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arb_probe.cxx

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Last change on this file was 18125, checked in by westram, 5 years ago
full update from 'trunk' into 'nameserver' adds: log:branches/cleanup@17627:17650,18105:18112 log:branches/clone@17813:17835 log:branches/config@17733:17737 log:branches/dbui@17881:17889 log:branches/fix@17597:17617 log:branches/fts@17653:18088,18090:18094 log:branches/gcc@17850:17876 log:branches/gui@17754:18092 log:branches/mix@17631:17633,17637:17640 log:trunk@17594:18123
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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	using namespace PT; // use AISC interface for ptserver
27
28	struct apd_sequence {
29	apd_sequence *next;
30	const char *sequence;
31	};
32
33	struct Params {
34	int DESIGNCLIPOUTPUT;
35	int SERVERID;
36	const char *DESIGNNAMES;
37	int DESIGNPROBELEN;
38	int DESIGNMAXPROBELEN;
39	const char *DESIGNSEQUENCE;
40
41	int MINTEMP;
42	int MAXTEMP;
43	int MINGC;
44	int MAXGC;
45	int MAXBOND;
46	int MINPOS;
47	int MAXPOS;
48	int MISHIT;
49	int MINTARGETS;
50	const char *SEQUENCE;
51	int MISMATCHES;
52	int ACCEPTN;
53	int LIMITN;
54	int MAXRESULT;
55	int ALSO_REVCOMPL;
56	int WEIGHTED;
57
58	apd_sequence *sequence;
59
60	int ITERATE;
61	int ITERATE_AMOUNT;
62	int ITERATE_READABLE;
63	const char *ITERATE_SEPARATOR;
64	const char *ITERATE_TU;
65
66	const char *DUMP;
67	};
68
69
70	struct gl_struct {
71	aisc_com *link;
72	T_PT_MAIN com;
73	T_PT_LOCS locs;
74	int pd_design_id;
75
76	gl_struct()
77	: link(NULp),
78	pd_design_id(0)
79	{}
80
81	};
82
83	static Params P;
84	static gl_struct pd_gl;
85
86	static int init_local_com_struct() {
87	const char *user = GB_getenvUSER();
88
89	if (aisc_create(pd_gl.link, PT_MAIN, pd_gl.com,
90	MAIN_LOCS, PT_LOCS, pd_gl.locs,
91	LOCS_USER, user,
92	NULp)) {
93	return 1;
94	}
95
96	return 0;
97	}
98
99	static const char *AP_probe_pt_look_for_server(ARB_ERROR& error) {
100	// DRY vs ../MULTI_PROBE/MP_noclass.cxx@MP_probe_pt_look_for_server
101	// DRY vs ../PROBE_DESIGN/probe_design.cxx@PD_probe_pt_look_for_server
102	const char *server_tag = GBS_ptserver_tag(P.SERVERID);
103	error = arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag);
104
105	const char *result = NULp;
106	if (!error) {
107	result = GBS_read_arb_tcp(server_tag);
108	if (!result) error = GB_await_error();
109	}
110	return result;
111	}
112
113	class PTserverConnection {
114	static int count;
115	bool need_close;
116	public:
117	PTserverConnection(ARB_ERROR& error)
118	: need_close(false)
119	{
120	if (count) {
121	error = "Only 1 PTserverConnection allowed";
122	}
123	else {
124	++count;
125	const char *servername = AP_probe_pt_look_for_server(error);
126	if (servername) {
127	GB_ERROR openerr = NULp;
128	pd_gl.link = aisc_open(servername, pd_gl.com, AISC_MAGIC_NUMBER, &openerr);
129	if (openerr) {
130	error = openerr;
131	}
132	else {
133	if (!pd_gl.link) {
134	error = "Cannot contact PT_SERVER [1]";
135	}
136	else if (init_local_com_struct()) {
137	error = "Cannot contact PT_SERVER [2]";
138	}
139	else {
140	need_close = true;
141	}
142	}
143	}
144	}
145	}
146	~PTserverConnection() {
147	if (need_close) {
148	aisc_close(pd_gl.link, pd_gl.com);
149	pd_gl.link = NULp;
150	}
151	--count;
152	}
153	};
154	int PTserverConnection::count = 0;
155
156	static char *AP_dump_index_event(ARB_ERROR& error) {
157	PTserverConnection contact(error);
158
159	char *result = NULp;
160	if (!error) {
161	aisc_put(pd_gl.link, PT_MAIN, pd_gl.com,
162	MAIN_DUMP_NAME, P.DUMP,
163	NULp);
164
165	if (aisc_get(pd_gl.link, PT_MAIN, pd_gl.com,
166	MAIN_DUMP_INDEX, &result,
167	NULp)) {
168	error = "Connection to PT_SERVER lost (1)";
169	}
170	else {
171	result = ARB_strdup("ok");
172	}
173	}
174	return result;
175	}
176
177	static char *AP_probe_iterate_event(ARB_ERROR& error) {
178	PTserverConnection contact(error);
179
180	char *result = NULp;
181	if (!error) {
182	T_PT_PEP pep;
183	int length = P.ITERATE;
184
185	if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs,
186	LOCS_PROBE_FIND_CONFIG, PT_PEP, pep,
187	PEP_PLENGTH, (long)length,
188	PEP_RESTART, (long)1,
189	PEP_READABLE, (long)P.ITERATE_READABLE,
190	PEP_TU, (long)P.ITERATE_TU[0],
191	PEP_SEPARATOR, (long)P.ITERATE_SEPARATOR[0],
192	NULp))
193	{
194	error = "Connection to PT_SERVER lost (1)";
195	}
196
197	if (!error) {
198	int amount = P.ITERATE_AMOUNT;
199	int amount_per_call = AISC_MAX_STRING_LEN/(length+2);
200
201	GBS_strstruct out(50000);
202	bool first = true;
203
204	while (amount && !error) {
205	int this_amount = std::min(amount, amount_per_call);
206
207	aisc_put(pd_gl.link, PT_PEP, pep,
208	PEP_NUMGET, (long)this_amount,
209	PEP_FIND_PROBES, (long)0,
210	NULp);
211
212	char *pep_result = NULp;
213	if (aisc_get(pd_gl.link, PT_PEP, pep,
214	PEP_RESULT, &pep_result,
215	NULp)) {
216	error = "Connection to PT_SERVER lost (2)";
217	}
218
219	if (!error) {
220	if (pep_result[0]) {
221	if (first) first = false;
222	else out.put(P.ITERATE_SEPARATOR[0]);
223
224	out.cat(pep_result);
225	amount -= this_amount;
226	}
227	else {
228	amount = 0; // terminate loop
229	}
230	}
231	free(pep_result);
232	}
233
234	if (!error) {
235	result = out.release();
236	}
237	}
238	}
239
240	if (error) freenull(result);
241	return result;
242	}
243
244	static char *AP_probe_design_event(ARB_ERROR& error) {
245	PTserverConnection contact(error);
246
247	if (!error) {
248	bytestring bs;
249	bs.data = (char*)(P.DESIGNNAMES);
250	bs.size = strlen(bs.data)+1;
251
252	T_PT_PDC pdc;
253	if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs,
254	LOCS_PROBE_DESIGN_CONFIG, PT_PDC, pdc,
255	PDC_MIN_PROBELEN, (long)P.DESIGNPROBELEN,
256	PDC_MAX_PROBELEN, (long)P.DESIGNMAXPROBELEN,
257	PDC_MINTEMP, (double)P.MINTEMP,
258	PDC_MAXTEMP, (double)P.MAXTEMP,
259	PDC_MINGC, (double)P.MINGC/100.0,
260	PDC_MAXGC, (double)P.MAXGC/100.0,
261	PDC_MAXBOND, (double)P.MAXBOND,
262	PDC_MIN_ECOLIPOS, (long)P.MINPOS,
263	PDC_MAX_ECOLIPOS, (long)P.MAXPOS,
264	PDC_MISHIT, (long)P.MISHIT,
265	PDC_MINTARGETS, (double)P.MINTARGETS/100.0,
266	PDC_CLIPRESULT, (long)P.DESIGNCLIPOUTPUT,
267	NULp))
268	{
269	error = "Connection to PT_SERVER lost (1)";
270	}
271
272	if (!error) {
273	for (apd_sequence *s = P.sequence; s; ) {
274	apd_sequence *next = s->next;
275
276	bytestring bs_seq;
277	T_PT_SEQUENCE pts;
278
279	bs_seq.data = (char*)s->sequence;
280	bs_seq.size = strlen(bs_seq.data)+1;
281	aisc_create(pd_gl.link, PT_PDC, pdc,
282	PDC_SEQUENCE, PT_SEQUENCE, pts,
283	SEQUENCE_SEQUENCE, &bs_seq,
284	NULp);
285
286	delete s;
287	s = next;
288	}
289
290	aisc_put(pd_gl.link, PT_PDC, pdc,
291	PDC_NAMES, &bs,
292	PDC_GO, (long)0,
293	NULp);
294
295	{
296	char *locs_error = NULp;
297	if (aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs,
298	LOCS_ERROR, &locs_error,
299	NULp)) {
300	error = "Connection to PT_SERVER lost (2)";
301	}
302	else {
303	if (*locs_error) error = GBS_static_string(locs_error);
304	free(locs_error);
305	}
306	}
307
308	if (!error) {
309	T_PT_TPROBE tprobe;
310	aisc_get(pd_gl.link, PT_PDC, pdc,
311	PDC_TPROBE, tprobe.as_result_param(),
312	NULp);
313
314
315	GBS_strstruct *outstr = GBS_stropen(1000);
316
317	if (tprobe.exists()) {
318	char *match_info = NULp;
319	aisc_get(pd_gl.link, PT_PDC, pdc,
320	PDC_INFO_HEADER, &match_info,
321	NULp);
322	GBS_strcat(outstr, match_info);
323	GBS_chrcat(outstr, '\n');
324	free(match_info);
325	}
326
327
328	while (tprobe.exists()) {
329	char *match_info = NULp;
330	if (aisc_get(pd_gl.link, PT_TPROBE, tprobe,
331	TPROBE_NEXT, tprobe.as_result_param(),
332	TPROBE_INFO, &match_info,
333	NULp)) break;
334	GBS_strcat(outstr, match_info);
335	GBS_chrcat(outstr, '\n');
336	free(match_info);
337	}
338
339	return GBS_strclose(outstr);
340	}
341	}
342	}
343	return NULp;
344	}
345
346	static char *AP_probe_match_event(ARB_ERROR& error) {
347	PTserverConnection contact(error);
348
349	if (!error &&
350	aisc_nput(pd_gl.link, PT_LOCS, pd_gl.locs,
351	LOCS_MATCH_ALSO_REVCOMP, (long)P.ALSO_REVCOMPL,
352	LOCS_COMPLEMENT_FIRST, (long)0, // (use sequence passed below as is. do not complement it.)
353	LOCS_MATCH_SORT_BY, (long)P.WEIGHTED,
354	LOCS_MATCH_MAX_MISMATCHES, (long)P.MISMATCHES,
355	LOCS_MATCH_N_ACCEPT, (long)P.ACCEPTN,
356	LOCS_MATCH_N_LIMIT, (long)P.LIMITN,
357	LOCS_MATCH_MAX_HITS, (long)P.MAXRESULT,
358	LOCS_SEARCHMATCH, P.SEQUENCE,
359	NULp)) {
360	error = "Connection to PT_SERVER lost (1)";
361	}
362
363	if (!error) {
364	bytestring bs;
365	bs.data = NULp;
366	{
367	char *locs_error = NULp;
368	T_PT_MATCHLIST match_list;
369	long match_list_cnt;
370
371	aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs,
372	LOCS_MATCH_LIST, match_list.as_result_param(),
373	LOCS_MATCH_LIST_CNT, &match_list_cnt,
374	LOCS_MATCH_STRING, &bs,
375	LOCS_ERROR, &locs_error,
376	NULp);
377	if (*locs_error) error = GBS_static_string(locs_error);
378	free(locs_error);
379	}
380
381	if (!error) return bs.data; // freed by caller
382	free(bs.data);
383	}
384	return NULp;
385	}
386
387	static int pargc;
388	static const char **pargv = NULp;
389	static bool showhelp;
390	static bool outOfRange;
391
392	static int getInt(const char param, int val, int min, int max, const char description) {
393	if (showhelp) {
394	printf(" %s=%i [%i .. ", param, val, min);
395	if (max != INT_MAX) printf("%i", max);
396	printf("] %s\n", description);
397	return 0;
398	}
399	int i;
400	const char *s = NULp;
401
402	arb_assert(min<=val && val<=max); // wrong default value
403
404	arb_assert(pargc >= 1); // otherwise s stays 0
405
406	for (i=1; i<pargc; i++) {
407	s = pargv[i];
408	if (*s == '-') s++;
409	if (!strncasecmp(s, param, strlen(param))) break;
410	}
411	if (i==pargc) return val;
412	s += strlen(param);
413	if (*s == '=') {
414	s++;
415	val = atoi(s);
416
417	if (val<min \|\| val>max) {
418	outOfRange = true;
419	printf("Parameter '%s=%s' is outside allowed range:\n", param, s);
420	showhelp = true;
421	getInt(param, val, min, max, description);
422	showhelp = false;
423	val = 0;
424	}
425	}
426
427	pargc--; // remove parameter
428	for (; i<pargc; i++) {
429	pargv[i] = pargv[i+1];
430	}
431
432	return val;
433	}
434
435	static const char getString(const char param, const char val, const char description) {
436	if (showhelp) {
437	if (!val) val = "";
438	printf(" %s=%s %s\n", param, val, description);
439	return NULp;
440	}
441	int i;
442	const char *s = NULp;
443
444	arb_assert(pargc >= 1); // otherwise s stays 0
445
446	for (i=1; i<pargc; i++) {
447	s = pargv[i];
448	if (*s == '-') s++;
449	if (!strncasecmp(s, param, strlen(param))) break;
450	}
451	if (i==pargc) return val;
452	s += strlen(param);
453	if (*s != '=') return val;
454	s++;
455	pargc--; // remove parameter
456	for (; i<pargc; i++) {
457	pargv[i] = pargv[i+1];
458	}
459	return s;
460	}
461
462	static bool parseCommandLine(int argc, const char * const * const argv) {
463	pargc = argc;
464
465	// copy argv (since parser will remove matched arguments)
466	free(pargv);
467	ARB_alloc(pargv, pargc);
468	for (int i=0; i<pargc; i++) pargv[i] = argv[i];
469
470	showhelp = (pargc <= 1);
471	outOfRange = false;
472
473	#ifdef UNIT_TESTS // UT_DIFF
474	const int minServerID = TEST_GENESERVER_ID;
475	#else // !UNIT_TESTS
476	const int minServerID = 0;
477	#endif
478
479	P.SERVERID = getInt("serverid", 0, minServerID, 100, "Server Id, look into $ARBHOME/lib/arb_tcp.dat");
480	#ifdef UNIT_TESTS // UT_DIFF
481	if (P.SERVERID<0) { arb_assert(P.SERVERID == TEST_SERVER_ID \|\| P.SERVERID == TEST_GENESERVER_ID); }
482	#endif
483
484	P.DESIGNCLIPOUTPUT = getInt("designmaxhits", 100, 10, 10000, "Maximum Number of Probe Design Suggestions");
485	P.DESIGNNAMES = getString("designnames", "", "List of short names separated by '#'");
486
487	P.sequence = NULp;
488	while ((P.DESIGNSEQUENCE = getString("designsequence", NULp, "Additional Sequences, will be added to the target group"))) {
489	apd_sequence *s = new apd_sequence;
490	s->next = P.sequence;
491	P.sequence = s;
492	s->sequence = P.DESIGNSEQUENCE;
493	P.DESIGNSEQUENCE = NULp;
494	}
495	P.DESIGNPROBELEN = getInt("designprobelength", 18, 2, 100, "(min.) length of probe");
496	P.DESIGNMAXPROBELEN = getInt("designmaxprobelength", -1, -1, 100, "max. length of probe (if specified)");
497	P.MINTEMP = getInt("designmintemp", 0, 0, 400, "Minimum melting temperature of probe");
498	P.MAXTEMP = getInt("designmaxtemp", 400, 0, 400, "Maximum melting temperature of probe");
499	P.MINGC = getInt("designmingc", 30, 0, 100, "Minimum gc content");
500	P.MAXGC = getInt("designmaxgc", 80, 0, 100, "Maximum gc content");
501	P.MAXBOND = getInt("designmaxbond", 0, 0, 10, "Not implemented");
502	P.MINPOS = getInt("designminpos", -1, -1, INT_MAX, "Minimum ecoli position (-1=none)");
503	P.MAXPOS = getInt("designmaxpos", -1, -1, INT_MAX, "Maximum ecoli position (-1=none)");
504	P.MISHIT = getInt("designmishit", 0, 0, 10000, "Number of allowed hits outside the selected group");
505	P.MINTARGETS = getInt("designmintargets", 50, 0, 100, "Minimum percentage of hits within the selected species");
506
507	P.SEQUENCE = getString("matchsequence", "agtagtagt", "The sequence to search for");
508
509	P.MISMATCHES = getInt("matchmismatches", 0, 0, INT_MAX, "Maximum Number of allowed mismatches");
510	P.ALSO_REVCOMPL = getInt("matchAlsoRevcomp", 0, 0, 1, "Also match reverse-complemented probe");
511	P.WEIGHTED = getInt("matchweighted", 0, 0, 1, "Use weighted mismatches");
512	P.ACCEPTN = getInt("matchacceptN", 1, 0, INT_MAX, "Amount of N-matches not counted as mismatch");
513	P.LIMITN = getInt("matchlimitN", 4, 0, INT_MAX, "Limit for N-matches. If reached N-matches are mismatches");
514	P.MAXRESULT = getInt("matchmaxresults", 1000000, 0, INT_MAX, "Max. number of matches reported (0=unlimited)");
515
516	P.ITERATE = getInt("iterate", 0, 0, 20, "Iterate over probes of given length");
517	P.ITERATE_AMOUNT = getInt("iterate_amount", 100, 1, INT_MAX, "Number of results per answer");
518	P.ITERATE_READABLE = getInt("iterate_readable", 1, 0, 1, "readable results");
519
520	P.ITERATE_TU = getString("iterate_tu", "T", "use T or U in readable result");
521	P.ITERATE_SEPARATOR = getString("iterate_separator", ";", "Number of results per answer");
522
523	P.DUMP = getString("dump", "", "dump ptserver index to file (may be huge!)");
524
525	if (pargc>1) {
526	printf("Unknown (or duplicate) parameter %s\n", pargv[1]);
527	return false;
528	}
529	if (outOfRange) {
530	puts("Not all parameters were inside allowed range\n");
531	return false;
532	}
533
534	return !showhelp;
535	}
536
537	// --------------------------------------------------------------------------------
538
539	#ifdef UNIT_TESTS
540	#ifndef TEST_UNIT_H
541	#include <test_unit.h>
542	#endif
543
544	void TEST_BASIC_parseCommandLine() {
545	{
546	const char *args[] = { NULp, "serverid=0"};
547	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
548
549	// test default values here
550	TEST_EXPECT_EQUAL(P.ACCEPTN, 1);
551	TEST_EXPECT_EQUAL(P.LIMITN, 4);
552	TEST_EXPECT_EQUAL(P.MISMATCHES, 0);
553	TEST_EXPECT_EQUAL(P.MAXRESULT, 1000000);
554	}
555
556	{
557	const char *args[] = {NULp, "serverid=4", "matchmismatches=2"};
558	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
559	TEST_EXPECT_EQUAL(P.SERVERID, 4);
560	TEST_EXPECT_EQUAL(P.MISMATCHES, 2);
561	TEST_EXPECT_EQUAL(args[1], "serverid=4"); // check array args was not modified
562	}
563
564	{
565	const char *args[] = { NULp, "matchacceptN=0", "matchlimitN=5"};
566	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
567	TEST_EXPECT_EQUAL(P.ACCEPTN, 0);
568	TEST_EXPECT_EQUAL(P.LIMITN, 5);
569	}
570
571	{
572	const char *args[] = { NULp, "matchmaxresults=100"};
573	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
574	TEST_EXPECT_EQUAL(P.MAXRESULT, 100);
575	}
576	}
577
578	#endif // UNIT_TESTS
579
580	// --------------------------------------------------------------------------------
581
582
583	static char *execute(ARB_ERROR& error) {
584	char *answer;
585	if (*P.DESIGNNAMES \|\| P.sequence) {
586	answer = AP_probe_design_event(error);
587	}
588	else if (P.ITERATE>0) {
589	answer = AP_probe_iterate_event(error);
590	}
591	else if (P.DUMP[0]) {
592	answer = AP_dump_index_event(error);
593	}
594	else {
595	answer = AP_probe_match_event(error);
596	}
597	pd_gl.locs.clear();
598	return answer;
599	}
600
601	int ARB_main(int argc, char *argv[]) {
602	bool ok = parseCommandLine(argc, argv);
603	if (ok) {
604	ARB_ERROR error;
605	char *answer = execute(error);
606
607	arb_assert(contradicted(answer, error));
608
609	if (!answer) {
610	fprintf(stderr,
611	"arb_probe: Failed to process your request\n"
612	" Reason: %s",
613	error.deliver());
614	ok = false;
615	}
616	else {
617	fputs(answer, stdout);
618	free(answer);
619	error.expect_no_error();
620	}
621	}
622	return ok ? EXIT_SUCCESS : EXIT_FAILURE;
623	}
624
625	// --------------------------------------------------------------------------------
626
627	#ifdef UNIT_TESTS
628	#ifndef TEST_UNIT_H
629	#include <test_unit.h>
630	#endif
631
632	static int test_setup(bool use_gene_ptserver) {
633	static bool setup[2] = { false, false };
634	if (!setup[use_gene_ptserver]) {
635	TEST_SETUP_GLOBAL_ENVIRONMENT(use_gene_ptserver ? "ptserver_gene" : "ptserver"); // first call will recreate the test pt-server
636	setup[use_gene_ptserver] = true;
637	}
638	return use_gene_ptserver ? TEST_GENESERVER_ID : TEST_SERVER_ID;
639	}
640
641	// ----------------------------------
642	// test probe design / match
643
644	#define TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv) \
645	int serverid = test_setup(use_gene_ptserver); \
646	TEST_EXPECT_EQUAL(true, parseCommandLine(fake_argc, fake_argv)); \
647	TEST_EXPECT((serverid == TEST_SERVER_ID)\|\|(serverid == TEST_GENESERVER_ID)); \
648	P.SERVERID = serverid; \
649	ARB_ERROR error; \
650	char *answer = execute(error)
651
652	#define TEST_ARB_PROBE__REPORTS_ERROR(fake_argc,fake_argv,expected_error) \
653	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
654	free(answer); \
655	TEST_EXPECT_ERROR_CONTAINS(error.deliver(), expected_error)
656
657	#define TEST_ARB_PROBE__REPORTS_ERROR__BROKEN(fake_argc,fake_argv,expected_error) \
658	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
659	free(answer); \
660	TEST_EXPECT_ANY_ERROR(error.preserve()); \
661	TEST_EXPECT_ERROR_CONTAINS__BROKEN(error.deliver(), expected_error)
662
663
664	#define TEST_RUN_ARB_PROBE(fake_argc,fake_argv) \
665	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
666	TEST_EXPECT_NO_ERROR(error.deliver())
667
668	#define TEST_ARB_PROBE(fake_argc,fake_argv,expected) do { \
669	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
670	TEST_EXPECT_EQUAL(answer, expected); \
671	free(answer); \
672	} while(0)
673
674	#define TEST_ARB_PROBE__BROKEN(fake_argc,fake_argv,expected) do { \
675	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
676	TEST_EXPECT_EQUAL__BROKEN(answer, expected); \
677	free(answer); \
678	} while(0)
679
680	#define TEST_ARB_PROBE_FILT(fake_argc,fake_argv,filter,expected) do { \
681	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
682	char *filtered = filter(answer); \
683	TEST_EXPECT_EQUAL(filtered, expected); \
684	free(filtered); \
685	free(answer); \
686	} while(0)
687
688	typedef const char *CCP;
689
690	void TEST_SLOW_match_geneprobe() {
691	// test here runs versus database ../UNIT_TESTER/run/TEST_gpt_src.arb
692
693	bool use_gene_ptserver = true;
694	{
695	const char *arguments[] = {
696	"prgnamefake",
697	"matchsequence=NNUCNN",
698	"matchacceptN=4",
699	"matchlimitN=5",
700	};
701	CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NNUCNN'\1"
702	"genome2\1" " genome2 gene3 0 4 2.6 2 1 0 .........-UU==GG-UUGAUC.\1"
703	"genome2\1" " genome2 joined1 0 4 2.6 2 1 0 .........-UU==GG-UUGAUCCUG\1"
704	"genome2\1" " genome2 gene1 0 4 2.6 2 2 0 ........A-UU==GG-U.\1"
705	"genome2\1" " genome2 intergene_19_65 0 4 2.7 31 12 0 GGUUACUGC-AU==GG-UGUUCGCCU\1"
706	"genome1\1" " genome1 intergene_17_65 0 4 2.7 31 14 0 GGUUACUGC-UA==GG-UGUUCGCCU\1"
707	"genome2\1" " genome2 intergene_19_65 0 4 2.7 38 19 0 GCAUUCGGU-GU==GC-CUAAGCACU\1"
708	"genome1\1" " genome1 intergene_17_65 0 4 2.7 38 21 0 GCUAUCGGU-GU==GC-CUAAGCCAU\1"
709	"genome2\1" " genome2 gene3 0 4 2.9 10 9 0 .UUUCGGUU-GA==..-\1"
710	"genome2\1" " genome2 intergene_19_65 0 4 3.1 56 37 0 AGCACUGCG-AG==AU-AUGUA.\1"
711	"genome1\1" " genome1 intergene_17_65 0 4 3.1 56 39 0 AGCCAUGCG-AG==AU-AUGUA.\1"
712	"genome1\1" " genome1 gene2 0 4 3.1 10 2 0 ........U-GA==CU-GC.\1"
713	"genome2\1" " genome2 gene2 0 4 3.1 10 4 0 ......GUU-GA==CU-GCCA.\1"
714	"genome1\1" " genome1 joined1 0 4 3.1 10 7 0 ...CUGGUU-GA==CU-GC.\1"
715	"genome2\1" " genome2 joined1 0 4 3.1 10 9 0 .UUUCGGUU-GA==CU-GCCA.\1";
716
717	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd);
718	}
719
720	{
721	const char *arguments[] = {
722	"prgnamefake",
723	"matchsequence=NGGUUN",
724	"matchacceptN=2",
725	"matchlimitN=3",
726	};
727	CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NGGUUN'\1"
728	"genome1\1" " genome1 gene3 0 2 1.3 5 2 0 ........C-U====G-A.\1"
729	"genome1\1" " genome1 joined1 0 2 1.3 5 2 0 ........C-U====G-AUCCUGC.\1"
730	"genome2\1" " genome2 gene3 0 2 1.4 5 4 0 ......UUU-C====G-AUC.\1"
731	"genome2\1" " genome2 joined1 0 2 1.4 5 4 0 ......UUU-C====G-AUCCUGCCA\1"
732	"genome2\1" " genome2 intergene_19_65 0 2 1.8 21 2 0 ........G-A====A-CUGCAUUCG\1"
733	"genome1\1" " genome1 intergene_17_65 0 2 1.8 21 4 0 ......CAG-A====A-CUGCUAUCG\1";
734
735	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd);
736	}
737
738	{
739	const char *arguments[] = {
740	"prgnamefake",
741	"matchsequence=UGAUCCU", // exists in data
742	};
743	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UGAUCCU'\1"
744	"genome1\1" " genome1 gene2 0 0 0.0 9 1 0 .........-=======-GC.\1"
745	"genome2\1" " genome2 gene2 0 0 0.0 9 3 0 .......GU-=======-GCCA.\1"
746	"genome1\1" " genome1 joined1 0 0 0.0 9 6 0 ....CUGGU-=======-GC.\1"
747	"genome2\1" " genome2 joined1 0 0 0.0 9 8 0 ..UUUCGGU-=======-GCCA.\1";
748
749	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hits in 'joined1' (of both genomes)]
750	}
751	{
752	const char *arguments[] = {
753	"prgnamefake",
754	"matchsequence=GAUCCU",
755	};
756	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'GAUCCU'\1"
757	"genome1\1" " genome1 gene2 0 0 0.0 10 2 0 ........U-======-GC.\1"
758	"genome2\1" " genome2 gene2 0 0 0.0 10 4 0 ......GUU-======-GCCA.\1"
759	"genome1\1" " genome1 joined1 0 0 0.0 10 7 0 ...CUGGUU-======-GC.\1"
760	"genome2\1" " genome2 joined1 0 0 0.0 10 9 0 .UUUCGGUU-======-GCCA.\1";
761
762	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]
763	}
764	{
765	const char *arguments[] = {
766	"prgnamefake",
767	"matchsequence=UUUCGG", // exists only in genome2
768	};
769	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUUCGG'\1"
770	"genome2\1" " genome2 gene3 0 0 0.0 2 1 0 .........-======-UUGAUC.\1"
771	"genome2\1" " genome2 joined1 0 0 0.0 2 1 0 .........-======-UUGAUCCUG\1"
772	"genome2\1" " genome2 gene1 0 0 0.0 2 2 0 ........A-======-U.\1";
773
774	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hit in genome2/gene1]
775	}
776	{
777	const char *arguments[] = {
778	"prgnamefake",
779	"matchsequence=AUCCUG",
780	};
781	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'AUCCUG'\1"
782	"genome1\1" " genome1 gene2 0 0 0.0 11 3 0 .......UG-======-C.\1"
783	"genome2\1" " genome2 gene2 0 0 0.0 11 5 0 .....GUUG-======-CCA.\1"
784	"genome1\1" " genome1 joined1 0 0 0.0 11 8 0 ..CUGGUUG-======-C.\1"
785	"genome2\1" " genome2 joined1 0 0 0.0 11 10 0 UUUCGGUUG-======-CCA.\1";
786
787	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hits in 'gene2' and 'joined1' of both genomes]
788	}
789	{
790	const char *arguments[] = {
791	"prgnamefake",
792	"matchsequence=UUGAUCCUGC",
793	};
794	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUGAUCCUGC'\1"
795	"genome2\1" " genome2 gene2 0 0 0.0 8 2 0 ........G-==========-CA.\1"
796	"genome1\1" " genome1 joined1 0 0 0.0 8 5 0 .....CUGG-==========-.\1"
797	"genome2\1" " genome2 joined1 0 0 0.0 8 7 0 ...UUUCGG-==========-CA.\1";
798
799	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hit in 'genome2/joined1']
800	}
801	}
802
803	__ATTR__REDUCED_OPTIMIZE void TEST_SLOW_match_probe() {
804	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
805
806	bool use_gene_ptserver = false;
807	{
808	const char *arguments[] = {
809	"prgnamefake",
810	"matchsequence=UAUCGGAGAGUUUGA",
811	};
812	CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UAUCGGAGAGUUUGA'\1"
813	"BcSSSS00\1" " BcSSSS00 0 0 0.0 3 2 0 .......UU-===============-UCAAGUCGA\1";
814
815	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
816	}
817
818	// ----------------------------------------------------------------------------
819	// match with old(=default) N-mismatch-behavior (accepting 1 N-match)
820
821	{
822	const char *arguments[] = {
823	"prgnamefake",
824	"matchsequence=CANCUCCUUUC", // contains 1 N
825	NULp // matchmismatches
826	};
827
828	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
829	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"; // only N-mismatch accepted
830
831	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
832	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
833	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
834	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
835	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
836	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
837	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
838	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
839	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
840	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1";
841
842	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
843	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
844	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
845	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
846	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
847	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
848	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
849	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
850	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
851	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
852	"AclPleur\1" " AclPleur 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
853	"PtVVVulg\1" " PtVVVulg 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
854	"DlcTolu2\1" " DlcTolu2 2 3 2.3 176 162 0 CGGCUGGAU-==C======NN-N.\1"
855	"FrhhPhil\1" " FrhhPhil 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
856	"HllHalod\1" " HllHalod 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
857	"CPPParap\1" " CPPParap 2 3 2.3 177 163 0 CGGNUGGAU-==C======..-\1";
858
859	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
860	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
861	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
862	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
863	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
864	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
865	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
866	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
867	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
868	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
869	"AclPleur\1" " AclPleur 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
870	"PtVVVulg\1" " PtVVVulg 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
871	"DlcTolu2\1" " DlcTolu2 2 3 2.3 176 162 0 CGGCUGGAU-==C======NN-N.\1"
872	"FrhhPhil\1" " FrhhPhil 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
873	"HllHalod\1" " HllHalod 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
874	"CPPParap\1" " CPPParap 2 3 2.3 177 163 0 CGGNUGGAU-==C======..-\1"
875	"VblVulni\1" " VblVulni 3 1 3.6 49 44 0 AGCACAGAG-a=A==uG====-UCGGGUGGC\1";
876
877	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
878	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
879	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
880	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
881	}
882
883	{
884	const char *arguments[] = {
885	"prgnamefake",
886	"matchsequence=UCACCUCCUUUC", // contains no N
887	NULp // matchmismatches
888	};
889
890	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
891	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
892	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
893	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
894	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
895	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
896	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
897	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
898	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1";
899
900	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
901	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
902	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
903	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
904	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
905	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
906	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
907	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
908	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
909	"AclPleur\1" " AclPleur 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
910	"PtVVVulg\1" " PtVVVulg 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
911	"DlcTolu2\1" " DlcTolu2 1 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
912	"FrhhPhil\1" " FrhhPhil 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
913	"HllHalod\1" " HllHalod 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
914	"CPPParap\1" " CPPParap 1 2 1.4 176 162 0 GCGGNUGGA-==========..-\1";
915
916	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
917	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
918	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
919	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
920	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
921	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
922	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
923	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
924	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
925	"AclPleur\1" " AclPleur 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
926	"PtVVVulg\1" " PtVVVulg 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
927	"DlcTolu2\1" " DlcTolu2 1 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
928	"FrhhPhil\1" " FrhhPhil 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
929	"HllHalod\1" " HllHalod 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
930	"CPPParap\1" " CPPParap 1 2 1.4 176 162 0 GCGGNUGGA-==========..-\1"
931	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C=========-U.\1"
932	"LgtLytic\1" " LgtLytic 2 3 2.1 175 161 0 GCGGCUGGA-=========N..-\1"
933	"PslFlave\1" " PslFlave 2 3 2.1 175 161 0 GCGGCUGGA-=========...-\1";
934
935	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
936	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
937	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
938	}
939
940	{
941	const char *arguments[] = {
942	"prgnamefake",
943	"matchsequence=UCACCUCCUUUC", // contains no N
944	NULp, // matchmismatches
945	"matchweighted=1", // use weighted mismatches
946	};
947
948	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
949	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
950	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
951	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
952	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
953	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
954	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
955	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
956	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1";
957
958	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
959	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
960	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
961	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
962	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
963	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
964	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
965	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
966	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
967	"DlcTolu2\1" " DlcTolu2 1 2 0.6 175 161 0 GCGGCUGGA-==========NN-N.\1"
968	"FrhhPhil\1" " FrhhPhil 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
969	"HllHalod\1" " HllHalod 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
970	"CPPParap\1" " CPPParap 1 2 0.6 176 162 0 GCGGNUGGA-==========..-\1"
971	"AclPleur\1" " AclPleur 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
972	"PtVVVulg\1" " PtVVVulg 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
973	"LgtLytic\1" " LgtLytic 2 3 1.3 175 161 0 GCGGCUGGA-=========N..-\1"
974	"PslFlave\1" " PslFlave 2 3 1.3 175 161 0 GCGGCUGGA-=========...-\1"
975	"ClfPerfr\1" " ClfPerfr 2 0 1.3 175 161 0 AAGAUUAAU-A=C=========-U.\1";
976
977	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
978	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
979	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
980	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
981	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
982	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
983	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
984	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
985	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
986	"DlcTolu2\1" " DlcTolu2 1 2 0.6 175 161 0 GCGGCUGGA-==========NN-N.\1"
987	"FrhhPhil\1" " FrhhPhil 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
988	"HllHalod\1" " HllHalod 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
989	"CPPParap\1" " CPPParap 1 2 0.6 176 162 0 GCGGNUGGA-==========..-\1"
990	"AclPleur\1" " AclPleur 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
991	"PtVVVulg\1" " PtVVVulg 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
992	"LgtLytic\1" " LgtLytic 2 3 1.3 175 161 0 GCGGCUGGA-=========N..-\1"
993	"PslFlave\1" " PslFlave 2 3 1.3 175 161 0 GCGGCUGGA-=========...-\1"
994	"ClfPerfr\1" " ClfPerfr 2 0 1.3 175 161 0 AAGAUUAAU-A=C=========-U.\1"
995	"AclPleur\1" " AclPleur 5 0 2.4 50 45 0 GAAGGGAGC-=ug=u=u====G-CCGACGAGU\1"
996	"PtVVVulg\1" " PtVVVulg 5 0 2.4 50 45 0 GGAGAAAGC-=ug=u=u===g=-UGACGAGCG\1";
997
998	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
999	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1000	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1001	}
1002
1003	// ----------------------------------------------
1004	// do not accept any N-matches as match
1005
1006	{
1007	const char *arguments[] = {
1008	"prgnamefake",
1009	"matchsequence=CANCUCCUUUC", // contains 1 N
1010	NULp, // matchmismatches
1011	"matchacceptN=0",
1012	};
1013
1014	CCP expectd0 = ""; // nothing matches
1015
1016	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
1017	"BcSSSS00\1" " BcSSSS00 1 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1";
1018
1019	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
1020	"BcSSSS00\1" " BcSSSS00 1 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
1021	"ClfPerfr\1" " ClfPerfr 2 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
1022	"PbcAcet2\1" " PbcAcet2 2 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1023	"PbrPropi\1" " PbrPropi 2 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1024	"Stsssola\1" " Stsssola 2 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
1025	"DcdNodos\1" " DcdNodos 2 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
1026	"VbrFurni\1" " VbrFurni 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
1027	"VblVulni\1" " VblVulni 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
1028	"VbhChole\1" " VbhChole 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1";
1029
1030	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1031	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1032	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1033	}
1034	{
1035	const char *arguments[] = {
1036	"prgnamefake",
1037	"matchsequence=UUUCUUU", // contains no N
1038	NULp, // matchmismatches
1039	"matchacceptN=0",
1040	};
1041
1042	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1043	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1";
1044
1045	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1046	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1"
1047	"AclPleur\1" " AclPleur 1 0 0.6 50 45 0 GAAGGGAGC-==g====-CUUUGCCGA\1"
1048	"PtVVVulg\1" " PtVVVulg 1 0 0.6 50 45 0 GGAGAAAGC-==g====-CUUGCUGAC\1"
1049	"PtVVVulg\1" " PtVVVulg 1 0 0.6 54 49 0 AAAGCUUGC-======g-CUGACGAGC\1"
1050	"ClfPerfr\1" " ClfPerfr 1 0 1.1 49 44 0 GCGAUGAAG-====C==-CGGGAAACG\1";
1051
1052	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1053	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1"
1054	"AclPleur\1" " AclPleur 1 0 0.6 50 45 0 GAAGGGAGC-==g====-CUUUGCCGA\1"
1055	"PtVVVulg\1" " PtVVVulg 1 0 0.6 50 45 0 GGAGAAAGC-==g====-CUUGCUGAC\1"
1056	"PtVVVulg\1" " PtVVVulg 1 0 0.6 54 49 0 AAAGCUUGC-======g-CUGACGAGC\1"
1057	"ClfPerfr\1" " ClfPerfr 1 0 1.1 49 44 0 GCGAUGAAG-====C==-CGGGAAACG\1"
1058	"DlcTolu2\1" " DlcTolu2 2 0 1.2 47 42 0 AGAAAGGGA-==g===g-CAAUCCUGA\1"
1059	"ClnCorin\1" " ClnCorin 2 0 1.7 48 43 0 AGCGAUGAA-g===C==-CGGGAAUGG\1"
1060	"CPPParap\1" " CPPParap 2 0 1.7 48 43 0 AGCGAUGAA-g===C==-CGGGAACGG\1"
1061	"HllHalod\1" " HllHalod 2 0 1.7 49 44 0 GAUGGAAGC-==g===C-CAGGCGUCG\1"
1062	"DcdNodos\1" " DcdNodos 2 0 1.7 50 45 0 UUAUGUAGC-==g==A=-GUAACCUAG\1"
1063	"VbhChole\1" " VbhChole 2 0 1.7 55 50 0 GAGGAACUU-g===C==-GGGUGGCGA\1"
1064	"VbrFurni\1" " VbrFurni 2 0 1.7 62 57 0 UUCGGGGGA-===G==g-GGCGGCGAG\1"
1065	"VblVulni\1" " VblVulni 2 0 1.7 62 57 0 AGAAACUUG-=====Cg-GGUGGCGAG\1"
1066	"VbhChole\1" " VbhChole 2 0 1.7 62 57 0 AGGAACUUG-==C===g-GGUGGCGAG\1"
1067	"ClnCorin\1" " ClnCorin 2 0 2.2 49 44 0 GCGAUGAAG-==C===C-GGGAAUGGA\1"
1068	"CltBotul\1" " CltBotul 2 0 2.2 49 44 0 GCGAUGAAG-C=====C-GGAAGUGGA\1"
1069	"CPPParap\1" " CPPParap 2 0 2.2 49 44 0 GCGAUGAAG-==C===C-GGGAACGGA\1"
1070	"ClfPerfr\1" " ClfPerfr 2 0 2.2 50 45 0 CGAUGAAGU-==C===C-GGGAAACGG\1"
1071	"VblVulni\1" " VblVulni 2 0 2.2 52 47 0 ACAGAGAAA-C==G===-CUCGGGUGG\1"
1072	"BcSSSS00\1" " BcSSSS00 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-CU.\1"
1073	"ClfPerfr\1" " ClfPerfr 2 0 2.2 179 165 0 UUAAUACCC-C=C====-CU.\1"
1074	"PbcAcet2\1" " PbcAcet2 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-NN.\1"
1075	"PbrPropi\1" " PbrPropi 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-NN.\1"
1076	"Stsssola\1" " Stsssola 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1077	"DcdNodos\1" " DcdNodos 2 0 2.2 179 165 0 UUGGAUCAC-C=C====-.\1"
1078	"VbrFurni\1" " VbrFurni 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1079	"VblVulni\1" " VblVulni 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1080	"VbhChole\1" " VbhChole 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1081	"BcSSSS00\1" " BcSSSS00 2 2 1.4 183 169 0 AUCACCUCC-=====..-\1"
1082	"ClfPerfr\1" " ClfPerfr 2 2 1.4 183 169 0 UACCCCUCC-=====..-\1";
1083
1084	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1085	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1086	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1087	}
1088	{
1089	const char *arguments[] = {
1090	"prgnamefake",
1091	"matchsequence=UCACCUCCUUUC", // contains no N
1092	NULp, // matchmismatches
1093	"matchacceptN=0",
1094	};
1095
1096	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1097	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "";
1098
1099	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1100	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
1101	"PbcAcet2\1" " PbcAcet2 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1102	"PbrPropi\1" " PbrPropi 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1103	"Stsssola\1" " Stsssola 1 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
1104	"DcdNodos\1" " DcdNodos 1 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
1105	"VbrFurni\1" " VbrFurni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1106	"VblVulni\1" " VblVulni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1107	"VbhChole\1" " VbhChole 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1";
1108
1109	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1110	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
1111	"PbcAcet2\1" " PbcAcet2 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1112	"PbrPropi\1" " PbrPropi 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1113	"Stsssola\1" " Stsssola 1 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
1114	"DcdNodos\1" " DcdNodos 1 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
1115	"VbrFurni\1" " VbrFurni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1116	"VblVulni\1" " VblVulni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1117	"VbhChole\1" " VbhChole 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1118	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C=========-U.\1"
1119	"AclPleur\1" " AclPleur 2 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
1120	"PtVVVulg\1" " PtVVVulg 2 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
1121	"DlcTolu2\1" " DlcTolu2 2 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
1122	"FrhhPhil\1" " FrhhPhil 2 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
1123	"HllHalod\1" " HllHalod 2 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
1124	"CPPParap\1" " CPPParap 2 2 1.4 176 162 0 GCGGNUGGA-==========..-\1";
1125
1126	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1127	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1128	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1129	}
1130	{
1131	const char *arguments[] = {
1132	"prgnamefake",
1133	"matchsequence=UCACCUCCUUUCU", // contains no N
1134	NULp, // matchmismatches
1135	"matchacceptN=0",
1136	};
1137
1138	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1139	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1";
1140
1141	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1142	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1143	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1144	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1145	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1146	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1147	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1148	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1149	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1150	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1";
1151
1152	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1153	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1154	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1155	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1156	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1157	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1158	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1159	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1160	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1161	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1162	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1163	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1164	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1165	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1166	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1167	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1";
1168
1169	CCP expectd4 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1170	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1171	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1172	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1173	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1174	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1175	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1176	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1177	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1178	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1179	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1180	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1181	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1182	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1183	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1184	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1"
1185	"LgtLytic\1" " LgtLytic 4 4 2.8 175 161 0 GCGGCUGGA-=========N...-\1"
1186	"PslFlave\1" " PslFlave 4 4 2.8 175 161 0 GCGGCUGGA-=========....-\1";
1187
1188	CCP expectd5 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1189	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1190	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1191	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1192	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1193	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1194	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1195	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1196	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1197	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1198	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1199	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1200	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1201	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1202	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1203	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1"
1204	"LgtLytic\1" " LgtLytic 4 4 2.8 175 161 0 GCGGCUGGA-=========N...-\1"
1205	"PslFlave\1" " PslFlave 4 4 2.8 175 161 0 GCGGCUGGA-=========....-\1"
1206	"PtVVVulg\1" " PtVVVulg 5 0 2.6 50 45 0 GGAGAAAGC-=ug=u=u===g==-GACGAGCGG\1"
1207	"AclPleur\1" " AclPleur 5 0 3.5 46 41 0 ACGGGAAGG-gag=u=G======-UUGCCGACG\1"
1208	"PtVVVulg\1" " PtVVVulg 5 0 4.0 45 40 0 ...AGGAGA-Aag=u=G======-UGCUGACGA\1"
1209	"VblVulni\1" " VblVulni 5 0 4.3 48 43 0 CAGCACAGA-ga=a==uG=====-CGGGUGGCG\1";
1210
1211	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1212	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1213	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1214	arguments[2] = "matchmismatches=4"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd4);
1215	arguments[2] = "matchmismatches=5"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd5);
1216	}
1217
1218	// ----------------------------------
1219	// accept several N-matches
1220
1221	{
1222	const char *arguments[] = {
1223	"prgnamefake",
1224	"matchsequence=CANCUCCUUNC", // contains 2 N
1225	NULp, // matchmismatches
1226	"matchacceptN=2",
1227	"matchlimitN=4",
1228	};
1229
1230	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1231	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1";
1232
1233	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1234	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1"
1235	"ClfPerfr\1" " ClfPerfr 1 2 2.8 176 162 0 AGAUUAAUA-=CC======U=-U.\1"
1236	"DlcTolu2\1" " DlcTolu2 1 3 2.4 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1237	"FrhhPhil\1" " FrhhPhil 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1238	"HllHalod\1" " HllHalod 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1239	"CPPParap\1" " CPPParap 1 3 2.4 177 163 0 CGGNUGGAU-==C======..-\1"
1240	"PbcAcet2\1" " PbcAcet2 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1241	"PbrPropi\1" " PbrPropi 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1242	"Stsssola\1" " Stsssola 1 3 2.4 176 162 0 CGGCUGGAU-==C======U.-\1"
1243	"DcdNodos\1" " DcdNodos 1 3 2.4 176 162 0 CGGUUGGAU-==C======U.-\1"
1244	"VbrFurni\1" " VbrFurni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1245	"VblVulni\1" " VblVulni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1246	"VbhChole\1" " VbhChole 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1247	"AclPleur\1" " AclPleur 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1"
1248	"PtVVVulg\1" " PtVVVulg 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1";
1249
1250	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1251	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1"
1252	"ClfPerfr\1" " ClfPerfr 1 2 2.8 176 162 0 AGAUUAAUA-=CC======U=-U.\1"
1253	"DlcTolu2\1" " DlcTolu2 1 3 2.4 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1254	"FrhhPhil\1" " FrhhPhil 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1255	"HllHalod\1" " HllHalod 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1256	"CPPParap\1" " CPPParap 1 3 2.4 177 163 0 CGGNUGGAU-==C======..-\1"
1257	"PbcAcet2\1" " PbcAcet2 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1258	"PbrPropi\1" " PbrPropi 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1259	"Stsssola\1" " Stsssola 1 3 2.4 176 162 0 CGGCUGGAU-==C======U.-\1"
1260	"DcdNodos\1" " DcdNodos 1 3 2.4 176 162 0 CGGUUGGAU-==C======U.-\1"
1261	"VbrFurni\1" " VbrFurni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1262	"VblVulni\1" " VblVulni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1263	"VbhChole\1" " VbhChole 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1264	"AclPleur\1" " AclPleur 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1"
1265	"PtVVVulg\1" " PtVVVulg 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1";
1266
1267	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1268	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1269	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1270	}
1271
1272	{
1273	const char *arguments[] = {
1274	"prgnamefake",
1275	"matchsequence=GAGCGGUCAG", // similar to a region where dots occur in seqdata
1276	NULp, // matchmismatches
1277	"matchacceptN=0",
1278	"matchlimitN=4",
1279	};
1280
1281	CCP expectd0 = "";
1282
1283	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1284	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1";
1285
1286	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1287	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1"
1288	"Bl0LLL00\1" " Bl0LLL00 2 0 2.2 25 21 0 GAUCAAGUC-======A=C=-ACGGGAGCU\1";
1289
1290	// this probe-match is also tested with 'arb_probe_match'. see arb_test.cxx@TEST_arb_probe_match
1291	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1292	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1"
1293	"Bl0LLL00\1" " Bl0LLL00 2 0 2.2 25 21 0 GAUCAAGUC-======A=C=-ACGGGAGCU\1"
1294	"VbrFurni\1" " VbrFurni 3 0 2.4 68 60 0 GGAUUUGUU-=g====CG==-CGGCGGACG\1"
1295	"FrhhPhil\1" " FrhhPhil 3 0 2.8 82 70 0 ACGAGUGGC-=gA===C===-UUGGAAACG\1"
1296	"ClfPerfr\1" " ClfPerfr 3 0 3.2 86 74 0 CGGCGGGAC-=g==CU====-AACCUGCGG\1"
1297	"HllHalod\1" " HllHalod 3 0 3.6 25 21 0 GAUCAAGUC-======Aa=C-GAUGGAAGC\1"
1298	"DlcTolu2\1" " DlcTolu2 3 0 3.6 95 83 0 GGACUGCCC-==Aa==A===-CUAAUACCG\1"
1299	"FrhhPhil\1" " FrhhPhil 3 0 4.0 25 21 0 GAUCAAGUC-==A====a=C-AGGUCUUCG\1"
1300	"AclPleur\1" " AclPleur 3 0 4.0 29 24 0 GAUCAAGUC-==A====a=C-GGGAAGGGA\1"
1301	"ClnCorin\1" " ClnCorin 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUCCUUCG\1"
1302	"CltBotul\1" " CltBotul 3 0 4.1 25 21 0 .AUCAAGUC-=====A=G=A-GCUUCUUCG\1"
1303	"CPPParap\1" " CPPParap 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUCCUUCG\1"
1304	"ClfPerfr\1" " ClfPerfr 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUUCCUUC\1"
1305	"DlcTolu2\1" " DlcTolu2 3 0 4.1 157 143 0 GUAGCCGUU-===GAA====-CGGCUGGAU\1"
1306	"PslFlave\1" " PslFlave 3 3 2.4 25 21 0 GAUCAAGUC-=======...-<more>\1"
1307	"PtVVVulg\1" " PtVVVulg 3 3 2.4 29 24 0 GAUCAAGUC-=======...-<more>\1";
1308
1309	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1310	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1311	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1312	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1313	}
1314
1315	{
1316	const char *arguments[] = {
1317	"prgnamefake",
1318	"matchsequence=GAGCGGUCAGGAG", // as above, but continues behind '...'
1319	NULp, // matchmismatches
1320	"matchweighted=1", // use weighted mismatches
1321	};
1322
1323	CCP expectd2 = "";
1324	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAGGAG'\1"
1325	"ClnCorin\1" " ClnCorin 6 0 3.4 77 66 0 AUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1326	"CltBotul\1" " CltBotul 6 0 3.4 77 66 0 GUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1327	"CPPParap\1" " CPPParap 6 0 3.4 77 66 0 ACGGAUUAG-Cg====A=g==CC-UUCCGAAAG\1"
1328	"BcSSSS00\1" " BcSSSS00 3 0 3.4 25 21 0 GAUCAAGUC-======A===AU=-GGAGCUUGC\1";
1329
1330	CCP expectd4 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAGGAG'\1"
1331	"ClnCorin\1" " ClnCorin 6 0 3.4 77 66 0 AUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1332	"CltBotul\1" " CltBotul 6 0 3.4 77 66 0 GUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1333	"CPPParap\1" " CPPParap 6 0 3.4 77 66 0 ACGGAUUAG-Cg====A=g==CC-UUCCGAAAG\1"
1334	"BcSSSS00\1" " BcSSSS00 3 0 3.4 25 21 0 GAUCAAGUC-======A===AU=-GGAGCUUGC\1"
1335	"ClfPerfr\1" " ClfPerfr 6 0 3.9 121 108 0 AUCAUAAUG-C====A=ug==gU-GAAGUCGUA\1"
1336	"ClnCorin\1" " ClnCorin 6 0 3.9 122 109 0 CGCAUAAGA-C====A=ug==gU-GAAGUCGUA\1"
1337	"CltBotul\1" " CltBotul 6 0 3.9 122 109 0 CUCAUAAGA-C====A=ug==gU-GAAGUCGUA\1"
1338	"CPPParap\1" " CPPParap 6 0 3.9 122 109 0 GCAUAAGAU-C====A=ug==gU-AAGUCGUAA\1"
1339	"DcdNodos\1" " DcdNodos 6 0 4.2 77 66 0 GUAACCUAG-Ug====A=g=AC=-UAUGGAAAC\1"
1340	"PsAAAA00\1" " PsAAAA00 6 0 4.2 77 66 0 UGGAUUCAG-Cg====A=g=AC=-UCCGGAAAC\1"
1341	"PslFlave\1" " PslFlave 6 0 4.2 77 66 0 CUGAUUCAG-Cg====A=g=AC=-UUUCGAAAG\1"
1342	"FrhhPhil\1" " FrhhPhil 5 0 4.2 149 135 0 UAACAAUGG-U===C==ag===A-CCUGCGGCU\1"
1343	"AclPleur\1" " AclPleur 4 0 4.3 29 24 0 GAUCAAGUC-==A====a=C=g=-AAGGGAGCU\1"
1344	"PbcAcet2\1" " PbcAcet2 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1345	"PbrPropi\1" " PbrPropi 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1346	"Stsssola\1" " Stsssola 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1347	"LgtLytic\1" " LgtLytic 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1348	"PslFlave\1" " PslFlave 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1349	"HllHalod\1" " HllHalod 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1350	"VbrFurni\1" " VbrFurni 5 0 4.4 68 60 0 GGAUUUGUU-=g====CG==Cg=-CGGACGGAC\1"
1351	"AclPleur\1" " AclPleur 6 0 4.4 35 30 0 GUCGAACGG-U=A===ga===gA-GCUUGCUUU\1"
1352	"PslFlave\1" " PslFlave 6 6 4.4 25 21 0 GAUCAAGUC-=======......-<more>\1"
1353	"PtVVVulg\1" " PtVVVulg 6 6 4.4 29 24 0 GAUCAAGUC-=======......-<more>\1"
1354	"VbrFurni\1" " VbrFurni 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1"
1355	"VblVulni\1" " VblVulni 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1"
1356	"VbhChole\1" " VbhChole 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1";
1357
1358	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1359	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1360	arguments[2] = "matchmismatches=4"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd4);
1361	}
1362
1363	// --------------------------
1364	// truncate results
1365
1366	{
1367	const char *arguments[] = {
1368	"prgnamefake",
1369	"matchsequence=CANCNCNNUNC", // contains 5N
1370	NULp, // matchmismatches
1371	"matchacceptN=5",
1372	"matchlimitN=7",
1373	"matchmaxresults=5",
1374	};
1375
1376	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1377	"BcSSSS00\1" " BcSSSS00 0 5 4.2 176 162 0 CGGCUGGAU-==C=U=CU=U=-U.\1";
1378
1379	// many hits are truncated here:
1380	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1381	"DlcTolu2\1" " DlcTolu2 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU==N-N.\1"
1382	"FrhhPhil\1" " FrhhPhil 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU=..-\1"
1383	"HllHalod\1" " HllHalod 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU=..-\1"
1384	"CPPParap\1" " CPPParap 1 6 4.9 177 163 0 CGGNUGGAU-==C=U=CU=..-\1"
1385	"AclPleur\1" " AclPleur 1 6 5.0 176 162 0 CGGUUGGAU-==C=U=CU=A.-\1";
1386
1387	// many hits are truncated here:
1388	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1389	"HllHalod\1" " HllHalod 2 5 5.1 45 40 0 AAACGAUGG-a=G=UuGC=U=-CAGGCGUCG\1"
1390	"VblVulni\1" " VblVulni 2 5 5.4 49 44 0 AGCACAGAG-a=A=UuGU=U=-UCGGGUGGC\1"
1391	"VbrFurni\1" " VbrFurni 2 5 5.7 40 35 0 CGGCAGCGA-==A=AuUGAA=-CUUCGGGGG\1"
1392	"LgtLytic\1" " LgtLytic 2 5 6.2 101 89 0 GGGGAAACU-==AGCuAA=A=-CGCAUAAUC\1"
1393	"ClfPerfr\1" " ClfPerfr 2 5 6.5 172 158 0 AGGAAGAUU-a=UaC=CC=C=-UUUCU.\1";
1394
1395	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1396	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1397	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1398	}
1399
1400	// -------------------------------------------------------------
1401	// tests related to http://bugs.arb-home.de/ticket/410
1402	{
1403	const char *arguments[] = {
1404	"prgnamefake",
1405	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACC", // length=29
1406	NULp, // matchmismatches
1407	"matchacceptN=5",
1408	"matchlimitN=7",
1409	"matchmaxresults=10",
1410	};
1411
1412	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'ACGGACUCCGGGAAACCGGGGCUAAUACC'\1"
1413	"BcSSSS00\1" " BcSSSS00 0 0 0.0 84 72 0 UAGCGGCGG-=============================-GGAUGGUGA\1"
1414	"Bl0LLL00\1" " Bl0LLL00 0 0 0.0 84 72 0 CAGCGGCGG-=============================-GGAUGCUGA\1"
1415	"AclPleur\1" " AclPleur 4 0 4.6 84 72 0 GAGUGGCGG-=======a========u=UA=========-GCGUAAUCA\1"
1416	"PtVVVulg\1" " PtVVVulg 4 0 5.1 84 72 0 GAGCGGCGG-=======a=U======G=U==========-GCAUGACCA\1"
1417	"DsssDesu\1" " DsssDesu 5 0 5.3 84 72 0 GAGUGGCGC-========u=C====Gu==A=========-GGAUACAGA\1"
1418	"PsAAAA00\1" " PsAAAA00 5 0 5.3 84 72 0 CAGCGGCGG-======gu=C======G==C=========-GCAUACGCA\1";
1419
1420	arguments[2] = "matchmismatches=5"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1421	}
1422	{
1423	const char *arguments[] = {
1424	"prgnamefake",
1425	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA", // length=38
1426	NULp, // matchmismatches
1427	"matchacceptN=5",
1428	"matchlimitN=7",
1429	"matchmaxresults=100",
1430	};
1431
1432	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA'\1"
1433	"BcSSSS00\1" " BcSSSS00 0 0 0.0 84 72 0 UAGCGGCGG-======================================-UGAUUGGGG\1"
1434	"Bl0LLL00\1" " Bl0LLL00 1 0 1.5 84 72 0 CAGCGGCGG-==================================C===-UGAUUGGGG\1"
1435	"DsssDesu\1" " DsssDesu 8 0 9.4 84 72 0 GAGUGGCGC-========u=C====Gu==A=============ACA==-G.\1"
1436	"PtVVVulg\1" " PtVVVulg 8 0 10.7 84 72 0 GAGCGGCGG-=======a=U======G=U===========C===ACC=-UGACUGGGG\1"
1437	"AclPleur\1" " AclPleur 9 0 10.8 84 72 0 GAGUGGCGG-=======a========u=UA==========Cg=AA=C=-UGACUGGGG\1"
1438	"PsAAAA00\1" " PsAAAA00 10 0 11.9 84 72 0 CAGCGGCGG-======gu=C======G==C==========C==ACgC=-UGGUAACAA\1"
1439	"LgtLytic\1" " LgtLytic 10 0 12.8 84 72 0 GAGNGGCGA-=======uG=======uCAA==========C==AA=C=-UGACUGGGG\1"
1440	"VbrFurni\1" " VbrFurni 10 0 12.8 84 72 0 GAGCGGCGG-======CauU======GAU===========C===A=C=-UGACUGGGG\1"
1441	"VblVulni\1" " VblVulni 10 0 12.8 84 72 0 GAGCGGCGG-======CauU======GAU===========C===A=C=-UGACUGGGG\1"
1442	"Stsssola\1" " Stsssola 10 0 12.9 84 72 0 AAGUGGCGC-======gG=U======G=UC=============AACA=-UGAUUGGGG\1"
1443	"DlcTolu2\1" " DlcTolu2 10 0 13.4 84 72 0 GAGUGGCGC-=======G=CC====GGACA==============AA==-UAAUUGGGG\1"
1444	"PbcAcet2\1" " PbcAcet2 11 0 12.2 84 72 0 AAGUGGCGC-======A=uUC====GG==U=============AAg=g-UAACUGGGG\1"
1445	"HllHalod\1" " HllHalod 11 0 13.0 84 72 0 GAGCGGCGG-======CuG=======uCA===========C==ACgC=-UGACUGGGG\1"
1446	"PbrPropi\1" " PbrPropi 12 0 13.6 84 72 0 UAGUGGCGC-======A=uUC====Ga==U=========U===AAg=g-UGACUGGGG\1"
1447	"DcdNodos\1" " DcdNodos 12 0 14.4 84 72 0 UAGUGGCGG-======guaU======GUAC==========C==AAg==-UGACUGGGG\1"
1448	"VbhChole\1" " VbhChole 12 0 15.4 84 72 0 GAGCGGCGG-======CauU======GAU===========C==AACC=-UGACUGGGG\1";
1449
1450	arguments[2] = "matchmismatches=12"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1451	}
1452
1453
1454	// test expected errors
1455	{
1456	const char *arguments[] = {
1457	"prgnamefake",
1458	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA", // length = 38
1459	"matchmismatches=20",
1460	};
1461
1462	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, "Max. 19 mismatches are allowed for probes of length 38");
1463	}
1464	}
1465
1466	static char extract_locations(const char probe_design_result) {
1467	const char *Target = strstr(probe_design_result, "\nTarget");
1468	if (Target) {
1469	const char *designed = strchr(Target+7, '\n');
1470	if (designed) {
1471	++designed;
1472
1473	GBS_strstruct result(300);
1474	RegExpr reg_designed("^[A-Z]+"
1475	"[[:space:]]+[0-9]+"
1476	"[[:space:]]+([A-Z][=+-])" // subexpr #1 (loc+-=)
1477	"[[:space:]]*([0-9]+)", // subexpr #2 (abs or locrel)
1478	true);
1479
1480
1481	while (designed) {
1482	const char *eol = strchr(designed, '\n');
1483	const RegMatch *match = reg_designed.match(designed); if (!match) break;
1484
1485	match = reg_designed.subexpr_match(1); if (!match) break;
1486	std::string loc = match->extract(designed);
1487
1488	match = reg_designed.subexpr_match(2); if (!match) break;
1489	std::string pos = match->extract(designed);
1490
1491	result.cat(loc.c_str());
1492	result.cat(pos.c_str());
1493
1494	designed = eol ? eol+1 : NULp;
1495	}
1496	arb_assert(implicated(designed, !reg_designed.has_failed())); // assert RegExpr compiled
1497
1498	return result.release();
1499	}
1500	}
1501	return ARB_strdup("can't extract");
1502	}
1503
1504	inline const char next_line(const char this_line) {
1505	const char *lf = strchr(this_line, '\n');
1506	return (lf && lf[1] && strchr("ACGTU", lf[1])) ? lf+1 : NULp;
1507	}
1508	inline int count_hits(const char *design_result) {
1509	const char *target = strstr(design_result, "\nTarget");
1510	if (target) {
1511	const char *hit = next_line(target+1);
1512	int hits = 0;
1513
1514	while (hit) {
1515	++hits;
1516	hit = next_line(hit);
1517	}
1518	return hits;
1519	}
1520	return -1;
1521	}
1522
1523	void TEST_SLOW_design_probe() {
1524	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
1525
1526	bool use_gene_ptserver = false;
1527	{
1528	int hits_len_18;
1529	{
1530	const char *arguments[] = {
1531	"prgnamefake",
1532	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1533	"designmintargets=100",
1534	};
1535	const char *expected =
1536	"Probe design parameters:\n"
1537	"Length of probe 18\n"
1538	"Temperature [ 0.0 -400.0]\n"
1539	"GC-content [30.0 - 80.0]\n"
1540	"E.Coli position [any]\n"
1541	"Max. nongroup hits 0\n"
1542	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1543	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1544	"CGAAAGGAAGAUUAAUAC 18 A=94 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1545	"GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC \| - - - - - - - - - - - - - - - - - - - -\n"
1546	"UCAAGUCGAGCGAUGAAG 18 B=18 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA \| - - - - - - - - - - - - - - - 2 2 2 2 2\n"
1547	"AUCAAGUCGAGCGAUGAA 18 B- 1 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU \| - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n";
1548
1549	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1550	hits_len_18 = count_hits(expected);
1551	TEST_EXPECT_EQUAL(hits_len_18, 4);
1552
1553	// test extraction of positions:
1554	{
1555	char *positions = extract_locations(expected);
1556	TEST_EXPECT_EQUAL(positions, "A=94A+1B=18B-1");
1557	free(positions);
1558	}
1559	}
1560	// same as above with probelength 17
1561	int hits_len_17;
1562	{
1563	const char *arguments[] = {
1564	"prgnamefake",
1565	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1566	"designmintargets=100",
1567	"designprobelength=17",
1568	};
1569	const char *expected =
1570	"Probe design parameters:\n"
1571	"Length of probe 17\n"
1572	"Temperature [ 0.0 -400.0]\n"
1573	"GC-content [30.0 - 80.0]\n"
1574	"E.Coli position [any]\n"
1575	"Max. nongroup hits 0\n"
1576	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1577	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1578	"CAAGUCGAGCGAUGAAG 17 A=19 18 65 4 52.9 52.0 CUUCAUCGCUCGACUUG \| - - - - - - - - - - - - - - - - 2 2 2 2\n"
1579	"UCAAGUCGAGCGAUGAA 17 A- 1 17 49 4 47.1 50.0 UUCAUCGCUCGACUUGA \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1580	"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";
1581
1582	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1583	hits_len_17 = count_hits(expected);
1584	TEST_EXPECT_EQUAL(hits_len_17, 3);
1585	}
1586	// same as above with probelength 16
1587	int hits_len_16;
1588	{
1589	const char *arguments[] = {
1590	"prgnamefake",
1591	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1592	"designmintargets=100",
1593	"designprobelength=16",
1594	};
1595	const char *expected =
1596	"Probe design parameters:\n"
1597	"Length of probe 16\n"
1598	"Temperature [ 0.0 -400.0]\n"
1599	"GC-content [30.0 - 80.0]\n"
1600	"E.Coli position [any]\n"
1601	"Max. nongroup hits 0\n"
1602	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1603	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1604	"CGAAAGGAAGAUUAAU 16 A=94 82 77 4 31.2 42.0 AUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1605	"AAGGAAGAUUAAUACC 16 A+ 3 85 77 4 31.2 42.0 GGUAUUAAUCUUCCUU \| - - - - - - - - - - - - - - - - - - - -\n"
1606	"AAGUCGAGCGAUGAAG 16 B=20 19 69 4 50.0 48.0 CUUCAUCGCUCGACUU \| - - - - - - - - - - - - - - - - - 2 2 2\n"
1607	"CAAGUCGAGCGAUGAA 16 B- 1 18 49 4 50.0 48.0 UUCAUCGCUCGACUUG \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1608	"UCAAGUCGAGCGAUGA 16 B- 2 17 37 4 50.0 48.0 UCAUCGCUCGACUUGA \| - - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2\n"
1609	"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";
1610
1611	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1612	hits_len_16 = count_hits(expected);
1613	TEST_EXPECT_EQUAL(hits_len_16, 6);
1614	}
1615	// combine the 3 preceeding designs
1616	int combined_hits;
1617	{
1618	const char *arguments[] = {
1619	"prgnamefake",
1620	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1621	"designmintargets=100",
1622	"designprobelength=16",
1623	"designmaxprobelength=18",
1624	};
1625	const char *expected =
1626	"Probe design parameters:\n"
1627	"Length of probe 16-18\n"
1628	"Temperature [ 0.0 -400.0]\n"
1629	"GC-content [30.0 - 80.0]\n"
1630	"E.Coli position [any]\n"
1631	"Max. nongroup hits 0\n"
1632	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1633	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1634	"CGAAAGGAAGAUUAAU 16 A=94 82 77 4 31.2 42.0 AUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1635	"CGAAAGGAAGAUUAAUAC 18 A+ 0 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1636	"GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC \| - - - - - - - - - - - - - - - - - - - -\n"
1637	"AAGGAAGAUUAAUACC 16 A+ 3 85 77 4 31.2 42.0 GGUAUUAAUCUUCCUU \| - - - - - - - - - - - - - - - - - - - -\n"
1638	"AAGUCGAGCGAUGAAG 16 B=20 19 69 4 50.0 48.0 CUUCAUCGCUCGACUU \| - - - - - - - - - - - - - - - - - 2 2 2\n"
1639	"CAAGUCGAGCGAUGAAG 17 B- 1 18 65 4 52.9 52.0 CUUCAUCGCUCGACUUG \| - - - - - - - - - - - - - - - - 2 2 2 2\n"
1640	"UCAAGUCGAGCGAUGAAG 18 B- 2 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA \| - - - - - - - - - - - - - - - 2 2 2 2 2\n"
1641	"UCAAGUCGAGCGAUGAA 17 B- 2 17 49 4 47.1 50.0 UUCAUCGCUCGACUUGA \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1642	"CAAGUCGAGCGAUGAA 16 B- 1 18 49 4 50.0 48.0 UUCAUCGCUCGACUUG \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1643	"AUCAAGUCGAGCGAUGAA 18 B- 3 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU \| - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n"
1644	"UCAAGUCGAGCGAUGA 16 B- 2 17 37 4 50.0 48.0 UCAUCGCUCGACUUGA \| - - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2\n"
1645	"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"
1646	"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";
1647
1648	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1649	combined_hits = count_hits(expected);
1650	}
1651
1652	// check that combined design reports all probes reported by single designs:
1653	TEST_EXPECT_EQUAL(combined_hits, hits_len_16+hits_len_17+hits_len_18);
1654	}
1655	// test vs bug (fails with [8988] .. [9175])
1656	{
1657	const char *arguments[] = {
1658	"prgnamefake",
1659	"designnames=VbhChole#VblVulni",
1660	"designmintargets=50", // hit at least 1 of the 2 targets
1661	"designmingc=60", "designmaxgc=75", // specific GC range
1662	};
1663
1664	const char *expected =
1665	"Probe design parameters:\n"
1666	"Length of probe 18\n"
1667	"Temperature [ 0.0 -400.0]\n"
1668	"GC-content [60.0 - 75.0]\n"
1669	"E.Coli position [any]\n"
1670	"Max. nongroup hits 0 (lowest rejected nongroup hits: 1)\n"
1671	"Min. group hits 50%\n"
1672	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1673	"AGUCGAGCGGCAGCACAG 18 A=21 20 39 2 66.7 60.0 CUGUGCUGCCGCUCGACU \| - - - - - - - - - - - - - - - - - - - -\n"
1674	"GUCGAGCGGCAGCACAGA 18 A+ 1 21 39 2 66.7 60.0 UCUGUGCUGCCGCUCGAC \| - - - - - - - - - - - - - - - - - - - -\n"
1675	"UCGAGCGGCAGCACAGAG 18 A+ 2 21 39 2 66.7 60.0 CUCUGUGCUGCCGCUCGA \| - - - - - - - - - - - - - - - - - - - -\n"
1676	"AAGUCGAGCGGCAGCACA 18 A- 1 19 25 2 61.1 58.0 UGUGCUGCCGCUCGACUU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1677	"CGAGCGGCAGCACAGAGA 18 A+ 3 21 20 1 66.7 60.0 UCUCUGUGCUGCCGCUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1678	"CGAGCGGCAGCACAGAGG 18 A+ 3 21 20 1 72.2 62.0 CCUCUGUGCUGCCGCUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1679	"GAGCGGCAGCACAGAGAA 18 A+ 4 21 20 1 61.1 58.0 UUCUCUGUGCUGCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1680	"GAGCGGCAGCACAGAGGA 18 A+ 4 21 20 1 66.7 60.0 UCCUCUGUGCUGCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1681	"AGCGGCAGCACAGAGGAA 18 A+ 5 21 20 1 61.1 58.0 UUCCUCUGUGCUGCCGCU \| - - - - - - - - - - - - - - - - - - - -\n"
1682	"GCGGCAGCACAGAGAAAC 18 A+ 6 22 20 1 61.1 58.0 GUUUCUCUGUGCUGCCGC \| - - - - - - - - - - - - - - - - - - - -\n"
1683	"GCGGCAGCACAGAGGAAC 18 A+ 6 22 20 1 66.7 60.0 GUUCCUCUGUGCUGCCGC \| - - - - - - - - - - - - - - - - - - - -\n"
1684	"CGGCAGCACAGAGGAACU 18 A+ 7 23 20 1 61.1 58.0 AGUUCCUCUGUGCUGCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1685	"CUUGUUCCUUGGGUGGCG 18 B=52 47 20 1 61.1 58.0 CGCCACCCAAGGAACAAG \| - - - - - - - - - - - - - - - - - - - -\n"
1686	"CUUGUUUCUCGGGUGGCG 18 B+ 0 47 20 1 61.1 58.0 CGCCACCCGAGAAACAAG \| - - - - - - - - - - - - - - - - - - - -\n"
1687	"UGUUCCUUGGGUGGCGAG 18 B+ 2 49 20 1 61.1 58.0 CUCGCCACCCAAGGAACA \| - - - - - - - - - - - - - - - - - - - -\n"
1688	"UGUUUCUCGGGUGGCGAG 18 B+ 2 49 20 1 61.1 58.0 CUCGCCACCCGAGAAACA \| - - - - - - - - - - - - - - - - - - - -\n"
1689	"GUUCCUUGGGUGGCGAGC 18 B+ 3 50 20 1 66.7 60.0 GCUCGCCACCCAAGGAAC \| - - - - - - - - - - - - - - - - - - - -\n"
1690	"GUUUCUCGGGUGGCGAGC 18 B+ 3 50 20 1 66.7 60.0 GCUCGCCACCCGAGAAAC \| - - - - - - - - - - - - - - - - - - - -\n"
1691	"UUCCUUGGGUGGCGAGCG 18 B+10 57 20 1 66.7 60.0 CGCUCGCCACCCAAGGAA \| - - - - - - - - - - - - - - - - - - - -\n"
1692	"UUUCUCGGGUGGCGAGCG 18 B+10 57 20 1 66.7 60.0 CGCUCGCCACCCGAGAAA \| - - - - - - - - - - - - - - - - - - - -\n"
1693	"UCCUUGGGUGGCGAGCGG 18 B+11 58 20 1 72.2 62.0 CCGCUCGCCACCCAAGGA \| - - - - - - - - - - - - - - - - - - - -\n"
1694	"UUCUCGGGUGGCGAGCGG 18 B+11 58 20 1 72.2 62.0 CCGCUCGCCACCCGAGAA \| - - - - - - - - - - - - - - - - - - - -\n"
1695	"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"
1696	"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";
1697
1698	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1699	}
1700
1701	// design MANY probes to test location specifier
1702	{
1703	const char *arguments_loc[] = {
1704	"prgnamefake",
1705	// "designnames=Stsssola#Stsssola", // @@@ crashes the ptserver
1706	"designnames=CPPParap#PsAAAA00",
1707	"designmintargets=50", // hit at least 1 of the 2 targets
1708	"designmingc=0", "designmaxgc=100", // allow all GCs
1709	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1710	"designmishit=7", // allow enough outgroup hits
1711	"designprobelength=9",
1712	};
1713
1714	const char *expected_loc =
1715	"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";
1716
1717	TEST_ARB_PROBE_FILT(ARRAY_ELEMS(arguments_loc), arguments_loc, extract_locations, expected_loc);
1718	}
1719
1720	// same as above
1721	{
1722	const char *arguments[] = {
1723	"prgnamefake",
1724	"designnames=CPPParap#PsAAAA00",
1725	"designmintargets=50", // hit at least 1 of the 2 targets
1726	"designmingc=0", "designmaxgc=100", // allow all GCs
1727	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1728	"designmishit=7", // allow enough outgroup hits
1729	"designprobelength=9",
1730	};
1731
1732	const char *expected =
1733	"Probe design parameters:\n"
1734	"Length of probe 9\n"
1735	"Temperature [30.0 -100.0]\n"
1736	"GC-content [ 0.0 -100.0]\n"
1737	"E.Coli position [any]\n"
1738	"Max. nongroup hits 7 (lowest rejected nongroup hits: 9)\n"
1739	"Min. group hits 50%\n"
1740	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1741	"GAGCGGAUG 9 A= 29 24 20 1 66.7 30.0 CAUCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1742	"UGCUCCUGG 9 B= 51 46 20 1 66.7 30.0 CCAGGAGCA \| - - - - - - - - - - - - - - - - - - - -\n"
1743	"GCUCCUGGA 9 B+ 1 47 20 1 66.7 30.0 UCCAGGAGC \| - - - - - - - - - - - - - - - - - - - -\n"
1744	"CGGGCGCUA 9 C= 99 87 20 1 77.8 32.0 UAGCGCCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1745	"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"
1746	"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"
1747	"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"
1748	"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"
1749	"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"
1750	"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"
1751	"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"
1752	"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"
1753	"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"
1754	"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"
1755	"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"
1756	"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"
1757	"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"
1758	"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"
1759	"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"
1760	"GGAAACGGG 9 C- 5 82 17 1 66.7 30.0 CCCGUUUCC \| - - - - - - - - - - - - - - - - 3 3 3 3\n"
1761	"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"
1762	"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"
1763	"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"
1764	"GGACGUCCG 9 E+ 6 74 14 1 77.8 32.0 CGGACGUCC \| - - - - - - - - - - - - - 1 1 1 1 3 3 3\n"
1765	"GACGUCCGG 9 E+ 7 75 14 1 77.8 32.0 CCGGACGUC \| - - - - - - - - - - - - - 1 1 1 1 2 2 14\n"
1766	"ACGUCCGGA 9 E+ 8 76 14 1 66.7 30.0 UCCGGACGU \| - - - - - - - - - - - - - 1 1 11 11 12 12 17\n"
1767	"CGUCCGGAA 9 G= 89 77 14 1 66.7 30.0 UUCCGGACG \| - - - - - - - - - - - - - 1 1 1 1 2 2 2\n"
1768	"AACGGGCGC 9 C- 2 85 14 1 77.8 32.0 GCGCCCGUU \| - - - - - - - - - - - - - 1 1 1 1 1 1 2\n"
1769	"CGAGCGGAU 9 A- 1 23 13 1 66.7 30.0 AUCCGCUCG \| - - - - - - - - - - - - 3 3 3 3 3 3 3 3\n"
1770	"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"
1771	"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"
1772	"ACGGGCGCU 9 C- 1 86 12 1 77.8 32.0 AGCGCCCGU \| - - - - - - - - - - - 1 1 1 1 1 1 2 2 2\n"
1773	"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"
1774	"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"
1775	"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"
1776	"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"
1777	"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"
1778	"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"
1779	"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"
1780	"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"
1781	"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"
1782	"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"
1783	"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"
1784	"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"
1785	"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"
1786	"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"
1787	"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"
1788	"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"
1789	"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"
1790	"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"
1791	"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"
1792	"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"
1793	"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";
1794
1795	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1796	}
1797
1798	#if defined(ARB_64)
1799	#define RES_64
1800	#else // !defined(ARB_64)
1801	// results below differ for some(!) 32 bit arb versions (numeric issues?)
1802	// (e.g. u1004 behaves like 64bit version; u1204 doesnt in NDEBUG mode)
1803	// #define RES_64 // uncomment for u1004
1804	#if defined(DEBUG)
1805	#define RES_64
1806	#endif
1807
1808	#endif
1809
1810
1811	// same as above (with probelen == 8)
1812	{
1813	const char *arguments[] = {
1814	"prgnamefake",
1815	"designnames=CPPParap#PsAAAA00",
1816	"designmintargets=50", // hit at least 1 of the 2 targets
1817	"designmingc=0", "designmaxgc=100", // allow all GCs
1818	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1819	// "designmishit=7",
1820	"designmishit=15", // @@@ reports more results than with 7 mishits, but no mishits reported below!
1821	"designprobelength=8",
1822	};
1823
1824	const char *expected =
1825	"Probe design parameters:\n"
1826	"Length of probe 8\n"
1827	"Temperature [30.0 -100.0]\n"
1828	"GC-content [ 0.0 -100.0]\n"
1829	"E.Coli position [any]\n"
1830	"Max. nongroup hits 15\n"
1831	"Min. group hits 50%\n"
1832	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1833	"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"
1834	"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"
1835	"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"
1836	"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"
1837	"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"
1838	"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"
1839	"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"
1840	"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"
1841	#if defined(RES_64)
1842	"ACGGGCGC 8 B=98 86 13 1 87.5 30.0 GCGCCCGU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1843	"CGGGCGCU 8 B+ 1 87 13 1 87.5 30.0 AGCGCCCG \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1844	"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";
1845	#else // !defined(RES_64)
1846	"ACGGGCGC 8 B=98 86 13 1 87.5 30.0 GCGCCCGU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 2\n"
1847	"CGGGCGCU 8 B+ 1 87 13 1 87.5 30.0 AGCGCCCG \| - - - - - - - - - - - - 1 1 1 1 1 1 1 2\n"
1848	"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";
1849	#endif
1850
1851	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1852	}
1853
1854	// same as above (but restricting ecoli-range)
1855	{
1856	const char *arguments[] = {
1857	"prgnamefake",
1858	"designnames=CPPParap#PsAAAA00",
1859	"designmintargets=50", // hit at least 1 of the 2 targets
1860	"designmingc=0", "designmaxgc=100", // allow all GCs
1861	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1862	"designmishit=15",
1863	"designprobelength=8",
1864	"designminpos=65", "designmaxpos=69", // restrict ecoli-range
1865	};
1866
1867	const char *expected =
1868	"Probe design parameters:\n"
1869	"Length of probe 8\n"
1870	"Temperature [30.0 -100.0]\n"
1871	"GC-content [ 0.0 -100.0]\n"
1872	"E.Coli position [ 65 - 69]\n"
1873	"Max. nongroup hits 15\n"
1874	"Min. group hits 50%\n"
1875	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1876	"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"
1877	"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"
1878	"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"
1879	"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"
1880	"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";
1881
1882	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1883	}
1884
1885	{
1886	const char *arguments[] = {
1887	"prgnamefake",
1888	"designnames=ClnCorin#CPPParap#ClfPerfr",
1889	"designprobelength=16",
1890	"designmintargets=100",
1891	"designmishit=2",
1892	};
1893	const char *expected =
1894	"Probe design parameters:\n"
1895	"Length of probe 16\n"
1896	"Temperature [ 0.0 -400.0]\n"
1897	"GC-content [30.0 - 80.0]\n"
1898	"E.Coli position [any]\n"
1899	"Max. nongroup hits 2 (lowest rejected nongroup hits: 6)\n"
1900	"Min. group hits 100% (max. rejected coverage: 67%)\n"
1901	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1902	"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"
1903	"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"
1904	"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"
1905	"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"
1906	"GUCGAGCGAUGAAGUU 16 B+ 2 21 31 3 50.0 48.0 AACUUCAUCGCUCGAC \| - - - - - - - - - - 1 1 1 1 1 1 1 1 1 1\n"
1907	"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"
1908	"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"
1909	"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"
1910	"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"
1911	"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";
1912
1913	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1914	}
1915	// test same design as above, but add 2 "unknown species" each of which is missing one of the previously designed probes
1916	{
1917	const char *arguments[] = {
1918	"prgnamefake",
1919	"designnames=ClnCorin#Unknown1#CPPParap#ClfPerfr#Unknown2",
1920	"designprobelength=16",
1921	"designmintargets=100",
1922	"designmishit=2",
1923	// pass sequences for the unknown species
1924	"designsequence=---CGAAAGGAAGAUUAAU------------------AAGUCGAGCGAUGAAG-CAAGUCGAGCGAUGAA-GUCGAGCGAUGAAGUU-UCAAGUCGAGCGAUGA-AGUCGAGCGAUGAAGU-AUCAAGUCGAGCGAUG-GAUCAAGUCGAGCGAU-UGAUCAAGUCGAGCGA",
1925	"designsequence=---CGAAAGGAAGAUUAAU-AAGGAAGAUUAAUACC-AAGUCGAGCGAUGAAG-CAAGUCGAGCGAUGAA-GUCGAGCGAUGAAGUU-UCAAGUCGAGCGAUGA-AGUCGAGCGAUGAAGU-AUCAAGUCGAGCGAUG------------------UGAUCAAGUCGAGCGA",
1926	};
1927	const char *expected =
1928	"Probe design parameters:\n"
1929	"Length of probe 16\n"
1930	"Temperature [ 0.0 -400.0]\n"
1931	"GC-content [30.0 - 80.0]\n"
1932	"E.Coli position [any]\n"
1933	"Max. nongroup hits 2\n"
1934	"Min. group hits 100% (max. rejected coverage: 80%)\n"
1935	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1936	"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"
1937	// AAGGAAGAUUAAUACC is not designed here
1938	"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"
1939	"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"
1940	"GUCGAGCGAUGAAGUU 16 B+ 2 21 51 5 50.0 48.0 AACUUCAUCGCUCGAC \| - - - - - - - - - - 1 1 1 1 1 1 1 1 1 1\n"
1941	"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"
1942	"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"
1943	"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"
1944	// GAUCAAGUCGAGCGAU is not designed here
1945	"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";
1946
1947	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1948	}
1949	{
1950	const char *arguments[] = {
1951	"prgnamefake",
1952	"designnames=VbrFurni",
1953	"designprobelength=8",
1954	"designmingc=80",
1955	"designmaxgc=100",
1956	};
1957	const char *expected =
1958	"Probe design parameters:\n"
1959	"Length of probe 8\n"
1960	"Temperature [ 0.0 -400.0]\n"
1961	"GC-content [80.0 -100.0]\n"
1962	"E.Coli position [any]\n"
1963	"Max. nongroup hits 0 (lowest rejected nongroup hits: 2)\n"
1964	"Min. group hits 50%\n"
1965	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1966	#if defined(RES_64)
1967	"CGGCAGCG 8 A=28 23 20 1 87.5 30.0 CGCUGCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1968	#else // !defined(RES_64)
1969	"CGGCAGCG 8 A=28 23 20 1 87.5 30.0 CGCUGCCG \| - - - - - - - - - - - - - - - - - - - 3\n"
1970	#endif
1971	"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"
1972	#if defined(RES_64)
1973	"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"
1974	#else // !defined(RES_64)
1975	"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"
1976	#endif
1977	"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"
1978	"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"
1979	"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";
1980
1981	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1982	}
1983	{
1984	const char *arguments[] = {
1985	"prgnamefake",
1986	"designnames=HllHalod#VbhChole#VblVulni#VbrFurni#PtVVVulg",
1987	"designprobelength=14",
1988	"designmintargets=100",
1989	"designmishit=4",
1990	"designmingc=70",
1991	"designmaxgc=100",
1992	};
1993	const char *expected =
1994	"Probe design parameters:\n"
1995	"Length of probe 14\n"
1996	"Temperature [ 0.0 -400.0]\n"
1997	"GC-content [70.0 -100.0]\n"
1998	"E.Coli position [any]\n"
1999	"Max. nongroup hits 4\n"
2000	"Min. group hits 100% (max. rejected coverage: 80%)\n"
2001	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
2002	"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"
2003	"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"
2004	"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";
2005
2006	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2007	}
2008	{
2009	const char *arguments[] = {
2010	"prgnamefake",
2011	"designnames=HllHalod#VbhChole#VblVulni#VbrFurni#PtVVVulg",
2012	"designprobelength=14",
2013	"designmintargets=100",
2014	"designmishit=0",
2015	"designmingc=51",
2016	"designmaxgc=60",
2017	};
2018	const char *expected = ""; // no probes found!
2019
2020	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2021	}
2022
2023	}
2024
2025	void TEST_SLOW_probe_design_errors() {
2026	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2027
2028	bool use_gene_ptserver = false;
2029	{
2030	const char *arguments[] = {
2031	"prgnamefake",
2032	"designnames=CPPParap#PsAAAA00",
2033	"designprobelength=3",
2034	};
2035	const char *expected_error = "Specified min. probe length 3 is below the min. allowed probe length of 8";
2036
2037	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2038	}
2039	{
2040	const char *arguments[] = {
2041	"prgnamefake",
2042	"designnames=CPPParap#PsAAAA00",
2043	"designprobelength=15",
2044	"designmaxprobelength=12",
2045	};
2046	const char *expected_error = "Max. probe length 12 is below the specified min. probe length of 15";
2047
2048	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2049	}
2050	{
2051	const char *expected_error = "Sequence contains only 0 bp. Impossible design request for one of the added sequences";
2052	{
2053	const char *arguments[] = {
2054	"prgnamefake",
2055	"designsequence=", // pass an empty sequence
2056	"designprobelength=16",
2057	};
2058	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2059	}
2060	{
2061	const char *arguments[] = {
2062	"prgnamefake",
2063	"designsequence=-------------", // pass a gap-only sequence
2064	"designprobelength=16",
2065	};
2066	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2067	}
2068	}
2069	{
2070	const char *arguments[] = {
2071	"prgnamefake",
2072	"designsequence=ACGTACGTACGTACGT", // pass a long enough (unexpected) sequence
2073	"designprobelength=16",
2074	};
2075	const char *expected_error = "Got 0 unknown marked species, but 1 custom sequence was added (has to match)";
2076	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2077	}
2078	{
2079	const char *arguments[] = {
2080	"prgnamefake",
2081	"designnames=Unknown", // one unknown species
2082	"designprobelength=16",
2083	};
2084	const char *expected_error = "No species marked - no probes designed";
2085	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2086	}
2087	{
2088	const char *arguments[] = {
2089	"prgnamefake",
2090	"designnames=Unknown#CPPParap", // one unknown species, one known species
2091	"designprobelength=16",
2092	};
2093	const char *expected_error = "Got 1 unknown marked species, but 0 custom sequences were added (has to match)";
2094	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2095	}
2096	{
2097	const char *expected_error = "Sequence contains only 0 bp. Impossible design request for one of the added sequences";
2098	{
2099	const char *arguments[] = {
2100	"prgnamefake",
2101	"designnames=Unknown", // one unknown species
2102	"designsequence=", // pass an empty sequence
2103	"designprobelength=16",
2104	};
2105	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2106	}
2107	{
2108	const char *arguments[] = {
2109	"prgnamefake",
2110	"designnames=Unknown", // one unknown species
2111	"designsequence=-------------", // pass a gap-only sequence
2112	"designprobelength=16",
2113	};
2114	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2115	}
2116	}
2117	}
2118
2119	void TEST_SLOW_match_designed_probe() {
2120	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2121
2122	bool use_gene_ptserver = false;
2123	const char *arguments[] = {
2124	"prgnamefake",
2125	"matchsequence=UCAAGUCGAGCGAUGAAG",
2126	};
2127	CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UCAAGUCGAGCGAUGAAG'\1"
2128	"ClnCorin\1" " ClnCorin 0 0 0.0 18 17 0 .GAGUUUGA-==================-UUCCUUCGG\1"
2129	"CltBotul\1" " CltBotul 0 0 0.0 18 17 0 ........A-==================-CUUCUUCGG\1"
2130	"CPPParap\1" " CPPParap 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUCCUUCGG\1"
2131	"ClfPerfr\1" " ClfPerfr 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUUCCUUCG\1";
2132
2133	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2134	}
2135
2136	void TEST_SLOW_get_existing_probes() {
2137	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2138
2139	bool use_gene_ptserver = false;
2140	{
2141	const char *arguments[] = {
2142	"prgnamefake",
2143	"iterate=20",
2144	"iterate_amount=10",
2145	};
2146	CCP expected =
2147	"AAACCGGGGCTAATACCGGA;AAACGACTGTTAATACCGCA;AAACGATGGAAGCTTGCTTC;AAACGATGGCTAATACCGCA;AAACGGATTAGCGGCGGGAC;"
2148	"AAACGGGCGCTAATACCGCA;AAACGGTCGCTAATACCGGA;AAACGGTGGCTAATACCGCA;AAACGTACGCTAATACCGCA;AAACTCAAGCTAATACCGCA";
2149
2150	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2151	}
2152	{
2153	const char *arguments[] = {
2154	"prgnamefake",
2155	"iterate=15",
2156	"iterate_amount=20",
2157	"iterate_separator=:",
2158	};
2159	CCP expected =
2160	"AAACCGGGGCTAATA:AAACGACTGTTAATA:AAACGATGGAAGCTT:AAACGATGGCTAATA:AAACGGATTAGCGGC:AAACGGGCGCTAATA:AAACGGTCGCTAATA:"
2161	"AAACGGTGGCTAATA:AAACGTACGCTAATA:AAACTCAAGCTAATA:AAACTCAGGCTAATA:AAACTGGAGAGTTTG:AAACTGTAGCTAATA:AAACTTGTTTCTCGG:"
2162	"AAAGAGGTGCTAATA:AAAGCTTGCTTTCTT:AAAGGAACGCTAATA:AAAGGAAGATTAATA:AAAGGACAGCTAATA:AAAGGGACTTCGGTC";
2163
2164	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2165	}
2166	{
2167	const char *arguments[] = {
2168	"prgnamefake",
2169	"iterate=10",
2170	"iterate_amount=5",
2171	"iterate_readable=0",
2172	};
2173	CCP expected =
2174	"\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";
2175
2176	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2177	}
2178	{
2179	const char *arguments[] = {
2180	"prgnamefake",
2181	"iterate=3",
2182	"iterate_amount=70",
2183	"iterate_tu=U",
2184	};
2185	CCP expected =
2186	"AAA;AAC;AAG;AAU;ACA;ACC;ACG;ACU;AGA;AGC;AGG;AGU;AUA;AUC;AUG;AUU;"
2187	"CAA;CAC;CAG;CAU;CCA;CCC;CCG;CCU;CGA;CGC;CGG;CGU;CUA;CUC;CUG;CUU;"
2188	"GAA;GAC;GAG;GAU;GCA;GCC;GCG;GCU;GGA;GGC;GGG;GGU;GUA;GUC;GUG;GUU;"
2189	"UAA;UAC;UAG;UAU;UCA;UCC;UCG;UCU;UGA;UGC;UGG;UGU;UUA;UUC;UUG;UUU";
2190
2191	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2192	}
2193	{
2194	const char *arguments[] = {
2195	"prgnamefake",
2196	"iterate=2",
2197	"iterate_amount=20",
2198	};
2199	CCP expected =
2200	"AA;AC;AG;AT;"
2201	"CA;CC;CG;CT;"
2202	"GA;GC;GG;GT;"
2203	"TA;TC;TG;TT";
2204
2205	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2206	}
2207	}
2208
2209	// #define TEST_AUTO_UPDATE // uncomment to auto-update expected index dumps
2210
2211	void TEST_SLOW_index_dump() {
2212	for (int use_gene_ptserver = 0; use_gene_ptserver <= 1; use_gene_ptserver++) {
2213	const char *dumpfile = use_gene_ptserver ? "index_gpt.dump" : "index_pt.dump";
2214	char *dumpfile_exp = GBS_global_string_copy("%s.expected", dumpfile);
2215
2216	const char *arguments[] = {
2217	"prgnamefake",
2218	GBS_global_string_copy("dump=%s", dumpfile),
2219	};
2220	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, "ok");
2221
2222	#if defined(TEST_AUTO_UPDATE)
2223	TEST_COPY_FILE(dumpfile, dumpfile_exp);
2224	#else // !defined(TEST_AUTO_UPDATE)
2225	TEST_EXPECT_TEXTFILES_EQUAL(dumpfile_exp, dumpfile);
2226	#endif
2227	TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(dumpfile));
2228
2229	free((char*)arguments[1]);
2230	free(dumpfile_exp);
2231	}
2232	}
2233
2234	#undef TEST_AUTO_UPDATE
2235
2236	// --------------------------------------------------------------------------------
2237
2238	#include <arb_strarray.h>
2239	#include <set>
2240	#include <iterator>
2241
2242	using namespace std;
2243
2244	typedef set<string> Matches;
2245
2246	inline void parseMatches(char*& answer, Matches& matches) {
2247	ConstStrArray match_results;
2248
2249	GBT_splitNdestroy_string(match_results, answer, "\1", false);
2250
2251	for (size_t i = 1; i<match_results.size(); i += 2) {
2252	if (match_results[i][0]) {
2253	matches.insert(match_results[i]);
2254	}
2255	}
2256	}
2257
2258	inline void getMatches(const char *probe, Matches& matches) {
2259	bool use_gene_ptserver = false;
2260	char *matchseq = GBS_global_string_copy("matchsequence=%s", probe);
2261	const char *arguments[] = {
2262	"prgnamefake",
2263	matchseq,
2264	};
2265	TEST_RUN_ARB_PROBE(ARRAY_ELEMS(arguments), arguments);
2266	parseMatches(answer, matches);
2267	free(matchseq);
2268	}
2269
2270	inline string matches2hitlist(const Matches& matches) {
2271	string hitlist;
2272	if (!matches.empty()) {
2273	for (Matches::const_iterator m = matches.begin(); m != matches.end(); ++m) {
2274	hitlist = hitlist + ',' + *m;
2275	}
2276	hitlist = hitlist.substr(1);
2277	}
2278	return hitlist;
2279	}
2280
2281	inline void extract_first_but_not_second(const Matches& first, const Matches& second, Matches& result) {
2282	set_difference(first.begin(), first.end(),
2283	second.begin(), second.end(),
2284	inserter(result, result.begin()));
2285	}
2286
2287	// --------------------------------------------------------------------------------
2288
2289	// #define TEST_INDEX_COMPLETENESS // only uncomment temporarily (slow as hell)
2290
2291	#if defined(TEST_INDEX_COMPLETENESS)
2292
2293	void TEST_SLOW_find_unmatched_probes() {
2294	bool use_gene_ptserver = false;
2295
2296	// get all 20mers indexed in ptserver:
2297	ConstStrArray fullProbes;
2298	{
2299	const char *arguments[] = {
2300	"prgnamefake",
2301	"iterate=20",
2302	"iterate_amount=1000000",
2303	"iterate_tu=U",
2304	};
2305	TEST_RUN_ARB_PROBE(ARRAY_ELEMS(arguments), arguments);
2306
2307	GBT_splitNdestroy_string(fullProbes, answer, ";", false);
2308	TEST_EXPECT_EQUAL(fullProbes.size(), 2040);
2309	}
2310
2311	for (size_t lp = 0; lp<fullProbes.size(); ++lp) { // with all 20mers existing in ptserver
2312	const char *fullProbe = fullProbes[lp];
2313
2314	size_t fullLen = strlen(fullProbe);
2315	TEST_EXPECT_EQUAL(fullLen, 20);
2316
2317	Matches fullHits;
2318	getMatches(fullProbe, fullHits);
2319	TEST_EXPECT(fullHits.size()>0);
2320
2321	bool fewerHitsSeen = false;
2322
2323	for (size_t subLen = fullLen-1; !fewerHitsSeen && subLen >= 10; --subLen) { // for each partial sub-probe of 20mer
2324	char subProbe[20];
2325	subProbe[subLen] = 0;
2326
2327	for (size_t pos = 0; pos+subLen <= fullLen; ++pos) {
2328	Matches subHits, onlyFull;
2329
2330	memcpy(subProbe, fullProbe+pos, subLen);
2331	getMatches(subProbe, subHits);
2332	extract_first_but_not_second(fullHits, subHits, onlyFull);
2333
2334	if (!onlyFull.empty()) {
2335	fprintf(stderr, "TEST_PARTIAL_COVERS_FULL_PROBE__BROKEN(\"%s\", \"%s\");\n", subProbe, fullProbe);
2336	fewerHitsSeen = true; // only list first wrong hit for each fullProbe
2337	}
2338	}
2339	}
2340	}
2341	}
2342
2343	#endif
2344	// --------------------------------------------------------------------------------
2345
2346	static arb_test::match_expectation partial_covers_full_probe(const char part, const char full) {
2347	using namespace arb_test;
2348	using namespace std;
2349
2350	expectation_group expected;
2351	expected.add(that(strstr(full, part)).does_differ_from_NULL());
2352	expected.add(that(strlen(part)).is_less_than(strlen(full)));
2353
2354	{
2355	Matches matchFull, matchPart;
2356	getMatches(full, matchFull);
2357	getMatches(part, matchPart);
2358
2359	expected.add(that(matchFull.empty()).is_equal_to(false));
2360
2361	Matches onlyFirst;
2362	extract_first_but_not_second(matchFull, matchPart, onlyFirst);
2363
2364	string only_hit_by_full = matches2hitlist(onlyFirst);
2365	expected.add(that(only_hit_by_full).is_equal_to(""));
2366	}
2367
2368
2369	return all().ofgroup(expected);
2370	}
2371
2372	#define TEST_PARTIAL_COVERS_FULL_PROBE(part,full) TEST_EXPECTATION(partial_covers_full_probe(part, full))
2373	#define TEST_PARTIAL_COVERS_FULL_PROBE__BROKEN(part,full) TEST_EXPECTATION__BROKEN(partial_covers_full_probe(part, full))
2374
2375	void TEST_SLOW_unmatched_probes() {
2376	TEST_PARTIAL_COVERS_FULL_PROBE("CCUCCUUUCU", "GAUUAAUACCCCUCCUUUCU");
2377
2378	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUC", "GGGGAACCUGCGGUUGGAUC");
2379	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCA", "GGGAACCUGCGGUUGGAUCA");
2380	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCAC", "GGAACCUGCGGUUGGAUCAC");
2381	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACC", "GAACCUGCGGUUGGAUCACC");
2382	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCU", "AACCUGCGGUUGGAUCACCU");
2383	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUC", "ACCUGCGGUUGGAUCACCUC");
2384	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCC", "CCUGCGGUUGGAUCACCUCC");
2385	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCU", "CUGCGGUUGGAUCACCUCCU");
2386	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCUU", "UGCGGUUGGAUCACCUCCUU");
2387	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCUUA", "GCGGUUGGAUCACCUCCUUA");
2388
2389	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUC", "GGGGAACCUGGCGCUGGAUC");
2390	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCA", "GGGAACCUGGCGCUGGAUCA");
2391	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCAC", "GGAACCUGGCGCUGGAUCAC");
2392	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACC", "GAACCUGGCGCUGGAUCACC");
2393	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCU", "AACCUGGCGCUGGAUCACCU");
2394	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUC", "ACCUGGCGCUGGAUCACCUC");
2395	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCC", "CCUGGCGCUGGAUCACCUCC");
2396	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCU", "CUGGCGCUGGAUCACCUCCU");
2397	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCUU", "UGGCGCUGGAUCACCUCCUU");
2398	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCUUU", "GGCGCUGGAUCACCUCCUUU");
2399
2400	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCAC", "GGAACCUGCGGCUGGAUCAC");
2401	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACC", "GAACCUGCGGCUGGAUCACC");
2402	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCU", "AACCUGCGGCUGGAUCACCU");
2403	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUC", "ACCUGCGGCUGGAUCACCUC");
2404	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCC", "CCUGCGGCUGGAUCACCUCC");
2405	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCU", "CUGCGGCUGGAUCACCUCCU");
2406	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUU", "UGCGGCUGGAUCACCUCCUU");
2407	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUUU", "GCGGCUGGAUCACCUCCUUU");
2408	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUUUC", "CGGCUGGAUCACCUCCUUUC");
2409
2410	// the data of the following tests is located right in front of the dots inserted in [8962]
2411	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAG", "AAUUGAAGAGUUUGAUCAAG");
2412	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGU", "AUUGAAGAGUUUGAUCAAGU");
2413	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUC", "UUGAAGAGUUUGAUCAAGUC");
2414	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCG", "UGAAGAGUUUGAUCAAGUCG");
2415	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGA", "GAAGAGUUUGAUCAAGUCGA");
2416	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAG", "AAGAGUUUGAUCAAGUCGAG");
2417	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGC", "AGAGUUUGAUCAAGUCGAGC");
2418	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCG", "GAGUUUGAUCAAGUCGAGCG");
2419	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCGG", "AGUUUGAUCAAGUCGAGCGG");
2420	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCGGU", "GUUUGAUCAAGUCGAGCGGU");
2421	}
2422
2423	void TEST_SLOW_variable_defaults_in_server() {
2424	test_setup(false);
2425
2426	const char *server_tag = GBS_ptserver_tag(TEST_SERVER_ID);
2427	TEST_EXPECT_NO_ERROR(arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag));
2428
2429	const char *servername = GBS_read_arb_tcp(server_tag);
2430	{
2431	char *socketname = GBS_global_string_copy(":%s", GB_path_in_ARBHOME("UNIT_TESTER/sok/pt.socket"));
2432	TEST_EXPECT_EQUAL(servername, socketname); // as defined in ../lib/arb_tcp_org.dat@ARB_TEST_PT_SERVER
2433	free(socketname);
2434	}
2435
2436	T_PT_MAIN com;
2437	T_PT_LOCS locs;
2438	GB_ERROR error = NULp;
2439	aisc_com *link = aisc_open(servername, com, AISC_MAGIC_NUMBER, &error);
2440	TEST_EXPECT_NO_ERROR(error);
2441	TEST_REJECT_NULL(link);
2442
2443	TEST_EXPECT_ZERO(aisc_create(link, PT_MAIN, com,
2444	MAIN_LOCS, PT_LOCS, locs,
2445	NULp));
2446
2447	{
2448	#define LOCAL(rvar) prev_read_##rvar
2449
2450
2451	#define FREE_LOCAL_long(rvar)
2452	#define FREE_LOCAL_charp(rvar) free(LOCAL(rvar))
2453	#define FREE_LOCAL(type,rvar) FREE_LOCAL_##type(rvar)
2454
2455	#define TEST__READ(type,rvar,expected) \
2456	do { \
2457	TEST_EXPECT_ZERO(aisc_get(link, PT_LOCS, locs, rvar, &(LOCAL(rvar)), NULp)); \
2458	TEST_EXPECT_EQUAL(LOCAL(rvar), expected); \
2459	FREE_LOCAL(type,rvar); \
2460	} while(0)
2461	#define TEST_WRITE(type,rvar,val) \
2462	TEST_EXPECT_ZERO(aisc_put(link, PT_LOCS, locs, rvar, (type)val, NULp))
2463	#define TEST_CHANGE(type,rvar,val) \
2464	do { \
2465	TEST_WRITE(type, rvar, val); \
2466	TEST__READ(type, rvar, val); \
2467	} while(0)
2468	#define TEST_DEFAULT_CHANGE(ctype,type,remote_variable,default_value,other_value) \
2469	do { \
2470	ctype DEFAULT_VALUE = default_value; \
2471	ctype OTHER_VALUE = other_value; \
2472	type LOCAL(remote_variable); \
2473	TEST__READ(type, remote_variable, DEFAULT_VALUE); \
2474	TEST_CHANGE(type, remote_variable, OTHER_VALUE); \
2475	TEST_CHANGE(type, remote_variable, DEFAULT_VALUE); \
2476	} while(0)
2477
2478	TEST_DEFAULT_CHANGE(const long, long, LOCS_MATCH_ALSO_REVCOMP, 1, 67);
2479	typedef char *charp;
2480	typedef const char *ccharp;
2481	TEST_DEFAULT_CHANGE(ccharp, charp, LOCS_LOGINTIME, "notime", "sometime");
2482	}
2483
2484	TEST_EXPECT_ZERO(aisc_close(link, com));
2485	link = NULp;
2486	}
2487
2488	#endif // UNIT_TESTS

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