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source: branches/profile/TOOLS/arb_probe.cxx

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Last change on this file was 12398, checked in by westram, 10 years ago
GBS_read_arb_tcp() handle exported errors at callers changed error message to 'No such entry' related to [12396]
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 130.8 KB

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

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