	"UGUUUCUCGGGUGGCGAG 18 B+ 2 49 20 1 61.1 58.0 CUCGCCACCCGAGAAACA \| - - - - - - - - - - - - - - - - - - - -\n"
1678	"GUUCCUUGGGUGGCGAGC 18 B+ 3 50 20 1 66.7 60.0 GCUCGCCACCCAAGGAAC \| - - - - - - - - - - - - - - - - - - - -\n"
1679	"GUUUCUCGGGUGGCGAGC 18 B+ 3 50 20 1 66.7 60.0 GCUCGCCACCCGAGAAAC \| - - - - - - - - - - - - - - - - - - - -\n"
1680	"UUCCUUGGGUGGCGAGCG 18 B+10 57 20 1 66.7 60.0 CGCUCGCCACCCAAGGAA \| - - - - - - - - - - - - - - - - - - - -\n"
1681	"UUUCUCGGGUGGCGAGCG 18 B+10 57 20 1 66.7 60.0 CGCUCGCCACCCGAGAAA \| - - - - - - - - - - - - - - - - - - - -\n"
1682	"UCCUUGGGUGGCGAGCGG 18 B+11 58 20 1 72.2 62.0 CCGCUCGCCACCCAAGGA \| - - - - - - - - - - - - - - - - - - - -\n"
1683	"UUCUCGGGUGGCGAGCGG 18 B+11 58 20 1 72.2 62.0 CCGCUCGCCACCCGAGAA \| - - - - - - - - - - - - - - - - - - - -\n"
1684	"CAAGUCGAGCGGCAGCAC 18 A- 2 18 13 2 66.7 60.0 GUGCUGCCGCUCGACUUG \| - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1685	"UCAAGUCGAGCGGCAGCA 18 A- 3 17 3 2 61.1 58.0 UGCUGCCGCUCGACUUGA \| - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3\n";
1686
1687	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1688	}
1689
1690	// design MANY probes to test location specifier
1691	{
1692	const char *arguments_loc[] = {
1693	"prgnamefake",
1694	// "designnames=Stsssola#Stsssola", // @@@ crashes the ptserver
1695	"designnames=CPPParap#PsAAAA00",
1696	"designmintargets=50", // hit at least 1 of the 2 targets
1697	"designmingc=0", "designmaxgc=100", // allow all GCs
1698	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1699	"designmishit=7", // allow enough outgroup hits
1700	"designprobelength=9",
1701	};
1702
1703	const char *expected_loc =
1704	"A=29B=51B+1C=99A+8D=112E=80E+2E+3E+4B-1A-5B-6B-5F=124F+1B-2E-7B+0C-5E+2E-1D-1E+6E+7E+8G=89C-2A-1H=61A-6C-1C-3E+3B+3B+4B+5E+5C+1E+4E+6E+7E+8C-7C-6E+5H+1H+2E-6C-4I=152I+1A-7";
1705
1706	TEST_ARB_PROBE_FILT(ARRAY_ELEMS(arguments_loc), arguments_loc, extract_locations, expected_loc);
1707	}
1708
1709	// same as above
1710	{
1711	const char *arguments[] = {
1712	"prgnamefake",
1713	"designnames=CPPParap#PsAAAA00",
1714	"designmintargets=50", // hit at least 1 of the 2 targets
1715	"designmingc=0", "designmaxgc=100", // allow all GCs
1716	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1717	"designmishit=7", // allow enough outgroup hits
1718	"designprobelength=9",
1719	};
1720
1721	const char *expected =
1722	"Probe design parameters:\n"
1723	"Length of probe 9\n"
1724	"Temperature [30.0 -100.0]\n"
1725	"GC-content [ 0.0 -100.0]\n"
1726	"E.Coli position [any]\n"
1727	"Max. nongroup hits 7 (lowest rejected nongroup hits: 9)\n"
1728	"Min. group hits 50%\n"
1729	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1730	"GAGCGGAUG 9 A= 29 24 20 1 66.7 30.0 CAUCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1731	"UGCUCCUGG 9 B= 51 46 20 1 66.7 30.0 CCAGGAGCA \| - - - - - - - - - - - - - - - - - - - -\n"
1732	"GCUCCUGGA 9 B+ 1 47 20 1 66.7 30.0 UCCAGGAGC \| - - - - - - - - - - - - - - - - - - - -\n"
1733	"CGGGCGCUA 9 C= 99 87 20 1 77.8 32.0 UAGCGCCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1734	"GAAGGGAGC 9 A+ 8 32 20 1 66.7 30.0 GCUCCCUUC \| 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2\n"
1735	"CGCAUACGC 9 D=112 100 20 1 66.7 30.0 GCGUAUGCG \| 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2\n"
1736	"CGGACGGGC 9 E= 80 69 20 1 88.9 34.0 GCCCGUCCG \| 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3\n"
1737	"GGACGGGCC 9 E+ 2 70 20 1 88.9 34.0 GGCCCGUCC \| 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n"
1738	"GACGGGCCU 9 E+ 3 71 20 1 77.8 32.0 AGGCCCGUC \| 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n"
1739	"ACGGGCCUU 9 E+ 4 72 20 1 66.7 30.0 AAGGCCCGU \| 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n"
1740	"UCCUUCGGG 9 B- 1 45 20 1 66.7 30.0 CCCGAAGGA \| 2 2 2 2 2 2 2 2 2 2 2 2 3 4 4 4 4 4 4 4\n"
1741	"CGAGCGAUG 9 A- 5 21 20 1 66.7 30.0 CAUCGCUCG \| 3 3 3 3 3 3 3 3 3 3 5 5 5 5 5 5 5 5 5 5\n"
1742	"GGGAGCUUG 9 B- 6 40 20 1 66.7 30.0 CAAGCUCCC \| 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 5 5\n"
1743	"GGAGCUUGC 9 B- 5 41 20 1 66.7 30.0 GCAAGCUCC \| 4 4 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5\n"
1744	"GCGAUUGGG 9 F=124 111 20 1 66.7 30.0 CCCAAUCGC \| 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 6 6\n"
1745	"CGAUUGGGG 9 F+ 1 112 20 1 66.7 30.0 CCCCAAUCG \| 3 3 3 3 3 3 6 6 6 6 6 6 6 6 6 6 6 6 6 6\n"
1746	"GCUUGCUCC 9 B- 2 44 20 1 66.7 30.0 GGAGCAAGC \| 4 4 4 4 4 4 5 5 5 5 5 5 5 7 7 7 7 8 8 8\n"
1747	"UUAGCGGCG 9 E- 7 62 19 1 66.7 30.0 CGCCGCUAA \| 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 6 6 6 11 11\n"
1748	"CCUUCGGGA 9 B+ 0 46 18 1 66.7 30.0 UCCCGAAGG \| 2 2 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 5 5 13\n"
1749	"GGAAACGGG 9 C- 5 82 17 1 66.7 30.0 CCCGUUUCC \| - - - - - - - - - - - - - - - - 3 3 3 3\n"
1750	"GGACGGACG 9 E+ 2 70 17 1 77.8 32.0 CGUCCGUCC \| 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 10 10 14 14\n"
1751	"GCGGACGGG 9 E- 1 68 17 1 88.9 34.0 CCCGUCCGC \| 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 13 13 13 13\n"
1752	"CCGCAUACG 9 D- 1 99 16 1 66.7 30.0 CGUAUGCGG \| 2 2 2 2 2 2 2 2 2 2 2 4 4 4 4 5 5 5 5 5\n"
1753	"GGACGUCCG 9 E+ 6 74 14 1 77.8 32.0 CGGACGUCC \| - - - - - - - - - - - - - 1 1 1 1 3 3 3\n"
1754	"GACGUCCGG 9 E+ 7 75 14 1 77.8 32.0 CCGGACGUC \| - - - - - - - - - - - - - 1 1 1 1 2 2 14\n"
1755	"ACGUCCGGA 9 E+ 8 76 14 1 66.7 30.0 UCCGGACGU \| - - - - - - - - - - - - - 1 1 11 11 12 12 17\n"
1756	"CGUCCGGAA 9 G= 89 77 14 1 66.7 30.0 UUCCGGACG \| - - - - - - - - - - - - - 1 1 1 1 2 2 2\n"
1757	"AACGGGCGC 9 C- 2 85 14 1 77.8 32.0 GCGCCCGUU \| - - - - - - - - - - - - - 1 1 1 1 1 1 2\n"
1758	"CGAGCGGAU 9 A- 1 23 13 1 66.7 30.0 AUCCGCUCG \| - - - - - - - - - - - - 3 3 3 3 3 3 3 3\n"
1759	"UUCAGCGGC 9 H= 61 56 13 1 66.7 30.0 GCCGCUGAA \| 1 1 1 1 1 1 2 2 2 2 2 2 3 4 4 4 4 4 7 7\n"
1760	"UCGAGCGGA 9 A- 6 21 13 1 66.7 30.0 UCCGCUCGA \| 3 3 3 3 3 3 3 3 3 3 3 3 8 8 8 8 8 8 8 8\n"
1761	"ACGGGCGCU 9 C- 1 86 12 1 77.8 32.0 AGCGCCCGU \| - - - - - - - - - - - 1 1 1 1 1 1 2 2 2\n"
1762	"AAACGGGCG 9 C- 3 84 9 1 66.7 30.0 CGCCCGUUU \| - - - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1\n"
1763	"GACGGACGU 9 E+ 3 71 9 1 66.7 30.0 ACGUCCGUC \| 2 2 2 2 2 2 2 2 13 13 13 13 13 13 13 14 14 14 14 14\n"
1764	"UCGGGAACG 9 B+ 3 49 7 1 66.7 30.0 CGUUCCCGA \| - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1765	"CGGGAACGG 9 B+ 4 50 7 1 77.8 32.0 CCGUUCCCG \| - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1766	"GGGAACGGA 9 B+ 5 51 7 1 66.7 30.0 UCCGUUCCC \| - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1767	"CGGACGUCC 9 E+ 5 73 7 1 77.8 32.0 GGACGUCCG \| - - - - - - 1 1 1 1 1 1 1 3 3 3 3 12 12 12\n"
1768	"GGGCGCUAA 9 C+ 1 88 7 1 66.7 30.0 UUAGCGCCC \| - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1769	"ACGGACGUC 9 E+ 4 72 7 1 66.7 30.0 GACGUCCGU \| - - - - - - 2 2 3 3 3 4 4 4 4 5 5 5 5 13\n"
1770	"GGGCCUUCC 9 E+ 6 74 7 1 77.8 32.0 GGAAGGCCC \| - - - - - - 2 2 2 2 2 3 3 3 3 3 3 3 3 4\n"
1771	"GGCCUUCCG 9 E+ 7 75 7 1 77.8 32.0 CGGAAGGCC \| - - - - - - 2 2 2 2 2 3 3 3 3 3 3 3 3 3\n"
1772	"GCCUUCCGA 9 E+ 8 76 7 1 66.7 30.0 UCGGAAGGC \| - - - - - - 2 2 2 2 2 3 3 3 3 3 3 3 3 3\n"
1773	"CCGGAAACG 9 C- 7 80 7 1 66.7 30.0 CGUUUCCGG \| - - - - - - 2 2 2 2 2 2 2 6 7 9 9 10 10 10\n"
1774	"CGGAAACGG 9 C- 6 81 7 1 66.7 30.0 CCGUUUCCG \| - - - - - - 2 2 4 4 4 4 4 4 5 5 6 6 6 6\n"
1775	"CGGGCCUUC 9 E+ 5 73 7 1 77.8 32.0 GAAGGCCCG \| 1 1 1 1 1 1 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n"
1776	"UCAGCGGCG 9 H+ 1 57 7 1 77.8 32.0 CGCCGCUGA \| 2 2 2 2 2 2 6 6 6 6 6 6 6 6 6 6 7 7 7 7\n"
1777	"CAGCGGCGG 9 H+ 2 58 7 1 88.9 34.0 CCGCCGCUG \| 2 2 2 2 2 2 6 6 6 6 6 6 6 7 12 12 12 12 12 12\n"
1778	"UAGCGGCGG 9 E- 6 63 7 1 77.8 32.0 CCGCCGCUA \| 4 4 4 4 4 4 10 10 10 10 10 10 12 14 14 14 14 14 14 14\n"
1779	"GAAACGGGC 9 C- 4 83 5 1 66.7 30.0 GCCCGUUUC \| - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1780	"GCCGUAGGA 9 I=152 138 3 1 66.7 30.0 UCCUACGGC \| 1 1 8 8 8 8 8 8 8 8 8 8 9 9 9 9 9 9 12 12\n"
1781	"CCGUAGGAG 9 I+ 1 139 3 1 66.7 30.0 CUCCUACGG \| 1 1 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11\n"
1782	"GUCGAGCGA 9 A- 7 21 3 1 66.7 30.0 UCGCUCGAC \| 3 3 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 13\n";
1783
1784	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1785	}
1786
1787	#if defined(ARB_64)
1788	#define RES_64
1789	#else // !defined(ARB_64)
1790	// results below differ for some(!) 32 bit arb versions (numeric issues?)
1791	// (e.g. u1004 behaves like 64bit version; u1204 doesnt in NDEBUG mode)
1792	// #define RES_64 // uncomment for u1004
1793	#if defined(DEBUG)
1794	#define RES_64
1795	#endif
1796
1797	#endif
1798
1799
1800	// same as above (with probelen == 8)
1801	{
1802	const char *arguments[] = {
1803	"prgnamefake",
1804	"designnames=CPPParap#PsAAAA00",
1805	"designmintargets=50", // hit at least 1 of the 2 targets
1806	"designmingc=0", "designmaxgc=100", // allow all GCs
1807	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1808	// "designmishit=7",
1809	"designmishit=15", // @@@ reports more results than with 7 mishits, but no mishits reported below!
1810	"designprobelength=8",
1811	};
1812
1813	const char *expected =
1814	"Probe design parameters:\n"
1815	"Length of probe 8\n"
1816	"Temperature [30.0 -100.0]\n"
1817	"GC-content [ 0.0 -100.0]\n"
1818	"E.Coli position [any]\n"
1819	"Max. nongroup hits 15\n"
1820	"Min. group hits 50%\n"
1821	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1822	"GGCGGACG 8 A=78 67 39 2 87.5 30.0 CGUCCGCC \| 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13\n"
1823	"GCGGACGG 8 A+ 1 68 39 2 87.5 30.0 CCGUCCGC \| 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13\n"
1824	"AGCGGCGG 8 A- 3 64 39 2 87.5 30.0 CCGCCGCU \| 11 11 11 11 11 11 11 14 14 14 14 14 14 14 14 14 14 14 14 14\n"
1825	"GCGGCGGA 8 A- 2 65 39 2 87.5 30.0 UCCGCCGC \| 10 10 11 11 11 11 11 14 14 14 14 14 14 14 14 14 14 14 14 14\n"
1826	"CGGCGGAC 8 A- 1 66 39 2 87.5 30.0 GUCCGCCG \| 10 10 10 10 10 10 10 13 13 13 13 13 13 13 14 14 14 14 14 14\n"
1827	"CGGACGGG 8 A+ 2 69 20 1 87.5 30.0 CCCGUCCG \| 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2\n"
1828	"GGACGGGC 8 A+ 4 70 20 1 87.5 30.0 GCCCGUCC \| 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n"
1829	"GACGGGCC 8 A+ 5 71 20 1 87.5 30.0 GGCCCGUC \| 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n"
1830	#if defined(RES_64)
1831	"ACGGGCGC 8 B=98 86 13 1 87.5 30.0 GCGCCCGU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1832	"CGGGCGCU 8 B+ 1 87 13 1 87.5 30.0 AGCGCCCG \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1833	"CAGCGGCG 8 C=63 58 8 1 87.5 30.0 CGCCGCUG \| 2 2 2 2 2 2 2 6 6 6 6 6 6 6 8 8 8 8 8 8\n";
1834	#else // !defined(RES_64)
1835	"ACGGGCGC 8 B=98 86 13 1 87.5 30.0 GCGCCCGU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 2\n"
1836	"CGGGCGCU 8 B+ 1 87 13 1 87.5 30.0 AGCGCCCG \| - - - - - - - - - - - - 1 1 1 1 1 1 1 2\n"
1837	"CAGCGGCG 8 C=63 58 8 1 87.5 30.0 CGCCGCUG \| 2 2 2 2 2 2 2 6 6 6 6 6 6 6 8 8 8 8 8 10\n";
1838	#endif
1839
1840	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1841	}
1842
1843	// same as above (but restricting ecoli-range)
1844	{
1845	const char *arguments[] = {
1846	"prgnamefake",
1847	"designnames=CPPParap#PsAAAA00",
1848	"designmintargets=50", // hit at least 1 of the 2 targets
1849	"designmingc=0", "designmaxgc=100", // allow all GCs
1850	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1851	"designmishit=15",
1852	"designprobelength=8",
1853	"designminpos=65", "designmaxpos=69", // restrict ecoli-range
1854	};
1855
1856	const char *expected =
1857	"Probe design parameters:\n"
1858	"Length of probe 8\n"
1859	"Temperature [30.0 -100.0]\n"
1860	"GC-content [ 0.0 -100.0]\n"
1861	"E.Coli position [ 65 - 69]\n"
1862	"Max. nongroup hits 15\n"
1863	"Min. group hits 50%\n"
1864	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1865	"GGCGGACG 8 A=78 67 39 2 87.5 30.0 CGUCCGCC \| 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13\n"
1866	"GCGGACGG 8 A+ 1 68 39 2 87.5 30.0 CCGUCCGC \| 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13\n"
1867	"GCGGCGGA 8 A- 2 65 39 2 87.5 30.0 UCCGCCGC \| 10 10 11 11 11 11 11 14 14 14 14 14 14 14 14 14 14 14 14 14\n"
1868	"CGGCGGAC 8 A- 1 66 39 2 87.5 30.0 GUCCGCCG \| 10 10 10 10 10 10 10 13 13 13 13 13 13 13 14 14 14 14 14 14\n"
1869	"CGGACGGG 8 A+ 2 69 20 1 87.5 30.0 CCCGUCCG \| 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2\n";
1870
1871	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1872	}
1873
1874	{
1875	const char *arguments[] = {
1876	"prgnamefake",
1877	"designnames=ClnCorin#CPPParap#ClfPerfr",
1878	"designprobelength=16",
1879	"designmintargets=100",
1880	"designmishit=2",
1881	};
1882	const char *expected =
1883	"Probe design parameters:\n"
1884	"Length of probe 16\n"
1885	"Temperature [ 0.0 -400.0]\n"
1886	"GC-content [30.0 - 80.0]\n"
1887	"E.Coli position [any]\n"
1888	"Max. nongroup hits 2 (lowest rejected nongroup hits: 6)\n"
1889	"Min. group hits 100% (max. rejected coverage: 67%)\n"
1890	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1891	"CGAAAGGAAGAUUAAU 16 A=94 82 58 3 31.2 42.0 AUUAAUCUUCCUUUCG \| 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1892	"AAGGAAGAUUAAUACC 16 A+ 3 85 58 3 31.2 42.0 GGUAUUAAUCUUCCUU \| 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1893	"AAGUCGAGCGAUGAAG 16 B=20 19 52 3 50.0 48.0 CUUCAUCGCUCGACUU \| 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3\n"
1894	"CAAGUCGAGCGAUGAA 16 B- 1 18 37 3 50.0 48.0 UUCAUCGCUCGACUUG \| 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3 3 3 3 3 3\n"
1895	"GUCGAGCGAUGAAGUU 16 B+ 2 21 31 3 50.0 48.0 AACUUCAUCGCUCGAC \| - - - - - - - - - - 1 1 1 1 1 1 1 1 1 1\n"
1896	"UCAAGUCGAGCGAUGA 16 B- 2 17 28 3 50.0 48.0 UCAUCGCUCGACUUGA \| 1 1 1 1 1 1 1 1 1 3 3 3 3 3 3 3 3 3 3 3\n"
1897	"AGUCGAGCGAUGAAGU 16 B+ 1 20 19 3 50.0 48.0 ACUUCAUCGCUCGACU \| - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1898	"AUCAAGUCGAGCGAUG 16 B- 3 16 16 3 50.0 48.0 CAUCGCUCGACUUGAU \| 1 1 1 1 1 3 3 3 3 3 3 3 3 3 3 3 3 10 10 10\n"
1899	"GAUCAAGUCGAGCGAU 16 B- 4 15 4 3 50.0 48.0 AUCGCUCGACUUGAUC \| - 2 2 2 3 3 3 3 10 10 10 10 10 10 10 10 10 10 10 10\n"
1900	"UGAUCAAGUCGAGCGA 16 B- 5 14 4 3 50.0 48.0 UCGCUCGACUUGAUCA \| - 9 9 9 9 9 9 9 10 10 10 10 10 10 10 10 10 10 10 10\n";
1901
1902	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1903	}
1904	// test same design as above, but add 2 "unknown species" each of which is missing one of the previously designed probes
1905	{
1906	const char *arguments[] = {
1907	"prgnamefake",
1908	"designnames=ClnCorin#Unknown1#CPPParap#ClfPerfr#Unknown2",
1909	"designprobelength=16",
1910	"designmintargets=100",
1911	"designmishit=2",
1912	// pass sequences for the unknown species
1913	"designsequence=---CGAAAGGAAGAUUAAU------------------AAGUCGAGCGAUGAAG-CAAGUCGAGCGAUGAA-GUCGAGCGAUGAAGUU-UCAAGUCGAGCGAUGA-AGUCGAGCGAUGAAGU-AUCAAGUCGAGCGAUG-GAUCAAGUCGAGCGAU-UGAUCAAGUCGAGCGA",
1914	"designsequence=---CGAAAGGAAGAUUAAU-AAGGAAGAUUAAUACC-AAGUCGAGCGAUGAAG-CAAGUCGAGCGAUGAA-GUCGAGCGAUGAAGUU-UCAAGUCGAGCGAUGA-AGUCGAGCGAUGAAGU-AUCAAGUCGAGCGAUG------------------UGAUCAAGUCGAGCGA",
1915	};
1916	const char *expected =
1917	"Probe design parameters:\n"
1918	"Length of probe 16\n"
1919	"Temperature [ 0.0 -400.0]\n"
1920	"GC-content [30.0 - 80.0]\n"
1921	"E.Coli position [any]\n"
1922	"Max. nongroup hits 2\n"
1923	"Min. group hits 100% (max. rejected coverage: 80%)\n"
1924	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1925	"CGAAAGGAAGAUUAAU 16 A=94 82 96 5 31.2 42.0 AUUAAUCUUCCUUUCG \| 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1926	// AAGGAAGAUUAAUACC is not designed here
1927	"AAGUCGAGCGAUGAAG 16 B=20 19 86 5 50.0 48.0 CUUCAUCGCUCGACUU \| 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3\n"
1928	"CAAGUCGAGCGAUGAA 16 B- 1 18 61 5 50.0 48.0 UUCAUCGCUCGACUUG \| 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3 3 3 3 3 3\n"
1929	"GUCGAGCGAUGAAGUU 16 B+ 2 21 51 5 50.0 48.0 AACUUCAUCGCUCGAC \| - - - - - - - - - - 1 1 1 1 1 1 1 1 1 1\n"
1930	"UCAAGUCGAGCGAUGA 16 B- 2 17 46 5 50.0 48.0 UCAUCGCUCGACUUGA \| 1 1 1 1 1 1 1 1 1 3 3 3 3 3 3 3 3 3 3 3\n"
1931	"AGUCGAGCGAUGAAGU 16 B+ 1 20 31 5 50.0 48.0 ACUUCAUCGCUCGACU \| - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1932	"AUCAAGUCGAGCGAUG 16 B- 3 16 26 5 50.0 48.0 CAUCGCUCGACUUGAU \| 1 1 1 1 1 3 3 3 3 3 3 3 3 3 3 3 3 10 10 10\n"
1933	// GAUCAAGUCGAGCGAU is not designed here
1934	"UGAUCAAGUCGAGCGA 16 B- 5 14 6 5 50.0 48.0 UCGCUCGACUUGAUCA \| - 9 9 9 9 9 9 9 10 10 10 10 10 10 10 10 10 10 10 10\n";
1935
1936	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1937	}
1938	{
1939	const char *arguments[] = {
1940	"prgnamefake",
1941	"designnames=VbrFurni",
1942	"designprobelength=8",
1943	"designmingc=80",
1944	"designmaxgc=100",
1945	};
1946	const char *expected =
1947	"Probe design parameters:\n"
1948	"Length of probe 8\n"
1949	"Temperature [ 0.0 -400.0]\n"
1950	"GC-content [80.0 -100.0]\n"
1951	"E.Coli position [any]\n"
1952	"Max. nongroup hits 0 (lowest rejected nongroup hits: 2)\n"
1953	"Min. group hits 50%\n"
1954	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1955	#if defined(RES_64)
1956	"CGGCAGCG 8 A=28 23 20 1 87.5 30.0 CGCUGCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1957	#else // !defined(RES_64)
1958	"CGGCAGCG 8 A=28 23 20 1 87.5 30.0 CGCUGCCG \| - - - - - - - - - - - - - - - - - - - 3\n"
1959	#endif
1960	"UGGGCGGC 8 B=67 60 8 1 87.5 30.0 GCCGCCCA \| - - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1\n"
1961	#if defined(RES_64)
1962	"CGGCGAGC 8 B+ 4 60 8 1 87.5 30.0 GCUCGCCG \| - - - - - - - 2 2 2 2 2 2 2 3 3 3 3 3 3\n"
1963	#else // !defined(RES_64)
1964	"CGGCGAGC 8 B+ 4 60 8 1 87.5 30.0 GCUCGCCG \| - - - - - - - 2 2 2 2 2 2 2 4 4 4 4 4 5\n"
1965	#endif
1966	"GGGCGGCG 8 B+ 1 60 8 1 100.0 32.0 CGCCGCCC \| - - - - - - - 3 3 3 3 3 3 3 3 3 3 3 3 3\n"
1967	"GGCGGCGA 8 B+ 2 60 8 1 87.5 30.0 UCGCCGCC \| - - - - - - - 3 3 3 3 3 3 3 3 3 3 3 3 3\n"
1968	"GCGGCGAG 8 B+ 3 60 3 1 87.5 30.0 CUCGCCGC \| - - 1 1 1 1 1 4 4 4 4 4 4 4 4 4 4 4 4 4\n";
1969
1970	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1971	}
1972	{
1973	const char *arguments[] = {
1974	"prgnamefake",
1975	"designnames=HllHalod#VbhChole#VblVulni#VbrFurni#PtVVVulg",
1976	"designprobelength=14",
1977	"designmintargets=100",
1978	"designmishit=4",
1979	"designmingc=70",
1980	"designmaxgc=100",
1981	};
1982	const char *expected =
1983	"Probe design parameters:\n"
1984	"Length of probe 14\n"
1985	"Temperature [ 0.0 -400.0]\n"
1986	"GC-content [70.0 -100.0]\n"
1987	"E.Coli position [any]\n"
1988	"Max. nongroup hits 4\n"
1989	"Min. group hits 100% (max. rejected coverage: 80%)\n"
1990	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1991	"GAGCGGCGGACGGA 14 A=75 64 21 5 78.6 50.0 UCCGUCCGCCGCUC \| - - - - 1 1 1 1 1 1 5 5 9 9 10 10 10 10 10 10\n"
1992	"CGAGCGGCGGACGG 14 A- 1 63 21 5 85.7 52.0 CCGUCCGCCGCUCG \| - - - - 2 2 2 2 2 2 2 2 2 2 2 2 2 2 9 9\n"
1993	"AGCGGCGGACGGAC 14 A+ 0 64 21 5 78.6 50.0 GUCCGUCCGCCGCU \| 4 7 7 7 9 9 9 9 9 9 9 9 9 9 9 9 9 10 10 10\n";
1994
1995	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1996	}
1997	{
1998	const char *arguments[] = {
1999	"prgnamefake",
2000	"designnames=HllHalod#VbhChole#VblVulni#VbrFurni#PtVVVulg",
2001	"designprobelength=14",
2002	"designmintargets=100",
2003	"designmishit=0",
2004	"designmingc=51",
2005	"designmaxgc=60",
2006	};
2007	const char *expected = ""; // no probes found!
2008
2009	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2010	}
2011
2012	}
2013
2014	void TEST_SLOW_probe_design_errors() {
2015	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2016
2017	bool use_gene_ptserver = false;
2018	{
2019	const char *arguments[] = {
2020	"prgnamefake",
2021	"designnames=CPPParap#PsAAAA00",
2022	"designprobelength=3",
2023	};
2024	const char *expected_error = "Specified min. probe length 3 is below the min. allowed probe length of 8";
2025
2026	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2027	}
2028	{
2029	const char *arguments[] = {
2030	"prgnamefake",
2031	"designnames=CPPParap#PsAAAA00",
2032	"designprobelength=15",
2033	"designmaxprobelength=12",
2034	};
2035	const char *expected_error = "Max. probe length 12 is below the specified min. probe length of 15";
2036
2037	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2038	}
2039	{
2040	const char *expected_error = "Sequence contains only 0 bp. Impossible design request for one of the added sequences";
2041	{
2042	const char *arguments[] = {
2043	"prgnamefake",
2044	"designsequence=", // pass an empty sequence
2045	"designprobelength=16",
2046	};
2047	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2048	}
2049	{
2050	const char *arguments[] = {
2051	"prgnamefake",
2052	"designsequence=-------------", // pass a gap-only sequence
2053	"designprobelength=16",
2054	};
2055	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2056	}
2057	}
2058	{
2059	const char *arguments[] = {
2060	"prgnamefake",
2061	"designsequence=ACGTACGTACGTACGT", // pass a long enough (unexpected) sequence
2062	"designprobelength=16",
2063	};
2064	const char *expected_error = "Got 0 unknown marked species, but 1 custom sequence was added (has to match)";
2065	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2066	}
2067	{
2068	const char *arguments[] = {
2069	"prgnamefake",
2070	"designnames=Unknown", // one unknown species
2071	"designprobelength=16",
2072	};
2073	const char *expected_error = "No species marked - no probes designed";
2074	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2075	}
2076	{
2077	const char *arguments[] = {
2078	"prgnamefake",
2079	"designnames=Unknown#CPPParap", // one unknown species, one known species
2080	"designprobelength=16",
2081	};
2082	const char *expected_error = "Got 1 unknown marked species, but 0 custom sequences were added (has to match)";
2083	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2084	}
2085	{
2086	const char *expected_error = "Sequence contains only 0 bp. Impossible design request for one of the added sequences";
2087	{
2088	const char *arguments[] = {
2089	"prgnamefake",
2090	"designnames=Unknown", // one unknown species
2091	"designsequence=", // pass an empty sequence
2092	"designprobelength=16",
2093	};
2094	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2095	}
2096	{
2097	const char *arguments[] = {
2098	"prgnamefake",
2099	"designnames=Unknown", // one unknown species
2100	"designsequence=-------------", // pass a gap-only sequence
2101	"designprobelength=16",
2102	};
2103	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2104	}
2105	}
2106	}
2107
2108	void TEST_SLOW_match_designed_probe() {
2109	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2110
2111	bool use_gene_ptserver = false;
2112	const char *arguments[] = {
2113	"prgnamefake",
2114	"matchsequence=UCAAGUCGAGCGAUGAAG",
2115	};
2116	CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UCAAGUCGAGCGAUGAAG'\1"
2117	"ClnCorin\1" " ClnCorin 0 0 0.0 18 17 0 .GAGUUUGA-==================-UUCCUUCGG\1"
2118	"CltBotul\1" " CltBotul 0 0 0.0 18 17 0 ........A-==================-CUUCUUCGG\1"
2119	"CPPParap\1" " CPPParap 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUCCUUCGG\1"
2120	"ClfPerfr\1" " ClfPerfr 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUUCCUUCG\1";
2121
2122	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2123	}
2124
2125	void TEST_SLOW_get_existing_probes() {
2126	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2127
2128	bool use_gene_ptserver = false;
2129	{
2130	const char *arguments[] = {
2131	"prgnamefake",
2132	"iterate=20",
2133	"iterate_amount=10",
2134	};
2135	CCP expected =
2136	"AAACCGGGGCTAATACCGGA;AAACGACTGTTAATACCGCA;AAACGATGGAAGCTTGCTTC;AAACGATGGCTAATACCGCA;AAACGGATTAGCGGCGGGAC;"
2137	"AAACGGGCGCTAATACCGCA;AAACGGTCGCTAATACCGGA;AAACGGTGGCTAATACCGCA;AAACGTACGCTAATACCGCA;AAACTCAAGCTAATACCGCA";
2138
2139	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2140	}
2141	{
2142	const char *arguments[] = {
2143	"prgnamefake",
2144	"iterate=15",
2145	"iterate_amount=20",
2146	"iterate_separator=:",
2147	};
2148	CCP expected =
2149	"AAACCGGGGCTAATA:AAACGACTGTTAATA:AAACGATGGAAGCTT:AAACGATGGCTAATA:AAACGGATTAGCGGC:AAACGGGCGCTAATA:AAACGGTCGCTAATA:"
2150	"AAACGGTGGCTAATA:AAACGTACGCTAATA:AAACTCAAGCTAATA:AAACTCAGGCTAATA:AAACTGGAGAGTTTG:AAACTGTAGCTAATA:AAACTTGTTTCTCGG:"
2151	"AAAGAGGTGCTAATA:AAAGCTTGCTTTCTT:AAAGGAACGCTAATA:AAAGGAAGATTAATA:AAAGGACAGCTAATA:AAAGGGACTTCGGTC";
2152
2153	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2154	}
2155	{
2156	const char *arguments[] = {
2157	"prgnamefake",
2158	"iterate=10",
2159	"iterate_amount=5",
2160	"iterate_readable=0",
2161	};
2162	CCP expected =
2163	"\2\2\2\3\3\4\4\4\4\3;\2\2\2\3\4\2\3\5\4\5;\2\2\2\3\4\2\5\4\4\2;\2\2\2\3\4\2\5\4\4\3;\2\2\2\3\4\4\2\5\5\2";
2164
2165	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2166	}
2167	{
2168	const char *arguments[] = {
2169	"prgnamefake",
2170	"iterate=3",
2171	"iterate_amount=70",
2172	"iterate_tu=U",
2173	};
2174	CCP expected =
2175	"AAA;AAC;AAG;AAU;ACA;ACC;ACG;ACU;AGA;AGC;AGG;AGU;AUA;AUC;AUG;AUU;"
2176	"CAA;CAC;CAG;CAU;CCA;CCC;CCG;CCU;CGA;CGC;CGG;CGU;CUA;CUC;CUG;CUU;"
2177	"GAA;GAC;GAG;GAU;GCA;GCC;GCG;GCU;GGA;GGC;GGG;GGU;GUA;GUC;GUG;GUU;"
2178	"UAA;UAC;UAG;UAU;UCA;UCC;UCG;UCU;UGA;UGC;UGG;UGU;UUA;UUC;UUG;UUU";
2179
2180	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2181	}
2182	{
2183	const char *arguments[] = {
2184	"prgnamefake",
2185	"iterate=2",
2186	"iterate_amount=20",
2187	};
2188	CCP expected =
2189	"AA;AC;AG;AT;"
2190	"CA;CC;CG;CT;"
2191	"GA;GC;GG;GT;"
2192	"TA;TC;TG;TT";
2193
2194	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2195	}
2196	}
2197
2198	// #define TEST_AUTO_UPDATE // uncomment to auto-update expected index dumps
2199
2200	void TEST_SLOW_index_dump() {
2201	for (int use_gene_ptserver = 0; use_gene_ptserver <= 1; use_gene_ptserver++) {
2202	const char *dumpfile = use_gene_ptserver ? "index_gpt.dump" : "index_pt.dump";
2203	char *dumpfile_exp = GBS_global_string_copy("%s.expected", dumpfile);
2204
2205	const char *arguments[] = {
2206	"prgnamefake",
2207	GBS_global_string_copy("dump=%s", dumpfile),
2208	};
2209	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, "ok");
2210
2211	#if defined(TEST_AUTO_UPDATE)
2212	TEST_COPY_FILE(dumpfile, dumpfile_exp);
2213	#else // !defined(TEST_AUTO_UPDATE)
2214	TEST_EXPECT_TEXTFILES_EQUAL(dumpfile_exp, dumpfile);
2215	#endif
2216	TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(dumpfile));
2217
2218	free((char*)arguments[1]);
2219	free(dumpfile_exp);
2220	}
2221	}
2222
2223	#undef TEST_AUTO_UPDATE
2224
2225	// --------------------------------------------------------------------------------
2226
2227	#include <arb_strarray.h>
2228	#include <set>
2229	#include <iterator>
2230
2231	using namespace std;
2232
2233	typedef set<string> Matches;
2234
2235	inline void parseMatches(char*& answer, Matches& matches) {
2236	ConstStrArray match_results;
2237
2238	GBT_splitNdestroy_string(match_results, answer, "\1", SPLIT_KEEPEMPTY);
2239
2240	for (size_t i = 1; i<match_results.size(); i += 2) {
2241	if (match_results[i][0]) {
2242	matches.insert(match_results[i]);
2243	}
2244	}
2245	}
2246
2247	inline void getMatches(const char *probe, Matches& matches) {
2248	bool use_gene_ptserver = false;
2249	char *matchseq = GBS_global_string_copy("matchsequence=%s", probe);
2250	const char *arguments[] = {
2251	"prgnamefake",
2252	matchseq,
2253	};
2254	TEST_RUN_ARB_PROBE(ARRAY_ELEMS(arguments), arguments);
2255	parseMatches(answer, matches);
2256	free(matchseq);
2257	}
2258
2259	inline string matches2hitlist(const Matches& matches) {
2260	string hitlist;
2261	if (!matches.empty()) {
2262	for (Matches::const_iterator m = matches.begin(); m != matches.end(); ++m) {
2263	hitlist = hitlist + ',' + *m;
2264	}
2265	hitlist = hitlist.substr(1);
2266	}
2267	return hitlist;
2268	}
2269
2270	inline void extract_first_but_not_second(const Matches& first, const Matches& second, Matches& result) {
2271	set_difference(first.begin(), first.end(),
2272	second.begin(), second.end(),
2273	inserter(result, result.begin()));
2274	}
2275
2276	// --------------------------------------------------------------------------------
2277
2278	// #define TEST_INDEX_COMPLETENESS // only uncomment temporarily (slow as hell)
2279
2280	#if defined(TEST_INDEX_COMPLETENESS)
2281
2282	void TEST_SLOW_find_unmatched_probes() {
2283	bool use_gene_ptserver = false;
2284
2285	// get all 20mers indexed in ptserver:
2286	ConstStrArray fullProbes;
2287	{
2288	const char *arguments[] = {
2289	"prgnamefake",
2290	"iterate=20",
2291	"iterate_amount=1000000",
2292	"iterate_tu=U",
2293	};
2294	TEST_RUN_ARB_PROBE(ARRAY_ELEMS(arguments), arguments);
2295
2296	GBT_splitNdestroy_string(fullProbes, answer, ";", false);
2297	TEST_EXPECT_EQUAL(fullProbes.size(), 2040);
2298	}
2299
2300	for (size_t lp = 0; lp<fullProbes.size(); ++lp) { // with all 20mers existing in ptserver
2301	const char *fullProbe = fullProbes[lp];
2302
2303	size_t fullLen = strlen(fullProbe);
2304	TEST_EXPECT_EQUAL(fullLen, 20);
2305
2306	Matches fullHits;
2307	getMatches(fullProbe, fullHits);
2308	TEST_EXPECT(fullHits.size()>0);
2309
2310	bool fewerHitsSeen = false;
2311
2312	for (size_t subLen = fullLen-1; !fewerHitsSeen && subLen >= 10; --subLen) { // for each partial sub-probe of 20mer
2313	char subProbe[20];
2314	subProbe[subLen] = 0;
2315
2316	for (size_t pos = 0; pos+subLen <= fullLen; ++pos) {
2317	Matches subHits, onlyFull;
2318
2319	memcpy(subProbe, fullProbe+pos, subLen);
2320	getMatches(subProbe, subHits);
2321	extract_first_but_not_second(fullHits, subHits, onlyFull);
2322
2323	if (!onlyFull.empty()) {
2324	fprintf(stderr, "TEST_PARTIAL_COVERS_FULL_PROBE__BROKEN(\"%s\", \"%s\");\n", subProbe, fullProbe);
2325	fewerHitsSeen = true; // only list first wrong hit for each fullProbe
2326	}
2327	}
2328	}
2329	}
2330	}
2331
2332	#endif
2333	// --------------------------------------------------------------------------------
2334
2335	static arb_test::match_expectation partial_covers_full_probe(const char part, const char full) {
2336	using namespace arb_test;
2337	using namespace std;
2338
2339	expectation_group expected;
2340	expected.add(that(strstr(full, part)).does_differ_from_NULL());
2341	expected.add(that(strlen(part)).is_less_than(strlen(full)));
2342
2343	{
2344	Matches matchFull, matchPart;
2345	getMatches(full, matchFull);
2346	getMatches(part, matchPart);
2347
2348	expected.add(that(matchFull.empty()).is_equal_to(false));
2349
2350	Matches onlyFirst;
2351	extract_first_but_not_second(matchFull, matchPart, onlyFirst);
2352
2353	string only_hit_by_full = matches2hitlist(onlyFirst);
2354	expected.add(that(only_hit_by_full).is_equal_to(""));
2355	}
2356
2357
2358	return all().ofgroup(expected);
2359	}
2360
2361	#define TEST_PARTIAL_COVERS_FULL_PROBE(part,full) TEST_EXPECTATION(partial_covers_full_probe(part, full))
2362	#define TEST_PARTIAL_COVERS_FULL_PROBE__BROKEN(part,full) TEST_EXPECTATION__BROKEN(partial_covers_full_probe(part, full))
2363
2364	void TEST_SLOW_unmatched_probes() {
2365	TEST_PARTIAL_COVERS_FULL_PROBE("CCUCCUUUCU", "GAUUAAUACCCCUCCUUUCU");
2366
2367	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUC", "GGGGAACCUGCGGUUGGAUC");
2368	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCA", "GGGAACCUGCGGUUGGAUCA");
2369	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCAC", "GGAACCUGCGGUUGGAUCAC");
2370	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACC", "GAACCUGCGGUUGGAUCACC");
2371	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCU", "AACCUGCGGUUGGAUCACCU");
2372	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUC", "ACCUGCGGUUGGAUCACCUC");
2373	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCC", "CCUGCGGUUGGAUCACCUCC");
2374	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCU", "CUGCGGUUGGAUCACCUCCU");
2375	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCUU", "UGCGGUUGGAUCACCUCCUU");
2376	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCUUA", "GCGGUUGGAUCACCUCCUUA");
2377
2378	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUC", "GGGGAACCUGGCGCUGGAUC");
2379	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCA", "GGGAACCUGGCGCUGGAUCA");
2380	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCAC", "GGAACCUGGCGCUGGAUCAC");
2381	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACC", "GAACCUGGCGCUGGAUCACC");
2382	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCU", "AACCUGGCGCUGGAUCACCU");
2383	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUC", "ACCUGGCGCUGGAUCACCUC");
2384	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCC", "CCUGGCGCUGGAUCACCUCC");
2385	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCU", "CUGGCGCUGGAUCACCUCCU");
2386	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCUU", "UGGCGCUGGAUCACCUCCUU");
2387	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCUUU", "GGCGCUGGAUCACCUCCUUU");
2388
2389	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCAC", "GGAACCUGCGGCUGGAUCAC");
2390	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACC", "GAACCUGCGGCUGGAUCACC");
2391	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCU", "AACCUGCGGCUGGAUCACCU");
2392	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUC", "ACCUGCGGCUGGAUCACCUC");
2393	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCC", "CCUGCGGCUGGAUCACCUCC");
2394	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCU", "CUGCGGCUGGAUCACCUCCU");
2395	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUU", "UGCGGCUGGAUCACCUCCUU");
2396	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUUU", "GCGGCUGGAUCACCUCCUUU");
2397	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUUUC", "CGGCUGGAUCACCUCCUUUC");
2398
2399	// the data of the following tests is located right in front of the dots inserted in [8962]
2400	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAG", "AAUUGAAGAGUUUGAUCAAG");
2401	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGU", "AUUGAAGAGUUUGAUCAAGU");
2402	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUC", "UUGAAGAGUUUGAUCAAGUC");
2403	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCG", "UGAAGAGUUUGAUCAAGUCG");
2404	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGA", "GAAGAGUUUGAUCAAGUCGA");
2405	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAG", "AAGAGUUUGAUCAAGUCGAG");
2406	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGC", "AGAGUUUGAUCAAGUCGAGC");
2407	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCG", "GAGUUUGAUCAAGUCGAGCG");
2408	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCGG", "AGUUUGAUCAAGUCGAGCGG");
2409	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCGGU", "GUUUGAUCAAGUCGAGCGGU");
2410	}
2411
2412	void TEST_SLOW_variable_defaults_in_server() {
2413	test_setup(false);
2414
2415	const char *server_tag = GBS_ptserver_tag(TEST_SERVER_ID);
2416	TEST_EXPECT_NO_ERROR(arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag));
2417
2418	const char *servername = GBS_read_arb_tcp(server_tag);
2419	{
2420	char *socketname = GBS_global_string_copy(":%s", GB_path_in_ARBHOME("UNIT_TESTER/sok/pt.socket"));
2421	TEST_EXPECT_EQUAL(servername, socketname); // as defined in ../lib/arb_tcp_org.dat@ARB_TEST_PT_SERVER
2422	free(socketname);
2423	}
2424
2425	T_PT_MAIN com;
2426	T_PT_LOCS locs;
2427	GB_ERROR error = NULp;
2428	aisc_com *link = aisc_open(servername, com, AISC_MAGIC_NUMBER, &error);
2429	TEST_EXPECT_NO_ERROR(error);
2430	TEST_REJECT_NULL(link);
2431
2432	TEST_EXPECT_ZERO(aisc_create(link, PT_MAIN, com,
2433	MAIN_LOCS, PT_LOCS, locs,
2434	NULp));
2435
2436	{
2437	#define LOCAL(rvar) prev_read_##rvar
2438
2439
2440	#define FREE_LOCAL_long(rvar)
2441	#define FREE_LOCAL_charp(rvar) free(LOCAL(rvar))
2442	#define FREE_LOCAL(type,rvar) FREE_LOCAL_##type(rvar)
2443
2444	#define TEST__READ(type,rvar,expected) \
2445	do { \
2446	TEST_EXPECT_ZERO(aisc_get(link, PT_LOCS, locs, rvar, &(LOCAL(rvar)), NULp)); \
2447	TEST_EXPECT_EQUAL(LOCAL(rvar), expected); \
2448	FREE_LOCAL(type,rvar); \
2449	} while(0)
2450	#define TEST_WRITE(type,rvar,val) \
2451	TEST_EXPECT_ZERO(aisc_put(link, PT_LOCS, locs, rvar, (type)val, NULp))
2452	#define TEST_CHANGE(type,rvar,val) \
2453	do { \
2454	TEST_WRITE(type, rvar, val); \
2455	TEST__READ(type, rvar, val); \
2456	} while(0)
2457	#define TEST_DEFAULT_CHANGE(ctype,type,remote_variable,default_value,other_value) \
2458	do { \
2459	ctype DEFAULT_VALUE = default_value; \
2460	ctype OTHER_VALUE = other_value; \
2461	type LOCAL(remote_variable); \
2462	TEST__READ(type, remote_variable, DEFAULT_VALUE); \
2463	TEST_CHANGE(type, remote_variable, OTHER_VALUE); \
2464	TEST_CHANGE(type, remote_variable, DEFAULT_VALUE); \
2465	} while(0)
2466
2467	TEST_DEFAULT_CHANGE(const long, long, LOCS_MATCH_ALSO_REVCOMP, 1, 67);
2468	typedef char *charp;
2469	typedef const char *ccharp;
2470	TEST_DEFAULT_CHANGE(ccharp, charp, LOCS_LOGINTIME, "notime", "sometime");
2471	}
2472
2473	TEST_EXPECT_ZERO(aisc_close(link, com));
2474	link = NULp;
2475	}
2476
2477	#endif // UNIT_TESTS

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source: trunk/TOOLS/arb_probe.cxx

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