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source: branches/stable/TOOLS/arb_probe.cxx

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Last change on this file was 17991, checked in by westram, 6 years ago
rename CLI params: complement → complementFirst reversed → alsoRevCompl matchcomplement → matchAlsoRevcomp improve CLI help: mention precedence and interaction between complementFirst + alsoRevCompl.
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 134.0 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	static const char *AP_probe_pt_look_for_server(ARB_ERROR& error) {
98	// DRY vs ../MULTI_PROBE/MP_noclass.cxx@MP_probe_pt_look_for_server
99	// DRY vs ../PROBE_DESIGN/probe_design.cxx@PD_probe_pt_look_for_server
100	const char *server_tag = GBS_ptserver_tag(P.SERVERID);
101	error = arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag);
102
103	const char *result = NULp;
104	if (!error) {
105	result = GBS_read_arb_tcp(server_tag);
106	if (!result) error = GB_await_error();
107	}
108	return result;
109	}
110
111	class PTserverConnection {
112	static int count;
113	bool need_close;
114	public:
115	PTserverConnection(ARB_ERROR& error)
116	: need_close(false)
117	{
118	if (count) {
119	error = "Only 1 PTserverConnection allowed";
120	}
121	else {
122	++count;
123	const char *servername = AP_probe_pt_look_for_server(error);
124	if (servername) {
125	GB_ERROR openerr = NULp;
126	pd_gl.link = aisc_open(servername, pd_gl.com, AISC_MAGIC_NUMBER, &openerr);
127	if (openerr) {
128	error = openerr;
129	}
130	else {
131	if (!pd_gl.link) {
132	error = "Cannot contact PT_SERVER [1]";
133	}
134	else if (init_local_com_struct()) {
135	error = "Cannot contact PT_SERVER [2]";
136	}
137	else {
138	need_close = true;
139	}
140	}
141	}
142	}
143	}
144	~PTserverConnection() {
145	if (need_close) {
146	aisc_close(pd_gl.link, pd_gl.com);
147	pd_gl.link = NULp;
148	}
149	--count;
150	}
151	};
152	int PTserverConnection::count = 0;
153
154	static char *AP_dump_index_event(ARB_ERROR& error) {
155	PTserverConnection contact(error);
156
157	char *result = NULp;
158	if (!error) {
159	aisc_put(pd_gl.link, PT_MAIN, pd_gl.com,
160	MAIN_DUMP_NAME, P.DUMP,
161	NULp);
162
163	if (aisc_get(pd_gl.link, PT_MAIN, pd_gl.com,
164	MAIN_DUMP_INDEX, &result,
165	NULp)) {
166	error = "Connection to PT_SERVER lost (1)";
167	}
168	else {
169	result = ARB_strdup("ok");
170	}
171	}
172	return result;
173	}
174
175	static char *AP_probe_iterate_event(ARB_ERROR& error) {
176	PTserverConnection contact(error);
177
178	char *result = NULp;
179	if (!error) {
180	T_PT_PEP pep;
181	int length = P.ITERATE;
182
183	if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs,
184	LOCS_PROBE_FIND_CONFIG, PT_PEP, pep,
185	PEP_PLENGTH, (long)length,
186	PEP_RESTART, (long)1,
187	PEP_READABLE, (long)P.ITERATE_READABLE,
188	PEP_TU, (long)P.ITERATE_TU[0],
189	PEP_SEPARATOR, (long)P.ITERATE_SEPARATOR[0],
190	NULp))
191	{
192	error = "Connection to PT_SERVER lost (1)";
193	}
194
195	if (!error) {
196	int amount = P.ITERATE_AMOUNT;
197	int amount_per_call = AISC_MAX_STRING_LEN/(length+2);
198
199	GBS_strstruct out(50000);
200	bool first = true;
201
202	while (amount && !error) {
203	int this_amount = std::min(amount, amount_per_call);
204
205	aisc_put(pd_gl.link, PT_PEP, pep,
206	PEP_NUMGET, (long)this_amount,
207	PEP_FIND_PROBES, (long)0,
208	NULp);
209
210	char *pep_result = NULp;
211	if (aisc_get(pd_gl.link, PT_PEP, pep,
212	PEP_RESULT, &pep_result,
213	NULp)) {
214	error = "Connection to PT_SERVER lost (2)";
215	}
216
217	if (!error) {
218	if (pep_result[0]) {
219	if (first) first = false;
220	else out.put(P.ITERATE_SEPARATOR[0]);
221
222	out.cat(pep_result);
223	amount -= this_amount;
224	}
225	else {
226	amount = 0; // terminate loop
227	}
228	}
229	free(pep_result);
230	}
231
232	if (!error) {
233	result = out.release();
234	}
235	}
236	}
237
238	if (error) freenull(result);
239	return result;
240	}
241
242	static char *AP_probe_design_event(ARB_ERROR& error) {
243	PTserverConnection contact(error);
244
245	if (!error) {
246	bytestring bs;
247	bs.data = (char*)(P.DESIGNNAMES);
248	bs.size = strlen(bs.data)+1;
249
250	T_PT_PDC pdc;
251	if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs,
252	LOCS_PROBE_DESIGN_CONFIG, PT_PDC, pdc,
253	PDC_MIN_PROBELEN, (long)P.DESIGNPROBELEN,
254	PDC_MAX_PROBELEN, (long)P.DESIGNMAXPROBELEN,
255	PDC_MINTEMP, (double)P.MINTEMP,
256	PDC_MAXTEMP, (double)P.MAXTEMP,
257	PDC_MINGC, (double)P.MINGC/100.0,
258	PDC_MAXGC, (double)P.MAXGC/100.0,
259	PDC_MAXBOND, (double)P.MAXBOND,
260	PDC_MIN_ECOLIPOS, (long)P.MINPOS,
261	PDC_MAX_ECOLIPOS, (long)P.MAXPOS,
262	PDC_MISHIT, (long)P.MISHIT,
263	PDC_MINTARGETS, (double)P.MINTARGETS/100.0,
264	PDC_CLIPRESULT, (long)P.DESIGNCLIPOUTPUT,
265	NULp))
266	{
267	error = "Connection to PT_SERVER lost (1)";
268	}
269
270	if (!error) {
271	for (apd_sequence *s = P.sequence; s; ) {
272	apd_sequence *next = s->next;
273
274	bytestring bs_seq;
275	T_PT_SEQUENCE pts;
276
277	bs_seq.data = (char*)s->sequence;
278	bs_seq.size = strlen(bs_seq.data)+1;
279	aisc_create(pd_gl.link, PT_PDC, pdc,
280	PDC_SEQUENCE, PT_SEQUENCE, pts,
281	SEQUENCE_SEQUENCE, &bs_seq,
282	NULp);
283
284	delete s;
285	s = next;
286	}
287
288	aisc_put(pd_gl.link, PT_PDC, pdc,
289	PDC_NAMES, &bs,
290	PDC_GO, (long)0,
291	NULp);
292
293	{
294	char *locs_error = NULp;
295	if (aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs,
296	LOCS_ERROR, &locs_error,
297	NULp)) {
298	error = "Connection to PT_SERVER lost (2)";
299	}
300	else {
301	if (*locs_error) error = GBS_static_string(locs_error);
302	free(locs_error);
303	}
304	}
305
306	if (!error) {
307	T_PT_TPROBE tprobe;
308	aisc_get(pd_gl.link, PT_PDC, pdc,
309	PDC_TPROBE, tprobe.as_result_param(),
310	NULp);
311
312
313	GBS_strstruct *outstr = GBS_stropen(1000);
314
315	if (tprobe.exists()) {
316	char *match_info = NULp;
317	aisc_get(pd_gl.link, PT_PDC, pdc,
318	PDC_INFO_HEADER, &match_info,
319	NULp);
320	GBS_strcat(outstr, match_info);
321	GBS_chrcat(outstr, '\n');
322	free(match_info);
323	}
324
325
326	while (tprobe.exists()) {
327	char *match_info = NULp;
328	if (aisc_get(pd_gl.link, PT_TPROBE, tprobe,
329	TPROBE_NEXT, tprobe.as_result_param(),
330	TPROBE_INFO, &match_info,
331	NULp)) break;
332	GBS_strcat(outstr, match_info);
333	GBS_chrcat(outstr, '\n');
334	free(match_info);
335	}
336
337	return GBS_strclose(outstr);
338	}
339	}
340	}
341	return NULp;
342	}
343
344	static char *AP_probe_match_event(ARB_ERROR& error) {
345	PTserverConnection contact(error);
346
347	if (!error &&
348	aisc_nput(pd_gl.link, PT_LOCS, pd_gl.locs,
349	LOCS_MATCH_ALSO_REVCOMP, (long)P.ALSO_REVCOMPL,
350	LOCS_COMPLEMENT_FIRST, (long)0, // (use sequence passed below as is. do not complement it.)
351	LOCS_MATCH_SORT_BY, (long)P.WEIGHTED,
352	LOCS_MATCH_MAX_MISMATCHES, (long)P.MISMATCHES,
353	LOCS_MATCH_N_ACCEPT, (long)P.ACCEPTN,
354	LOCS_MATCH_N_LIMIT, (long)P.LIMITN,
355	LOCS_MATCH_MAX_HITS, (long)P.MAXRESULT,
356	LOCS_SEARCHMATCH, P.SEQUENCE,
357	NULp)) {
358	error = "Connection to PT_SERVER lost (1)";
359	}
360
361	if (!error) {
362	bytestring bs;
363	bs.data = NULp;
364	{
365	char *locs_error = NULp;
366	T_PT_MATCHLIST match_list;
367	long match_list_cnt;
368
369	aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs,
370	LOCS_MATCH_LIST, match_list.as_result_param(),
371	LOCS_MATCH_LIST_CNT, &match_list_cnt,
372	LOCS_MATCH_STRING, &bs,
373	LOCS_ERROR, &locs_error,
374	NULp);
375	if (*locs_error) error = GBS_static_string(locs_error);
376	free(locs_error);
377	}
378
379	if (!error) return bs.data; // freed by caller
380	free(bs.data);
381	}
382	return NULp;
383	}
384
385	static int pargc;
386	static const char **pargv = NULp;
387	static bool showhelp;
388	static bool outOfRange;
389
390	static int getInt(const char param, int val, int min, int max, const char description) {
391	if (showhelp) {
392	printf(" %s=%i [%i .. ", param, val, min);
393	if (max != INT_MAX) printf("%i", max);
394	printf("] %s\n", description);
395	return 0;
396	}
397	int i;
398	const char *s = NULp;
399
400	arb_assert(min<=val && val<=max); // wrong default value
401
402	arb_assert(pargc >= 1); // otherwise s stays 0
403
404	for (i=1; i<pargc; i++) {
405	s = pargv[i];
406	if (*s == '-') s++;
407	if (!strncasecmp(s, param, strlen(param))) break;
408	}
409	if (i==pargc) return val;
410	s += strlen(param);
411	if (*s == '=') {
412	s++;
413	val = atoi(s);
414
415	if (val<min \|\| val>max) {
416	outOfRange = true;
417	printf("Parameter '%s=%s' is outside allowed range:\n", param, s);
418	showhelp = true;
419	getInt(param, val, min, max, description);
420	showhelp = false;
421	val = 0;
422	}
423	}
424
425	pargc--; // remove parameter
426	for (; i<pargc; i++) {
427	pargv[i] = pargv[i+1];
428	}
429
430	return val;
431	}
432
433	static const char getString(const char param, const char val, const char description) {
434	if (showhelp) {
435	if (!val) val = "";
436	printf(" %s=%s %s\n", param, val, description);
437	return NULp;
438	}
439	int i;
440	const char *s = NULp;
441
442	arb_assert(pargc >= 1); // otherwise s stays 0
443
444	for (i=1; i<pargc; i++) {
445	s = pargv[i];
446	if (*s == '-') s++;
447	if (!strncasecmp(s, param, strlen(param))) break;
448	}
449	if (i==pargc) return val;
450	s += strlen(param);
451	if (*s != '=') return val;
452	s++;
453	pargc--; // remove parameter
454	for (; i<pargc; i++) {
455	pargv[i] = pargv[i+1];
456	}
457	return s;
458	}
459
460	static bool parseCommandLine(int argc, const char * const * const argv) {
461	pargc = argc;
462
463	// copy argv (since parser will remove matched arguments)
464	free(pargv);
465	ARB_alloc(pargv, pargc);
466	for (int i=0; i<pargc; i++) pargv[i] = argv[i];
467
468	showhelp = (pargc <= 1);
469	outOfRange = false;
470
471	#ifdef UNIT_TESTS // UT_DIFF
472	const int minServerID = TEST_GENESERVER_ID;
473	#else // !UNIT_TESTS
474	const int minServerID = 0;
475	#endif
476
477	P.SERVERID = getInt("serverid", 0, minServerID, 100, "Server Id, look into $ARBHOME/lib/arb_tcp.dat");
478	#ifdef UNIT_TESTS // UT_DIFF
479	if (P.SERVERID<0) { arb_assert(P.SERVERID == TEST_SERVER_ID \|\| P.SERVERID == TEST_GENESERVER_ID); }
480	#endif
481
482	P.DESIGNCLIPOUTPUT = getInt("designmaxhits", 100, 10, 10000, "Maximum Number of Probe Design Suggestions");
483	P.DESIGNNAMES = getString("designnames", "", "List of short names separated by '#'");
484
485	P.sequence = NULp;
486	while ((P.DESIGNSEQUENCE = getString("designsequence", NULp, "Additional Sequences, will be added to the target group"))) {
487	apd_sequence *s = new apd_sequence;
488	s->next = P.sequence;
489	P.sequence = s;
490	s->sequence = P.DESIGNSEQUENCE;
491	P.DESIGNSEQUENCE = NULp;
492	}
493	P.DESIGNPROBELEN = getInt("designprobelength", 18, 2, 100, "(min.) length of probe");
494	P.DESIGNMAXPROBELEN = getInt("designmaxprobelength", -1, -1, 100, "max. length of probe (if specified)");
495	P.MINTEMP = getInt("designmintemp", 0, 0, 400, "Minimum melting temperature of probe");
496	P.MAXTEMP = getInt("designmaxtemp", 400, 0, 400, "Maximum melting temperature of probe");
497	P.MINGC = getInt("designmingc", 30, 0, 100, "Minimum gc content");
498	P.MAXGC = getInt("designmaxgc", 80, 0, 100, "Maximum gc content");
499	P.MAXBOND = getInt("designmaxbond", 0, 0, 10, "Not implemented");
500	P.MINPOS = getInt("designminpos", -1, -1, INT_MAX, "Minimum ecoli position (-1=none)");
501	P.MAXPOS = getInt("designmaxpos", -1, -1, INT_MAX, "Maximum ecoli position (-1=none)");
502	P.MISHIT = getInt("designmishit", 0, 0, 10000, "Number of allowed hits outside the selected group");
503	P.MINTARGETS = getInt("designmintargets", 50, 0, 100, "Minimum percentage of hits within the selected species");
504
505	P.SEQUENCE = getString("matchsequence", "agtagtagt", "The sequence to search for");
506
507	P.MISMATCHES = getInt("matchmismatches", 0, 0, INT_MAX, "Maximum Number of allowed mismatches");
508	P.ALSO_REVCOMPL = getInt("matchAlsoRevcomp", 0, 0, 1, "Also match reverse-complemented probe");
509	P.WEIGHTED = getInt("matchweighted", 0, 0, 1, "Use weighted mismatches");
510	P.ACCEPTN = getInt("matchacceptN", 1, 0, INT_MAX, "Amount of N-matches not counted as mismatch");
511	P.LIMITN = getInt("matchlimitN", 4, 0, INT_MAX, "Limit for N-matches. If reached N-matches are mismatches");
512	P.MAXRESULT = getInt("matchmaxresults", 1000000, 0, INT_MAX, "Max. number of matches reported (0=unlimited)");
513
514	P.ITERATE = getInt("iterate", 0, 0, 20, "Iterate over probes of given length");
515	P.ITERATE_AMOUNT = getInt("iterate_amount", 100, 1, INT_MAX, "Number of results per answer");
516	P.ITERATE_READABLE = getInt("iterate_readable", 1, 0, 1, "readable results");
517
518	P.ITERATE_TU = getString("iterate_tu", "T", "use T or U in readable result");
519	P.ITERATE_SEPARATOR = getString("iterate_separator", ";", "Number of results per answer");
520
521	P.DUMP = getString("dump", "", "dump ptserver index to file (may be huge!)");
522
523	if (pargc>1) {
524	printf("Unknown (or duplicate) parameter %s\n", pargv[1]);
525	return false;
526	}
527	if (outOfRange) {
528	puts("Not all parameters were inside allowed range\n");
529	return false;
530	}
531
532	return !showhelp;
533	}
534
535	// --------------------------------------------------------------------------------
536
537	#ifdef UNIT_TESTS
538	#ifndef TEST_UNIT_H
539	#include <test_unit.h>
540	#endif
541
542	void TEST_BASIC_parseCommandLine() {
543	{
544	const char *args[] = { NULp, "serverid=0"};
545	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
546
547	// test default values here
548	TEST_EXPECT_EQUAL(P.ACCEPTN, 1);
549	TEST_EXPECT_EQUAL(P.LIMITN, 4);
550	TEST_EXPECT_EQUAL(P.MISMATCHES, 0);
551	TEST_EXPECT_EQUAL(P.MAXRESULT, 1000000);
552	}
553
554	{
555	const char *args[] = {NULp, "serverid=4", "matchmismatches=2"};
556	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
557	TEST_EXPECT_EQUAL(P.SERVERID, 4);
558	TEST_EXPECT_EQUAL(P.MISMATCHES, 2);
559	TEST_EXPECT_EQUAL(args[1], "serverid=4"); // check array args was not modified
560	}
561
562	{
563	const char *args[] = { NULp, "matchacceptN=0", "matchlimitN=5"};
564	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
565	TEST_EXPECT_EQUAL(P.ACCEPTN, 0);
566	TEST_EXPECT_EQUAL(P.LIMITN, 5);
567	}
568
569	{
570	const char *args[] = { NULp, "matchmaxresults=100"};
571	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
572	TEST_EXPECT_EQUAL(P.MAXRESULT, 100);
573	}
574	}
575
576	#endif // UNIT_TESTS
577
578	// --------------------------------------------------------------------------------
579
580
581	static char *execute(ARB_ERROR& error) {
582	char *answer;
583	if (*P.DESIGNNAMES \|\| P.sequence) {
584	answer = AP_probe_design_event(error);
585	}
586	else if (P.ITERATE>0) {
587	answer = AP_probe_iterate_event(error);
588	}
589	else if (P.DUMP[0]) {
590	answer = AP_dump_index_event(error);
591	}
592	else {
593	answer = AP_probe_match_event(error);
594	}
595	pd_gl.locs.clear();
596	return answer;
597	}
598
599	int ARB_main(int argc, char *argv[]) {
600	bool ok = parseCommandLine(argc, argv);
601	if (ok) {
602	ARB_ERROR error;
603	char *answer = execute(error);
604
605	arb_assert(contradicted(answer, error));
606
607	if (!answer) {
608	fprintf(stderr,
609	"arb_probe: Failed to process your request\n"
610	" Reason: %s",
611	error.deliver());
612	ok = false;
613	}
614	else {
615	fputs(answer, stdout);
616	free(answer);
617	error.expect_no_error();
618	}
619	}
620	return ok ? EXIT_SUCCESS : EXIT_FAILURE;
621	}
622
623	// --------------------------------------------------------------------------------
624
625	#ifdef UNIT_TESTS
626	#ifndef TEST_UNIT_H
627	#include <test_unit.h>
628	#endif
629
630	static int test_setup(bool use_gene_ptserver) {
631	static bool setup[2] = { false, false };
632	if (!setup[use_gene_ptserver]) {
633	TEST_SETUP_GLOBAL_ENVIRONMENT(use_gene_ptserver ? "ptserver_gene" : "ptserver"); // first call will recreate the test pt-server
634	setup[use_gene_ptserver] = true;
635	}
636	return use_gene_ptserver ? TEST_GENESERVER_ID : TEST_SERVER_ID;
637	}
638
639	// ----------------------------------
640	// test probe design / match
641
642	#define TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv) \
643	int serverid = test_setup(use_gene_ptserver); \
644	TEST_EXPECT_EQUAL(true, parseCommandLine(fake_argc, fake_argv)); \
645	TEST_EXPECT((serverid == TEST_SERVER_ID)\|\|(serverid == TEST_GENESERVER_ID)); \
646	P.SERVERID = serverid; \
647	ARB_ERROR error; \
648	char *answer = execute(error)
649
650	#define TEST_ARB_PROBE__REPORTS_ERROR(fake_argc,fake_argv,expected_error) \
651	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
652	free(answer); \
653	TEST_EXPECT_ERROR_CONTAINS(error.deliver(), expected_error)
654
655	#define TEST_ARB_PROBE__REPORTS_ERROR__BROKEN(fake_argc,fake_argv,expected_error) \
656	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
657	free(answer); \
658	TEST_EXPECT_ANY_ERROR(error.preserve()); \
659	TEST_EXPECT_ERROR_CONTAINS__BROKEN(error.deliver(), expected_error)
660
661
662	#define TEST_RUN_ARB_PROBE(fake_argc,fake_argv) \
663	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
664	TEST_EXPECT_NO_ERROR(error.deliver())
665
666	#define TEST_ARB_PROBE(fake_argc,fake_argv,expected) do { \
667	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
668	TEST_EXPECT_EQUAL(answer, expected); \
669	free(answer); \
670	} while(0)
671
672	#define TEST_ARB_PROBE__BROKEN(fake_argc,fake_argv,expected) do { \
673	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
674	TEST_EXPECT_EQUAL__BROKEN(answer, expected); \
675	free(answer); \
676	} while(0)
677
678	#define TEST_ARB_PROBE_FILT(fake_argc,fake_argv,filter,expected) do { \
679	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
680	char *filtered = filter(answer); \
681	TEST_EXPECT_EQUAL(filtered, expected); \
682	free(filtered); \
683	free(answer); \
684	} while(0)
685
686	typedef const char *CCP;
687
688	void TEST_SLOW_match_geneprobe() {
689	// test here runs versus database ../UNIT_TESTER/run/TEST_gpt_src.arb
690
691	bool use_gene_ptserver = true;
692	{
693	const char *arguments[] = {
694	"prgnamefake",
695	"matchsequence=NNUCNN",
696	"matchacceptN=4",
697	"matchlimitN=5",
698	};
699	CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NNUCNN'\1"
700	"genome2\1" " genome2 gene3 0 4 2.6 2 1 0 .........-UU==GG-UUGAUC.\1"
701	"genome2\1" " genome2 joined1 0 4 2.6 2 1 0 .........-UU==GG-UUGAUCCUG\1"
702	"genome2\1" " genome2 gene1 0 4 2.6 2 2 0 ........A-UU==GG-U.\1"
703	"genome2\1" " genome2 intergene_19_65 0 4 2.7 31 12 0 GGUUACUGC-AU==GG-UGUUCGCCU\1"
704	"genome1\1" " genome1 intergene_17_65 0 4 2.7 31 14 0 GGUUACUGC-UA==GG-UGUUCGCCU\1"
705	"genome2\1" " genome2 intergene_19_65 0 4 2.7 38 19 0 GCAUUCGGU-GU==GC-CUAAGCACU\1"
706	"genome1\1" " genome1 intergene_17_65 0 4 2.7 38 21 0 GCUAUCGGU-GU==GC-CUAAGCCAU\1"
707	"genome2\1" " genome2 gene3 0 4 2.9 10 9 0 .UUUCGGUU-GA==..-\1"
708	"genome2\1" " genome2 intergene_19_65 0 4 3.1 56 37 0 AGCACUGCG-AG==AU-AUGUA.\1"
709	"genome1\1" " genome1 intergene_17_65 0 4 3.1 56 39 0 AGCCAUGCG-AG==AU-AUGUA.\1"
710	"genome1\1" " genome1 gene2 0 4 3.1 10 2 0 ........U-GA==CU-GC.\1"
711	"genome2\1" " genome2 gene2 0 4 3.1 10 4 0 ......GUU-GA==CU-GCCA.\1"
712	"genome1\1" " genome1 joined1 0 4 3.1 10 7 0 ...CUGGUU-GA==CU-GC.\1"
713	"genome2\1" " genome2 joined1 0 4 3.1 10 9 0 .UUUCGGUU-GA==CU-GCCA.\1";
714
715	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd);
716	}
717
718	{
719	const char *arguments[] = {
720	"prgnamefake",
721	"matchsequence=NGGUUN",
722	"matchacceptN=2",
723	"matchlimitN=3",
724	};
725	CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NGGUUN'\1"
726	"genome1\1" " genome1 gene3 0 2 1.3 5 2 0 ........C-U====G-A.\1"
727	"genome1\1" " genome1 joined1 0 2 1.3 5 2 0 ........C-U====G-AUCCUGC.\1"
728	"genome2\1" " genome2 gene3 0 2 1.4 5 4 0 ......UUU-C====G-AUC.\1"
729	"genome2\1" " genome2 joined1 0 2 1.4 5 4 0 ......UUU-C====G-AUCCUGCCA\1"
730	"genome2\1" " genome2 intergene_19_65 0 2 1.8 21 2 0 ........G-A====A-CUGCAUUCG\1"
731	"genome1\1" " genome1 intergene_17_65 0 2 1.8 21 4 0 ......CAG-A====A-CUGCUAUCG\1";
732
733	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd);
734	}
735
736	{
737	const char *arguments[] = {
738	"prgnamefake",
739	"matchsequence=UGAUCCU", // exists in data
740	};
741	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UGAUCCU'\1"
742	"genome1\1" " genome1 gene2 0 0 0.0 9 1 0 .........-=======-GC.\1"
743	"genome2\1" " genome2 gene2 0 0 0.0 9 3 0 .......GU-=======-GCCA.\1"
744	"genome1\1" " genome1 joined1 0 0 0.0 9 6 0 ....CUGGU-=======-GC.\1"
745	"genome2\1" " genome2 joined1 0 0 0.0 9 8 0 ..UUUCGGU-=======-GCCA.\1";
746
747	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hits in 'joined1' (of both genomes)]
748	}
749	{
750	const char *arguments[] = {
751	"prgnamefake",
752	"matchsequence=GAUCCU",
753	};
754	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'GAUCCU'\1"
755	"genome1\1" " genome1 gene2 0 0 0.0 10 2 0 ........U-======-GC.\1"
756	"genome2\1" " genome2 gene2 0 0 0.0 10 4 0 ......GUU-======-GCCA.\1"
757	"genome1\1" " genome1 joined1 0 0 0.0 10 7 0 ...CUGGUU-======-GC.\1"
758	"genome2\1" " genome2 joined1 0 0 0.0 10 9 0 .UUUCGGUU-======-GCCA.\1";
759
760	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]
761	}
762	{
763	const char *arguments[] = {
764	"prgnamefake",
765	"matchsequence=UUUCGG", // exists only in genome2
766	};
767	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUUCGG'\1"
768	"genome2\1" " genome2 gene3 0 0 0.0 2 1 0 .........-======-UUGAUC.\1"
769	"genome2\1" " genome2 joined1 0 0 0.0 2 1 0 .........-======-UUGAUCCUG\1"
770	"genome2\1" " genome2 gene1 0 0 0.0 2 2 0 ........A-======-U.\1";
771
772	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hit in genome2/gene1]
773	}
774	{
775	const char *arguments[] = {
776	"prgnamefake",
777	"matchsequence=AUCCUG",
778	};
779	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'AUCCUG'\1"
780	"genome1\1" " genome1 gene2 0 0 0.0 11 3 0 .......UG-======-C.\1"
781	"genome2\1" " genome2 gene2 0 0 0.0 11 5 0 .....GUUG-======-CCA.\1"
782	"genome1\1" " genome1 joined1 0 0 0.0 11 8 0 ..CUGGUUG-======-C.\1"
783	"genome2\1" " genome2 joined1 0 0 0.0 11 10 0 UUUCGGUUG-======-CCA.\1";
784
785	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hits in 'gene2' and 'joined1' of both genomes]
786	}
787	{
788	const char *arguments[] = {
789	"prgnamefake",
790	"matchsequence=UUGAUCCUGC",
791	};
792	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUGAUCCUGC'\1"
793	"genome2\1" " genome2 gene2 0 0 0.0 8 2 0 ........G-==========-CA.\1"
794	"genome1\1" " genome1 joined1 0 0 0.0 8 5 0 .....CUGG-==========-.\1"
795	"genome2\1" " genome2 joined1 0 0 0.0 8 7 0 ...UUUCGG-==========-CA.\1";
796
797	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hit in 'genome2/joined1']
798	}
799	}
800
801	__ATTR__REDUCED_OPTIMIZE void TEST_SLOW_match_probe() {
802	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
803
804	bool use_gene_ptserver = false;
805	{
806	const char *arguments[] = {
807	"prgnamefake",
808	"matchsequence=UAUCGGAGAGUUUGA",
809	};
810	CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UAUCGGAGAGUUUGA'\1"
811	"BcSSSS00\1" " BcSSSS00 0 0 0.0 3 2 0 .......UU-===============-UCAAGUCGA\1";
812
813	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
814	}
815
816	// ----------------------------------------------------------------------------
817	// match with old(=default) N-mismatch-behavior (accepting 1 N-match)
818
819	{
820	const char *arguments[] = {
821	"prgnamefake",
822	"matchsequence=CANCUCCUUUC", // contains 1 N
823	NULp // matchmismatches
824	};
825
826	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
827	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"; // only N-mismatch accepted
828
829	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
830	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
831	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
832	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
833	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
834	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
835	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
836	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
837	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
838	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1";
839
840	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
841	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
842	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
843	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
844	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
845	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
846	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
847	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
848	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
849	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
850	"AclPleur\1" " AclPleur 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
851	"PtVVVulg\1" " PtVVVulg 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
852	"DlcTolu2\1" " DlcTolu2 2 3 2.3 176 162 0 CGGCUGGAU-==C======NN-N.\1"
853	"FrhhPhil\1" " FrhhPhil 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
854	"HllHalod\1" " HllHalod 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
855	"CPPParap\1" " CPPParap 2 3 2.3 177 163 0 CGGNUGGAU-==C======..-\1";
856
857	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
858	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
859	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
860	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
861	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
862	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
863	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
864	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
865	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
866	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
867	"AclPleur\1" " AclPleur 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
868	"PtVVVulg\1" " PtVVVulg 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
869	"DlcTolu2\1" " DlcTolu2 2 3 2.3 176 162 0 CGGCUGGAU-==C======NN-N.\1"
870	"FrhhPhil\1" " FrhhPhil 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
871	"HllHalod\1" " HllHalod 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
872	"CPPParap\1" " CPPParap 2 3 2.3 177 163 0 CGGNUGGAU-==C======..-\1"
873	"VblVulni\1" " VblVulni 3 1 3.6 49 44 0 AGCACAGAG-a=A==uG====-UCGGGUGGC\1";
874
875	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
876	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
877	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
878	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
879	}
880
881	{
882	const char *arguments[] = {
883	"prgnamefake",
884	"matchsequence=UCACCUCCUUUC", // contains no N
885	NULp // matchmismatches
886	};
887
888	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
889	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
890	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
891	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
892	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
893	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
894	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
895	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
896	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1";
897
898	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
899	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
900	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
901	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
902	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
903	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
904	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
905	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
906	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
907	"AclPleur\1" " AclPleur 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
908	"PtVVVulg\1" " PtVVVulg 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
909	"DlcTolu2\1" " DlcTolu2 1 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
910	"FrhhPhil\1" " FrhhPhil 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
911	"HllHalod\1" " HllHalod 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
912	"CPPParap\1" " CPPParap 1 2 1.4 176 162 0 GCGGNUGGA-==========..-\1";
913
914	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
915	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
916	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
917	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
918	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
919	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
920	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
921	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
922	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
923	"AclPleur\1" " AclPleur 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
924	"PtVVVulg\1" " PtVVVulg 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
925	"DlcTolu2\1" " DlcTolu2 1 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
926	"FrhhPhil\1" " FrhhPhil 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
927	"HllHalod\1" " HllHalod 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
928	"CPPParap\1" " CPPParap 1 2 1.4 176 162 0 GCGGNUGGA-==========..-\1"
929	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C=========-U.\1"
930	"LgtLytic\1" " LgtLytic 2 3 2.1 175 161 0 GCGGCUGGA-=========N..-\1"
931	"PslFlave\1" " PslFlave 2 3 2.1 175 161 0 GCGGCUGGA-=========...-\1";
932
933	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
934	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
935	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
936	}
937
938	{
939	const char *arguments[] = {
940	"prgnamefake",
941	"matchsequence=UCACCUCCUUUC", // contains no N
942	NULp, // matchmismatches
943	"matchweighted=1", // use weighted mismatches
944	};
945
946	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
947	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
948	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
949	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
950	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
951	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
952	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
953	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
954	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1";
955
956	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
957	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
958	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
959	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
960	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
961	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
962	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
963	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
964	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
965	"DlcTolu2\1" " DlcTolu2 1 2 0.6 175 161 0 GCGGCUGGA-==========NN-N.\1"
966	"FrhhPhil\1" " FrhhPhil 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
967	"HllHalod\1" " HllHalod 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
968	"CPPParap\1" " CPPParap 1 2 0.6 176 162 0 GCGGNUGGA-==========..-\1"
969	"AclPleur\1" " AclPleur 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
970	"PtVVVulg\1" " PtVVVulg 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
971	"LgtLytic\1" " LgtLytic 2 3 1.3 175 161 0 GCGGCUGGA-=========N..-\1"
972	"PslFlave\1" " PslFlave 2 3 1.3 175 161 0 GCGGCUGGA-=========...-\1"
973	"ClfPerfr\1" " ClfPerfr 2 0 1.3 175 161 0 AAGAUUAAU-A=C=========-U.\1";
974
975	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
976	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
977	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
978	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
979	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
980	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
981	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
982	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
983	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
984	"DlcTolu2\1" " DlcTolu2 1 2 0.6 175 161 0 GCGGCUGGA-==========NN-N.\1"
985	"FrhhPhil\1" " FrhhPhil 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
986	"HllHalod\1" " HllHalod 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
987	"CPPParap\1" " CPPParap 1 2 0.6 176 162 0 GCGGNUGGA-==========..-\1"
988	"AclPleur\1" " AclPleur 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
989	"PtVVVulg\1" " PtVVVulg 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
990	"LgtLytic\1" " LgtLytic 2 3 1.3 175 161 0 GCGGCUGGA-=========N..-\1"
991	"PslFlave\1" " PslFlave 2 3 1.3 175 161 0 GCGGCUGGA-=========...-\1"
992	"ClfPerfr\1" " ClfPerfr 2 0 1.3 175 161 0 AAGAUUAAU-A=C=========-U.\1"
993	"AclPleur\1" " AclPleur 5 0 2.4 50 45 0 GAAGGGAGC-=ug=u=u====G-CCGACGAGU\1"
994	"PtVVVulg\1" " PtVVVulg 5 0 2.4 50 45 0 GGAGAAAGC-=ug=u=u===g=-UGACGAGCG\1";
995
996	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
997	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
998	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
999	}
1000
1001	// ----------------------------------------------
1002	// do not accept any N-matches as match
1003
1004	{
1005	const char *arguments[] = {
1006	"prgnamefake",
1007	"matchsequence=CANCUCCUUUC", // contains 1 N
1008	NULp, // matchmismatches
1009	"matchacceptN=0",
1010	};
1011
1012	CCP expectd0 = ""; // nothing matches
1013
1014	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
1015	"BcSSSS00\1" " BcSSSS00 1 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1";
1016
1017	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
1018	"BcSSSS00\1" " BcSSSS00 1 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
1019	"ClfPerfr\1" " ClfPerfr 2 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
1020	"PbcAcet2\1" " PbcAcet2 2 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1021	"PbrPropi\1" " PbrPropi 2 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1022	"Stsssola\1" " Stsssola 2 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
1023	"DcdNodos\1" " DcdNodos 2 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
1024	"VbrFurni\1" " VbrFurni 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
1025	"VblVulni\1" " VblVulni 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
1026	"VbhChole\1" " VbhChole 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1";
1027
1028	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1029	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1030	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1031	}
1032	{
1033	const char *arguments[] = {
1034	"prgnamefake",
1035	"matchsequence=UUUCUUU", // contains no N
1036	NULp, // matchmismatches
1037	"matchacceptN=0",
1038	};
1039
1040	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1041	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1";
1042
1043	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1044	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1"
1045	"AclPleur\1" " AclPleur 1 0 0.6 50 45 0 GAAGGGAGC-==g====-CUUUGCCGA\1"
1046	"PtVVVulg\1" " PtVVVulg 1 0 0.6 50 45 0 GGAGAAAGC-==g====-CUUGCUGAC\1"
1047	"PtVVVulg\1" " PtVVVulg 1 0 0.6 54 49 0 AAAGCUUGC-======g-CUGACGAGC\1"
1048	"ClfPerfr\1" " ClfPerfr 1 0 1.1 49 44 0 GCGAUGAAG-====C==-CGGGAAACG\1";
1049
1050	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1051	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1"
1052	"AclPleur\1" " AclPleur 1 0 0.6 50 45 0 GAAGGGAGC-==g====-CUUUGCCGA\1"
1053	"PtVVVulg\1" " PtVVVulg 1 0 0.6 50 45 0 GGAGAAAGC-==g====-CUUGCUGAC\1"
1054	"PtVVVulg\1" " PtVVVulg 1 0 0.6 54 49 0 AAAGCUUGC-======g-CUGACGAGC\1"
1055	"ClfPerfr\1" " ClfPerfr 1 0 1.1 49 44 0 GCGAUGAAG-====C==-CGGGAAACG\1"
1056	"DlcTolu2\1" " DlcTolu2 2 0 1.2 47 42 0 AGAAAGGGA-==g===g-CAAUCCUGA\1"
1057	"ClnCorin\1" " ClnCorin 2 0 1.7 48 43 0 AGCGAUGAA-g===C==-CGGGAAUGG\1"
1058	"CPPParap\1" " CPPParap 2 0 1.7 48 43 0 AGCGAUGAA-g===C==-CGGGAACGG\1"
1059	"HllHalod\1" " HllHalod 2 0 1.7 49 44 0 GAUGGAAGC-==g===C-CAGGCGUCG\1"
1060	"DcdNodos\1" " DcdNodos 2 0 1.7 50 45 0 UUAUGUAGC-==g==A=-GUAACCUAG\1"
1061	"VbhChole\1" " VbhChole 2 0 1.7 55 50 0 GAGGAACUU-g===C==-GGGUGGCGA\1"
1062	"VbrFurni\1" " VbrFurni 2 0 1.7 62 57 0 UUCGGGGGA-===G==g-GGCGGCGAG\1"
1063	"VblVulni\1" " VblVulni 2 0 1.7 62 57 0 AGAAACUUG-=====Cg-GGUGGCGAG\1"
1064	"VbhChole\1" " VbhChole 2 0 1.7 62 57 0 AGGAACUUG-==C===g-GGUGGCGAG\1"
1065	"ClnCorin\1" " ClnCorin 2 0 2.2 49 44 0 GCGAUGAAG-==C===C-GGGAAUGGA\1"
1066	"CltBotul\1" " CltBotul 2 0 2.2 49 44 0 GCGAUGAAG-C=====C-GGAAGUGGA\1"
1067	"CPPParap\1" " CPPParap 2 0 2.2 49 44 0 GCGAUGAAG-==C===C-GGGAACGGA\1"
1068	"ClfPerfr\1" " ClfPerfr 2 0 2.2 50 45 0 CGAUGAAGU-==C===C-GGGAAACGG\1"
1069	"VblVulni\1" " VblVulni 2 0 2.2 52 47 0 ACAGAGAAA-C==G===-CUCGGGUGG\1"
1070	"BcSSSS00\1" " BcSSSS00 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-CU.\1"
1071	"ClfPerfr\1" " ClfPerfr 2 0 2.2 179 165 0 UUAAUACCC-C=C====-CU.\1"
1072	"PbcAcet2\1" " PbcAcet2 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-NN.\1"
1073	"PbrPropi\1" " PbrPropi 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-NN.\1"
1074	"Stsssola\1" " Stsssola 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1075	"DcdNodos\1" " DcdNodos 2 0 2.2 179 165 0 UUGGAUCAC-C=C====-.\1"
1076	"VbrFurni\1" " VbrFurni 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1077	"VblVulni\1" " VblVulni 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1078	"VbhChole\1" " VbhChole 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1079	"BcSSSS00\1" " BcSSSS00 2 2 1.4 183 169 0 AUCACCUCC-=====..-\1"
1080	"ClfPerfr\1" " ClfPerfr 2 2 1.4 183 169 0 UACCCCUCC-=====..-\1";
1081
1082	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1083	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1084	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1085	}
1086	{
1087	const char *arguments[] = {
1088	"prgnamefake",
1089	"matchsequence=UCACCUCCUUUC", // contains no N
1090	NULp, // matchmismatches
1091	"matchacceptN=0",
1092	};
1093
1094	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1095	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "";
1096
1097	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1098	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
1099	"PbcAcet2\1" " PbcAcet2 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1100	"PbrPropi\1" " PbrPropi 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1101	"Stsssola\1" " Stsssola 1 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
1102	"DcdNodos\1" " DcdNodos 1 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
1103	"VbrFurni\1" " VbrFurni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1104	"VblVulni\1" " VblVulni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1105	"VbhChole\1" " VbhChole 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1";
1106
1107	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1108	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
1109	"PbcAcet2\1" " PbcAcet2 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1110	"PbrPropi\1" " PbrPropi 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1111	"Stsssola\1" " Stsssola 1 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
1112	"DcdNodos\1" " DcdNodos 1 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
1113	"VbrFurni\1" " VbrFurni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1114	"VblVulni\1" " VblVulni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1115	"VbhChole\1" " VbhChole 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1116	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C=========-U.\1"
1117	"AclPleur\1" " AclPleur 2 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
1118	"PtVVVulg\1" " PtVVVulg 2 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
1119	"DlcTolu2\1" " DlcTolu2 2 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
1120	"FrhhPhil\1" " FrhhPhil 2 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
1121	"HllHalod\1" " HllHalod 2 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
1122	"CPPParap\1" " CPPParap 2 2 1.4 176 162 0 GCGGNUGGA-==========..-\1";
1123
1124	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1125	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1126	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1127	}
1128	{
1129	const char *arguments[] = {
1130	"prgnamefake",
1131	"matchsequence=UCACCUCCUUUCU", // contains no N
1132	NULp, // matchmismatches
1133	"matchacceptN=0",
1134	};
1135
1136	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1137	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1";
1138
1139	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1140	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1141	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1142	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1143	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1144	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1145	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1146	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1147	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1148	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1";
1149
1150	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1151	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1152	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1153	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1154	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1155	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1156	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1157	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1158	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1159	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1160	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1161	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1162	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1163	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1164	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1165	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1";
1166
1167	CCP expectd4 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1168	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1169	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1170	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1171	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1172	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1173	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1174	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1175	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1176	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1177	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1178	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1179	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1180	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1181	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1182	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1"
1183	"LgtLytic\1" " LgtLytic 4 4 2.8 175 161 0 GCGGCUGGA-=========N...-\1"
1184	"PslFlave\1" " PslFlave 4 4 2.8 175 161 0 GCGGCUGGA-=========....-\1";
1185
1186	CCP expectd5 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1187	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1188	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1189	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1190	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1191	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1192	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1193	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1194	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1195	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1196	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1197	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1198	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1199	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1200	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1201	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1"
1202	"LgtLytic\1" " LgtLytic 4 4 2.8 175 161 0 GCGGCUGGA-=========N...-\1"
1203	"PslFlave\1" " PslFlave 4 4 2.8 175 161 0 GCGGCUGGA-=========....-\1"
1204	"PtVVVulg\1" " PtVVVulg 5 0 2.6 50 45 0 GGAGAAAGC-=ug=u=u===g==-GACGAGCGG\1"
1205	"AclPleur\1" " AclPleur 5 0 3.5 46 41 0 ACGGGAAGG-gag=u=G======-UUGCCGACG\1"
1206	"PtVVVulg\1" " PtVVVulg 5 0 4.0 45 40 0 ...AGGAGA-Aag=u=G======-UGCUGACGA\1"
1207	"VblVulni\1" " VblVulni 5 0 4.3 48 43 0 CAGCACAGA-ga=a==uG=====-CGGGUGGCG\1";
1208
1209	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1210	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1211	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1212	arguments[2] = "matchmismatches=4"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd4);
1213	arguments[2] = "matchmismatches=5"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd5);
1214	}
1215
1216	// ----------------------------------
1217	// accept several N-matches
1218
1219	{
1220	const char *arguments[] = {
1221	"prgnamefake",
1222	"matchsequence=CANCUCCUUNC", // contains 2 N
1223	NULp, // matchmismatches
1224	"matchacceptN=2",
1225	"matchlimitN=4",
1226	};
1227
1228	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1229	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1";
1230
1231	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1232	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1"
1233	"ClfPerfr\1" " ClfPerfr 1 2 2.8 176 162 0 AGAUUAAUA-=CC======U=-U.\1"
1234	"DlcTolu2\1" " DlcTolu2 1 3 2.4 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1235	"FrhhPhil\1" " FrhhPhil 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1236	"HllHalod\1" " HllHalod 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1237	"CPPParap\1" " CPPParap 1 3 2.4 177 163 0 CGGNUGGAU-==C======..-\1"
1238	"PbcAcet2\1" " PbcAcet2 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1239	"PbrPropi\1" " PbrPropi 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1240	"Stsssola\1" " Stsssola 1 3 2.4 176 162 0 CGGCUGGAU-==C======U.-\1"
1241	"DcdNodos\1" " DcdNodos 1 3 2.4 176 162 0 CGGUUGGAU-==C======U.-\1"
1242	"VbrFurni\1" " VbrFurni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1243	"VblVulni\1" " VblVulni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1244	"VbhChole\1" " VbhChole 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1245	"AclPleur\1" " AclPleur 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1"
1246	"PtVVVulg\1" " PtVVVulg 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1";
1247
1248	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1249	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1"
1250	"ClfPerfr\1" " ClfPerfr 1 2 2.8 176 162 0 AGAUUAAUA-=CC======U=-U.\1"
1251	"DlcTolu2\1" " DlcTolu2 1 3 2.4 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1252	"FrhhPhil\1" " FrhhPhil 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1253	"HllHalod\1" " HllHalod 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1254	"CPPParap\1" " CPPParap 1 3 2.4 177 163 0 CGGNUGGAU-==C======..-\1"
1255	"PbcAcet2\1" " PbcAcet2 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1256	"PbrPropi\1" " PbrPropi 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1257	"Stsssola\1" " Stsssola 1 3 2.4 176 162 0 CGGCUGGAU-==C======U.-\1"
1258	"DcdNodos\1" " DcdNodos 1 3 2.4 176 162 0 CGGUUGGAU-==C======U.-\1"
1259	"VbrFurni\1" " VbrFurni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1260	"VblVulni\1" " VblVulni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1261	"VbhChole\1" " VbhChole 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1262	"AclPleur\1" " AclPleur 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1"
1263	"PtVVVulg\1" " PtVVVulg 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1";
1264
1265	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1266	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1267	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1268	}
1269
1270	{
1271	const char *arguments[] = {
1272	"prgnamefake",
1273	"matchsequence=GAGCGGUCAG", // similar to a region where dots occur in seqdata
1274	NULp, // matchmismatches
1275	"matchacceptN=0",
1276	"matchlimitN=4",
1277	};
1278
1279	CCP expectd0 = "";
1280
1281	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1282	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1";
1283
1284	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1285	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1"
1286	"Bl0LLL00\1" " Bl0LLL00 2 0 2.2 25 21 0 GAUCAAGUC-======A=C=-ACGGGAGCU\1";
1287
1288	// this probe-match is also tested with 'arb_probe_match'. see arb_test.cxx@TEST_arb_probe_match
1289	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1290	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1"
1291	"Bl0LLL00\1" " Bl0LLL00 2 0 2.2 25 21 0 GAUCAAGUC-======A=C=-ACGGGAGCU\1"
1292	"VbrFurni\1" " VbrFurni 3 0 2.4 68 60 0 GGAUUUGUU-=g====CG==-CGGCGGACG\1"
1293	"FrhhPhil\1" " FrhhPhil 3 0 2.8 82 70 0 ACGAGUGGC-=gA===C===-UUGGAAACG\1"
1294	"ClfPerfr\1" " ClfPerfr 3 0 3.2 86 74 0 CGGCGGGAC-=g==CU====-AACCUGCGG\1"
1295	"HllHalod\1" " HllHalod 3 0 3.6 25 21 0 GAUCAAGUC-======Aa=C-GAUGGAAGC\1"
1296	"DlcTolu2\1" " DlcTolu2 3 0 3.6 95 83 0 GGACUGCCC-==Aa==A===-CUAAUACCG\1"
1297	"FrhhPhil\1" " FrhhPhil 3 0 4.0 25 21 0 GAUCAAGUC-==A====a=C-AGGUCUUCG\1"
1298	"AclPleur\1" " AclPleur 3 0 4.0 29 24 0 GAUCAAGUC-==A====a=C-GGGAAGGGA\1"
1299	"ClnCorin\1" " ClnCorin 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUCCUUCG\1"
1300	"CltBotul\1" " CltBotul 3 0 4.1 25 21 0 .AUCAAGUC-=====A=G=A-GCUUCUUCG\1"
1301	"CPPParap\1" " CPPParap 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUCCUUCG\1"
1302	"ClfPerfr\1" " ClfPerfr 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUUCCUUC\1"
1303	"DlcTolu2\1" " DlcTolu2 3 0 4.1 157 143 0 GUAGCCGUU-===GAA====-CGGCUGGAU\1"
1304	"PslFlave\1" " PslFlave 3 3 2.4 25 21 0 GAUCAAGUC-=======...-<more>\1"
1305	"PtVVVulg\1" " PtVVVulg 3 3 2.4 29 24 0 GAUCAAGUC-=======...-<more>\1";
1306
1307	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1308	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1309	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1310	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1311	}
1312
1313	{
1314	const char *arguments[] = {
1315	"prgnamefake",
1316	"matchsequence=GAGCGGUCAGGAG", // as above, but continues behind '...'
1317	NULp, // matchmismatches
1318	"matchweighted=1", // use weighted mismatches
1319	};
1320
1321	CCP expectd2 = "";
1322	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAGGAG'\1"
1323	"ClnCorin\1" " ClnCorin 6 0 3.4 77 66 0 AUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1324	"CltBotul\1" " CltBotul 6 0 3.4 77 66 0 GUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1325	"CPPParap\1" " CPPParap 6 0 3.4 77 66 0 ACGGAUUAG-Cg====A=g==CC-UUCCGAAAG\1"
1326	"BcSSSS00\1" " BcSSSS00 3 0 3.4 25 21 0 GAUCAAGUC-======A===AU=-GGAGCUUGC\1";
1327
1328	CCP expectd4 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAGGAG'\1"
1329	"ClnCorin\1" " ClnCorin 6 0 3.4 77 66 0 AUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1330	"CltBotul\1" " CltBotul 6 0 3.4 77 66 0 GUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1331	"CPPParap\1" " CPPParap 6 0 3.4 77 66 0 ACGGAUUAG-Cg====A=g==CC-UUCCGAAAG\1"
1332	"BcSSSS00\1" " BcSSSS00 3 0 3.4 25 21 0 GAUCAAGUC-======A===AU=-GGAGCUUGC\1"
1333	"ClfPerfr\1" " ClfPerfr 6 0 3.9 121 108 0 AUCAUAAUG-C====A=ug==gU-GAAGUCGUA\1"
1334	"ClnCorin\1" " ClnCorin 6 0 3.9 122 109 0 CGCAUAAGA-C====A=ug==gU-GAAGUCGUA\1"
1335	"CltBotul\1" " CltBotul 6 0 3.9 122 109 0 CUCAUAAGA-C====A=ug==gU-GAAGUCGUA\1"
1336	"CPPParap\1" " CPPParap 6 0 3.9 122 109 0 GCAUAAGAU-C====A=ug==gU-AAGUCGUAA\1"
1337	"DcdNodos\1" " DcdNodos 6 0 4.2 77 66 0 GUAACCUAG-Ug====A=g=AC=-UAUGGAAAC\1"
1338	"PsAAAA00\1" " PsAAAA00 6 0 4.2 77 66 0 UGGAUUCAG-Cg====A=g=AC=-UCCGGAAAC\1"
1339	"PslFlave\1" " PslFlave 6 0 4.2 77 66 0 CUGAUUCAG-Cg====A=g=AC=-UUUCGAAAG\1"
1340	"FrhhPhil\1" " FrhhPhil 5 0 4.2 149 135 0 UAACAAUGG-U===C==ag===A-CCUGCGGCU\1"
1341	"AclPleur\1" " AclPleur 4 0 4.3 29 24 0 GAUCAAGUC-==A====a=C=g=-AAGGGAGCU\1"
1342	"PbcAcet2\1" " PbcAcet2 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1343	"PbrPropi\1" " PbrPropi 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1344	"Stsssola\1" " Stsssola 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1345	"LgtLytic\1" " LgtLytic 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1346	"PslFlave\1" " PslFlave 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1347	"HllHalod\1" " HllHalod 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1348	"VbrFurni\1" " VbrFurni 5 0 4.4 68 60 0 GGAUUUGUU-=g====CG==Cg=-CGGACGGAC\1"
1349	"AclPleur\1" " AclPleur 6 0 4.4 35 30 0 GUCGAACGG-U=A===ga===gA-GCUUGCUUU\1"
1350	"PslFlave\1" " PslFlave 6 6 4.4 25 21 0 GAUCAAGUC-=======......-<more>\1"
1351	"PtVVVulg\1" " PtVVVulg 6 6 4.4 29 24 0 GAUCAAGUC-=======......-<more>\1"
1352	"VbrFurni\1" " VbrFurni 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1"
1353	"VblVulni\1" " VblVulni 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1"
1354	"VbhChole\1" " VbhChole 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1";
1355
1356	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1357	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1358	arguments[2] = "matchmismatches=4"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd4);
1359	}
1360
1361	// --------------------------
1362	// truncate results
1363
1364	{
1365	const char *arguments[] = {
1366	"prgnamefake",
1367	"matchsequence=CANCNCNNUNC", // contains 5N
1368	NULp, // matchmismatches
1369	"matchacceptN=5",
1370	"matchlimitN=7",
1371	"matchmaxresults=5",
1372	};
1373
1374	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1375	"BcSSSS00\1" " BcSSSS00 0 5 4.2 176 162 0 CGGCUGGAU-==C=U=CU=U=-U.\1";
1376
1377	// many hits are truncated here:
1378	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1379	"DlcTolu2\1" " DlcTolu2 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU==N-N.\1"
1380	"FrhhPhil\1" " FrhhPhil 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU=..-\1"
1381	"HllHalod\1" " HllHalod 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU=..-\1"
1382	"CPPParap\1" " CPPParap 1 6 4.9 177 163 0 CGGNUGGAU-==C=U=CU=..-\1"
1383	"AclPleur\1" " AclPleur 1 6 5.0 176 162 0 CGGUUGGAU-==C=U=CU=A.-\1";
1384
1385	// many hits are truncated here:
1386	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1387	"HllHalod\1" " HllHalod 2 5 5.1 45 40 0 AAACGAUGG-a=G=UuGC=U=-CAGGCGUCG\1"
1388	"VblVulni\1" " VblVulni 2 5 5.4 49 44 0 AGCACAGAG-a=A=UuGU=U=-UCGGGUGGC\1"
1389	"VbrFurni\1" " VbrFurni 2 5 5.7 40 35 0 CGGCAGCGA-==A=AuUGAA=-CUUCGGGGG\1"
1390	"LgtLytic\1" " LgtLytic 2 5 6.2 101 89 0 GGGGAAACU-==AGCuAA=A=-CGCAUAAUC\1"
1391	"ClfPerfr\1" " ClfPerfr 2 5 6.5 172 158 0 AGGAAGAUU-a=UaC=CC=C=-UUUCU.\1";
1392
1393	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1394	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1395	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1396	}
1397
1398	// -------------------------------------------------------------
1399	// tests related to http://bugs.arb-home.de/ticket/410
1400	{
1401	const char *arguments[] = {
1402	"prgnamefake",
1403	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACC", // length=29
1404	NULp, // matchmismatches
1405	"matchacceptN=5",
1406	"matchlimitN=7",
1407	"matchmaxresults=10",
1408	};
1409
1410	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'ACGGACUCCGGGAAACCGGGGCUAAUACC'\1"
1411	"BcSSSS00\1" " BcSSSS00 0 0 0.0 84 72 0 UAGCGGCGG-=============================-GGAUGGUGA\1"
1412	"Bl0LLL00\1" " Bl0LLL00 0 0 0.0 84 72 0 CAGCGGCGG-=============================-GGAUGCUGA\1"
1413	"AclPleur\1" " AclPleur 4 0 4.6 84 72 0 GAGUGGCGG-=======a========u=UA=========-GCGUAAUCA\1"
1414	"PtVVVulg\1" " PtVVVulg 4 0 5.1 84 72 0 GAGCGGCGG-=======a=U======G=U==========-GCAUGACCA\1"
1415	"DsssDesu\1" " DsssDesu 5 0 5.3 84 72 0 GAGUGGCGC-========u=C====Gu==A=========-GGAUACAGA\1"
1416	"PsAAAA00\1" " PsAAAA00 5 0 5.3 84 72 0 CAGCGGCGG-======gu=C======G==C=========-GCAUACGCA\1";
1417
1418	arguments[2] = "matchmismatches=5"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1419	}
1420	{
1421	const char *arguments[] = {
1422	"prgnamefake",
1423	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA", // length=38
1424	NULp, // matchmismatches
1425	"matchacceptN=5",
1426	"matchlimitN=7",
1427	"matchmaxresults=100",
1428	};
1429
1430	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA'\1"
1431	"BcSSSS00\1" " BcSSSS00 0 0 0.0 84 72 0 UAGCGGCGG-======================================-UGAUUGGGG\1"
1432	"Bl0LLL00\1" " Bl0LLL00 1 0 1.5 84 72 0 CAGCGGCGG-==================================C===-UGAUUGGGG\1"
1433	"DsssDesu\1" " DsssDesu 8 0 9.4 84 72 0 GAGUGGCGC-========u=C====Gu==A=============ACA==-G.\1"
1434	"PtVVVulg\1" " PtVVVulg 8 0 10.7 84 72 0 GAGCGGCGG-=======a=U======G=U===========C===ACC=-UGACUGGGG\1"
1435	"AclPleur\1" " AclPleur 9 0 10.8 84 72 0 GAGUGGCGG-=======a========u=UA==========Cg=AA=C=-UGACUGGGG\1"
1436	"PsAAAA00\1" " PsAAAA00 10 0 11.9 84 72 0 CAGCGGCGG-======gu=C======G==C==========C==ACgC=-UGGUAACAA\1"
1437	"LgtLytic\1" " LgtLytic 10 0 12.8 84 72 0 GAGNGGCGA-=======uG=======uCAA==========C==AA=C=-UGACUGGGG\1"
1438	"VbrFurni\1" " VbrFurni 10 0 12.8 84 72 0 GAGCGGCGG-======CauU======GAU===========C===A=C=-UGACUGGGG\1"
1439	"VblVulni\1" " VblVulni 10 0 12.8 84 72 0 GAGCGGCGG-======CauU======GAU===========C===A=C=-UGACUGGGG\1"
1440	"Stsssola\1" " Stsssola 10 0 12.9 84 72 0 AAGUGGCGC-======gG=U======G=UC=============AACA=-UGAUUGGGG\1"
1441	"DlcTolu2\1" " DlcTolu2 10 0 13.4 84 72 0 GAGUGGCGC-=======G=CC====GGACA==============AA==-UAAUUGGGG\1"
1442	"PbcAcet2\1" " PbcAcet2 11 0 12.2 84 72 0 AAGUGGCGC-======A=uUC====GG==U=============AAg=g-UAACUGGGG\1"
1443	"HllHalod\1" " HllHalod 11 0 13.0 84 72 0 GAGCGGCGG-======CuG=======uCA===========C==ACgC=-UGACUGGGG\1"
1444	"PbrPropi\1" " PbrPropi 12 0 13.6 84 72 0 UAGUGGCGC-======A=uUC====Ga==U=========U===AAg=g-UGACUGGGG\1"
1445	"DcdNodos\1" " DcdNodos 12 0 14.4 84 72 0 UAGUGGCGG-======guaU======GUAC==========C==AAg==-UGACUGGGG\1"
1446	"VbhChole\1" " VbhChole 12 0 15.4 84 72 0 GAGCGGCGG-======CauU======GAU===========C==AACC=-UGACUGGGG\1";
1447
1448	arguments[2] = "matchmismatches=12"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1449	}
1450
1451
1452	// test expected errors
1453	{
1454	const char *arguments[] = {
1455	"prgnamefake",
1456	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA", // length = 38
1457	"matchmismatches=20",
1458	};
1459
1460	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, "Max. 19 mismatches are allowed for probes of length 38");
1461	}
1462	}
1463
1464	static char extract_locations(const char probe_design_result) {
1465	const char *Target = strstr(probe_design_result, "\nTarget");
1466	if (Target) {
1467	const char *designed = strchr(Target+7, '\n');
1468	if (designed) {
1469	++designed;
1470
1471	GBS_strstruct result(300);
1472	RegExpr reg_designed("^[A-Z]+"
1473	"[[:space:]]+[0-9]+"
1474	"[[:space:]]+([A-Z][=+-])" // subexpr #1 (loc+-=)
1475	"[[:space:]]*([0-9]+)", // subexpr #2 (abs or locrel)
1476	true);
1477
1478
1479	while (designed) {
1480	const char *eol = strchr(designed, '\n');
1481	const RegMatch *match = reg_designed.match(designed); if (!match) break;
1482
1483	match = reg_designed.subexpr_match(1); if (!match) break;
1484	std::string loc = match->extract(designed);
1485
1486	match = reg_designed.subexpr_match(2); if (!match) break;
1487	std::string pos = match->extract(designed);
1488
1489	result.cat(loc.c_str());
1490	result.cat(pos.c_str());
1491
1492	designed = eol ? eol+1 : NULp;
1493	}
1494	arb_assert(implicated(designed, !reg_designed.has_failed())); // assert RegExpr compiled
1495
1496	return result.release();
1497	}
1498	}
1499	return ARB_strdup("can't extract");
1500	}
1501
1502	inline const char next_line(const char this_line) {
1503	const char *lf = strchr(this_line, '\n');
1504	return (lf && lf[1] && strchr("ACGTU", lf[1])) ? lf+1 : NULp;
1505	}
1506	inline int count_hits(const char *design_result) {
1507	const char *target = strstr(design_result, "\nTarget");
1508	if (target) {
1509	const char *hit = next_line(target+1);
1510	int hits = 0;
1511
1512	while (hit) {
1513	++hits;
1514	hit = next_line(hit);
1515	}
1516	return hits;
1517	}
1518	return -1;
1519	}
1520
1521	void TEST_SLOW_design_probe() {
1522	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
1523
1524	bool use_gene_ptserver = false;
1525	{
1526	int hits_len_18;
1527	{
1528	const char *arguments[] = {
1529	"prgnamefake",
1530	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1531	"designmintargets=100",
1532	};
1533	const char *expected =
1534	"Probe design parameters:\n"
1535	"Length of probe 18\n"
1536	"Temperature [ 0.0 -400.0]\n"
1537	"GC-content [30.0 - 80.0]\n"
1538	"E.Coli position [any]\n"
1539	"Max. nongroup hits 0\n"
1540	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1541	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1542	"CGAAAGGAAGAUUAAUAC 18 A=94 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1543	"GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC \| - - - - - - - - - - - - - - - - - - - -\n"
1544	"UCAAGUCGAGCGAUGAAG 18 B=18 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA \| - - - - - - - - - - - - - - - 2 2 2 2 2\n"
1545	"AUCAAGUCGAGCGAUGAA 18 B- 1 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU \| - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n";
1546
1547	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1548	hits_len_18 = count_hits(expected);
1549	TEST_EXPECT_EQUAL(hits_len_18, 4);
1550
1551	// test extraction of positions:
1552	{
1553	char *positions = extract_locations(expected);
1554	TEST_EXPECT_EQUAL(positions, "A=94A+1B=18B-1");
1555	free(positions);
1556	}
1557	}
1558	// same as above with probelength 17
1559	int hits_len_17;
1560	{
1561	const char *arguments[] = {
1562	"prgnamefake",
1563	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1564	"designmintargets=100",
1565	"designprobelength=17",
1566	};
1567	const char *expected =
1568	"Probe design parameters:\n"
1569	"Length of probe 17\n"
1570	"Temperature [ 0.0 -400.0]\n"
1571	"GC-content [30.0 - 80.0]\n"
1572	"E.Coli position [any]\n"
1573	"Max. nongroup hits 0\n"
1574	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1575	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1576	"CAAGUCGAGCGAUGAAG 17 A=19 18 65 4 52.9 52.0 CUUCAUCGCUCGACUUG \| - - - - - - - - - - - - - - - - 2 2 2 2\n"
1577	"UCAAGUCGAGCGAUGAA 17 A- 1 17 49 4 47.1 50.0 UUCAUCGCUCGACUUGA \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1578	"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";
1579
1580	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1581	hits_len_17 = count_hits(expected);
1582	TEST_EXPECT_EQUAL(hits_len_17, 3);
1583	}
1584	// same as above with probelength 16
1585	int hits_len_16;
1586	{
1587	const char *arguments[] = {
1588	"prgnamefake",
1589	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1590	"designmintargets=100",
1591	"designprobelength=16",
1592	};
1593	const char *expected =
1594	"Probe design parameters:\n"
1595	"Length of probe 16\n"
1596	"Temperature [ 0.0 -400.0]\n"
1597	"GC-content [30.0 - 80.0]\n"
1598	"E.Coli position [any]\n"
1599	"Max. nongroup hits 0\n"
1600	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1601	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1602	"CGAAAGGAAGAUUAAU 16 A=94 82 77 4 31.2 42.0 AUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1603	"AAGGAAGAUUAAUACC 16 A+ 3 85 77 4 31.2 42.0 GGUAUUAAUCUUCCUU \| - - - - - - - - - - - - - - - - - - - -\n"
1604	"AAGUCGAGCGAUGAAG 16 B=20 19 69 4 50.0 48.0 CUUCAUCGCUCGACUU \| - - - - - - - - - - - - - - - - - 2 2 2\n"
1605	"CAAGUCGAGCGAUGAA 16 B- 1 18 49 4 50.0 48.0 UUCAUCGCUCGACUUG \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1606	"UCAAGUCGAGCGAUGA 16 B- 2 17 37 4 50.0 48.0 UCAUCGCUCGACUUGA \| - - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2\n"
1607	"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";
1608
1609	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1610	hits_len_16 = count_hits(expected);
1611	TEST_EXPECT_EQUAL(hits_len_16, 6);
1612	}
1613	// combine the 3 preceeding designs
1614	int combined_hits;
1615	{
1616	const char *arguments[] = {
1617	"prgnamefake",
1618	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1619	"designmintargets=100",
1620	"designprobelength=16",
1621	"designmaxprobelength=18",
1622	};
1623	const char *expected =
1624	"Probe design parameters:\n"
1625	"Length of probe 16-18\n"
1626	"Temperature [ 0.0 -400.0]\n"
1627	"GC-content [30.0 - 80.0]\n"
1628	"E.Coli position [any]\n"
1629	"Max. nongroup hits 0\n"
1630	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1631	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1632	"CGAAAGGAAGAUUAAU 16 A=94 82 77 4 31.2 42.0 AUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1633	"CGAAAGGAAGAUUAAUAC 18 A+ 0 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1634	"GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC \| - - - - - - - - - - - - - - - - - - - -\n"
1635	"AAGGAAGAUUAAUACC 16 A+ 3 85 77 4 31.2 42.0 GGUAUUAAUCUUCCUU \| - - - - - - - - - - - - - - - - - - - -\n"
1636	"AAGUCGAGCGAUGAAG 16 B=20 19 69 4 50.0 48.0 CUUCAUCGCUCGACUU \| - - - - - - - - - - - - - - - - - 2 2 2\n"
1637	"CAAGUCGAGCGAUGAAG 17 B- 1 18 65 4 52.9 52.0 CUUCAUCGCUCGACUUG \| - - - - - - - - - - - - - - - - 2 2 2 2\n"
1638	"UCAAGUCGAGCGAUGAAG 18 B- 2 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA \| - - - - - - - - - - - - - - - 2 2 2 2 2\n"
1639	"UCAAGUCGAGCGAUGAA 17 B- 2 17 49 4 47.1 50.0 UUCAUCGCUCGACUUGA \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1640	"CAAGUCGAGCGAUGAA 16 B- 1 18 49 4 50.0 48.0 UUCAUCGCUCGACUUG \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1641	"AUCAAGUCGAGCGAUGAA 18 B- 3 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU \| - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n"
1642	"UCAAGUCGAGCGAUGA 16 B- 2 17 37 4 50.0 48.0 UCAUCGCUCGACUUGA \| - - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2\n"
1643	"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"
1644	"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";
1645
1646	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1647	combined_hits = count_hits(expected);
1648	}
1649
1650	// check that combined design reports all probes reported by single designs:
1651	TEST_EXPECT_EQUAL(combined_hits, hits_len_16+hits_len_17+hits_len_18);
1652	}
1653	// test vs bug (fails with [8988] .. [9175])
1654	{
1655	const char *arguments[] = {
1656	"prgnamefake",
1657	"designnames=VbhChole#VblVulni",
1658	"designmintargets=50", // hit at least 1 of the 2 targets
1659	"designmingc=60", "designmaxgc=75", // specific GC range
1660	};
1661
1662	const char *expected =
1663	"Probe design parameters:\n"
1664	"Length of probe 18\n"
1665	"Temperature [ 0.0 -400.0]\n"
1666	"GC-content [60.0 - 75.0]\n"
1667	"E.Coli position [any]\n"
1668	"Max. nongroup hits 0 (lowest rejected nongroup hits: 1)\n"
1669	"Min. group hits 50%\n"
1670	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1671	"AGUCGAGCGGCAGCACAG 18 A=21 20 39 2 66.7 60.0 CUGUGCUGCCGCUCGACU \| - - - - - - - - - - - - - - - - - - - -\n"
1672	"GUCGAGCGGCAGCACAGA 18 A+ 1 21 39 2 66.7 60.0 UCUGUGCUGCCGCUCGAC \| - - - - - - - - - - - - - - - - - - - -\n"
1673	"UCGAGCGGCAGCACAGAG 18 A+ 2 21 39 2 66.7 60.0 CUCUGUGCUGCCGCUCGA \| - - - - - - - - - - - - - - - - - - - -\n"
1674	"AAGUCGAGCGGCAGCACA 18 A- 1 19 25 2 61.1 58.0 UGUGCUGCCGCUCGACUU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1675	"CGAGCGGCAGCACAGAGA 18 A+ 3 21 20 1 66.7 60.0 UCUCUGUGCUGCCGCUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1676	"CGAGCGGCAGCACAGAGG 18 A+ 3 21 20 1 72.2 62.0 CCUCUGUGCUGCCGCUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1677	"GAGCGGCAGCACAGAGAA 18 A+ 4 21 20 1 61.1 58.0 UUCUCUGUGCUGCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1678	"GAGCGGCAGCACAGAGGA 18 A+ 4 21 20 1 66.7 60.0 UCCUCUGUGCUGCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1679	"AGCGGCAGCACAGAGGAA 18 A+ 5 21 20 1 61.1 58.0 UUCCUCUGUGCUGCCGCU \| - - - - - - - - - - - - - - - - - - - -\n"
1680	"GCGGCAGCACAGAGAAAC 18 A+ 6 22 20 1 61.1 58.0 GUUUCUCUGUGCUGCCGC \| - - - - - - - - - - - - - - - - - - - -\n"
1681	"GCGGCAGCACAGAGGAAC 18 A+ 6 22 20 1 66.7 60.0 GUUCCUCUGUGCUGCCGC \| - - - - - - - - - - - - - - - - - - - -\n"
1682	"CGGCAGCACAGAGGAACU 18 A+ 7 23 20 1 61.1 58.0 AGUUCCUCUGUGCUGCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1683	"CUUGUUCCUUGGGUGGCG 18 B=52 47 20 1 61.1 58.0 CGCCACCCAAGGAACAAG \| - - - - - - - - - - - - - - - - - - - -\n"
1684	"CUUGUUUCUCGGGUGGCG 18 B+ 0 47 20 1 61.1 58.0 CGCCACCCGAGAAACAAG \| - - - - - - - - - - - - - - - - - - - -\n"
1685	"UGUUCCUUGGGUGGCGAG 18 B+ 2 49 20 1 61.1 58.0 CUCGCCACCCAAGGAACA \| - - - - - - - - - - - - - - - - - - - -\n"
1686	"UGUUUCUCGGGUGGCGAG 18 B+ 2 49 20 1 61.1 58.0 CUCGCCACCCGAGAAACA \| - - - - - - - - - - - - - - - - - - - -\n"
1687	"GUUCCUUGGGUGGCGAGC 18 B+ 3 50 20 1 66.7 60.0 GCUCGCCACCCAAGGAAC \| - - - - - - - - - - - - - - - - - - - -\n"
1688	"GUUUCUCGGGUGGCGAGC 18 B+ 3 50 20 1 66.7 60.0 GCUCGCCACCCGAGAAAC \| - - - - - - - - - - - - - - - - - - - -\n"
1689	"UUCCUUGGGUGGCGAGCG 18 B+10 57 20 1 66.7 60.0 CGCUCGCCACCCAAGGAA \| - - - - - - - - - - - - - - - - - - - -\n"
1690	"UUUCUCGGGUGGCGAGCG 18 B+10 57 20 1 66.7 60.0 CGCUCGCCACCCGAGAAA \| - - - - - - - - - - - - - - - - - - - -\n"
1691	"UCCUUGGGUGGCGAGCGG 18 B+11 58 20 1 72.2 62.0 CCGCUCGCCACCCAAGGA \| - - - - - - - - - - - - - - - - - - - -\n"
1692	"UUCUCGGGUGGCGAGCGG 18 B+11 58 20 1 72.2 62.0 CCGCUCGCCACCCGAGAA \| - - - - - - - - - - - - - - - - - - - -\n"
1693	"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"
1694	"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";
1695
1696	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1697	}
1698
1699	// design MANY probes to test location specifier
1700	{
1701	const char *arguments_loc[] = {
1702	"prgnamefake",
1703	// "designnames=Stsssola#Stsssola", // @@@ crashes the ptserver
1704	"designnames=CPPParap#PsAAAA00",
1705	"designmintargets=50", // hit at least 1 of the 2 targets
1706	"designmingc=0", "designmaxgc=100", // allow all GCs
1707	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1708	"designmishit=7", // allow enough outgroup hits
1709	"designprobelength=9",
1710	};
1711
1712	const char *expected_loc =
1713	"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";
1714
1715	TEST_ARB_PROBE_FILT(ARRAY_ELEMS(arguments_loc), arguments_loc, extract_locations, expected_loc);
1716	}
1717
1718	// same as above
1719	{
1720	const char *arguments[] = {
1721	"prgnamefake",
1722	"designnames=CPPParap#PsAAAA00",
1723	"designmintargets=50", // hit at least 1 of the 2 targets
1724	"designmingc=0", "designmaxgc=100", // allow all GCs
1725	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1726	"designmishit=7", // allow enough outgroup hits
1727	"designprobelength=9",
1728	};
1729
1730	const char *expected =
1731	"Probe design parameters:\n"
1732	"Length of probe 9\n"
1733	"Temperature [30.0 -100.0]\n"
1734	"GC-content [ 0.0 -100.0]\n"
1735	"E.Coli position [any]\n"
1736	"Max. nongroup hits 7 (lowest rejected nongroup hits: 9)\n"
1737	"Min. group hits 50%\n"
1738	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1739	"GAGCGGAUG 9 A= 29 24 20 1 66.7 30.0 CAUCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1740	"UGCUCCUGG 9 B= 51 46 20 1 66.7 30.0 CCAGGAGCA \| - - - - - - - - - - - - - - - - - - - -\n"
1741	"GCUCCUGGA 9 B+ 1 47 20 1 66.7 30.0 UCCAGGAGC \| - - - - - - - - - - - - - - - - - - - -\n"
1742	"CGGGCGCUA 9 C= 99 87 20 1 77.8 32.0 UAGCGCCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1743	"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"
1744	"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"
1745	"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"
1746	"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"
1747	"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"
1748	"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"
1749	"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"
1750	"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"
1751	"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"
1752	"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"
1753	"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"
1754	"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"
1755	"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"
1756	"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"
1757	"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"
1758	"GGAAACGGG 9 C- 5 82 17 1 66.7 30.0 CCCGUUUCC \| - - - - - - - - - - - - - - - - 3 3 3 3\n"
1759	"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"
1760	"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"
1761	"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"
1762	"GGACGUCCG 9 E+ 6 74 14 1 77.8 32.0 CGGACGUCC \| - - - - - - - - - - - - - 1 1 1 1 3 3 3\n"
1763	"GACGUCCGG 9 E+ 7 75 14 1 77.8 32.0 CCGGACGUC \| - - - - - - - - - - - - - 1 1 1 1 2 2 14\n"
1764	"ACGUCCGGA 9 E+ 8 76 14 1 66.7 30.0 UCCGGACGU \| - - - - - - - - - - - - - 1 1 11 11 12 12 17\n"
1765	"CGUCCGGAA 9 G= 89 77 14 1 66.7 30.0 UUCCGGACG \| - - - - - - - - - - - - - 1 1 1 1 2 2 2\n"
1766	"AACGGGCGC 9 C- 2 85 14 1 77.8 32.0 GCGCCCGUU \| - - - - - - - - - - - - - 1 1 1 1 1 1 2\n"
1767	"CGAGCGGAU 9 A- 1 23 13 1 66.7 30.0 AUCCGCUCG \| - - - - - - - - - - - - 3 3 3 3 3 3 3 3\n"
1768	"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"
1769	"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"
1770	"ACGGGCGCU 9 C- 1 86 12 1 77.8 32.0 AGCGCCCGU \| - - - - - - - - - - - 1 1 1 1 1 1 2 2 2\n"
1771	"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"
1772	"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"
1773	"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"
1774	"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"
1775	"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"
1776	"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"
1777	"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"
1778	"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"
1779	"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"
1780	"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"
1781	"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"
1782	"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"
1783	"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"
1784	"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"
1785	"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"
1786	"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"
1787	"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"
1788	"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"
1789	"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"
1790	"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"
1791	"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";
1792
1793	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1794	}
1795
1796	#if defined(ARB_64)
1797	#define RES_64
1798	#else // !defined(ARB_64)
1799	// results below differ for some(!) 32 bit arb versions (numeric issues?)
1800	// (e.g. u1004 behaves like 64bit version; u1204 doesnt in NDEBUG mode)
1801	// #define RES_64 // uncomment for u1004
1802	#if defined(DEBUG)
1803	#define RES_64
1804	#endif
1805
1806	#endif
1807
1808
1809	// same as above (with probelen == 8)
1810	{
1811	const char *arguments[] = {
1812	"prgnamefake",
1813	"designnames=CPPParap#PsAAAA00",
1814	"designmintargets=50", // hit at least 1 of the 2 targets
1815	"designmingc=0", "designmaxgc=100", // allow all GCs
1816	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1817	// "designmishit=7",
1818	"designmishit=15", // @@@ reports more results than with 7 mishits, but no mishits reported below!
1819	"designprobelength=8",
1820	};
1821
1822	const char *expected =
1823	"Probe design parameters:\n"
1824	"Length of probe 8\n"
1825	"Temperature [30.0 -100.0]\n"
1826	"GC-content [ 0.0 -100.0]\n"
1827	"E.Coli position [any]\n"
1828	"Max. nongroup hits 15\n"
1829	"Min. group hits 50%\n"
1830	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1831	"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"
1832	"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"
1833	"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"
1834	"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"
1835	"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"
1836	"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"
1837	"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"
1838	"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"
1839	#if defined(RES_64)
1840	"ACGGGCGC 8 B=98 86 13 1 87.5 30.0 GCGCCCGU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1841	"CGGGCGCU 8 B+ 1 87 13 1 87.5 30.0 AGCGCCCG \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1842	"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";
1843	#else // !defined(RES_64)
1844	"ACGGGCGC 8 B=98 86 13 1 87.5 30.0 GCGCCCGU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 2\n"
1845	"CGGGCGCU 8 B+ 1 87 13 1 87.5 30.0 AGCGCCCG \| - - - - - - - - - - - - 1 1 1 1 1 1 1 2\n"
1846	"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";
1847	#endif
1848
1849	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1850	}
1851
1852	// same as above (but restricting ecoli-range)
1853	{
1854	const char *arguments[] = {
1855	"prgnamefake",
1856	"designnames=CPPParap#PsAAAA00",
1857	"designmintargets=50", // hit at least 1 of the 2 targets
1858	"designmingc=0", "designmaxgc=100", // allow all GCs
1859	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1860	"designmishit=15",
1861	"designprobelength=8",
1862	"designminpos=65", "designmaxpos=69", // restrict ecoli-range
1863	};
1864
1865	const char *expected =
1866	"Probe design parameters:\n"
1867	"Length of probe 8\n"
1868	"Temperature [30.0 -100.0]\n"
1869	"GC-content [ 0.0 -100.0]\n"
1870	"E.Coli position [ 65 - 69]\n"
1871	"Max. nongroup hits 15\n"
1872	"Min. group hits 50%\n"
1873	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1874	"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"
1875	"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"
1876	"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"
1877	"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"
1878	"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";
1879
1880	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1881	}
1882
1883	{
1884	const char *arguments[] = {
1885	"prgnamefake",
1886	"designnames=ClnCorin#CPPParap#ClfPerfr",
1887	"designprobelength=16",
1888	"designmintargets=100",
1889	"designmishit=2",
1890	};
1891	const char *expected =
1892	"Probe design parameters:\n"
1893	"Length of probe 16\n"
1894	"Temperature [ 0.0 -400.0]\n"
1895	"GC-content [30.0 - 80.0]\n"
1896	"E.Coli position [any]\n"
1897	"Max. nongroup hits 2 (lowest rejected nongroup hits: 6)\n"
1898	"Min. group hits 100% (max. rejected coverage: 67%)\n"
1899	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1900	"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"
1901	"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"
1902	"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"
1903	"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"
1904	"GUCGAGCGAUGAAGUU 16 B+ 2 21 31 3 50.0 48.0 AACUUCAUCGCUCGAC \| - - - - - - - - - - 1 1 1 1 1 1 1 1 1 1\n"
1905	"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"
1906	"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"
1907	"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"
1908	"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"
1909	"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";
1910
1911	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1912	}
1913	// test same design as above, but add 2 "unknown species" each of which is missing one of the previously designed probes
1914	{
1915	const char *arguments[] = {
1916	"prgnamefake",
1917	"designnames=ClnCorin#Unknown1#CPPParap#ClfPerfr#Unknown2",
1918	"designprobelength=16",
1919	"designmintargets=100",
1920	"designmishit=2",
1921	// pass sequences for the unknown species
1922	"designsequence=---CGAAAGGAAGAUUAAU------------------AAGUCGAGCGAUGAAG-CAAGUCGAGCGAUGAA-GUCGAGCGAUGAAGUU-UCAAGUCGAGCGAUGA-AGUCGAGCGAUGAAGU-AUCAAGUCGAGCGAUG-GAUCAAGUCGAGCGAU-UGAUCAAGUCGAGCGA",
1923	"designsequence=---CGAAAGGAAGAUUAAU-AAGGAAGAUUAAUACC-AAGUCGAGCGAUGAAG-CAAGUCGAGCGAUGAA-GUCGAGCGAUGAAGUU-UCAAGUCGAGCGAUGA-AGUCGAGCGAUGAAGU-AUCAAGUCGAGCGAUG------------------UGAUCAAGUCGAGCGA",
1924	};
1925	const char *expected =
1926	"Probe design parameters:\n"
1927	"Length of probe 16\n"
1928	"Temperature [ 0.0 -400.0]\n"
1929	"GC-content [30.0 - 80.0]\n"
1930	"E.Coli position [any]\n"
1931	"Max. nongroup hits 2\n"
1932	"Min. group hits 100% (max. rejected coverage: 80%)\n"
1933	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1934	"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"
1935	// AAGGAAGAUUAAUACC is not designed here
1936	"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"
1937	"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"
1938	"GUCGAGCGAUGAAGUU 16 B+ 2 21 51 5 50.0 48.0 AACUUCAUCGCUCGAC \| - - - - - - - - - - 1 1 1 1 1 1 1 1 1 1\n"
1939	"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"
1940	"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"
1941	"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"
1942	// GAUCAAGUCGAGCGAU is not designed here
1943	"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";
1944
1945	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1946	}
1947	{
1948	const char *arguments[] = {
1949	"prgnamefake",
1950	"designnames=VbrFurni",
1951	"designprobelength=8",
1952	"designmingc=80",
1953	"designmaxgc=100",
1954	};
1955	const char *expected =
1956	"Probe design parameters:\n"
1957	"Length of probe 8\n"
1958	"Temperature [ 0.0 -400.0]\n"
1959	"GC-content [80.0 -100.0]\n"
1960	"E.Coli position [any]\n"
1961	"Max. nongroup hits 0 (lowest rejected nongroup hits: 2)\n"
1962	"Min. group hits 50%\n"
1963	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1964	#if defined(RES_64)
1965	"CGGCAGCG 8 A=28 23 20 1 87.5 30.0 CGCUGCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1966	#else // !defined(RES_64)
1967	"CGGCAGCG 8 A=28 23 20 1 87.5 30.0 CGCUGCCG \| - - - - - - - - - - - - - - - - - - - 3\n"
1968	#endif
1969	"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"
1970	#if defined(RES_64)
1971	"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"
1972	#else // !defined(RES_64)
1973	"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"
1974	#endif
1975	"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"
1976	"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"
1977	"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";
1978
1979	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1980	}
1981	{
1982	const char *arguments[] = {
1983	"prgnamefake",
1984	"designnames=HllHalod#VbhChole#VblVulni#VbrFurni#PtVVVulg",
1985	"designprobelength=14",
1986	"designmintargets=100",
1987	"designmishit=4",
1988	"designmingc=70",
1989	"designmaxgc=100",
1990	};
1991	const char *expected =
1992	"Probe design parameters:\n"
1993	"Length of probe 14\n"
1994	"Temperature [ 0.0 -400.0]\n"
1995	"GC-content [70.0 -100.0]\n"
1996	"E.Coli position [any]\n"
1997	"Max. nongroup hits 4\n"
1998	"Min. group hits 100% (max. rejected coverage: 80%)\n"
1999	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
2000	"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"
2001	"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"
2002	"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";
2003
2004	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2005	}
2006	{
2007	const char *arguments[] = {
2008	"prgnamefake",
2009	"designnames=HllHalod#VbhChole#VblVulni#VbrFurni#PtVVVulg",
2010	"designprobelength=14",
2011	"designmintargets=100",
2012	"designmishit=0",
2013	"designmingc=51",
2014	"designmaxgc=60",
2015	};
2016	const char *expected = ""; // no probes found!
2017
2018	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2019	}
2020
2021	}
2022
2023	void TEST_SLOW_probe_design_errors() {
2024	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2025
2026	bool use_gene_ptserver = false;
2027	{
2028	const char *arguments[] = {
2029	"prgnamefake",
2030	"designnames=CPPParap#PsAAAA00",
2031	"designprobelength=3",
2032	};
2033	const char *expected_error = "Specified min. probe length 3 is below the min. allowed probe length of 8";
2034
2035	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2036	}
2037	{
2038	const char *arguments[] = {
2039	"prgnamefake",
2040	"designnames=CPPParap#PsAAAA00",
2041	"designprobelength=15",
2042	"designmaxprobelength=12",
2043	};
2044	const char *expected_error = "Max. probe length 12 is below the specified min. probe length of 15";
2045
2046	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2047	}
2048	{
2049	const char *expected_error = "Sequence contains only 0 bp. Impossible design request for one of the added sequences";
2050	{
2051	const char *arguments[] = {
2052	"prgnamefake",
2053	"designsequence=", // pass an empty sequence
2054	"designprobelength=16",
2055	};
2056	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2057	}
2058	{
2059	const char *arguments[] = {
2060	"prgnamefake",
2061	"designsequence=-------------", // pass a gap-only sequence
2062	"designprobelength=16",
2063	};
2064	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2065	}
2066	}
2067	{
2068	const char *arguments[] = {
2069	"prgnamefake",
2070	"designsequence=ACGTACGTACGTACGT", // pass a long enough (unexpected) sequence
2071	"designprobelength=16",
2072	};
2073	const char *expected_error = "Got 0 unknown marked species, but 1 custom sequence was added (has to match)";
2074	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2075	}
2076	{
2077	const char *arguments[] = {
2078	"prgnamefake",
2079	"designnames=Unknown", // one unknown species
2080	"designprobelength=16",
2081	};
2082	const char *expected_error = "No species marked - no probes designed";
2083	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2084	}
2085	{
2086	const char *arguments[] = {
2087	"prgnamefake",
2088	"designnames=Unknown#CPPParap", // one unknown species, one known species
2089	"designprobelength=16",
2090	};
2091	const char *expected_error = "Got 1 unknown marked species, but 0 custom sequences were added (has to match)";
2092	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2093	}
2094	{
2095	const char *expected_error = "Sequence contains only 0 bp. Impossible design request for one of the added sequences";
2096	{
2097	const char *arguments[] = {
2098	"prgnamefake",
2099	"designnames=Unknown", // one unknown species
2100	"designsequence=", // pass an empty sequence
2101	"designprobelength=16",
2102	};
2103	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2104	}
2105	{
2106	const char *arguments[] = {
2107	"prgnamefake",
2108	"designnames=Unknown", // one unknown species
2109	"designsequence=-------------", // pass a gap-only sequence
2110	"designprobelength=16",
2111	};
2112	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2113	}
2114	}
2115	}
2116
2117	void TEST_SLOW_match_designed_probe() {
2118	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2119
2120	bool use_gene_ptserver = false;
2121	const char *arguments[] = {
2122	"prgnamefake",
2123	"matchsequence=UCAAGUCGAGCGAUGAAG",
2124	};
2125	CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UCAAGUCGAGCGAUGAAG'\1"
2126	"ClnCorin\1" " ClnCorin 0 0 0.0 18 17 0 .GAGUUUGA-==================-UUCCUUCGG\1"
2127	"CltBotul\1" " CltBotul 0 0 0.0 18 17 0 ........A-==================-CUUCUUCGG\1"
2128	"CPPParap\1" " CPPParap 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUCCUUCGG\1"
2129	"ClfPerfr\1" " ClfPerfr 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUUCCUUCG\1";
2130
2131	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2132	}
2133
2134	void TEST_SLOW_get_existing_probes() {
2135	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2136
2137	bool use_gene_ptserver = false;
2138	{
2139	const char *arguments[] = {
2140	"prgnamefake",
2141	"iterate=20",
2142	"iterate_amount=10",
2143	};
2144	CCP expected =
2145	"AAACCGGGGCTAATACCGGA;AAACGACTGTTAATACCGCA;AAACGATGGAAGCTTGCTTC;AAACGATGGCTAATACCGCA;AAACGGATTAGCGGCGGGAC;"
2146	"AAACGGGCGCTAATACCGCA;AAACGGTCGCTAATACCGGA;AAACGGTGGCTAATACCGCA;AAACGTACGCTAATACCGCA;AAACTCAAGCTAATACCGCA";
2147
2148	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2149	}
2150	{
2151	const char *arguments[] = {
2152	"prgnamefake",
2153	"iterate=15",
2154	"iterate_amount=20",
2155	"iterate_separator=:",
2156	};
2157	CCP expected =
2158	"AAACCGGGGCTAATA:AAACGACTGTTAATA:AAACGATGGAAGCTT:AAACGATGGCTAATA:AAACGGATTAGCGGC:AAACGGGCGCTAATA:AAACGGTCGCTAATA:"
2159	"AAACGGTGGCTAATA:AAACGTACGCTAATA:AAACTCAAGCTAATA:AAACTCAGGCTAATA:AAACTGGAGAGTTTG:AAACTGTAGCTAATA:AAACTTGTTTCTCGG:"
2160	"AAAGAGGTGCTAATA:AAAGCTTGCTTTCTT:AAAGGAACGCTAATA:AAAGGAAGATTAATA:AAAGGACAGCTAATA:AAAGGGACTTCGGTC";
2161
2162	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2163	}
2164	{
2165	const char *arguments[] = {
2166	"prgnamefake",
2167	"iterate=10",
2168	"iterate_amount=5",
2169	"iterate_readable=0",
2170	};
2171	CCP expected =
2172	"\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";
2173
2174	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2175	}
2176	{
2177	const char *arguments[] = {
2178	"prgnamefake",
2179	"iterate=3",
2180	"iterate_amount=70",
2181	"iterate_tu=U",
2182	};
2183	CCP expected =
2184	"AAA;AAC;AAG;AAU;ACA;ACC;ACG;ACU;AGA;AGC;AGG;AGU;AUA;AUC;AUG;AUU;"
2185	"CAA;CAC;CAG;CAU;CCA;CCC;CCG;CCU;CGA;CGC;CGG;CGU;CUA;CUC;CUG;CUU;"
2186	"GAA;GAC;GAG;GAU;GCA;GCC;GCG;GCU;GGA;GGC;GGG;GGU;GUA;GUC;GUG;GUU;"
2187	"UAA;UAC;UAG;UAU;UCA;UCC;UCG;UCU;UGA;UGC;UGG;UGU;UUA;UUC;UUG;UUU";
2188
2189	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2190	}
2191	{
2192	const char *arguments[] = {
2193	"prgnamefake",
2194	"iterate=2",
2195	"iterate_amount=20",
2196	};
2197	CCP expected =
2198	"AA;AC;AG;AT;"
2199	"CA;CC;CG;CT;"
2200	"GA;GC;GG;GT;"
2201	"TA;TC;TG;TT";
2202
2203	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2204	}
2205	}
2206
2207	// #define TEST_AUTO_UPDATE // uncomment to auto-update expected index dumps
2208
2209	void TEST_SLOW_index_dump() {
2210	for (int use_gene_ptserver = 0; use_gene_ptserver <= 1; use_gene_ptserver++) {
2211	const char *dumpfile = use_gene_ptserver ? "index_gpt.dump" : "index_pt.dump";
2212	char *dumpfile_exp = GBS_global_string_copy("%s.expected", dumpfile);
2213
2214	const char *arguments[] = {
2215	"prgnamefake",
2216	GBS_global_string_copy("dump=%s", dumpfile),
2217	};
2218	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, "ok");
2219
2220	#if defined(TEST_AUTO_UPDATE)
2221	TEST_COPY_FILE(dumpfile, dumpfile_exp);
2222	#else // !defined(TEST_AUTO_UPDATE)
2223	TEST_EXPECT_TEXTFILES_EQUAL(dumpfile_exp, dumpfile);
2224	#endif
2225	TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(dumpfile));
2226
2227	free((char*)arguments[1]);
2228	free(dumpfile_exp);
2229	}
2230	}
2231
2232	#undef TEST_AUTO_UPDATE
2233
2234	// --------------------------------------------------------------------------------
2235
2236	#include <arb_strarray.h>
2237	#include <set>
2238	#include <iterator>
2239
2240	using namespace std;
2241
2242	typedef set<string> Matches;
2243
2244	inline void parseMatches(char*& answer, Matches& matches) {
2245	ConstStrArray match_results;
2246
2247	GBT_splitNdestroy_string(match_results, answer, "\1", false);
2248
2249	for (size_t i = 1; i<match_results.size(); i += 2) {
2250	if (match_results[i][0]) {
2251	matches.insert(match_results[i]);
2252	}
2253	}
2254	}
2255
2256	inline void getMatches(const char *probe, Matches& matches) {
2257	bool use_gene_ptserver = false;
2258	char *matchseq = GBS_global_string_copy("matchsequence=%s", probe);
2259	const char *arguments[] = {
2260	"prgnamefake",
2261	matchseq,
2262	};
2263	TEST_RUN_ARB_PROBE(ARRAY_ELEMS(arguments), arguments);
2264	parseMatches(answer, matches);
2265	free(matchseq);
2266	}
2267
2268	inline string matches2hitlist(const Matches& matches) {
2269	string hitlist;
2270	if (!matches.empty()) {
2271	for (Matches::const_iterator m = matches.begin(); m != matches.end(); ++m) {
2272	hitlist = hitlist + ',' + *m;
2273	}
2274	hitlist = hitlist.substr(1);
2275	}
2276	return hitlist;
2277	}
2278
2279	inline void extract_first_but_not_second(const Matches& first, const Matches& second, Matches& result) {
2280	set_difference(first.begin(), first.end(),
2281	second.begin(), second.end(),
2282	inserter(result, result.begin()));
2283	}
2284
2285	// --------------------------------------------------------------------------------
2286
2287	// #define TEST_INDEX_COMPLETENESS // only uncomment temporarily (slow as hell)
2288
2289	#if defined(TEST_INDEX_COMPLETENESS)
2290
2291	void TEST_SLOW_find_unmatched_probes() {
2292	bool use_gene_ptserver = false;
2293
2294	// get all 20mers indexed in ptserver:
2295	ConstStrArray fullProbes;
2296	{
2297	const char *arguments[] = {
2298	"prgnamefake",
2299	"iterate=20",
2300	"iterate_amount=1000000",
2301	"iterate_tu=U",
2302	};
2303	TEST_RUN_ARB_PROBE(ARRAY_ELEMS(arguments), arguments);
2304
2305	GBT_splitNdestroy_string(fullProbes, answer, ";", false);
2306	TEST_EXPECT_EQUAL(fullProbes.size(), 2040);
2307	}
2308
2309	for (size_t lp = 0; lp<fullProbes.size(); ++lp) { // with all 20mers existing in ptserver
2310	const char *fullProbe = fullProbes[lp];
2311
2312	size_t fullLen = strlen(fullProbe);
2313	TEST_EXPECT_EQUAL(fullLen, 20);
2314
2315	Matches fullHits;
2316	getMatches(fullProbe, fullHits);
2317	TEST_EXPECT(fullHits.size()>0);
2318
2319	bool fewerHitsSeen = false;
2320
2321	for (size_t subLen = fullLen-1; !fewerHitsSeen && subLen >= 10; --subLen) { // for each partial sub-probe of 20mer
2322	char subProbe[20];
2323	subProbe[subLen] = 0;
2324
2325	for (size_t pos = 0; pos+subLen <= fullLen; ++pos) {
2326	Matches subHits, onlyFull;
2327
2328	memcpy(subProbe, fullProbe+pos, subLen);
2329	getMatches(subProbe, subHits);
2330	extract_first_but_not_second(fullHits, subHits, onlyFull);
2331
2332	if (!onlyFull.empty()) {
2333	fprintf(stderr, "TEST_PARTIAL_COVERS_FULL_PROBE__BROKEN(\"%s\", \"%s\");\n", subProbe, fullProbe);
2334	fewerHitsSeen = true; // only list first wrong hit for each fullProbe
2335	}
2336	}
2337	}
2338	}
2339	}
2340
2341	#endif
2342	// --------------------------------------------------------------------------------
2343
2344	static arb_test::match_expectation partial_covers_full_probe(const char part, const char full) {
2345	using namespace arb_test;
2346	using namespace std;
2347
2348	expectation_group expected;
2349	expected.add(that(strstr(full, part)).does_differ_from_NULL());
2350	expected.add(that(strlen(part)).is_less_than(strlen(full)));
2351
2352	{
2353	Matches matchFull, matchPart;
2354	getMatches(full, matchFull);
2355	getMatches(part, matchPart);
2356
2357	expected.add(that(matchFull.empty()).is_equal_to(false));
2358
2359	Matches onlyFirst;
2360	extract_first_but_not_second(matchFull, matchPart, onlyFirst);
2361
2362	string only_hit_by_full = matches2hitlist(onlyFirst);
2363	expected.add(that(only_hit_by_full).is_equal_to(""));
2364	}
2365
2366
2367	return all().ofgroup(expected);
2368	}
2369
2370	#define TEST_PARTIAL_COVERS_FULL_PROBE(part,full) TEST_EXPECTATION(partial_covers_full_probe(part, full))
2371	#define TEST_PARTIAL_COVERS_FULL_PROBE__BROKEN(part,full) TEST_EXPECTATION__BROKEN(partial_covers_full_probe(part, full))
2372
2373	void TEST_SLOW_unmatched_probes() {
2374	TEST_PARTIAL_COVERS_FULL_PROBE("CCUCCUUUCU", "GAUUAAUACCCCUCCUUUCU");
2375
2376	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUC", "GGGGAACCUGCGGUUGGAUC");
2377	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCA", "GGGAACCUGCGGUUGGAUCA");
2378	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCAC", "GGAACCUGCGGUUGGAUCAC");
2379	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACC", "GAACCUGCGGUUGGAUCACC");
2380	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCU", "AACCUGCGGUUGGAUCACCU");
2381	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUC", "ACCUGCGGUUGGAUCACCUC");
2382	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCC", "CCUGCGGUUGGAUCACCUCC");
2383	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCU", "CUGCGGUUGGAUCACCUCCU");
2384	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCUU", "UGCGGUUGGAUCACCUCCUU");
2385	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCUUA", "GCGGUUGGAUCACCUCCUUA");
2386
2387	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUC", "GGGGAACCUGGCGCUGGAUC");
2388	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCA", "GGGAACCUGGCGCUGGAUCA");
2389	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCAC", "GGAACCUGGCGCUGGAUCAC");
2390	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACC", "GAACCUGGCGCUGGAUCACC");
2391	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCU", "AACCUGGCGCUGGAUCACCU");
2392	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUC", "ACCUGGCGCUGGAUCACCUC");
2393	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCC", "CCUGGCGCUGGAUCACCUCC");
2394	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCU", "CUGGCGCUGGAUCACCUCCU");
2395	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCUU", "UGGCGCUGGAUCACCUCCUU");
2396	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCUUU", "GGCGCUGGAUCACCUCCUUU");
2397
2398	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCAC", "GGAACCUGCGGCUGGAUCAC");
2399	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACC", "GAACCUGCGGCUGGAUCACC");
2400	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCU", "AACCUGCGGCUGGAUCACCU");
2401	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUC", "ACCUGCGGCUGGAUCACCUC");
2402	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCC", "CCUGCGGCUGGAUCACCUCC");
2403	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCU", "CUGCGGCUGGAUCACCUCCU");
2404	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUU", "UGCGGCUGGAUCACCUCCUU");
2405	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUUU", "GCGGCUGGAUCACCUCCUUU");
2406	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUUUC", "CGGCUGGAUCACCUCCUUUC");
2407
2408	// the data of the following tests is located right in front of the dots inserted in [8962]
2409	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAG", "AAUUGAAGAGUUUGAUCAAG");
2410	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGU", "AUUGAAGAGUUUGAUCAAGU");
2411	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUC", "UUGAAGAGUUUGAUCAAGUC");
2412	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCG", "UGAAGAGUUUGAUCAAGUCG");
2413	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGA", "GAAGAGUUUGAUCAAGUCGA");
2414	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAG", "AAGAGUUUGAUCAAGUCGAG");
2415	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGC", "AGAGUUUGAUCAAGUCGAGC");
2416	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCG", "GAGUUUGAUCAAGUCGAGCG");
2417	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCGG", "AGUUUGAUCAAGUCGAGCGG");
2418	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCGGU", "GUUUGAUCAAGUCGAGCGGU");
2419	}
2420
2421	void TEST_SLOW_variable_defaults_in_server() {
2422	test_setup(false);
2423
2424	const char *server_tag = GBS_ptserver_tag(TEST_SERVER_ID);
2425	TEST_EXPECT_NO_ERROR(arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag));
2426
2427	const char *servername = GBS_read_arb_tcp(server_tag);
2428	{
2429	char *socketname = GBS_global_string_copy(":%s", GB_path_in_ARBHOME("UNIT_TESTER/sok/pt.socket"));
2430	TEST_EXPECT_EQUAL(servername, socketname); // as defined in ../lib/arb_tcp_org.dat@ARB_TEST_PT_SERVER
2431	free(socketname);
2432	}
2433
2434	T_PT_MAIN com;
2435	T_PT_LOCS locs;
2436	GB_ERROR error = NULp;
2437	aisc_com *link = aisc_open(servername, com, AISC_MAGIC_NUMBER, &error);
2438	TEST_EXPECT_NO_ERROR(error);
2439	TEST_REJECT_NULL(link);
2440
2441	TEST_EXPECT_ZERO(aisc_create(link, PT_MAIN, com,
2442	MAIN_LOCS, PT_LOCS, locs,
2443	NULp));
2444
2445	{
2446	#define LOCAL(rvar) prev_read_##rvar
2447
2448
2449	#define FREE_LOCAL_long(rvar)
2450	#define FREE_LOCAL_charp(rvar) free(LOCAL(rvar))
2451	#define FREE_LOCAL(type,rvar) FREE_LOCAL_##type(rvar)
2452
2453	#define TEST__READ(type,rvar,expected) \
2454	do { \
2455	TEST_EXPECT_ZERO(aisc_get(link, PT_LOCS, locs, rvar, &(LOCAL(rvar)), NULp)); \
2456	TEST_EXPECT_EQUAL(LOCAL(rvar), expected); \
2457	FREE_LOCAL(type,rvar); \
2458	} while(0)
2459	#define TEST_WRITE(type,rvar,val) \
2460	TEST_EXPECT_ZERO(aisc_put(link, PT_LOCS, locs, rvar, (type)val, NULp))
2461	#define TEST_CHANGE(type,rvar,val) \
2462	do { \
2463	TEST_WRITE(type, rvar, val); \
2464	TEST__READ(type, rvar, val); \
2465	} while(0)
2466	#define TEST_DEFAULT_CHANGE(ctype,type,remote_variable,default_value,other_value) \
2467	do { \
2468	ctype DEFAULT_VALUE = default_value; \
2469	ctype OTHER_VALUE = other_value; \
2470	type LOCAL(remote_variable); \
2471	TEST__READ(type, remote_variable, DEFAULT_VALUE); \
2472	TEST_CHANGE(type, remote_variable, OTHER_VALUE); \
2473	TEST_CHANGE(type, remote_variable, DEFAULT_VALUE); \
2474	} while(0)
2475
2476	TEST_DEFAULT_CHANGE(const long, long, LOCS_MATCH_ALSO_REVCOMP, 1, 67);
2477	typedef char *charp;
2478	typedef const char *ccharp;
2479	TEST_DEFAULT_CHANGE(ccharp, charp, LOCS_LOGINTIME, "notime", "sometime");
2480	}
2481
2482	TEST_EXPECT_ZERO(aisc_close(link, com));
2483	link = NULp;
2484	}
2485
2486	#endif // UNIT_TESTS

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