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source: tags/arb-6.0/TOOLS/arb_probe.cxx

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Last change on this file was 11889, checked in by westram, 12 years ago
add missing comment to closing #endif of test-sections
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 130.4 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	const char *server_tag = GBS_ptserver_tag(P.SERVERID);
100
101	error = arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag);
102	if (error) return NULL;
103
104	return GBS_read_arb_tcp(server_tag);
105	}
106
107	class PTserverConnection {
108	static int count;
109	bool need_close;
110	public:
111	PTserverConnection(ARB_ERROR& error)
112	: need_close(false)
113	{
114	if (count) {
115	error = "Only 1 PTserverConnection allowed";
116	}
117	else {
118	++count;
119	const char *servername = AP_probe_pt_look_for_server(error);
120	if (servername) {
121	GB_ERROR openerr = NULL;
122	pd_gl.link = aisc_open(servername, pd_gl.com, AISC_MAGIC_NUMBER, &openerr);
123	if (openerr) {
124	error = openerr;
125	}
126	else {
127	if (!pd_gl.link) {
128	error = "Cannot contact PT_SERVER [1]";
129	}
130	else if (init_local_com_struct()) {
131	error = "Cannot contact PT_SERVER [2]";
132	}
133	else {
134	need_close = true;
135	}
136	}
137	}
138	}
139	}
140	~PTserverConnection() {
141	if (need_close) {
142	aisc_close(pd_gl.link, pd_gl.com);
143	pd_gl.link = 0;
144	}
145	--count;
146	}
147	};
148	int PTserverConnection::count = 0;
149
150	static char *AP_dump_index_event(ARB_ERROR& error) {
151	PTserverConnection contact(error);
152
153	char *result = NULL;
154	if (!error) {
155	aisc_put(pd_gl.link, PT_MAIN, pd_gl.com,
156	MAIN_DUMP_NAME, P.DUMP,
157	NULL);
158
159	if (aisc_get(pd_gl.link, PT_MAIN, pd_gl.com,
160	MAIN_DUMP_INDEX, &result,
161	NULL)) {
162	error = "Connection to PT_SERVER lost (1)";
163	}
164	else {
165	result = strdup("ok");
166	}
167	}
168	return result;
169	}
170
171	static char *AP_probe_iterate_event(ARB_ERROR& error) {
172	PTserverConnection contact(error);
173
174	char *result = NULL;
175	if (!error) {
176	T_PT_PEP pep;
177	int length = P.ITERATE;
178
179	if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs,
180	LOCS_PROBE_FIND_CONFIG, PT_PEP, pep,
181	PEP_PLENGTH, (long)length,
182	PEP_RESTART, (long)1,
183	PEP_READABLE, (long)P.ITERATE_READABLE,
184	PEP_TU, (long)P.ITERATE_TU[0],
185	PEP_SEPARATOR, (long)P.ITERATE_SEPARATOR[0],
186	NULL))
187	{
188	error = "Connection to PT_SERVER lost (1)";
189	}
190
191	if (!error) {
192	int amount = P.ITERATE_AMOUNT;
193	int amount_per_call = AISC_MAX_STRING_LEN/(length+2);
194
195	GBS_strstruct out(50000);
196	bool first = true;
197
198	while (amount && !error) {
199	int this_amount = std::min(amount, amount_per_call);
200
201	aisc_put(pd_gl.link, PT_PEP, pep,
202	PEP_NUMGET, (long)this_amount,
203	PEP_FIND_PROBES, 0,
204	NULL);
205
206	char *pep_result = 0;
207	if (aisc_get(pd_gl.link, PT_PEP, pep,
208	PEP_RESULT, &pep_result,
209	NULL)) {
210	error = "Connection to PT_SERVER lost (2)";
211	}
212
213	if (!error) {
214	if (pep_result[0]) {
215	if (first) first = false;
216	else out.put(P.ITERATE_SEPARATOR[0]);
217
218	out.cat(pep_result);
219	amount -= this_amount;
220	}
221	else {
222	amount = 0; // terminate loop
223	}
224	}
225	free(pep_result);
226	}
227
228	if (!error) {
229	result = out.release();
230	}
231	}
232	}
233
234	if (error) freenull(result);
235	return result;
236	}
237
238	static char *AP_probe_design_event(ARB_ERROR& error) {
239	PTserverConnection contact(error);
240
241	if (!error) {
242	bytestring bs;
243	bs.data = (char*)(P.DESIGNNAMES);
244	bs.size = strlen(bs.data)+1;
245
246	T_PT_PDC pdc;
247	if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs,
248	LOCS_PROBE_DESIGN_CONFIG, PT_PDC, pdc,
249	PDC_MIN_PROBELEN, (long)P.DESIGNPROBELEN,
250	PDC_MAX_PROBELEN, (long)P.DESIGNMAXPROBELEN,
251	PDC_MINTEMP, (double)P.MINTEMP,
252	PDC_MAXTEMP, (double)P.MAXTEMP,
253	PDC_MINGC, P.MINGC/100.0,
254	PDC_MAXGC, P.MAXGC/100.0,
255	PDC_MAXBOND, (double)P.MAXBOND,
256	PDC_MIN_ECOLIPOS, (long)P.MINPOS,
257	PDC_MAX_ECOLIPOS, (long)P.MAXPOS,
258	PDC_MISHIT, (long)P.MISHIT,
259	PDC_MINTARGETS, P.MINTARGETS/100.0,
260	PDC_CLIPRESULT, (long)P.DESIGNCLIPOUTPUT,
261	NULL))
262	{
263	error = "Connection to PT_SERVER lost (1)";
264	}
265
266	if (!error) {
267	for (apd_sequence *s = P.sequence; s; ) {
268	apd_sequence *next = s->next;
269
270	bytestring bs_seq;
271	T_PT_SEQUENCE pts;
272
273	bs_seq.data = (char*)s->sequence;
274	bs_seq.size = strlen(bs_seq.data)+1;
275	aisc_create(pd_gl.link, PT_PDC, pdc,
276	PDC_SEQUENCE, PT_SEQUENCE, pts,
277	SEQUENCE_SEQUENCE, &bs_seq,
278	NULL);
279
280	delete s;
281	s = next;
282	}
283
284	aisc_put(pd_gl.link, PT_PDC, pdc,
285	PDC_NAMES, &bs,
286	PDC_GO, 0,
287	NULL);
288
289	{
290	char *locs_error = 0;
291	if (aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs,
292	LOCS_ERROR, &locs_error,
293	NULL)) {
294	error = "Connection to PT_SERVER lost (2)";
295	}
296	else {
297	if (*locs_error) error = GBS_static_string(locs_error);
298	free(locs_error);
299	}
300	}
301
302	if (!error) {
303	T_PT_TPROBE tprobe;
304	aisc_get(pd_gl.link, PT_PDC, pdc,
305	PDC_TPROBE, tprobe.as_result_param(),
306	NULL);
307
308
309	GBS_strstruct *outstr = GBS_stropen(1000);
310
311	if (tprobe.exists()) {
312	char *match_info = 0;
313	aisc_get(pd_gl.link, PT_PDC, pdc,
314	PDC_INFO_HEADER, &match_info,
315	NULL);
316	GBS_strcat(outstr, match_info);
317	GBS_chrcat(outstr, '\n');
318	free(match_info);
319	}
320
321
322	while (tprobe.exists()) {
323	char *match_info = 0;
324	if (aisc_get(pd_gl.link, PT_TPROBE, tprobe,
325	TPROBE_NEXT, tprobe.as_result_param(),
326	TPROBE_INFO, &match_info,
327	NULL)) break;
328	GBS_strcat(outstr, match_info);
329	GBS_chrcat(outstr, '\n');
330	free(match_info);
331	}
332
333	return GBS_strclose(outstr);
334	}
335	}
336	}
337	return NULL;
338	}
339
340	static char *AP_probe_match_event(ARB_ERROR& error) {
341	PTserverConnection contact(error);
342
343	if (!error &&
344	aisc_nput(pd_gl.link, PT_LOCS, pd_gl.locs,
345	LOCS_MATCH_REVERSED, (long)P.COMPLEMENT,
346	LOCS_MATCH_SORT_BY, (long)P.WEIGHTED,
347	LOCS_MATCH_COMPLEMENT, 0L,
348	LOCS_MATCH_MAX_MISMATCHES, (long)P.MISMATCHES,
349	LOCS_MATCH_N_ACCEPT, (long)P.ACCEPTN,
350	LOCS_MATCH_N_LIMIT, (long)P.LIMITN,
351	LOCS_MATCH_MAX_HITS, (long)P.MAXRESULT,
352	LOCS_SEARCHMATCH, P.SEQUENCE,
353	NULL)) {
354	error = "Connection to PT_SERVER lost (1)";
355	}
356
357	if (!error) {
358	bytestring bs;
359	bs.data = 0;
360	{
361	char *locs_error = 0;
362	T_PT_MATCHLIST match_list;
363	long match_list_cnt;
364
365	aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs,
366	LOCS_MATCH_LIST, match_list.as_result_param(),
367	LOCS_MATCH_LIST_CNT, &match_list_cnt,
368	LOCS_MATCH_STRING, &bs,
369	LOCS_ERROR, &locs_error,
370	NULL);
371	if (*locs_error) error = GBS_static_string(locs_error);
372	free(locs_error);
373	}
374
375	if (!error) return bs.data; // freed by caller
376	free(bs.data);
377	}
378	return NULL;
379	}
380
381	static int pargc;
382	static const char **pargv = NULL;
383	static bool showhelp;
384
385	static int getInt(const char param, int val, int min, int max, const char description) {
386	if (showhelp) {
387	printf(" %s=%i [%i .. %i] %s\n", param, val, min, max, description);
388	return 0;
389	}
390	int i;
391	const char *s = 0;
392
393	arb_assert(pargc >= 1); // otherwise s stays 0
394
395	for (i=1; i<pargc; i++) {
396	s = pargv[i];
397	if (*s == '-') s++;
398	if (!strncasecmp(s, param, strlen(param))) break;
399	}
400	if (i==pargc) return val;
401	s += strlen(param);
402	if (*s != '=') return val;
403	s++;
404	val = atoi(s);
405	pargc--; // remove parameter
406	for (; i<pargc; i++) {
407	pargv[i] = pargv[i+1];
408	}
409
410	if (val<min) val = min;
411	if (val>max) val = max;
412	return val;
413	}
414
415	static const char getString(const char param, const char val, const char description) {
416	if (showhelp) {
417	if (!val) val = "";
418	printf(" %s=%s %s\n", param, val, description);
419	return 0;
420	}
421	int i;
422	const char *s = 0;
423
424	arb_assert(pargc >= 1); // otherwise s stays 0
425
426	for (i=1; i<pargc; i++) {
427	s = pargv[i];
428	if (*s == '-') s++;
429	if (!strncasecmp(s, param, strlen(param))) break;
430	}
431	if (i==pargc) return val;
432	s += strlen(param);
433	if (*s != '=') return val;
434	s++;
435	pargc--; // remove parameter
436	for (; i<pargc; i++) {
437	pargv[i] = pargv[i+1];
438	}
439	return s;
440	}
441
442	static bool parseCommandLine(int argc, const char * const * const argv) {
443	pargc = argc;
444
445	// copy argv (since parser will remove matched arguments)
446	free(pargv);
447	pargv = (const char *)malloc(sizeof(pargv)*pargc);
448	for (int i=0; i<pargc; i++) pargv[i] = argv[i];
449
450	showhelp = (pargc <= 1);
451
452	#ifdef UNIT_TESTS // UT_DIFF
453	const int minServerID = TEST_GENESERVER_ID;
454	#else // !UNIT_TESTS
455	const int minServerID = 0;
456	#endif
457
458	P.SERVERID = getInt("serverid", 0, minServerID, 100, "Server Id, look into $ARBHOME/lib/arb_tcp.dat");
459	#ifdef UNIT_TESTS // UT_DIFF
460	if (P.SERVERID<0) { arb_assert(P.SERVERID == TEST_SERVER_ID \|\| P.SERVERID == TEST_GENESERVER_ID); }
461	#endif
462
463	P.DESIGNCLIPOUTPUT = getInt("designmaxhits", 100, 10, 10000, "Maximum Number of Probe Design Suggestions");
464	P.DESIGNNAMES = getString("designnames", "", "List of short names separated by '#'");
465
466	P.sequence = 0;
467	while ((P.DESIGNSEQUENCE = getString("designsequence", 0, "Additional Sequences, will be added to the target group"))) {
468	apd_sequence *s = new apd_sequence;
469	s->next = P.sequence;
470	P.sequence = s;
471	s->sequence = P.DESIGNSEQUENCE;
472	P.DESIGNSEQUENCE = 0;
473	}
474	P.DESIGNPROBELEN = getInt("designprobelength", 18, 2, 100, "(min.) length of probe");
475	P.DESIGNMAXPROBELEN = getInt("designmaxprobelength", -1, -1, 100, "max. length of probe (if specified)");
476	P.MINTEMP = getInt("designmintemp", 0, 0, 400, "Minimum melting temperature of probe");
477	P.MAXTEMP = getInt("designmaxtemp", 400, 0, 400, "Maximum melting temperature of probe");
478	P.MINGC = getInt("designmingc", 30, 0, 100, "Minimum gc content");
479	P.MAXGC = getInt("designmaxgc", 80, 0, 100, "Maximum gc content");
480	P.MAXBOND = getInt("designmaxbond", 0, 0, 10, "Not implemented");
481	P.MINPOS = getInt("designminpos", -1, -1, INT_MAX, "Minimum ecoli position (-1=none)");
482	P.MAXPOS = getInt("designmaxpos", -1, -1, INT_MAX, "Maximum ecoli position (-1=none)");
483	P.MISHIT = getInt("designmishit", 0, 0, 10000, "Number of allowed hits outside the selected group");
484	P.MINTARGETS = getInt("designmintargets", 50, 0, 100, "Minimum percentage of hits within the selected species");
485
486	P.SEQUENCE = getString("matchsequence", "agtagtagt", "The sequence to search for");
487
488	P.MISMATCHES = getInt("matchmismatches", 0, 0, 5, "Maximum Number of allowed mismatches");
489	P.COMPLEMENT = getInt("matchcomplement", 0, 0, 1, "Match reversed and complemented probe");
490	P.WEIGHTED = getInt("matchweighted", 0, 0, 1, "Use weighted mismatches");
491	P.ACCEPTN = getInt("matchacceptN", 1, 0, 20, "Amount of N-matches not counted as mismatch");
492	P.LIMITN = getInt("matchlimitN", 4, 0, 20, "Limit for N-matches. If reached N-matches are mismatches");
493	P.MAXRESULT = getInt("matchmaxresults", 1000000, 0, INT_MAX, "Max. number of matches reported (0=unlimited)");
494
495	P.ITERATE = getInt("iterate", 0, 1, 20, "Iterate over probes of given length");
496	P.ITERATE_AMOUNT = getInt("iterate_amount", 100, 1, INT_MAX, "Number of results per answer");
497	P.ITERATE_READABLE = getInt("iterate_readable", 1, 0, 1, "readable results");
498
499	P.ITERATE_TU = getString("iterate_tu", "T", "use T or U in readable result");
500	P.ITERATE_SEPARATOR = getString("iterate_separator", ";", "Number of results per answer");
501
502	P.DUMP = getString("dump", "", "dump ptserver index to file (may be huge!)");
503
504	if (pargc>1) {
505	printf("Unknown (or duplicate) parameter %s\n", pargv[1]);
506	return false;
507	}
508	return !showhelp;
509	}
510
511	// --------------------------------------------------------------------------------
512
513	#ifdef UNIT_TESTS
514	#ifndef TEST_UNIT_H
515	#include <test_unit.h>
516	#endif
517
518	void TEST_BASIC_parseCommandLine() {
519	{
520	const char *args[] = { NULL, "serverid=0"};
521	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
522
523	// test default values here
524	TEST_EXPECT_EQUAL(P.ACCEPTN, 1);
525	TEST_EXPECT_EQUAL(P.LIMITN, 4);
526	TEST_EXPECT_EQUAL(P.MISMATCHES, 0);
527	TEST_EXPECT_EQUAL(P.MAXRESULT, 1000000);
528	}
529
530	{
531	const char *args[] = {NULL, "serverid=4", "matchmismatches=2"};
532	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
533	TEST_EXPECT_EQUAL(P.SERVERID, 4);
534	TEST_EXPECT_EQUAL(P.MISMATCHES, 2);
535	TEST_EXPECT_EQUAL(args[1], "serverid=4"); // check array args was not modified
536	}
537
538	{
539	const char *args[] = { NULL, "matchacceptN=0", "matchlimitN=5"};
540	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
541	TEST_EXPECT_EQUAL(P.ACCEPTN, 0);
542	TEST_EXPECT_EQUAL(P.LIMITN, 5);
543	}
544
545	{
546	const char *args[] = { NULL, "matchmaxresults=100"};
547	TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args));
548	TEST_EXPECT_EQUAL(P.MAXRESULT, 100);
549	}
550	}
551
552	#endif // UNIT_TESTS
553
554	// --------------------------------------------------------------------------------
555
556
557	static char *execute(ARB_ERROR& error) {
558	char *answer;
559	if (*P.DESIGNNAMES \|\| P.sequence) {
560	answer = AP_probe_design_event(error);
561	}
562	else if (P.ITERATE>0) {
563	answer = AP_probe_iterate_event(error);
564	}
565	else if (P.DUMP[0]) {
566	answer = AP_dump_index_event(error);
567	}
568	else {
569	answer = AP_probe_match_event(error);
570	}
571	pd_gl.locs.clear();
572	return answer;
573	}
574
575	int ARB_main(int argc, char *argv[]) {
576	bool ok = parseCommandLine(argc, argv);
577	if (ok) {
578	ARB_ERROR error;
579	char *answer = execute(error);
580
581	arb_assert(contradicted(answer, error));
582
583	if (!answer) {
584	fprintf(stderr,
585	"arb_probe: Failed to process your request\n"
586	" Reason: %s",
587	error.deliver());
588	ok = false;
589	}
590	else {
591	fputs(answer, stdout);
592	free(answer);
593	error.expect_no_error();
594	}
595	}
596	return ok ? EXIT_SUCCESS : EXIT_FAILURE;
597	}
598
599	// --------------------------------------------------------------------------------
600
601	#ifdef UNIT_TESTS
602	#ifndef TEST_UNIT_H
603	#include <test_unit.h>
604	#endif
605
606	static int test_setup(bool use_gene_ptserver) {
607	static bool setup[2] = { false, false };
608	if (!setup[use_gene_ptserver]) {
609	TEST_SETUP_GLOBAL_ENVIRONMENT(use_gene_ptserver ? "ptserver_gene" : "ptserver"); // first call will recreate the test pt-server
610	setup[use_gene_ptserver] = true;
611	}
612	return use_gene_ptserver ? TEST_GENESERVER_ID : TEST_SERVER_ID;
613	}
614
615	// ----------------------------------
616	// test probe design / match
617
618	#define TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv) \
619	int serverid = test_setup(use_gene_ptserver); \
620	TEST_EXPECT_EQUAL(true, parseCommandLine(fake_argc, fake_argv)); \
621	TEST_EXPECT((serverid == TEST_SERVER_ID)\|\|(serverid == TEST_GENESERVER_ID)); \
622	P.SERVERID = serverid; \
623	ARB_ERROR error; \
624	char *answer = execute(error)
625
626	#define TEST_ARB_PROBE__REPORTS_ERROR(fake_argc,fake_argv,expected_error) \
627	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
628	free(answer); \
629	TEST_EXPECT_ERROR_CONTAINS(error.deliver(), expected_error)
630
631	#define TEST_ARB_PROBE__REPORTS_ERROR__BROKEN(fake_argc,fake_argv,expected_error) \
632	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
633	free(answer); \
634	TEST_EXPECT_ANY_ERROR(error.preserve()); \
635	TEST_EXPECT_ERROR_CONTAINS__BROKEN(error.deliver(), expected_error)
636
637
638	#define TEST_RUN_ARB_PROBE(fake_argc,fake_argv) \
639	TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \
640	TEST_EXPECT_NO_ERROR(error.deliver())
641
642	#define TEST_ARB_PROBE(fake_argc,fake_argv,expected) do { \
643	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
644	TEST_EXPECT_EQUAL(answer, expected); \
645	free(answer); \
646	} while(0)
647
648	#define TEST_ARB_PROBE__BROKEN(fake_argc,fake_argv,expected) do { \
649	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
650	TEST_EXPECT_EQUAL__BROKEN(answer, expected); \
651	free(answer); \
652	} while(0)
653
654	#define TEST_ARB_PROBE_FILT(fake_argc,fake_argv,filter,expected) do { \
655	TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \
656	char *filtered = filter(answer); \
657	TEST_EXPECT_EQUAL(filtered, expected); \
658	free(filtered); \
659	free(answer); \
660	} while(0)
661
662	typedef const char *CCP;
663
664	void TEST_SLOW_match_geneprobe() {
665	// test here runs versus database ../UNIT_TESTER/run/TEST_gpt_src.arb
666
667	bool use_gene_ptserver = true;
668	{
669	const char *arguments[] = {
670	"prgnamefake",
671	"matchsequence=NNUCNN",
672	"matchacceptN=4",
673	"matchlimitN=5",
674	};
675	CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NNUCNN'\1"
676	"genome2\1" " genome2 gene3 0 4 2.6 2 1 0 .........-UU==GG-UUGAUC.\1"
677	"genome2\1" " genome2 joined1 0 4 2.6 2 1 0 .........-UU==GG-UUGAUCCUG\1"
678	"genome2\1" " genome2 gene1 0 4 2.6 2 2 0 ........A-UU==GG-U.\1"
679	"genome2\1" " genome2 intergene_19_65 0 4 2.7 31 12 0 GGUUACUGC-AU==GG-UGUUCGCCU\1"
680	"genome1\1" " genome1 intergene_17_65 0 4 2.7 31 14 0 GGUUACUGC-UA==GG-UGUUCGCCU\1"
681	"genome2\1" " genome2 intergene_19_65 0 4 2.7 38 19 0 GCAUUCGGU-GU==GC-CUAAGCACU\1"
682	"genome1\1" " genome1 intergene_17_65 0 4 2.7 38 21 0 GCUAUCGGU-GU==GC-CUAAGCCAU\1"
683	"genome2\1" " genome2 gene3 0 4 2.9 10 9 0 .UUUCGGUU-GA==..-\1"
684	"genome2\1" " genome2 intergene_19_65 0 4 3.1 56 37 0 AGCACUGCG-AG==AU-AUGUA.\1"
685	"genome1\1" " genome1 intergene_17_65 0 4 3.1 56 39 0 AGCCAUGCG-AG==AU-AUGUA.\1"
686	"genome1\1" " genome1 gene2 0 4 3.1 10 2 0 ........U-GA==CU-GC.\1"
687	"genome2\1" " genome2 gene2 0 4 3.1 10 4 0 ......GUU-GA==CU-GCCA.\1"
688	"genome1\1" " genome1 joined1 0 4 3.1 10 7 0 ...CUGGUU-GA==CU-GC.\1"
689	"genome2\1" " genome2 joined1 0 4 3.1 10 9 0 .UUUCGGUU-GA==CU-GCCA.\1";
690
691	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd);
692	}
693
694	{
695	const char *arguments[] = {
696	"prgnamefake",
697	"matchsequence=NGGUUN",
698	"matchacceptN=2",
699	"matchlimitN=3",
700	};
701	CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NGGUUN'\1"
702	"genome1\1" " genome1 gene3 0 2 1.3 5 2 0 ........C-U====G-A.\1"
703	"genome1\1" " genome1 joined1 0 2 1.3 5 2 0 ........C-U====G-AUCCUGC.\1"
704	"genome2\1" " genome2 gene3 0 2 1.4 5 4 0 ......UUU-C====G-AUC.\1"
705	"genome2\1" " genome2 joined1 0 2 1.4 5 4 0 ......UUU-C====G-AUCCUGCCA\1"
706	"genome2\1" " genome2 intergene_19_65 0 2 1.8 21 2 0 ........G-A====A-CUGCAUUCG\1"
707	"genome1\1" " genome1 intergene_17_65 0 2 1.8 21 4 0 ......CAG-A====A-CUGCUAUCG\1";
708
709	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd);
710	}
711
712	{
713	const char *arguments[] = {
714	"prgnamefake",
715	"matchsequence=UGAUCCU", // exists in data
716	};
717	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UGAUCCU'\1"
718	"genome1\1" " genome1 gene2 0 0 0.0 9 1 0 .........-=======-GC.\1"
719	"genome2\1" " genome2 gene2 0 0 0.0 9 3 0 .......GU-=======-GCCA.\1"
720	"genome1\1" " genome1 joined1 0 0 0.0 9 6 0 ....CUGGU-=======-GC.\1"
721	"genome2\1" " genome2 joined1 0 0 0.0 9 8 0 ..UUUCGGU-=======-GCCA.\1";
722
723	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hits in 'joined1' (of both genomes)]
724	}
725	{
726	const char *arguments[] = {
727	"prgnamefake",
728	"matchsequence=GAUCCU",
729	};
730	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'GAUCCU'\1"
731	"genome1\1" " genome1 gene2 0 0 0.0 10 2 0 ........U-======-GC.\1"
732	"genome2\1" " genome2 gene2 0 0 0.0 10 4 0 ......GUU-======-GCCA.\1"
733	"genome1\1" " genome1 joined1 0 0 0.0 10 7 0 ...CUGGUU-======-GC.\1"
734	"genome2\1" " genome2 joined1 0 0 0.0 10 9 0 .UUUCGGUU-======-GCCA.\1";
735
736	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]
737	}
738	{
739	const char *arguments[] = {
740	"prgnamefake",
741	"matchsequence=UUUCGG", // exists only in genome2
742	};
743	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUUCGG'\1"
744	"genome2\1" " genome2 gene3 0 0 0.0 2 1 0 .........-======-UUGAUC.\1"
745	"genome2\1" " genome2 joined1 0 0 0.0 2 1 0 .........-======-UUGAUCCUG\1"
746	"genome2\1" " genome2 gene1 0 0 0.0 2 2 0 ........A-======-U.\1";
747
748	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hit in genome2/gene1]
749	}
750	{
751	const char *arguments[] = {
752	"prgnamefake",
753	"matchsequence=AUCCUG",
754	};
755	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'AUCCUG'\1"
756	"genome1\1" " genome1 gene2 0 0 0.0 11 3 0 .......UG-======-C.\1"
757	"genome2\1" " genome2 gene2 0 0 0.0 11 5 0 .....GUUG-======-CCA.\1"
758	"genome1\1" " genome1 joined1 0 0 0.0 11 8 0 ..CUGGUUG-======-C.\1"
759	"genome2\1" " genome2 joined1 0 0 0.0 11 10 0 UUUCGGUUG-======-CCA.\1";
760
761	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hits in 'gene2' and 'joined1' of both genomes]
762	}
763	{
764	const char *arguments[] = {
765	"prgnamefake",
766	"matchsequence=UUGAUCCUGC",
767	};
768	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUGAUCCUGC'\1"
769	"genome2\1" " genome2 gene2 0 0 0.0 8 2 0 ........G-==========-CA.\1"
770	"genome1\1" " genome1 joined1 0 0 0.0 8 5 0 .....CUGG-==========-.\1"
771	"genome2\1" " genome2 joined1 0 0 0.0 8 7 0 ...UUUCGG-==========-CA.\1";
772
773	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hit in 'genome2/joined1']
774	}
775	}
776
777	void TEST_SLOW_match_probe() {
778	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
779
780	bool use_gene_ptserver = false;
781	{
782	const char *arguments[] = {
783	"prgnamefake",
784	"matchsequence=UAUCGGAGAGUUUGA",
785	};
786	CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UAUCGGAGAGUUUGA'\1"
787	"BcSSSS00\1" " BcSSSS00 0 0 0.0 3 2 0 .......UU-===============-UCAAGUCGA\1";
788
789	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
790	}
791
792	// ----------------------------------------------------------------------------
793	// match with old(=default) N-mismatch-behavior (accepting 1 N-match)
794
795	{
796	const char *arguments[] = {
797	"prgnamefake",
798	"matchsequence=CANCUCCUUUC", // contains 1 N
799	NULL // matchmismatches
800	};
801
802	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
803	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"; // only N-mismatch accepted
804
805	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
806	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
807	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
808	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
809	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
810	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
811	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
812	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
813	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
814	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1";
815
816	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
817	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
818	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
819	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
820	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
821	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
822	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
823	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
824	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
825	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
826	"AclPleur\1" " AclPleur 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
827	"PtVVVulg\1" " PtVVVulg 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
828	"DlcTolu2\1" " DlcTolu2 2 3 2.3 176 162 0 CGGCUGGAU-==C======NN-N.\1"
829	"FrhhPhil\1" " FrhhPhil 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
830	"HllHalod\1" " HllHalod 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
831	"CPPParap\1" " CPPParap 2 3 2.3 177 163 0 CGGNUGGAU-==C======..-\1";
832
833	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
834	"BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
835	"ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
836	"PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
837	"PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
838	"Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
839	"DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
840	"VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
841	"VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
842	"VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
843	"AclPleur\1" " AclPleur 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
844	"PtVVVulg\1" " PtVVVulg 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1"
845	"DlcTolu2\1" " DlcTolu2 2 3 2.3 176 162 0 CGGCUGGAU-==C======NN-N.\1"
846	"FrhhPhil\1" " FrhhPhil 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
847	"HllHalod\1" " HllHalod 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1"
848	"CPPParap\1" " CPPParap 2 3 2.3 177 163 0 CGGNUGGAU-==C======..-\1"
849	"VblVulni\1" " VblVulni 3 1 3.6 49 44 0 AGCACAGAG-a=A==uG====-UCGGGUGGC\1";
850
851	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
852	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
853	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
854	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
855	}
856
857	{
858	const char *arguments[] = {
859	"prgnamefake",
860	"matchsequence=UCACCUCCUUUC", // contains no N
861	NULL // matchmismatches
862	};
863
864	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
865	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
866	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
867	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
868	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
869	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
870	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
871	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
872	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1";
873
874	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
875	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
876	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
877	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
878	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
879	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
880	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
881	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
882	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
883	"AclPleur\1" " AclPleur 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
884	"PtVVVulg\1" " PtVVVulg 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
885	"DlcTolu2\1" " DlcTolu2 1 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
886	"FrhhPhil\1" " FrhhPhil 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
887	"HllHalod\1" " HllHalod 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
888	"CPPParap\1" " CPPParap 1 2 1.4 176 162 0 GCGGNUGGA-==========..-\1";
889
890	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
891	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
892	"PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
893	"PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
894	"Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
895	"DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
896	"VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
897	"VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
898	"VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
899	"AclPleur\1" " AclPleur 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
900	"PtVVVulg\1" " PtVVVulg 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
901	"DlcTolu2\1" " DlcTolu2 1 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
902	"FrhhPhil\1" " FrhhPhil 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
903	"HllHalod\1" " HllHalod 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
904	"CPPParap\1" " CPPParap 1 2 1.4 176 162 0 GCGGNUGGA-==========..-\1"
905	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C=========-U.\1"
906	"LgtLytic\1" " LgtLytic 2 3 2.1 175 161 0 GCGGCUGGA-=========N..-\1"
907	"PslFlave\1" " PslFlave 2 3 2.1 175 161 0 GCGGCUGGA-=========...-\1";
908
909	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
910	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
911	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
912	}
913
914	{
915	const char *arguments[] = {
916	"prgnamefake",
917	"matchsequence=UCACCUCCUUUC", // contains no N
918	NULL, // matchmismatches
919	"matchweighted=1", // use weighted mismatches
920	};
921
922	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
923	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
924	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
925	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
926	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
927	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
928	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
929	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
930	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1";
931
932	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
933	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
934	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
935	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
936	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
937	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
938	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
939	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
940	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
941	"DlcTolu2\1" " DlcTolu2 1 2 0.6 175 161 0 GCGGCUGGA-==========NN-N.\1"
942	"FrhhPhil\1" " FrhhPhil 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
943	"HllHalod\1" " HllHalod 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
944	"CPPParap\1" " CPPParap 1 2 0.6 176 162 0 GCGGNUGGA-==========..-\1"
945	"AclPleur\1" " AclPleur 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
946	"PtVVVulg\1" " PtVVVulg 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
947	"LgtLytic\1" " LgtLytic 2 3 1.3 175 161 0 GCGGCUGGA-=========N..-\1"
948	"PslFlave\1" " PslFlave 2 3 1.3 175 161 0 GCGGCUGGA-=========...-\1"
949	"ClfPerfr\1" " ClfPerfr 2 0 1.3 175 161 0 AAGAUUAAU-A=C=========-U.\1";
950
951	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
952	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
953	"PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
954	"PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1"
955	"Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1"
956	"DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1"
957	"VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
958	"VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
959	"VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"
960	"DlcTolu2\1" " DlcTolu2 1 2 0.6 175 161 0 GCGGCUGGA-==========NN-N.\1"
961	"FrhhPhil\1" " FrhhPhil 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
962	"HllHalod\1" " HllHalod 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1"
963	"CPPParap\1" " CPPParap 1 2 0.6 176 162 0 GCGGNUGGA-==========..-\1"
964	"AclPleur\1" " AclPleur 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
965	"PtVVVulg\1" " PtVVVulg 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1"
966	"LgtLytic\1" " LgtLytic 2 3 1.3 175 161 0 GCGGCUGGA-=========N..-\1"
967	"PslFlave\1" " PslFlave 2 3 1.3 175 161 0 GCGGCUGGA-=========...-\1"
968	"ClfPerfr\1" " ClfPerfr 2 0 1.3 175 161 0 AAGAUUAAU-A=C=========-U.\1"
969	"AclPleur\1" " AclPleur 5 0 2.4 50 45 0 GAAGGGAGC-=ug=u=u====G-CCGACGAGU\1"
970	"PtVVVulg\1" " PtVVVulg 5 0 2.4 50 45 0 GGAGAAAGC-=ug=u=u===g=-UGACGAGCG\1";
971
972	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
973	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
974	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
975	}
976
977	// ----------------------------------------------
978	// do not accept any N-matches as match
979
980	{
981	const char *arguments[] = {
982	"prgnamefake",
983	"matchsequence=CANCUCCUUUC", // contains 1 N
984	NULL, // matchmismatches
985	"matchacceptN=0",
986	};
987
988	CCP expectd0 = ""; // nothing matches
989
990	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
991	"BcSSSS00\1" " BcSSSS00 1 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1";
992
993	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
994	"BcSSSS00\1" " BcSSSS00 1 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"
995	"ClfPerfr\1" " ClfPerfr 2 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1"
996	"PbcAcet2\1" " PbcAcet2 2 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
997	"PbrPropi\1" " PbrPropi 2 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1"
998	"Stsssola\1" " Stsssola 2 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1"
999	"DcdNodos\1" " DcdNodos 2 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1"
1000	"VbrFurni\1" " VbrFurni 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
1001	"VblVulni\1" " VblVulni 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"
1002	"VbhChole\1" " VbhChole 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1";
1003
1004	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1005	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1006	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1007	}
1008	{
1009	const char *arguments[] = {
1010	"prgnamefake",
1011	"matchsequence=UUUCUUU", // contains no N
1012	NULL, // matchmismatches
1013	"matchacceptN=0",
1014	};
1015
1016	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1017	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1";
1018
1019	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1020	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1"
1021	"AclPleur\1" " AclPleur 1 0 0.6 50 45 0 GAAGGGAGC-==g====-CUUUGCCGA\1"
1022	"PtVVVulg\1" " PtVVVulg 1 0 0.6 50 45 0 GGAGAAAGC-==g====-CUUGCUGAC\1"
1023	"PtVVVulg\1" " PtVVVulg 1 0 0.6 54 49 0 AAAGCUUGC-======g-CUGACGAGC\1"
1024	"ClfPerfr\1" " ClfPerfr 1 0 1.1 49 44 0 GCGAUGAAG-====C==-CGGGAAACG\1";
1025
1026	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1"
1027	"AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1"
1028	"AclPleur\1" " AclPleur 1 0 0.6 50 45 0 GAAGGGAGC-==g====-CUUUGCCGA\1"
1029	"PtVVVulg\1" " PtVVVulg 1 0 0.6 50 45 0 GGAGAAAGC-==g====-CUUGCUGAC\1"
1030	"PtVVVulg\1" " PtVVVulg 1 0 0.6 54 49 0 AAAGCUUGC-======g-CUGACGAGC\1"
1031	"ClfPerfr\1" " ClfPerfr 1 0 1.1 49 44 0 GCGAUGAAG-====C==-CGGGAAACG\1"
1032	"DlcTolu2\1" " DlcTolu2 2 0 1.2 47 42 0 AGAAAGGGA-==g===g-CAAUCCUGA\1"
1033	"ClnCorin\1" " ClnCorin 2 0 1.7 48 43 0 AGCGAUGAA-g===C==-CGGGAAUGG\1"
1034	"CPPParap\1" " CPPParap 2 0 1.7 48 43 0 AGCGAUGAA-g===C==-CGGGAACGG\1"
1035	"HllHalod\1" " HllHalod 2 0 1.7 49 44 0 GAUGGAAGC-==g===C-CAGGCGUCG\1"
1036	"DcdNodos\1" " DcdNodos 2 0 1.7 50 45 0 UUAUGUAGC-==g==A=-GUAACCUAG\1"
1037	"VbhChole\1" " VbhChole 2 0 1.7 55 50 0 GAGGAACUU-g===C==-GGGUGGCGA\1"
1038	"VbrFurni\1" " VbrFurni 2 0 1.7 62 57 0 UUCGGGGGA-===G==g-GGCGGCGAG\1"
1039	"VblVulni\1" " VblVulni 2 0 1.7 62 57 0 AGAAACUUG-=====Cg-GGUGGCGAG\1"
1040	"VbhChole\1" " VbhChole 2 0 1.7 62 57 0 AGGAACUUG-==C===g-GGUGGCGAG\1"
1041	"ClnCorin\1" " ClnCorin 2 0 2.2 49 44 0 GCGAUGAAG-==C===C-GGGAAUGGA\1"
1042	"CltBotul\1" " CltBotul 2 0 2.2 49 44 0 GCGAUGAAG-C=====C-GGAAGUGGA\1"
1043	"CPPParap\1" " CPPParap 2 0 2.2 49 44 0 GCGAUGAAG-==C===C-GGGAACGGA\1"
1044	"ClfPerfr\1" " ClfPerfr 2 0 2.2 50 45 0 CGAUGAAGU-==C===C-GGGAAACGG\1"
1045	"VblVulni\1" " VblVulni 2 0 2.2 52 47 0 ACAGAGAAA-C==G===-CUCGGGUGG\1"
1046	"BcSSSS00\1" " BcSSSS00 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-CU.\1"
1047	"ClfPerfr\1" " ClfPerfr 2 0 2.2 179 165 0 UUAAUACCC-C=C====-CU.\1"
1048	"PbcAcet2\1" " PbcAcet2 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-NN.\1"
1049	"PbrPropi\1" " PbrPropi 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-NN.\1"
1050	"Stsssola\1" " Stsssola 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1051	"DcdNodos\1" " DcdNodos 2 0 2.2 179 165 0 UUGGAUCAC-C=C====-.\1"
1052	"VbrFurni\1" " VbrFurni 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1053	"VblVulni\1" " VblVulni 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1054	"VbhChole\1" " VbhChole 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1"
1055	"BcSSSS00\1" " BcSSSS00 2 2 1.4 183 169 0 AUCACCUCC-=====..-\1"
1056	"ClfPerfr\1" " ClfPerfr 2 2 1.4 183 169 0 UACCCCUCC-=====..-\1";
1057
1058	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1059	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1060	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1061	}
1062	{
1063	const char *arguments[] = {
1064	"prgnamefake",
1065	"matchsequence=UCACCUCCUUUC", // contains no N
1066	NULL, // matchmismatches
1067	"matchacceptN=0",
1068	};
1069
1070	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1071	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "";
1072
1073	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1074	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
1075	"PbcAcet2\1" " PbcAcet2 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1076	"PbrPropi\1" " PbrPropi 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1077	"Stsssola\1" " Stsssola 1 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
1078	"DcdNodos\1" " DcdNodos 1 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
1079	"VbrFurni\1" " VbrFurni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1080	"VblVulni\1" " VblVulni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1081	"VbhChole\1" " VbhChole 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1";
1082
1083	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
1084	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1"
1085	"PbcAcet2\1" " PbcAcet2 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1086	"PbrPropi\1" " PbrPropi 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1"
1087	"Stsssola\1" " Stsssola 1 1 0.7 175 161 0 GCGGCUGGA-===========.-\1"
1088	"DcdNodos\1" " DcdNodos 1 1 0.7 175 161 0 GCGGUUGGA-===========.-\1"
1089	"VbrFurni\1" " VbrFurni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1090	"VblVulni\1" " VblVulni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1091	"VbhChole\1" " VbhChole 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"
1092	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C=========-U.\1"
1093	"AclPleur\1" " AclPleur 2 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
1094	"PtVVVulg\1" " PtVVVulg 2 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1"
1095	"DlcTolu2\1" " DlcTolu2 2 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1"
1096	"FrhhPhil\1" " FrhhPhil 2 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
1097	"HllHalod\1" " HllHalod 2 2 1.4 175 161 0 GCGGCUGGA-==========..-\1"
1098	"CPPParap\1" " CPPParap 2 2 1.4 176 162 0 GCGGNUGGA-==========..-\1";
1099
1100	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1101	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1102	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1103	}
1104	{
1105	const char *arguments[] = {
1106	"prgnamefake",
1107	"matchsequence=UCACCUCCUUUCU", // contains no N
1108	NULL, // matchmismatches
1109	"matchacceptN=0",
1110	};
1111
1112	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1113	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1";
1114
1115	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1116	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1117	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1118	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1119	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1120	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1121	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1122	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1123	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1124	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1";
1125
1126	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1127	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1128	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1129	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1130	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1131	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1132	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1133	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1134	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1135	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1136	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1137	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1138	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1139	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1140	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1141	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1";
1142
1143	CCP expectd4 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1144	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1145	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1146	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1147	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1148	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1149	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1150	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1151	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1152	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1153	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1154	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1155	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1156	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1157	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1158	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1"
1159	"LgtLytic\1" " LgtLytic 4 4 2.8 175 161 0 GCGGCUGGA-=========N...-\1"
1160	"PslFlave\1" " PslFlave 4 4 2.8 175 161 0 GCGGCUGGA-=========....-\1";
1161
1162	CCP expectd5 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1"
1163	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"
1164	"ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1"
1165	"PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1166	"PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1"
1167	"Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1"
1168	"DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1"
1169	"VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1170	"VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1171	"VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"
1172	"AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1173	"PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1"
1174	"DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1"
1175	"FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1176	"HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1"
1177	"CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1"
1178	"LgtLytic\1" " LgtLytic 4 4 2.8 175 161 0 GCGGCUGGA-=========N...-\1"
1179	"PslFlave\1" " PslFlave 4 4 2.8 175 161 0 GCGGCUGGA-=========....-\1"
1180	"PtVVVulg\1" " PtVVVulg 5 0 2.6 50 45 0 GGAGAAAGC-=ug=u=u===g==-GACGAGCGG\1"
1181	"AclPleur\1" " AclPleur 5 0 3.5 46 41 0 ACGGGAAGG-gag=u=G======-UUGCCGACG\1"
1182	"PtVVVulg\1" " PtVVVulg 5 0 4.0 45 40 0 ...AGGAGA-Aag=u=G======-UGCUGACGA\1"
1183	"VblVulni\1" " VblVulni 5 0 4.3 48 43 0 CAGCACAGA-ga=a==uG=====-CGGGUGGCG\1";
1184
1185	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1186	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1187	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1188	arguments[2] = "matchmismatches=4"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd4);
1189	arguments[2] = "matchmismatches=5"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd5);
1190	}
1191
1192	// ----------------------------------
1193	// accept several N-matches
1194
1195	{
1196	const char *arguments[] = {
1197	"prgnamefake",
1198	"matchsequence=CANCUCCUUNC", // contains 2 N
1199	NULL, // matchmismatches
1200	"matchacceptN=2",
1201	"matchlimitN=4",
1202	};
1203
1204	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1205	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1";
1206
1207	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1208	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1"
1209	"ClfPerfr\1" " ClfPerfr 1 2 2.8 176 162 0 AGAUUAAUA-=CC======U=-U.\1"
1210	"DlcTolu2\1" " DlcTolu2 1 3 2.4 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1211	"FrhhPhil\1" " FrhhPhil 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1212	"HllHalod\1" " HllHalod 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1213	"CPPParap\1" " CPPParap 1 3 2.4 177 163 0 CGGNUGGAU-==C======..-\1"
1214	"PbcAcet2\1" " PbcAcet2 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1215	"PbrPropi\1" " PbrPropi 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1216	"Stsssola\1" " Stsssola 1 3 2.4 176 162 0 CGGCUGGAU-==C======U.-\1"
1217	"DcdNodos\1" " DcdNodos 1 3 2.4 176 162 0 CGGUUGGAU-==C======U.-\1"
1218	"VbrFurni\1" " VbrFurni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1219	"VblVulni\1" " VblVulni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1220	"VbhChole\1" " VbhChole 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1221	"AclPleur\1" " AclPleur 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1"
1222	"PtVVVulg\1" " PtVVVulg 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1";
1223
1224	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
1225	"BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1"
1226	"ClfPerfr\1" " ClfPerfr 1 2 2.8 176 162 0 AGAUUAAUA-=CC======U=-U.\1"
1227	"DlcTolu2\1" " DlcTolu2 1 3 2.4 176 162 0 CGGCUGGAU-==C=======N-N.\1"
1228	"FrhhPhil\1" " FrhhPhil 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1229	"HllHalod\1" " HllHalod 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1"
1230	"CPPParap\1" " CPPParap 1 3 2.4 177 163 0 CGGNUGGAU-==C======..-\1"
1231	"PbcAcet2\1" " PbcAcet2 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1232	"PbrPropi\1" " PbrPropi 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1"
1233	"Stsssola\1" " Stsssola 1 3 2.4 176 162 0 CGGCUGGAU-==C======U.-\1"
1234	"DcdNodos\1" " DcdNodos 1 3 2.4 176 162 0 CGGUUGGAU-==C======U.-\1"
1235	"VbrFurni\1" " VbrFurni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1236	"VblVulni\1" " VblVulni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1237	"VbhChole\1" " VbhChole 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1"
1238	"AclPleur\1" " AclPleur 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1"
1239	"PtVVVulg\1" " PtVVVulg 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1";
1240
1241	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1242	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1243	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1244	}
1245
1246	{
1247	const char *arguments[] = {
1248	"prgnamefake",
1249	"matchsequence=GAGCGGUCAG", // similar to a region where dots occur in seqdata
1250	NULL, // matchmismatches
1251	"matchacceptN=0",
1252	"matchlimitN=4",
1253	};
1254
1255	CCP expectd0 = "";
1256
1257	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1258	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1";
1259
1260	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1261	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1"
1262	"Bl0LLL00\1" " Bl0LLL00 2 0 2.2 25 21 0 GAUCAAGUC-======A=C=-ACGGGAGCU\1";
1263
1264	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1"
1265	"BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1"
1266	"Bl0LLL00\1" " Bl0LLL00 2 0 2.2 25 21 0 GAUCAAGUC-======A=C=-ACGGGAGCU\1"
1267	"VbrFurni\1" " VbrFurni 3 0 2.4 68 60 0 GGAUUUGUU-=g====CG==-CGGCGGACG\1"
1268	"FrhhPhil\1" " FrhhPhil 3 0 2.8 82 70 0 ACGAGUGGC-=gA===C===-UUGGAAACG\1"
1269	"ClfPerfr\1" " ClfPerfr 3 0 3.2 86 74 0 CGGCGGGAC-=g==CU====-AACCUGCGG\1"
1270	"HllHalod\1" " HllHalod 3 0 3.6 25 21 0 GAUCAAGUC-======Aa=C-GAUGGAAGC\1"
1271	"DlcTolu2\1" " DlcTolu2 3 0 3.6 95 83 0 GGACUGCCC-==Aa==A===-CUAAUACCG\1"
1272	"FrhhPhil\1" " FrhhPhil 3 0 4.0 25 21 0 GAUCAAGUC-==A====a=C-AGGUCUUCG\1"
1273	"AclPleur\1" " AclPleur 3 0 4.0 29 24 0 GAUCAAGUC-==A====a=C-GGGAAGGGA\1"
1274	"ClnCorin\1" " ClnCorin 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUCCUUCG\1"
1275	"CltBotul\1" " CltBotul 3 0 4.1 25 21 0 .AUCAAGUC-=====A=G=A-GCUUCUUCG\1"
1276	"CPPParap\1" " CPPParap 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUCCUUCG\1"
1277	"ClfPerfr\1" " ClfPerfr 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUUCCUUC\1"
1278	"DlcTolu2\1" " DlcTolu2 3 0 4.1 157 143 0 GUAGCCGUU-===GAA====-CGGCUGGAU\1"
1279	"PslFlave\1" " PslFlave 3 3 2.4 25 21 0 GAUCAAGUC-=======...-<more>\1"
1280	"PtVVVulg\1" " PtVVVulg 3 3 2.4 29 24 0 GAUCAAGUC-=======...-<more>\1";
1281
1282	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1283	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1284	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1285	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1286	}
1287
1288	{
1289	const char *arguments[] = {
1290	"prgnamefake",
1291	"matchsequence=GAGCGGUCAGGAG", // as above, but continues behind '...'
1292	NULL, // matchmismatches
1293	"matchweighted=1", // use weighted mismatches
1294	};
1295
1296	CCP expectd2 = "";
1297	CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAGGAG'\1"
1298	"ClnCorin\1" " ClnCorin 6 0 3.4 77 66 0 AUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1299	"CltBotul\1" " CltBotul 6 0 3.4 77 66 0 GUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1300	"CPPParap\1" " CPPParap 6 0 3.4 77 66 0 ACGGAUUAG-Cg====A=g==CC-UUCCGAAAG\1"
1301	"BcSSSS00\1" " BcSSSS00 3 0 3.4 25 21 0 GAUCAAGUC-======A===AU=-GGAGCUUGC\1";
1302
1303	CCP expectd4 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAGGAG'\1"
1304	"ClnCorin\1" " ClnCorin 6 0 3.4 77 66 0 AUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1305	"CltBotul\1" " CltBotul 6 0 3.4 77 66 0 GUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1"
1306	"CPPParap\1" " CPPParap 6 0 3.4 77 66 0 ACGGAUUAG-Cg====A=g==CC-UUCCGAAAG\1"
1307	"BcSSSS00\1" " BcSSSS00 3 0 3.4 25 21 0 GAUCAAGUC-======A===AU=-GGAGCUUGC\1"
1308	"ClfPerfr\1" " ClfPerfr 6 0 3.9 121 108 0 AUCAUAAUG-C====A=ug==gU-GAAGUCGUA\1"
1309	"ClnCorin\1" " ClnCorin 6 0 3.9 122 109 0 CGCAUAAGA-C====A=ug==gU-GAAGUCGUA\1"
1310	"CltBotul\1" " CltBotul 6 0 3.9 122 109 0 CUCAUAAGA-C====A=ug==gU-GAAGUCGUA\1"
1311	"CPPParap\1" " CPPParap 6 0 3.9 122 109 0 GCAUAAGAU-C====A=ug==gU-AAGUCGUAA\1"
1312	"DcdNodos\1" " DcdNodos 6 0 4.2 77 66 0 GUAACCUAG-Ug====A=g=AC=-UAUGGAAAC\1"
1313	"PsAAAA00\1" " PsAAAA00 6 0 4.2 77 66 0 UGGAUUCAG-Cg====A=g=AC=-UCCGGAAAC\1"
1314	"PslFlave\1" " PslFlave 6 0 4.2 77 66 0 CUGAUUCAG-Cg====A=g=AC=-UUUCGAAAG\1"
1315	"FrhhPhil\1" " FrhhPhil 5 0 4.2 149 135 0 UAACAAUGG-U===C==ag===A-CCUGCGGCU\1"
1316	"AclPleur\1" " AclPleur 4 0 4.3 29 24 0 GAUCAAGUC-==A====a=C=g=-AAGGGAGCU\1"
1317	"PbcAcet2\1" " PbcAcet2 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1318	"PbrPropi\1" " PbrPropi 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1319	"Stsssola\1" " Stsssola 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1320	"LgtLytic\1" " LgtLytic 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1321	"PslFlave\1" " PslFlave 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1322	"HllHalod\1" " HllHalod 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1"
1323	"VbrFurni\1" " VbrFurni 5 0 4.4 68 60 0 GGAUUUGUU-=g====CG==Cg=-CGGACGGAC\1"
1324	"AclPleur\1" " AclPleur 6 0 4.4 35 30 0 GUCGAACGG-U=A===ga===gA-GCUUGCUUU\1"
1325	"PslFlave\1" " PslFlave 6 6 4.4 25 21 0 GAUCAAGUC-=======......-<more>\1"
1326	"PtVVVulg\1" " PtVVVulg 6 6 4.4 29 24 0 GAUCAAGUC-=======......-<more>\1"
1327	"VbrFurni\1" " VbrFurni 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1"
1328	"VblVulni\1" " VblVulni 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1"
1329	"VbhChole\1" " VbhChole 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1";
1330
1331	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1332	arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3);
1333	arguments[2] = "matchmismatches=4"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd4);
1334	}
1335
1336	// --------------------------
1337	// truncate results
1338
1339	{
1340	const char *arguments[] = {
1341	"prgnamefake",
1342	"matchsequence=CANCNCNNUNC", // contains 5N
1343	NULL, // matchmismatches
1344	"matchacceptN=5",
1345	"matchlimitN=7",
1346	"matchmaxresults=5",
1347	};
1348
1349	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1350	"BcSSSS00\1" " BcSSSS00 0 5 4.2 176 162 0 CGGCUGGAU-==C=U=CU=U=-U.\1";
1351
1352	// many hits are truncated here:
1353	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1354	"DlcTolu2\1" " DlcTolu2 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU==N-N.\1"
1355	"FrhhPhil\1" " FrhhPhil 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU=..-\1"
1356	"HllHalod\1" " HllHalod 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU=..-\1"
1357	"CPPParap\1" " CPPParap 1 6 4.9 177 163 0 CGGNUGGAU-==C=U=CU=..-\1"
1358	"AclPleur\1" " AclPleur 1 6 5.0 176 162 0 CGGUUGGAU-==C=U=CU=A.-\1";
1359
1360	// many hits are truncated here:
1361	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
1362	"HllHalod\1" " HllHalod 2 5 5.1 45 40 0 AAACGAUGG-a=G=UuGC=U=-CAGGCGUCG\1"
1363	"VblVulni\1" " VblVulni 2 5 5.4 49 44 0 AGCACAGAG-a=A=UuGU=U=-UCGGGUGGC\1"
1364	"VbrFurni\1" " VbrFurni 2 5 5.7 40 35 0 CGGCAGCGA-==A=AuUGAA=-CUUCGGGGG\1"
1365	"LgtLytic\1" " LgtLytic 2 5 6.2 101 89 0 GGGGAAACU-==AGCuAA=A=-CGCAUAAUC\1"
1366	"ClfPerfr\1" " ClfPerfr 2 5 6.5 172 158 0 AGGAAGAUU-a=UaC=CC=C=-UUUCU.\1";
1367
1368	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1369	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
1370	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
1371	}
1372
1373	// -------------------------------------------------------------
1374	// tests related to http://bugs.arb-home.de/ticket/410
1375	{
1376	const char *arguments[] = {
1377	"prgnamefake",
1378	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACC", // length=29
1379	NULL, // matchmismatches
1380	"matchacceptN=5",
1381	"matchlimitN=7",
1382	"matchmaxresults=10",
1383	};
1384
1385	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'ACGGACUCCGGGAAACCGGGGCUAAUACC'\1"
1386	"BcSSSS00\1" " BcSSSS00 0 0 0.0 84 72 0 UAGCGGCGG-=============================-GGAUGGUGA\1"
1387	"Bl0LLL00\1" " Bl0LLL00 0 0 0.0 84 72 0 CAGCGGCGG-=============================-GGAUGCUGA\1"
1388	"AclPleur\1" " AclPleur 4 0 4.6 84 72 0 GAGUGGCGG-=======a========u=UA=========-GCGUAAUCA\1"
1389	"PtVVVulg\1" " PtVVVulg 4 0 5.1 84 72 0 GAGCGGCGG-=======a=U======G=U==========-GCAUGACCA\1"
1390	"DsssDesu\1" " DsssDesu 5 0 5.3 84 72 0 GAGUGGCGC-========u=C====Gu==A=========-GGAUACAGA\1"
1391	"PsAAAA00\1" " PsAAAA00 5 0 5.3 84 72 0 CAGCGGCGG-======gu=C======G==C=========-GCAUACGCA\1";
1392
1393	arguments[2] = "matchmismatches=5"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1394	}
1395	{
1396	const char *arguments[] = {
1397	"prgnamefake",
1398	"matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA", // length=38
1399	NULL, // matchmismatches
1400	"matchacceptN=5",
1401	"matchlimitN=7",
1402	"matchmaxresults=10",
1403	};
1404
1405	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA'\1"
1406	"BcSSSS00\1" " BcSSSS00 0 0 0.0 84 72 0 UAGCGGCGG-======================================-UGAUUGGGG\1"
1407	"Bl0LLL00\1" " Bl0LLL00 1 0 1.5 84 72 0 CAGCGGCGG-==================================C===-UGAUUGGGG\1";
1408
1409	arguments[2] = "matchmismatches=18"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
1410	}
1411	}
1412
1413	static char extract_locations(const char probe_design_result) {
1414	const char *Target = strstr(probe_design_result, "\nTarget");
1415	if (Target) {
1416	const char *designed = strchr(Target+7, '\n');
1417	if (designed) {
1418	++designed;
1419
1420	GBS_strstruct result(300);
1421	RegExpr reg_designed("^[A-Z]+"
1422	"[[:space:]]+[0-9]+"
1423	"[[:space:]]+([A-Z][=+-])" // subexpr #1 (loc+-=)
1424	"[[:space:]]*([0-9]+)", // subexpr #2 (abs or locrel)
1425	true);
1426
1427
1428	while (designed) {
1429	const char *eol = strchr(designed, '\n');
1430	const RegMatch *match = reg_designed.match(designed); if (!match) break;
1431
1432	match = reg_designed.subexpr_match(1); if (!match) break;
1433	std::string loc = match->extract(designed);
1434
1435	match = reg_designed.subexpr_match(2); if (!match) break;
1436	std::string pos = match->extract(designed);
1437
1438	result.cat(loc.c_str());
1439	result.cat(pos.c_str());
1440
1441	designed = eol ? eol+1 : NULL;
1442	}
1443
1444	return result.release();
1445	}
1446	}
1447	return strdup("can't extract");
1448	}
1449
1450	inline const char next_line(const char this_line) {
1451	const char *lf = strchr(this_line, '\n');
1452	return (lf && lf[1] && strchr("ACGTU", lf[1])) ? lf+1 : NULL;
1453	}
1454	inline int count_hits(const char *design_result) {
1455	const char *target = strstr(design_result, "\nTarget");
1456	if (target) {
1457	const char *hit = next_line(target+1);
1458	int hits = 0;
1459
1460	while (hit) {
1461	++hits;
1462	hit = next_line(hit);
1463	}
1464	return hits;
1465	}
1466	return -1;
1467	}
1468
1469	void TEST_SLOW_design_probe() {
1470	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
1471
1472	bool use_gene_ptserver = false;
1473	{
1474	int hits_len_18;
1475	{
1476	const char *arguments[] = {
1477	"prgnamefake",
1478	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1479	"designmintargets=100",
1480	};
1481	const char *expected =
1482	"Probe design parameters:\n"
1483	"Length of probe 18\n"
1484	"Temperature [ 0.0 -400.0]\n"
1485	"GC-content [30.0 - 80.0]\n"
1486	"E.Coli position [any]\n"
1487	"Max. nongroup hits 0\n"
1488	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1489	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1490	"CGAAAGGAAGAUUAAUAC 18 A=94 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1491	"GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC \| - - - - - - - - - - - - - - - - - - - -\n"
1492	"UCAAGUCGAGCGAUGAAG 18 B=18 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA \| - - - - - - - - - - - - - - - 2 2 2 2 2\n"
1493	"AUCAAGUCGAGCGAUGAA 18 B- 1 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU \| - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n";
1494
1495	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1496	hits_len_18 = count_hits(expected);
1497	TEST_EXPECT_EQUAL(hits_len_18, 4);
1498
1499	// test extraction of positions:
1500	{
1501	char *positions = extract_locations(expected);
1502	TEST_EXPECT_EQUAL(positions, "A=94A+1B=18B-1");
1503	free(positions);
1504	}
1505	}
1506	// same as above with probelength 17
1507	int hits_len_17;
1508	{
1509	const char *arguments[] = {
1510	"prgnamefake",
1511	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1512	"designmintargets=100",
1513	"designprobelength=17",
1514	};
1515	const char *expected =
1516	"Probe design parameters:\n"
1517	"Length of probe 17\n"
1518	"Temperature [ 0.0 -400.0]\n"
1519	"GC-content [30.0 - 80.0]\n"
1520	"E.Coli position [any]\n"
1521	"Max. nongroup hits 0\n"
1522	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1523	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1524	"CAAGUCGAGCGAUGAAG 17 A=19 18 65 4 52.9 52.0 CUUCAUCGCUCGACUUG \| - - - - - - - - - - - - - - - - 2 2 2 2\n"
1525	"UCAAGUCGAGCGAUGAA 17 A- 1 17 49 4 47.1 50.0 UUCAUCGCUCGACUUGA \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1526	"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";
1527
1528	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1529	hits_len_17 = count_hits(expected);
1530	TEST_EXPECT_EQUAL(hits_len_17, 3);
1531	}
1532	// same as above with probelength 16
1533	int hits_len_16;
1534	{
1535	const char *arguments[] = {
1536	"prgnamefake",
1537	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1538	"designmintargets=100",
1539	"designprobelength=16",
1540	};
1541	const char *expected =
1542	"Probe design parameters:\n"
1543	"Length of probe 16\n"
1544	"Temperature [ 0.0 -400.0]\n"
1545	"GC-content [30.0 - 80.0]\n"
1546	"E.Coli position [any]\n"
1547	"Max. nongroup hits 0\n"
1548	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1549	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1550	"CGAAAGGAAGAUUAAU 16 A=94 82 77 4 31.2 42.0 AUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1551	"AAGGAAGAUUAAUACC 16 A+ 3 85 77 4 31.2 42.0 GGUAUUAAUCUUCCUU \| - - - - - - - - - - - - - - - - - - - -\n"
1552	"AAGUCGAGCGAUGAAG 16 B=20 19 69 4 50.0 48.0 CUUCAUCGCUCGACUU \| - - - - - - - - - - - - - - - - - 2 2 2\n"
1553	"CAAGUCGAGCGAUGAA 16 B- 1 18 49 4 50.0 48.0 UUCAUCGCUCGACUUG \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1554	"UCAAGUCGAGCGAUGA 16 B- 2 17 37 4 50.0 48.0 UCAUCGCUCGACUUGA \| - - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2\n"
1555	"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";
1556
1557	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1558	hits_len_16 = count_hits(expected);
1559	TEST_EXPECT_EQUAL(hits_len_16, 6);
1560	}
1561	// combine the 3 preceeding designs
1562	int combined_hits;
1563	{
1564	const char *arguments[] = {
1565	"prgnamefake",
1566	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
1567	"designmintargets=100",
1568	"designprobelength=16",
1569	"designmaxprobelength=18",
1570	};
1571	const char *expected =
1572	"Probe design parameters:\n"
1573	"Length of probe 16-18\n"
1574	"Temperature [ 0.0 -400.0]\n"
1575	"GC-content [30.0 - 80.0]\n"
1576	"E.Coli position [any]\n"
1577	"Max. nongroup hits 0\n"
1578	"Min. group hits 100% (max. rejected coverage: 75%)\n"
1579	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1580	"CGAAAGGAAGAUUAAU 16 A=94 82 77 4 31.2 42.0 AUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1581	"CGAAAGGAAGAUUAAUAC 18 A+ 0 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1582	"GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC \| - - - - - - - - - - - - - - - - - - - -\n"
1583	"AAGGAAGAUUAAUACC 16 A+ 3 85 77 4 31.2 42.0 GGUAUUAAUCUUCCUU \| - - - - - - - - - - - - - - - - - - - -\n"
1584	"AAGUCGAGCGAUGAAG 16 B=20 19 69 4 50.0 48.0 CUUCAUCGCUCGACUU \| - - - - - - - - - - - - - - - - - 2 2 2\n"
1585	"CAAGUCGAGCGAUGAAG 17 B- 1 18 65 4 52.9 52.0 CUUCAUCGCUCGACUUG \| - - - - - - - - - - - - - - - - 2 2 2 2\n"
1586	"UCAAGUCGAGCGAUGAAG 18 B- 2 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA \| - - - - - - - - - - - - - - - 2 2 2 2 2\n"
1587	"UCAAGUCGAGCGAUGAA 17 B- 2 17 49 4 47.1 50.0 UUCAUCGCUCGACUUGA \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1588	"CAAGUCGAGCGAUGAA 16 B- 1 18 49 4 50.0 48.0 UUCAUCGCUCGACUUG \| - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n"
1589	"AUCAAGUCGAGCGAUGAA 18 B- 3 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU \| - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n"
1590	"UCAAGUCGAGCGAUGA 16 B- 2 17 37 4 50.0 48.0 UCAUCGCUCGACUUGA \| - - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2\n"
1591	"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"
1592	"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";
1593
1594	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1595	combined_hits = count_hits(expected);
1596	}
1597
1598	// check that combined design reports all probes reported by single designs:
1599	TEST_EXPECT_EQUAL(combined_hits, hits_len_16+hits_len_17+hits_len_18);
1600	}
1601	// test vs bug (fails with [8988] .. [9175])
1602	{
1603	const char *arguments[] = {
1604	"prgnamefake",
1605	"designnames=VbhChole#VblVulni",
1606	"designmintargets=50", // hit at least 1 of the 2 targets
1607	"designmingc=60", "designmaxgc=75", // specific GC range
1608	};
1609
1610	const char *expected =
1611	"Probe design parameters:\n"
1612	"Length of probe 18\n"
1613	"Temperature [ 0.0 -400.0]\n"
1614	"GC-content [60.0 - 75.0]\n"
1615	"E.Coli position [any]\n"
1616	"Max. nongroup hits 0 (lowest rejected nongroup hits: 1)\n"
1617	"Min. group hits 50%\n"
1618	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1619	"AGUCGAGCGGCAGCACAG 18 A=21 20 39 2 66.7 60.0 CUGUGCUGCCGCUCGACU \| - - - - - - - - - - - - - - - - - - - -\n"
1620	"GUCGAGCGGCAGCACAGA 18 A+ 1 21 39 2 66.7 60.0 UCUGUGCUGCCGCUCGAC \| - - - - - - - - - - - - - - - - - - - -\n"
1621	"UCGAGCGGCAGCACAGAG 18 A+ 2 21 39 2 66.7 60.0 CUCUGUGCUGCCGCUCGA \| - - - - - - - - - - - - - - - - - - - -\n"
1622	"AAGUCGAGCGGCAGCACA 18 A- 1 19 25 2 61.1 58.0 UGUGCUGCCGCUCGACUU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1623	"CGAGCGGCAGCACAGAGA 18 A+ 3 21 20 1 66.7 60.0 UCUCUGUGCUGCCGCUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1624	"CGAGCGGCAGCACAGAGG 18 A+ 3 21 20 1 72.2 62.0 CCUCUGUGCUGCCGCUCG \| - - - - - - - - - - - - - - - - - - - -\n"
1625	"GAGCGGCAGCACAGAGAA 18 A+ 4 21 20 1 61.1 58.0 UUCUCUGUGCUGCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1626	"GAGCGGCAGCACAGAGGA 18 A+ 4 21 20 1 66.7 60.0 UCCUCUGUGCUGCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1627	"AGCGGCAGCACAGAGGAA 18 A+ 5 21 20 1 61.1 58.0 UUCCUCUGUGCUGCCGCU \| - - - - - - - - - - - - - - - - - - - -\n"
1628	"GCGGCAGCACAGAGAAAC 18 A+ 6 22 20 1 61.1 58.0 GUUUCUCUGUGCUGCCGC \| - - - - - - - - - - - - - - - - - - - -\n"
1629	"GCGGCAGCACAGAGGAAC 18 A+ 6 22 20 1 66.7 60.0 GUUCCUCUGUGCUGCCGC \| - - - - - - - - - - - - - - - - - - - -\n"
1630	"CGGCAGCACAGAGGAACU 18 A+ 7 23 20 1 61.1 58.0 AGUUCCUCUGUGCUGCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1631	"CUUGUUCCUUGGGUGGCG 18 B=52 47 20 1 61.1 58.0 CGCCACCCAAGGAACAAG \| - - - - - - - - - - - - - - - - - - - -\n"
1632	"CUUGUUUCUCGGGUGGCG 18 B+ 0 47 20 1 61.1 58.0 CGCCACCCGAGAAACAAG \| - - - - - - - - - - - - - - - - - - - -\n"
1633	"UGUUCCUUGGGUGGCGAG 18 B+ 2 49 20 1 61.1 58.0 CUCGCCACCCAAGGAACA \| - - - - - - - - - - - - - - - - - - - -\n"
1634	"UGUUUCUCGGGUGGCGAG 18 B+ 2 49 20 1 61.1 58.0 CUCGCCACCCGAGAAACA \| - - - - - - - - - - - - - - - - - - - -\n"
1635	"GUUCCUUGGGUGGCGAGC 18 B+ 3 50 20 1 66.7 60.0 GCUCGCCACCCAAGGAAC \| - - - - - - - - - - - - - - - - - - - -\n"
1636	"GUUUCUCGGGUGGCGAGC 18 B+ 3 50 20 1 66.7 60.0 GCUCGCCACCCGAGAAAC \| - - - - - - - - - - - - - - - - - - - -\n"
1637	"UUCCUUGGGUGGCGAGCG 18 B+10 57 20 1 66.7 60.0 CGCUCGCCACCCAAGGAA \| - - - - - - - - - - - - - - - - - - - -\n"
1638	"UUUCUCGGGUGGCGAGCG 18 B+10 57 20 1 66.7 60.0 CGCUCGCCACCCGAGAAA \| - - - - - - - - - - - - - - - - - - - -\n"
1639	"UCCUUGGGUGGCGAGCGG 18 B+11 58 20 1 72.2 62.0 CCGCUCGCCACCCAAGGA \| - - - - - - - - - - - - - - - - - - - -\n"
1640	"UUCUCGGGUGGCGAGCGG 18 B+11 58 20 1 72.2 62.0 CCGCUCGCCACCCGAGAA \| - - - - - - - - - - - - - - - - - - - -\n"
1641	"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"
1642	"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";
1643
1644	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1645	}
1646
1647	// design MANY probes to test location specifier
1648	{
1649	const char *arguments_loc[] = {
1650	"prgnamefake",
1651	// "designnames=Stsssola#Stsssola", // @@@ crashes the ptserver
1652	"designnames=CPPParap#PsAAAA00",
1653	"designmintargets=50", // hit at least 1 of the 2 targets
1654	"designmingc=0", "designmaxgc=100", // allow all GCs
1655	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1656	"designmishit=7", // allow enough outgroup hits
1657	"designprobelength=9",
1658	};
1659
1660	const char *expected_loc =
1661	"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";
1662
1663	TEST_ARB_PROBE_FILT(ARRAY_ELEMS(arguments_loc), arguments_loc, extract_locations, expected_loc);
1664	}
1665
1666	// same as above
1667	{
1668	const char *arguments[] = {
1669	"prgnamefake",
1670	"designnames=CPPParap#PsAAAA00",
1671	"designmintargets=50", // hit at least 1 of the 2 targets
1672	"designmingc=0", "designmaxgc=100", // allow all GCs
1673	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1674	"designmishit=7", // allow enough outgroup hits
1675	"designprobelength=9",
1676	};
1677
1678	const char *expected =
1679	"Probe design parameters:\n"
1680	"Length of probe 9\n"
1681	"Temperature [30.0 -100.0]\n"
1682	"GC-content [ 0.0 -100.0]\n"
1683	"E.Coli position [any]\n"
1684	"Max. nongroup hits 7 (lowest rejected nongroup hits: 9)\n"
1685	"Min. group hits 50%\n"
1686	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1687	"GAGCGGAUG 9 A= 29 24 20 1 66.7 30.0 CAUCCGCUC \| - - - - - - - - - - - - - - - - - - - -\n"
1688	"UGCUCCUGG 9 B= 51 46 20 1 66.7 30.0 CCAGGAGCA \| - - - - - - - - - - - - - - - - - - - -\n"
1689	"GCUCCUGGA 9 B+ 1 47 20 1 66.7 30.0 UCCAGGAGC \| - - - - - - - - - - - - - - - - - - - -\n"
1690	"CGGGCGCUA 9 C= 99 87 20 1 77.8 32.0 UAGCGCCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1691	"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"
1692	"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"
1693	"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"
1694	"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"
1695	"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"
1696	"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"
1697	"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"
1698	"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"
1699	"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"
1700	"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"
1701	"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"
1702	"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"
1703	"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"
1704	"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"
1705	"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"
1706	"GGAAACGGG 9 C- 5 82 17 1 66.7 30.0 CCCGUUUCC \| - - - - - - - - - - - - - - - - 3 3 3 3\n"
1707	"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"
1708	"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"
1709	"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"
1710	"GGACGUCCG 9 E+ 6 74 14 1 77.8 32.0 CGGACGUCC \| - - - - - - - - - - - - - 1 1 1 1 3 3 3\n"
1711	"GACGUCCGG 9 E+ 7 75 14 1 77.8 32.0 CCGGACGUC \| - - - - - - - - - - - - - 1 1 1 1 2 2 14\n"
1712	"ACGUCCGGA 9 E+ 8 76 14 1 66.7 30.0 UCCGGACGU \| - - - - - - - - - - - - - 1 1 11 11 12 12 17\n"
1713	"CGUCCGGAA 9 G= 89 77 14 1 66.7 30.0 UUCCGGACG \| - - - - - - - - - - - - - 1 1 1 1 2 2 2\n"
1714	"AACGGGCGC 9 C- 2 85 14 1 77.8 32.0 GCGCCCGUU \| - - - - - - - - - - - - - 1 1 1 1 1 1 2\n"
1715	"CGAGCGGAU 9 A- 1 23 13 1 66.7 30.0 AUCCGCUCG \| - - - - - - - - - - - - 3 3 3 3 3 3 3 3\n"
1716	"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"
1717	"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"
1718	"ACGGGCGCU 9 C- 1 86 12 1 77.8 32.0 AGCGCCCGU \| - - - - - - - - - - - 1 1 1 1 1 1 2 2 2\n"
1719	"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"
1720	"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"
1721	"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"
1722	"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"
1723	"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"
1724	"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"
1725	"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"
1726	"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"
1727	"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"
1728	"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"
1729	"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"
1730	"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"
1731	"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"
1732	"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"
1733	"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"
1734	"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"
1735	"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"
1736	"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"
1737	"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"
1738	"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"
1739	"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";
1740
1741	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1742	}
1743
1744	// same as above (with probelen == 8)
1745	{
1746	const char *arguments[] = {
1747	"prgnamefake",
1748	"designnames=CPPParap#PsAAAA00",
1749	"designmintargets=50", // hit at least 1 of the 2 targets
1750	"designmingc=0", "designmaxgc=100", // allow all GCs
1751	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1752	// "designmishit=7",
1753	"designmishit=15", // @@@ reports more results than with 7 mishits, but no mishits reported below!
1754	"designprobelength=8",
1755	};
1756
1757	const char *expected =
1758	"Probe design parameters:\n"
1759	"Length of probe 8\n"
1760	"Temperature [30.0 -100.0]\n"
1761	"GC-content [ 0.0 -100.0]\n"
1762	"E.Coli position [any]\n"
1763	"Max. nongroup hits 15\n"
1764	"Min. group hits 50%\n"
1765	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1766	"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"
1767	"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"
1768	"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"
1769	"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"
1770	"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"
1771	"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"
1772	"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"
1773	"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"
1774	#if defined(ARB_64)
1775	"ACGGGCGC 8 B=98 86 13 1 87.5 30.0 GCGCCCGU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1776	"CGGGCGCU 8 B+ 1 87 13 1 87.5 30.0 AGCGCCCG \| - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n"
1777	"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";
1778	#else // !defined(ARB_64)
1779	// @@@ 32bit version differs (possibly numeric issues?)
1780	"ACGGGCGC 8 B=98 86 13 1 87.5 30.0 GCGCCCGU \| - - - - - - - - - - - - 1 1 1 1 1 1 1 2\n"
1781	"CGGGCGCU 8 B+ 1 87 13 1 87.5 30.0 AGCGCCCG \| - - - - - - - - - - - - 1 1 1 1 1 1 1 2\n"
1782	"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";
1783	#endif
1784
1785	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1786	}
1787
1788	// same as above (but restricting ecoli-range)
1789	{
1790	const char *arguments[] = {
1791	"prgnamefake",
1792	"designnames=CPPParap#PsAAAA00",
1793	"designmintargets=50", // hit at least 1 of the 2 targets
1794	"designmingc=0", "designmaxgc=100", // allow all GCs
1795	"designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg
1796	"designmishit=15",
1797	"designprobelength=8",
1798	"designminpos=65", "designmaxpos=69", // restrict ecoli-range
1799	};
1800
1801	const char *expected =
1802	"Probe design parameters:\n"
1803	"Length of probe 8\n"
1804	"Temperature [30.0 -100.0]\n"
1805	"GC-content [ 0.0 -100.0]\n"
1806	"E.Coli position [ 65 - 69]\n"
1807	"Max. nongroup hits 15\n"
1808	"Min. group hits 50%\n"
1809	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1810	"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"
1811	"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"
1812	"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"
1813	"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"
1814	"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";
1815
1816	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1817	}
1818
1819	{
1820	const char *arguments[] = {
1821	"prgnamefake",
1822	"designnames=ClnCorin#CPPParap#ClfPerfr",
1823	"designprobelength=16",
1824	"designmintargets=100",
1825	"designmishit=2",
1826	};
1827	const char *expected =
1828	"Probe design parameters:\n"
1829	"Length of probe 16\n"
1830	"Temperature [ 0.0 -400.0]\n"
1831	"GC-content [30.0 - 80.0]\n"
1832	"E.Coli position [any]\n"
1833	"Max. nongroup hits 2 (lowest rejected nongroup hits: 6)\n"
1834	"Min. group hits 100% (max. rejected coverage: 67%)\n"
1835	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1836	"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"
1837	"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"
1838	"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"
1839	"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"
1840	"GUCGAGCGAUGAAGUU 16 B+ 2 21 31 3 50.0 48.0 AACUUCAUCGCUCGAC \| - - - - - - - - - - 1 1 1 1 1 1 1 1 1 1\n"
1841	"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"
1842	"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"
1843	"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"
1844	"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"
1845	"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";
1846
1847	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1848	}
1849	// test same design as above, but add 2 "unknown species" each of which is missing one of the previously designed probes
1850	{
1851	const char *arguments[] = {
1852	"prgnamefake",
1853	"designnames=ClnCorin#Unknown1#CPPParap#ClfPerfr#Unknown2",
1854	"designprobelength=16",
1855	"designmintargets=100",
1856	"designmishit=2",
1857	// pass sequences for the unknown species
1858	"designsequence=---CGAAAGGAAGAUUAAU------------------AAGUCGAGCGAUGAAG-CAAGUCGAGCGAUGAA-GUCGAGCGAUGAAGUU-UCAAGUCGAGCGAUGA-AGUCGAGCGAUGAAGU-AUCAAGUCGAGCGAUG-GAUCAAGUCGAGCGAU-UGAUCAAGUCGAGCGA",
1859	"designsequence=---CGAAAGGAAGAUUAAU-AAGGAAGAUUAAUACC-AAGUCGAGCGAUGAAG-CAAGUCGAGCGAUGAA-GUCGAGCGAUGAAGUU-UCAAGUCGAGCGAUGA-AGUCGAGCGAUGAAGU-AUCAAGUCGAGCGAUG------------------UGAUCAAGUCGAGCGA",
1860	};
1861	const char *expected =
1862	"Probe design parameters:\n"
1863	"Length of probe 16\n"
1864	"Temperature [ 0.0 -400.0]\n"
1865	"GC-content [30.0 - 80.0]\n"
1866	"E.Coli position [any]\n"
1867	"Max. nongroup hits 2\n"
1868	"Min. group hits 100% (max. rejected coverage: 80%)\n"
1869	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1870	"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"
1871	// AAGGAAGAUUAAUACC is not designed here
1872	"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"
1873	"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"
1874	"GUCGAGCGAUGAAGUU 16 B+ 2 21 51 5 50.0 48.0 AACUUCAUCGCUCGAC \| - - - - - - - - - - 1 1 1 1 1 1 1 1 1 1\n"
1875	"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"
1876	"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"
1877	"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"
1878	// GAUCAAGUCGAGCGAU is not designed here
1879	"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";
1880
1881	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1882	}
1883	{
1884	const char *arguments[] = {
1885	"prgnamefake",
1886	"designnames=VbrFurni",
1887	"designprobelength=8",
1888	"designmingc=80",
1889	"designmaxgc=100",
1890	};
1891	const char *expected =
1892	"Probe design parameters:\n"
1893	"Length of probe 8\n"
1894	"Temperature [ 0.0 -400.0]\n"
1895	"GC-content [80.0 -100.0]\n"
1896	"E.Coli position [any]\n"
1897	"Max. nongroup hits 0 (lowest rejected nongroup hits: 2)\n"
1898	"Min. group hits 50%\n"
1899	"Target le apos ecol qual grps G+C temp Probe \| Decrease T by n*.3C -> probe matches n non group species\n"
1900	#if defined(ARB_64)
1901	"CGGCAGCG 8 A=28 23 20 1 87.5 30.0 CGCUGCCG \| - - - - - - - - - - - - - - - - - - - -\n"
1902	#else // !defined(ARB_64)
1903	"CGGCAGCG 8 A=28 23 20 1 87.5 30.0 CGCUGCCG \| - - - - - - - - - - - - - - - - - - - 3\n"
1904	#endif
1905	"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"
1906	#if defined(ARB_64)
1907	"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"
1908	#else // !defined(ARB_64)
1909	"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"
1910	#endif
1911	"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"
1912	"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"
1913	"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";
1914
1915	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1916	}
1917	{
1918	const char *arguments[] = {
1919	"prgnamefake",
1920	"designnames=HllHalod#VbhChole#VblVulni#VbrFurni#PtVVVulg",
1921	"designprobelength=14",
1922	"designmintargets=100",
1923	"designmishit=4",
1924	"designmingc=70",
1925	"designmaxgc=100",
1926	};
1927	const char *expected =
1928	"Probe design parameters:\n"
1929	"Length of probe 14\n"
1930	"Temperature [ 0.0 -400.0]\n"
1931	"GC-content [70.0 -100.0]\n"
1932	"E.Coli position [any]\n"
1933	"Max. nongroup hits 4\n"
1934	"Min. group hits 100% (max. rejected coverage: 80%)\n"
1935	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
1936	"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"
1937	"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"
1938	"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";
1939
1940	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1941	}
1942	{
1943	const char *arguments[] = {
1944	"prgnamefake",
1945	"designnames=HllHalod#VbhChole#VblVulni#VbrFurni#PtVVVulg",
1946	"designprobelength=14",
1947	"designmintargets=100",
1948	"designmishit=0",
1949	"designmingc=51",
1950	"designmaxgc=60",
1951	};
1952	const char *expected = ""; // no probes found!
1953
1954	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
1955	}
1956
1957	}
1958
1959	void TEST_SLOW_probe_design_errors() {
1960	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
1961
1962	bool use_gene_ptserver = false;
1963	{
1964	const char *arguments[] = {
1965	"prgnamefake",
1966	"designnames=CPPParap#PsAAAA00",
1967	"designprobelength=3",
1968	};
1969	const char *expected_error = "Specified min. probe length 3 is below the min. allowed probe length of 8";
1970
1971	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
1972	}
1973	{
1974	const char *arguments[] = {
1975	"prgnamefake",
1976	"designnames=CPPParap#PsAAAA00",
1977	"designprobelength=15",
1978	"designmaxprobelength=12",
1979	};
1980	const char *expected_error = "Max. probe length 12 is below the specified min. probe length of 15";
1981
1982	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
1983	}
1984	{
1985	const char *expected_error = "Sequence contains only 0 bp. Impossible design request for one of the added sequences";
1986	{
1987	const char *arguments[] = {
1988	"prgnamefake",
1989	"designsequence=", // pass an empty sequence
1990	"designprobelength=16",
1991	};
1992	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
1993	}
1994	{
1995	const char *arguments[] = {
1996	"prgnamefake",
1997	"designsequence=-------------", // pass a gap-only sequence
1998	"designprobelength=16",
1999	};
2000	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2001	}
2002	}
2003	{
2004	const char *arguments[] = {
2005	"prgnamefake",
2006	"designsequence=ACGTACGTACGTACGT", // pass a long enough (unexpected) sequence
2007	"designprobelength=16",
2008	};
2009	const char *expected_error = "Got 0 unknown marked species, but 1 custom sequence was added (has to match)";
2010	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2011	}
2012	{
2013	const char *arguments[] = {
2014	"prgnamefake",
2015	"designnames=Unknown", // one unknown species
2016	"designprobelength=16",
2017	};
2018	const char *expected_error = "No species marked - no probes designed";
2019	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2020	}
2021	{
2022	const char *arguments[] = {
2023	"prgnamefake",
2024	"designnames=Unknown#CPPParap", // one unknown species, one known species
2025	"designprobelength=16",
2026	};
2027	const char *expected_error = "Got 1 unknown marked species, but 0 custom sequences were added (has to match)";
2028	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2029	}
2030	{
2031	const char *expected_error = "Sequence contains only 0 bp. Impossible design request for one of the added sequences";
2032	{
2033	const char *arguments[] = {
2034	"prgnamefake",
2035	"designnames=Unknown", // one unknown species
2036	"designsequence=", // pass an empty sequence
2037	"designprobelength=16",
2038	};
2039	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2040	}
2041	{
2042	const char *arguments[] = {
2043	"prgnamefake",
2044	"designnames=Unknown", // one unknown species
2045	"designsequence=-------------", // pass a gap-only sequence
2046	"designprobelength=16",
2047	};
2048	TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error);
2049	}
2050	}
2051	}
2052
2053	void TEST_SLOW_match_designed_probe() {
2054	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2055
2056	bool use_gene_ptserver = false;
2057	const char *arguments[] = {
2058	"prgnamefake",
2059	"matchsequence=UCAAGUCGAGCGAUGAAG",
2060	};
2061	CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UCAAGUCGAGCGAUGAAG'\1"
2062	"ClnCorin\1" " ClnCorin 0 0 0.0 18 17 0 .GAGUUUGA-==================-UUCCUUCGG\1"
2063	"CltBotul\1" " CltBotul 0 0 0.0 18 17 0 ........A-==================-CUUCUUCGG\1"
2064	"CPPParap\1" " CPPParap 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUCCUUCGG\1"
2065	"ClfPerfr\1" " ClfPerfr 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUUCCUUCG\1";
2066
2067	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2068	}
2069
2070	void TEST_SLOW_get_existing_probes() {
2071	// test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb
2072
2073	bool use_gene_ptserver = false;
2074	{
2075	const char *arguments[] = {
2076	"prgnamefake",
2077	"iterate=20",
2078	"iterate_amount=10",
2079	};
2080	CCP expected =
2081	"AAACCGGGGCTAATACCGGA;AAACGACTGTTAATACCGCA;AAACGATGGAAGCTTGCTTC;AAACGATGGCTAATACCGCA;AAACGGATTAGCGGCGGGAC;"
2082	"AAACGGGCGCTAATACCGCA;AAACGGTCGCTAATACCGGA;AAACGGTGGCTAATACCGCA;AAACGTACGCTAATACCGCA;AAACTCAAGCTAATACCGCA";
2083
2084	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2085	}
2086	{
2087	const char *arguments[] = {
2088	"prgnamefake",
2089	"iterate=15",
2090	"iterate_amount=20",
2091	"iterate_separator=:",
2092	};
2093	CCP expected =
2094	"AAACCGGGGCTAATA:AAACGACTGTTAATA:AAACGATGGAAGCTT:AAACGATGGCTAATA:AAACGGATTAGCGGC:AAACGGGCGCTAATA:AAACGGTCGCTAATA:"
2095	"AAACGGTGGCTAATA:AAACGTACGCTAATA:AAACTCAAGCTAATA:AAACTCAGGCTAATA:AAACTGGAGAGTTTG:AAACTGTAGCTAATA:AAACTTGTTTCTCGG:"
2096	"AAAGAGGTGCTAATA:AAAGCTTGCTTTCTT:AAAGGAACGCTAATA:AAAGGAAGATTAATA:AAAGGACAGCTAATA:AAAGGGACTTCGGTC";
2097
2098	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2099	}
2100	{
2101	const char *arguments[] = {
2102	"prgnamefake",
2103	"iterate=10",
2104	"iterate_amount=5",
2105	"iterate_readable=0",
2106	};
2107	CCP expected =
2108	"\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";
2109
2110	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2111	}
2112	{
2113	const char *arguments[] = {
2114	"prgnamefake",
2115	"iterate=3",
2116	"iterate_amount=70",
2117	"iterate_tu=U",
2118	};
2119	CCP expected =
2120	"AAA;AAC;AAG;AAU;ACA;ACC;ACG;ACU;AGA;AGC;AGG;AGU;AUA;AUC;AUG;AUU;"
2121	"CAA;CAC;CAG;CAU;CCA;CCC;CCG;CCU;CGA;CGC;CGG;CGU;CUA;CUC;CUG;CUU;"
2122	"GAA;GAC;GAG;GAU;GCA;GCC;GCG;GCU;GGA;GGC;GGG;GGU;GUA;GUC;GUG;GUU;"
2123	"UAA;UAC;UAG;UAU;UCA;UCC;UCG;UCU;UGA;UGC;UGG;UGU;UUA;UUC;UUG;UUU";
2124
2125	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2126	}
2127	{
2128	const char *arguments[] = {
2129	"prgnamefake",
2130	"iterate=2",
2131	"iterate_amount=20",
2132	};
2133	CCP expected =
2134	"AA;AC;AG;AT;"
2135	"CA;CC;CG;CT;"
2136	"GA;GC;GG;GT;"
2137	"TA;TC;TG;TT";
2138
2139	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
2140	}
2141	}
2142
2143	// #define TEST_AUTO_UPDATE // uncomment to auto-update expected index dumps
2144
2145	void TEST_SLOW_index_dump() {
2146	for (int use_gene_ptserver = 0; use_gene_ptserver <= 1; use_gene_ptserver++) {
2147	const char *dumpfile = use_gene_ptserver ? "index_gpt.dump" : "index_pt.dump";
2148	char *dumpfile_exp = GBS_global_string_copy("%s.expected", dumpfile);
2149
2150	const char *arguments[] = {
2151	"prgnamefake",
2152	GBS_global_string_copy("dump=%s", dumpfile),
2153	};
2154	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, "ok");
2155
2156	#if defined(TEST_AUTO_UPDATE)
2157	TEST_COPY_FILE(dumpfile, dumpfile_exp);
2158	#else // !defined(TEST_AUTO_UPDATE)
2159	TEST_EXPECT_TEXTFILES_EQUAL(dumpfile_exp, dumpfile);
2160	#endif
2161	TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(dumpfile));
2162
2163	free((char*)arguments[1]);
2164	free(dumpfile_exp);
2165	}
2166	}
2167
2168	#undef TEST_AUTO_UPDATE
2169
2170	// --------------------------------------------------------------------------------
2171
2172	#include <arb_strarray.h>
2173	#include <set>
2174	#include <iterator>
2175
2176	using namespace std;
2177
2178	typedef set<string> Matches;
2179
2180	inline void parseMatches(char*& answer, Matches& matches) {
2181	ConstStrArray match_results;
2182
2183	GBT_splitNdestroy_string(match_results, answer, "\1", false);
2184
2185	for (size_t i = 1; i<match_results.size(); i += 2) {
2186	if (match_results[i][0]) {
2187	matches.insert(match_results[i]);
2188	}
2189	}
2190	}
2191
2192	inline void getMatches(const char *probe, Matches& matches) {
2193	bool use_gene_ptserver = false;
2194	char *matchseq = GBS_global_string_copy("matchsequence=%s", probe);
2195	const char *arguments[] = {
2196	"prgnamefake",
2197	matchseq,
2198	};
2199	TEST_RUN_ARB_PROBE(ARRAY_ELEMS(arguments), arguments);
2200	parseMatches(answer, matches);
2201	free(matchseq);
2202	}
2203
2204	inline string matches2hitlist(const Matches& matches) {
2205	string hitlist;
2206	if (!matches.empty()) {
2207	for (Matches::const_iterator m = matches.begin(); m != matches.end(); ++m) {
2208	hitlist = hitlist + ',' + *m;
2209	}
2210	hitlist = hitlist.substr(1);
2211	}
2212	return hitlist;
2213	}
2214
2215	inline void extract_first_but_not_second(const Matches& first, const Matches& second, Matches& result) {
2216	set_difference(first.begin(), first.end(),
2217	second.begin(), second.end(),
2218	inserter(result, result.begin()));
2219	}
2220
2221	// --------------------------------------------------------------------------------
2222
2223	// #define TEST_INDEX_COMPLETENESS // only uncomment temporarily (slow as hell)
2224
2225	#if defined(TEST_INDEX_COMPLETENESS)
2226
2227	void TEST_SLOW_find_unmatched_probes() {
2228	bool use_gene_ptserver = false;
2229
2230	// get all 20mers indexed in ptserver:
2231	ConstStrArray fullProbes;
2232	{
2233	const char *arguments[] = {
2234	"prgnamefake",
2235	"iterate=20",
2236	"iterate_amount=1000000",
2237	"iterate_tu=U",
2238	};
2239	TEST_RUN_ARB_PROBE(ARRAY_ELEMS(arguments), arguments);
2240
2241	GBT_splitNdestroy_string(fullProbes, answer, ";", false);
2242	TEST_EXPECT_EQUAL(fullProbes.size(), 2040);
2243	}
2244
2245	for (size_t lp = 0; lp<fullProbes.size(); ++lp) { // with all 20mers existing in ptserver
2246	const char *fullProbe = fullProbes[lp];
2247
2248	size_t fullLen = strlen(fullProbe);
2249	TEST_EXPECT_EQUAL(fullLen, 20);
2250
2251	Matches fullHits;
2252	getMatches(fullProbe, fullHits);
2253	TEST_EXPECT(fullHits.size()>0);
2254
2255	bool fewerHitsSeen = false;
2256
2257	for (size_t subLen = fullLen-1; !fewerHitsSeen && subLen >= 10; --subLen) { // for each partial sub-probe of 20mer
2258	char subProbe[20];
2259	subProbe[subLen] = 0;
2260
2261	for (size_t pos = 0; pos+subLen <= fullLen; ++pos) {
2262	Matches subHits, onlyFull;
2263
2264	memcpy(subProbe, fullProbe+pos, subLen);
2265	getMatches(subProbe, subHits);
2266	extract_first_but_not_second(fullHits, subHits, onlyFull);
2267
2268	if (!onlyFull.empty()) {
2269	fprintf(stderr, "TEST_PARTIAL_COVERS_FULL_PROBE__BROKEN(\"%s\", \"%s\");\n", subProbe, fullProbe);
2270	fewerHitsSeen = true; // only list first wrong hit for each fullProbe
2271	}
2272	}
2273	}
2274	}
2275	}
2276
2277	#endif
2278	// --------------------------------------------------------------------------------
2279
2280	static arb_test::match_expectation partial_covers_full_probe(const char part, const char full) {
2281	using namespace arb_test;
2282	using namespace std;
2283
2284	expectation_group expected;
2285	expected.add(that(strstr(full, part)).does_differ_from_NULL());
2286	expected.add(that(strlen(part)).is_less_than(strlen(full)));
2287
2288	{
2289	Matches matchFull, matchPart;
2290	getMatches(full, matchFull);
2291	getMatches(part, matchPart);
2292
2293	expected.add(that(matchFull.empty()).is_equal_to(false));
2294
2295	Matches onlyFirst;
2296	extract_first_but_not_second(matchFull, matchPart, onlyFirst);
2297
2298	string only_hit_by_full = matches2hitlist(onlyFirst);
2299	expected.add(that(only_hit_by_full).is_equal_to(""));
2300	}
2301
2302
2303	return all().ofgroup(expected);
2304	}
2305
2306	#define TEST_PARTIAL_COVERS_FULL_PROBE(part,full) TEST_EXPECTATION(partial_covers_full_probe(part, full))
2307	#define TEST_PARTIAL_COVERS_FULL_PROBE__BROKEN(part,full) TEST_EXPECTATION__BROKEN(partial_covers_full_probe(part, full))
2308
2309	void TEST_SLOW_unmatched_probes() {
2310	TEST_PARTIAL_COVERS_FULL_PROBE("CCUCCUUUCU", "GAUUAAUACCCCUCCUUUCU");
2311
2312	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUC", "GGGGAACCUGCGGUUGGAUC");
2313	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCA", "GGGAACCUGCGGUUGGAUCA");
2314	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCAC", "GGAACCUGCGGUUGGAUCAC");
2315	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACC", "GAACCUGCGGUUGGAUCACC");
2316	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCU", "AACCUGCGGUUGGAUCACCU");
2317	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUC", "ACCUGCGGUUGGAUCACCUC");
2318	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCC", "CCUGCGGUUGGAUCACCUCC");
2319	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCU", "CUGCGGUUGGAUCACCUCCU");
2320	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCUU", "UGCGGUUGGAUCACCUCCUU");
2321	TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCUUA", "GCGGUUGGAUCACCUCCUUA");
2322
2323	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUC", "GGGGAACCUGGCGCUGGAUC");
2324	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCA", "GGGAACCUGGCGCUGGAUCA");
2325	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCAC", "GGAACCUGGCGCUGGAUCAC");
2326	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACC", "GAACCUGGCGCUGGAUCACC");
2327	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCU", "AACCUGGCGCUGGAUCACCU");
2328	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUC", "ACCUGGCGCUGGAUCACCUC");
2329	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCC", "CCUGGCGCUGGAUCACCUCC");
2330	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCU", "CUGGCGCUGGAUCACCUCCU");
2331	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCUU", "UGGCGCUGGAUCACCUCCUU");
2332	TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCUUU", "GGCGCUGGAUCACCUCCUUU");
2333
2334	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCAC", "GGAACCUGCGGCUGGAUCAC");
2335	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACC", "GAACCUGCGGCUGGAUCACC");
2336	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCU", "AACCUGCGGCUGGAUCACCU");
2337	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUC", "ACCUGCGGCUGGAUCACCUC");
2338	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCC", "CCUGCGGCUGGAUCACCUCC");
2339	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCU", "CUGCGGCUGGAUCACCUCCU");
2340	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUU", "UGCGGCUGGAUCACCUCCUU");
2341	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUUU", "GCGGCUGGAUCACCUCCUUU");
2342	TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUUUC", "CGGCUGGAUCACCUCCUUUC");
2343
2344	// the data of the following tests is located right in front of the dots inserted in [8962]
2345	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAG", "AAUUGAAGAGUUUGAUCAAG");
2346	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGU", "AUUGAAGAGUUUGAUCAAGU");
2347	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUC", "UUGAAGAGUUUGAUCAAGUC");
2348	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCG", "UGAAGAGUUUGAUCAAGUCG");
2349	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGA", "GAAGAGUUUGAUCAAGUCGA");
2350	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAG", "AAGAGUUUGAUCAAGUCGAG");
2351	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGC", "AGAGUUUGAUCAAGUCGAGC");
2352	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCG", "GAGUUUGAUCAAGUCGAGCG");
2353	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCGG", "AGUUUGAUCAAGUCGAGCGG");
2354	TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCGGU", "GUUUGAUCAAGUCGAGCGGU");
2355	}
2356
2357	void TEST_SLOW_variable_defaults_in_server() {
2358	test_setup(false);
2359
2360	const char *server_tag = GBS_ptserver_tag(TEST_SERVER_ID);
2361	TEST_EXPECT_NO_ERROR(arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag));
2362
2363	const char *servername = GBS_read_arb_tcp(server_tag);
2364	{
2365	char *socketname = GBS_global_string_copy(":%s", GB_path_in_ARBHOME("UNIT_TESTER/sockets/pt.socket"));
2366	TEST_EXPECT_EQUAL(servername, socketname); // as defined in ../lib/arb_tcp.dat@ARB_TEST_PT_SERVER
2367	free(socketname);
2368	}
2369
2370	T_PT_MAIN com;
2371	T_PT_LOCS locs;
2372	GB_ERROR error = NULL;
2373	aisc_com *link = aisc_open(servername, com, AISC_MAGIC_NUMBER, &error);
2374	TEST_EXPECT_NO_ERROR(error);
2375	TEST_REJECT_NULL(link);
2376
2377	TEST_EXPECT_ZERO(aisc_create(link, PT_MAIN, com,
2378	MAIN_LOCS, PT_LOCS, locs,
2379	NULL));
2380
2381	{
2382	#define LOCAL(rvar) (prev_read_##rvar)
2383
2384
2385	#define FREE_LOCAL_long(rvar)
2386	#define FREE_LOCAL_charp(rvar) free(LOCAL(rvar))
2387	#define FREE_LOCAL(type,rvar) FREE_LOCAL_##type(rvar)
2388
2389	#define TEST__READ(type,rvar,expected) \
2390	do { \
2391	TEST_EXPECT_ZERO(aisc_get(link, PT_LOCS, locs, rvar, &(LOCAL(rvar)), NULL)); \
2392	TEST_EXPECT_EQUAL(LOCAL(rvar), expected); \
2393	FREE_LOCAL(type,rvar); \
2394	} while(0)
2395	#define TEST_WRITE(type,rvar,val) \
2396	TEST_EXPECT_ZERO(aisc_put(link, PT_LOCS, locs, rvar, (type)val, NULL))
2397	#define TEST_CHANGE(type,rvar,val) \
2398	do { \
2399	TEST_WRITE(type, rvar, val); \
2400	TEST__READ(type, rvar, val); \
2401	} while(0)
2402	#define TEST_DEFAULT_CHANGE(ctype,type,remote_variable,default_value,other_value) \
2403	do { \
2404	ctype DEFAULT_VALUE = default_value; \
2405	ctype OTHER_VALUE = other_value; \
2406	type LOCAL(remote_variable); \
2407	TEST__READ(type, remote_variable, DEFAULT_VALUE); \
2408	TEST_CHANGE(type, remote_variable, OTHER_VALUE); \
2409	TEST_CHANGE(type, remote_variable, DEFAULT_VALUE); \
2410	} while(0)
2411
2412	TEST_DEFAULT_CHANGE(const long, long, LOCS_MATCH_REVERSED, 1, 67);
2413	typedef char *charp;
2414	typedef const char *ccharp;
2415	TEST_DEFAULT_CHANGE(ccharp, charp, LOCS_LOGINTIME, "notime", "sometime");
2416	}
2417
2418	TEST_EXPECT_ZERO(aisc_close(link, com));
2419	link = 0;
2420	}
2421
2422	#endif // UNIT_TESTS

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