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source: tags/svn.1.5.4/TOOLS/arb_probe.cxx

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Last change on this file was 8309, checked in by westram, 14 years ago

moved much code into static scope

(partly reverted by [8310])

Property svn:eol-style set to native
Property svn:keywords set to Author Date Id Revision

File size: 38.7 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
20	struct apd_sequence {
21	apd_sequence *next;
22	const char *sequence;
23	};
24
25	struct Params {
26	int DESIGNCLIPOUTPUT;
27	int SERVERID;
28	const char *DESIGNNAMES;
29	int DESIGNPROBELENGTH;
30	const char *DESIGNSEQUENCE;
31
32	int MINTEMP;
33	int MAXTEMP;
34	int MINGC;
35	int MAXGC;
36	int MAXBOND;
37	int MINPOS;
38	int MAXPOS;
39	int MISHIT;
40	int MINTARGETS;
41	const char *SEQUENCE;
42	int MISMATCHES;
43	int ACCEPTN;
44	int LIMITN;
45	int MAXRESULT;
46	int COMPLEMENT;
47	int WEIGHTED;
48
49	apd_sequence *sequence;
50	};
51
52
53	struct gl_struct {
54	aisc_com *link;
55	T_PT_LOCS locs;
56	T_PT_MAIN com;
57	int pd_design_id;
58	};
59
60	static Params P;
61	static gl_struct pd_gl;
62
63	static int init_local_com_struct()
64	{
65	const char *user = GB_getenvUSER();
66
67	if (aisc_create(pd_gl.link, PT_MAIN, pd_gl.com,
68	MAIN_LOCS, PT_LOCS, &pd_gl.locs,
69	LOCS_USER, user,
70	NULL)) {
71	return 1;
72	}
73	return 0;
74	}
75
76	static void aw_message(const char *error) {
77	printf("%s\n", error);
78	}
79
80	static const char *AP_probe_pt_look_for_server(ARB_ERROR& error) {
81	const char *server_tag = GBS_ptserver_tag(P.SERVERID);
82
83	error = arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag);
84	if (error) return NULL;
85
86	return GBS_read_arb_tcp(server_tag);
87	}
88
89	static char *AP_probe_design_event(ARB_ERROR& error) {
90	T_PT_PDC pdc;
91	T_PT_TPROBE tprobe;
92	bytestring bs;
93	char *match_info;
94
95	{
96	const char *servername = AP_probe_pt_look_for_server(error);
97	if (!servername) return NULL;
98
99	pd_gl.link = aisc_open(servername, &pd_gl.com, AISC_MAGIC_NUMBER);
100	}
101
102	if (!pd_gl.link) {
103	error = "Cannot contact PT_SERVER [1]";
104	return NULL;
105	}
106	if (init_local_com_struct()) {
107	error = "Cannot contact PT_SERVER [2]";
108	return NULL;
109	}
110
111	bs.data = (char*)(P.DESIGNNAMES);
112	bs.size = strlen(bs.data)+1;
113
114	if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs,
115	LOCS_PROBE_DESIGN_CONFIG, PT_PDC, &pdc,
116	PDC_PROBELENGTH, (long)P.DESIGNPROBELENGTH,
117	PDC_MINTEMP, (double)P.MINTEMP,
118	PDC_MAXTEMP, (double)P.MAXTEMP,
119	PDC_MINGC, P.MINGC/100.0,
120	PDC_MAXGC, P.MAXGC/100.0,
121	PDC_MAXBOND, (double)P.MAXBOND,
122	PDC_MIN_ECOLIPOS, (long)P.MINPOS,
123	PDC_MAX_ECOLIPOS, (long)P.MAXPOS,
124	PDC_MISHIT, (long)P.MISHIT,
125	PDC_MINTARGETS, P.MINTARGETS/100.0,
126	PDC_CLIPRESULT, (long)P.DESIGNCLIPOUTPUT,
127	NULL))
128	{
129	error = "Connection to PT_SERVER lost (1)";
130	return NULL;
131	}
132
133	apd_sequence *s;
134	for (s = P.sequence; s; s = s->next) {
135	bytestring bs_seq;
136	T_PT_SEQUENCE pts;
137	bs_seq.data = (char*)s->sequence;
138	bs_seq.size = strlen(bs_seq.data)+1;
139	aisc_create(pd_gl.link, PT_PDC, pdc,
140	PDC_SEQUENCE, PT_SEQUENCE, &pts,
141	SEQUENCE_SEQUENCE, &bs_seq,
142	NULL);
143	}
144
145	aisc_put(pd_gl.link, PT_PDC, pdc,
146	PDC_NAMES, &bs,
147	PDC_GO, 0,
148	NULL);
149
150	{
151	char *locs_error = 0;
152	if (aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs,
153	LOCS_ERROR, &locs_error,
154	NULL)) {
155	aw_message ("Connection to PT_SERVER lost (1)");
156	return NULL;
157	}
158	if (*locs_error) {
159	aw_message(locs_error);
160	}
161	free(locs_error);
162	}
163
164	aisc_get(pd_gl.link, PT_PDC, pdc,
165	PDC_TPROBE, &tprobe,
166	NULL);
167
168
169	GBS_strstruct *outstr = GBS_stropen(1000);
170
171	if (tprobe) {
172	aisc_get(pd_gl.link, PT_TPROBE, tprobe,
173	TPROBE_INFO_HEADER, &match_info,
174	NULL);
175	GBS_strcat(outstr, match_info);
176	GBS_chrcat(outstr, '\n');
177	free(match_info);
178	}
179
180
181	while (tprobe) {
182	if (aisc_get(pd_gl.link, PT_TPROBE, tprobe,
183	TPROBE_NEXT, &tprobe,
184	TPROBE_INFO, &match_info,
185	NULL)) break;
186	GBS_strcat(outstr, match_info);
187	GBS_chrcat(outstr, '\n');
188	free(match_info);
189	}
190
191	aisc_close(pd_gl.link); pd_gl.link = 0;
192
193	return GBS_strclose(outstr);
194	}
195
196	static char *AP_probe_match_event(ARB_ERROR& error) {
197	T_PT_MATCHLIST match_list;
198	char *probe = 0;
199
200	{
201	const char *servername = AP_probe_pt_look_for_server(error);
202	if (!servername) return NULL;
203
204	pd_gl.link = aisc_open(servername, &pd_gl.com, AISC_MAGIC_NUMBER);
205	}
206
207	if (!pd_gl.link) {
208	error = "Cannot contact PT_SERVER [1]";
209	return NULL;
210	}
211	if (init_local_com_struct()) {
212	error = "Cannot contact PT_SERVER [2]";
213	return NULL;
214	}
215
216	if (aisc_nput(pd_gl.link, PT_LOCS, pd_gl.locs,
217	LOCS_MATCH_REVERSED, (long)P.COMPLEMENT,
218	LOCS_MATCH_SORT_BY, (long)P.WEIGHTED,
219	LOCS_MATCH_COMPLEMENT, 0L,
220	LOCS_MATCH_MAX_MISMATCHES, (long)P.MISMATCHES,
221	LOCS_MATCH_N_ACCEPT, (long)P.ACCEPTN,
222	LOCS_MATCH_N_LIMIT, (long)P.LIMITN,
223	LOCS_MATCH_MAX_HITS, (long)P.MAXRESULT,
224	LOCS_SEARCHMATCH, P.SEQUENCE,
225	NULL)) {
226	free(probe);
227	error = "Connection to PT_SERVER lost (1)";
228	return NULL;
229	}
230
231	long match_list_cnt;
232
233	bytestring bs;
234	bs.data = 0;
235	{
236	char *locs_error;
237	aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs,
238	LOCS_MATCH_LIST, &match_list,
239	LOCS_MATCH_LIST_CNT, &match_list_cnt,
240	LOCS_MATCH_STRING, &bs,
241	LOCS_ERROR, &locs_error,
242	NULL);
243	if (*locs_error) error = locs_error;
244	free(locs_error);
245	}
246	aisc_close(pd_gl.link);
247
248	return bs.data; // freed by caller
249	}
250
251	static int pargc;
252	static const char **pargv = NULL;
253	static bool showhelp;
254
255	static int getInt(const char param, int val, int min, int max, const char description) {
256	if (showhelp) {
257	printf(" %s=%i [%i .. %i] %s\n", param, val, min, max, description);
258	return 0;
259	}
260	int i;
261	const char *s = 0;
262
263	arb_assert(pargc >= 1); // otherwise s stays 0
264
265	for (i=1; i<pargc; i++) {
266	s = pargv[i];
267	if (*s == '-') s++;
268	if (!strncasecmp(s, param, strlen(param))) break;
269	}
270	if (i==pargc) return val;
271	s += strlen(param);
272	if (*s != '=') return val;
273	s++;
274	val = atoi(s);
275	pargc--; // remove parameter
276	for (; i<pargc; i++) {
277	pargv[i] = pargv[i+1];
278	}
279
280	if (val<min) val = min;
281	if (val>max) val = max;
282	return val;
283	}
284
285	static const char getString(const char param, const char val, const char description) {
286	if (showhelp) {
287	if (!val) val = "";
288	printf(" %s=%s %s\n", param, val, description);
289	return 0;
290	}
291	int i;
292	const char *s = 0;
293
294	arb_assert(pargc >= 1); // otherwise s stays 0
295
296	for (i=1; i<pargc; i++) {
297	s = pargv[i];
298	if (*s == '-') s++;
299	if (!strncasecmp(s, param, strlen(param))) break;
300	}
301	if (i==pargc) return val;
302	s += strlen(param);
303	if (*s != '=') return val;
304	s++;
305	pargc--; // remove parameter
306	for (; i<pargc; i++) {
307	pargv[i] = pargv[i+1];
308	}
309	return s;
310	}
311
312	static bool parseCommandLine(int argc, const char * const * const argv) {
313	pargc = argc;
314
315	// copy argv (since parser will remove matched arguments)
316	free(pargv);
317	pargv = (const char *)malloc(sizeof(pargv)*pargc);
318	for (int i=0; i<pargc; i++) pargv[i] = argv[i];
319
320	showhelp = (pargc <= 1);
321
322	#ifdef UNIT_TESTS
323	const int minServerID = TEST_GENESERVER_ID;
324	#else // !UNIT_TESTS
325	const int minServerID = 0;
326	#endif
327
328	P.SERVERID = getInt("serverid", 0, minServerID, 100, "Server Id, look into $ARBHOME/lib/arb_tcp.dat");
329	#ifdef UNIT_TESTS
330	if (P.SERVERID<0) { arb_assert(P.SERVERID == TEST_SERVER_ID \|\| P.SERVERID == TEST_GENESERVER_ID); }
331	#endif
332
333	P.DESIGNCLIPOUTPUT = getInt("designmaxhits", 100, 10, 10000, "Maximum Number of Probe Design Suggestions");
334	P.DESIGNNAMES = getString("designnames", "", "List of short names separated by '#'");
335
336	P.sequence = 0;
337	while ((P.DESIGNSEQUENCE = getString("designsequence", 0, "Additional Sequences, will be added to the target group"))) {
338	apd_sequence *s = new apd_sequence;
339	s->next = P.sequence;
340	P.sequence = s;
341	s->sequence = P.DESIGNSEQUENCE;
342	P.DESIGNSEQUENCE = 0;
343	}
344	P.DESIGNPROBELENGTH = getInt("designprobelength", 18, 2, 100, "Length of probe");
345	P.MINTEMP = getInt("designmintemp", 0, 0, 400, "Minimum melting temperature of probe");
346	P.MAXTEMP = getInt("designmaxtemp", 400, 0, 400, "Maximum melting temperature of probe");
347	P.MINGC = getInt("designmingc", 30, 0, 100, "Minimum gc content");
348	P.MAXGC = getInt("designmaxgc", 80, 0, 100, "Maximum gc content");
349	P.MAXBOND = getInt("designmaxbond", 0, 0, 10, "Not implemented");
350	P.MINPOS = getInt("designminpos", -1, -1, INT_MAX, "Minimum ecoli position (-1=none)");
351	P.MAXPOS = getInt("designmaxpos", -1, -1, INT_MAX, "Maximum ecoli position (-1=none)");
352	P.MISHIT = getInt("designmishit", 0, 0, 10000, "Number of allowed hits outside the selected group");
353	P.MINTARGETS = getInt("designmintargets", 50, 0, 100, "Minimum percentage of hits within the selected species");
354
355	P.SEQUENCE = getString("matchsequence", "agtagtagt", "The sequence to search for");
356
357	P.MISMATCHES = getInt("matchmismatches", 0, 0, 5, "Maximum Number of allowed mismatches");
358	P.COMPLEMENT = getInt("matchcomplement", 0, 0, 1, "Match reversed and complemented probe");
359	P.WEIGHTED = getInt("matchweighted", 0, 0, 1, "Use weighted mismatches");
360	P.ACCEPTN = getInt("matchacceptN", 1, 0, 20, "Amount of N-matches not counted as mismatch");
361	P.LIMITN = getInt("matchlimitN", 4, 0, 20, "Limit for N-matches. If reached N-matches are mismatches");
362	P.MAXRESULT = getInt("matchmaxresults", 1000000, 0, INT_MAX, "Max. number of matches reported (0=unlimited)");
363
364	if (pargc>1) {
365	printf("Unknown (or duplicate) parameter %s\n", pargv[1]);
366	return false;
367	}
368	return !showhelp;
369	}
370
371	// --------------------------------------------------------------------------------
372
373	#ifdef UNIT_TESTS
374	#ifndef TEST_UNIT_H
375	#include <test_unit.h>
376	#endif
377
378	void TEST_BASIC_parseCommandLine() {
379	{
380	const char *args[] = { NULL, "serverid=0"};
381	TEST_ASSERT(parseCommandLine(ARRAY_ELEMS(args), args));
382
383	// test default values here
384	TEST_ASSERT_EQUAL(P.ACCEPTN, 1);
385	TEST_ASSERT_EQUAL(P.LIMITN, 4);
386	TEST_ASSERT_EQUAL(P.MISMATCHES, 0);
387	TEST_ASSERT_EQUAL(P.MAXRESULT, 1000000);
388	}
389
390	{
391	const char *args[] = {NULL, "serverid=4", "matchmismatches=2"};
392	TEST_ASSERT(parseCommandLine(ARRAY_ELEMS(args), args));
393	TEST_ASSERT_EQUAL(P.SERVERID, 4);
394	TEST_ASSERT_EQUAL(P.MISMATCHES, 2);
395	TEST_ASSERT_EQUAL(args[1], "serverid=4"); // check array args was not modified
396	}
397
398	{
399	const char *args[] = { NULL, "matchacceptN=0", "matchlimitN=5"};
400	TEST_ASSERT(parseCommandLine(ARRAY_ELEMS(args), args));
401	TEST_ASSERT_EQUAL(P.ACCEPTN, 0);
402	TEST_ASSERT_EQUAL(P.LIMITN, 5);
403	}
404
405	{
406	const char *args[] = { NULL, "matchmaxresults=100"};
407	TEST_ASSERT(parseCommandLine(ARRAY_ELEMS(args), args));
408	TEST_ASSERT_EQUAL(P.MAXRESULT, 100);
409	}
410	}
411
412	#endif // UNIT_TESTS
413
414	// --------------------------------------------------------------------------------
415
416
417	static char *execute(ARB_ERROR& error) {
418	char *answer;
419	if (*P.DESIGNNAMES \|\| P.sequence) {
420	answer = AP_probe_design_event(error);
421	}
422	else {
423	answer = AP_probe_match_event(error);
424	}
425	return answer;
426	}
427
428	int ARB_main(int argc, const char *argv[]) {
429	bool ok = parseCommandLine(argc, argv);
430	if (ok) {
431	ARB_ERROR error;
432	char *answer = execute(error);
433
434	arb_assert(contradicted(answer, error));
435
436	if (!answer) {
437	fprintf(stderr,
438	"arb_probe: Failed to process your request\n"
439	" Reason: %s",
440	error.deliver());
441	ok = false;
442	}
443	else {
444	fputs(answer, stdout);
445	free(answer);
446	error.expect_no_error();
447	}
448	}
449	return ok ? EXIT_SUCCESS : EXIT_FAILURE;
450	}
451
452	// --------------------------------------------------------------------------------
453
454	#ifdef UNIT_TESTS
455	#ifndef TEST_UNIT_H
456	#include <test_unit.h>
457	#endif
458
459	static int test_setup(bool use_gene_ptserver) {
460	static bool setup[2] = { false, false };
461	if (!setup[use_gene_ptserver]) {
462	TEST_SETUP_GLOBAL_ENVIRONMENT(use_gene_ptserver ? "ptserver_gene" : "ptserver"); // first call will recreate the test pt-server
463	setup[use_gene_ptserver] = true;
464	}
465	return use_gene_ptserver ? TEST_GENESERVER_ID : TEST_SERVER_ID;
466	}
467
468	// ----------------------------------
469	// test probe design / match
470
471	#define TEST_PART1(fake_argc,fake_argv) \
472	int serverid = test_setup(use_gene_ptserver); \
473	TEST_ASSERT_EQUAL(true, parseCommandLine(fake_argc, fake_argv)); \
474	TEST_ASSERT((serverid == TEST_SERVER_ID)\|\|(serverid == TEST_GENESERVER_ID)); \
475	P.SERVERID = serverid; \
476	ARB_ERROR error; \
477	char *answer = execute(error); \
478	TEST_ASSERT_NO_ERROR(error.deliver())
479
480
481	#define TEST_ARB_PROBE(fake_argc,fake_argv,expected) do { \
482	TEST_PART1(fake_argc,fake_argv); \
483	TEST_ASSERT_EQUAL(answer, expected); \
484	free(answer); \
485	} while(0)
486
487	#define TEST_ARB_PROBE__BROKEN(fake_argc,fake_argv,expected) do { \
488	TEST_PART1(fake_argc,fake_argv); \
489	TEST_ASSERT_EQUAL__BROKEN(answer, expected); \
490	free(answer); \
491	} while(0)
492
493	#define TEST_ARB_PROBE_FILT(fake_argc,fake_argv,filter,expected) do { \
494	TEST_PART1(fake_argc,fake_argv); \
495	char *filtered = filter(answer); \
496	TEST_ASSERT_EQUAL(filtered, expected); \
497	free(filtered); \
498	free(answer); \
499	} while(0)
500
501	typedef const char *CCP;
502
503	void TEST_SLOW_match_geneprobe() {
504	bool use_gene_ptserver = true;
505	{
506	const char *arguments[] = {
507	"prgnamefake",
508	"matchsequence=NNUCNN",
509	"matchacceptN=4",
510	"matchlimitN=5",
511	};
512	CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NNUCNN'\1"
513	"genome2\1" " genome2 gene3 0 4 0.0 2 1 0 .........-UU==GG-UUGAUC\1"
514	"genome2\1" " genome2 joined1 0 4 0.0 2 1 0 .........-UU==GG-UUGAUCCUG\1"
515	"genome2\1" " genome2 gene2 0 4 0.0 10 4 0 ......GUU-GA==CU-GCCA\1"
516	"genome2\1" " genome2 intergene_19_65 0 4 0.0 31 12 0 GGUUACUGC-AU==GG-UGUUCGCCU\1"
517	"genome1\1" " genome1 intergene_17_65 0 4 0.0 31 14 0 GGUUACUGC-UA==GG-UGUUCGCCU\1"
518	"genome2\1" " genome2 intergene_19_65 0 4 0.0 38 19 0 GCAUUCGGU-GU==GC-CUAAGCACU\1"
519	"genome1\1" " genome1 intergene_17_65 0 4 0.0 38 21 0 GCUAUCGGU-GU==GC-CUAAGCCAU\1"
520	"genome1\1" " genome1 intergene_17_65 0 4 0.0 56 39 0 AGCCAUGCG-AG==AU-AUGUA\1" "";
521
522	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd);
523	}
524	{
525	const char *arguments[] = {
526	"prgnamefake",
527	"matchsequence=NGGUUN",
528	"matchacceptN=2",
529	"matchlimitN=3",
530	};
531	CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NGGUUN'\1"
532	"genome1\1" " genome1 joined1 0 2 0.0 5 2 0 ........C-U====G-AUCCUGC\1"
533	"genome2\1" " genome2 intergene_19_65 0 2 0.0 21 2 0 ........G-A====A-CUGCAUUCG\1"
534	"genome1\1" " genome1 intergene_17_65 0 2 0.0 21 4 0 ......CAG-A====A-CUGCUAUCG\1"
535	"genome2\1" " genome2 gene3 0 2 0.0 5 4 0 ......UUU-C====G-AUC\1"
536	"genome2\1" " genome2 joined1 0 2 0.0 5 4 0 ......UUU-C====G-AUCCUGCCA\1" "";
537
538	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd);
539	}
540
541	{
542	const char *arguments[] = {
543	"prgnamefake",
544	"matchsequence=UGAUCCU", // exists in data
545	};
546	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UGAUCCU'\1"
547	"genome1\1" " genome1 gene2 0 0 0.0 9 1 0 .........-=======-GC\1"
548	"genome2\1" " genome2 gene2 0 0 0.0 9 3 0 .......GU-=======-GCCA\1" "";
549
550	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // @@@ defect: probe exists as well in 'joined1' (of both genomes)
551	}
552	{
553	const char *arguments[] = {
554	"prgnamefake",
555	"matchsequence=GAUCCU",
556	};
557	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'GAUCCU'\1"
558	"genome2\1" " genome2 gene2 0 0 0.0 10 4 0 ......GUU-======-GCCA\1" "";
559
560	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // @@@ defect: probe is part of above probe, but reports less hits
561	}
562	{
563	const char *arguments[] = {
564	"prgnamefake",
565	"matchsequence=UUUCGG", // exists only in genome2
566	};
567	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUUCGG'\1"
568	"genome2\1" " genome2 gene3 0 0 0.0 2 1 0 .........-======-UUGAUC\1"
569	"genome2\1" " genome2 joined1 0 0 0.0 2 1 0 .........-======-UUGAUCCUG\1" "";
570
571	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // @@@ defect: also exists in genome2/gene1
572	}
573	{
574	const char *arguments[] = {
575	"prgnamefake",
576	"matchsequence=AUCCUG",
577	};
578	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'AUCCUG'\1"
579	"genome2\1" " genome2 gene2 0 0 0.0 11 5 0 .....GUUG-======-CCA\1" "";
580
581	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // @@@ defect: exists in 'gene2' and 'joined1' of both genomes
582	}
583	{
584	const char *arguments[] = {
585	"prgnamefake",
586	"matchsequence=UUGAUCCUGC",
587	};
588	CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUGAUCCUGC'\1"
589	"genome2\1" " genome2 gene2 0 0 0.0 8 2 0 ........G-==========-CA\1"
590	"genome1\1" " genome1 joined1 0 0 0.0 8 5 0 .....CUGG-==========-\1" "";
591
592	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // @@@ defect: also exists in 'genome2/joined1'
593	}
594	}
595
596	void TEST_SLOW_match_probe() {
597	bool use_gene_ptserver = false;
598	{
599	const char *arguments[] = {
600	"prgnamefake",
601	"matchsequence=UAUCGGAGAGUUUGA",
602	};
603	CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UAUCGGAGAGUUUGA'\1"
604	"BcSSSS00\1" " BcSSSS00 0 0 0.0 3 2 0 .......UU-===============-UCAAGUCGA\1";
605
606	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
607	}
608
609	// ----------------------------------------------------------------------------
610	// match with old(=default) N-mismatch-behavior (accepting 1 N-match)
611
612	{
613	const char *arguments[] = {
614	"prgnamefake",
615	"matchsequence=CANCUCCUUUC", // contains 1 N
616	NULL // matchmismatches
617	};
618
619	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
620	"BcSSSS00\1" " BcSSSS00 0 1 0.0 176 162 0 CGGCUGGAU-==C========-U\1" ""; // only N-mismatch accepted
621
622	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
623	"BcSSSS00\1" " BcSSSS00 0 1 0.0 176 162 0 CGGCUGGAU-==C========-U\1"
624	"PbcAcet2\1" " PbcAcet2 0 2 0.0 176 162 0 CGGCUGGAU-==C=======N-N\1"
625	"ClfPerfr\1" " ClfPerfr 1 1 0.0 176 162 0 AGAUUAAUA-=CC========-U\1";
626
627	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
628	"BcSSSS00\1" " BcSSSS00 0 1 0.0 176 162 0 CGGCUGGAU-==C========-U\1"
629	"PbcAcet2\1" " PbcAcet2 0 2 0.0 176 162 0 CGGCUGGAU-==C=======N-N\1"
630	"DlcTolu2\1" " DlcTolu2 0 3 0.0 176 162 0 CGGCUGGAU-==C======NN-N\1"
631	"ClfPerfr\1" " ClfPerfr 1 1 0.0 176 162 0 AGAUUAAUA-=CC========-U\1";
632
633	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
634	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
635	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
636	}
637	{
638	const char *arguments[] = {
639	"prgnamefake",
640	"matchsequence=UCACCUCCUUUC", // contains no N
641	NULL // matchmismatches
642	};
643
644	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
645	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U\1"
646	"PbcAcet2\1" " PbcAcet2 0 1 0.0 175 161 0 GCGGCUGGA-===========N-N\1";
647
648	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
649	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U\1"
650	"PbcAcet2\1" " PbcAcet2 0 1 0.0 175 161 0 GCGGCUGGA-===========N-N\1"
651	"DlcTolu2\1" " DlcTolu2 0 2 0.0 175 161 0 GCGGCUGGA-==========NN-N\1" "";
652
653	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
654	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U\1"
655	"PbcAcet2\1" " PbcAcet2 0 1 0.0 175 161 0 GCGGCUGGA-===========N-N\1"
656	"DlcTolu2\1" " DlcTolu2 0 2 0.0 175 161 0 GCGGCUGGA-==========NN-N\1"
657	"ClfPerfr\1" " ClfPerfr 2 0 0.0 175 161 0 AAGAUUAAU-A=C=========-U\1" "";
658
659	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
660	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
661	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
662	}
663
664	// ----------------------------------------------
665	// do not accept any N-matches as match
666
667	{
668	const char *arguments[] = {
669	"prgnamefake",
670	"matchsequence=CANCUCCUUUC", // contains 1 N
671	NULL, // matchmismatches
672	"matchacceptN=0",
673	};
674
675	CCP expectd0 = ""; // nothing matches
676
677	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
678	"BcSSSS00\1" " BcSSSS00 0 1 0.0 176 162 0 CGGCUGGAU-==C========-U\1" "";
679
680	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1"
681	"BcSSSS00\1" " BcSSSS00 0 1 0.0 176 162 0 CGGCUGGAU-==C========-U\1"
682	"PbcAcet2\1" " PbcAcet2 0 2 0.0 176 162 0 CGGCUGGAU-==C=======N-N\1"
683	"ClfPerfr\1" " ClfPerfr 1 1 0.0 176 162 0 AGAUUAAUA-=CC========-U\1" "";
684
685	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
686	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
687	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
688	}
689	{
690	const char *arguments[] = {
691	"prgnamefake",
692	"matchsequence=UCACCUCCUUUC", // contains no N
693	NULL, // matchmismatches
694	"matchacceptN=0",
695	};
696
697	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
698	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U\1" "";
699
700	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
701	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U\1"
702	"PbcAcet2\1" " PbcAcet2 0 1 0.0 175 161 0 GCGGCUGGA-===========N-N\1" "";
703
704	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1"
705	"BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U\1"
706	"PbcAcet2\1" " PbcAcet2 0 1 0.0 175 161 0 GCGGCUGGA-===========N-N\1"
707	"DlcTolu2\1" " DlcTolu2 0 2 0.0 175 161 0 GCGGCUGGA-==========NN-N\1"
708	"ClfPerfr\1" " ClfPerfr 2 0 0.0 175 161 0 AAGAUUAAU-A=C=========-U\1" "";
709
710	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
711	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
712	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
713	}
714
715	// ----------------------------------
716	// accept several N-matches
717
718	{
719	const char *arguments[] = {
720	"prgnamefake",
721	"matchsequence=CANCUCCUUNC", // contains 2 N
722	NULL, // matchmismatches
723	"matchacceptN=2",
724	"matchlimitN=4",
725	};
726
727	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
728	"BcSSSS00\1" " BcSSSS00 0 2 0.0 176 162 0 CGGCUGGAU-==C======U=-U\1" "";
729
730	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
731	"BcSSSS00\1" " BcSSSS00 0 2 0.0 176 162 0 CGGCUGGAU-==C======U=-U\1"
732	"DlcTolu2\1" " DlcTolu2 0 3 0.0 176 162 0 CGGCUGGAU-==C=======N-N\1"
733	"PbcAcet2\1" " PbcAcet2 0 3 0.0 176 162 0 CGGCUGGAU-==C======UN-N\1"
734	"ClfPerfr\1" " ClfPerfr 1 2 0.0 176 162 0 AGAUUAAUA-=CC======U=-U\1" "";
735
736	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1"
737	"BcSSSS00\1" " BcSSSS00 0 2 0.0 176 162 0 CGGCUGGAU-==C======U=-U\1"
738	"DlcTolu2\1" " DlcTolu2 0 3 0.0 176 162 0 CGGCUGGAU-==C=======N-N\1"
739	"PbcAcet2\1" " PbcAcet2 0 3 0.0 176 162 0 CGGCUGGAU-==C======UN-N\1"
740	"ClfPerfr\1" " ClfPerfr 1 2 0.0 176 162 0 AGAUUAAUA-=CC======U=-U\1" "";
741
742	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
743	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
744	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
745	}
746
747	// --------------------------
748	// truncate results
749
750	{
751	const char *arguments[] = {
752	"prgnamefake",
753	"matchsequence=CANCNCNNUNC", // contains 5N
754	NULL, // matchmismatches
755	"matchacceptN=5",
756	"matchlimitN=7",
757	"matchmaxresults=5",
758	};
759
760	CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
761	"BcSSSS00\1" " BcSSSS00 0 5 0.0 176 162 0 CGGCUGGAU-==C=U=CU=U=-U\1" "";
762
763	CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
764	"BcSSSS00\1" " BcSSSS00 0 5 0.0 176 162 0 CGGCUGGAU-==C=U=CU=U=-U\1"
765	"DlcTolu2\1" " DlcTolu2 0 6 0.0 176 162 0 CGGCUGGAU-==C=U=CU==N-N\1"
766	"PbcAcet2\1" " PbcAcet2 0 6 0.0 176 162 0 CGGCUGGAU-==C=U=CU=UN-N\1"
767	"LgtLytic\1" " LgtLytic 1 5 0.0 31 26 0 GUCGAACGG-==G=A=AG=CU-AGCUUGCUA\1"
768	"ClfPerfr\1" " ClfPerfr 1 5 0.0 111 99 0 CGGCUGGAU-==U=AUAA=G=-AGCGAUUGG\1"; // one hit is truncated here
769
770	CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1"
771	"VbrFurni\1" " VbrFurni 2 5 0.0 40 35 0 CGGCAGCGA-==A=AUUGAA=-CUUCGGGGG\1"
772	"HllHalod\1" " HllHalod 2 5 0.0 45 40 0 AAACGAUGG-A=G=UUGC=U=-CAGGCGUCG\1"
773	"VblVulni\1" " VblVulni 2 5 0.0 49 44 0 AGCACAGAG-A=A=UUGU=U=-UCGGGUGGC\1"
774	"LgtLytic\1" " LgtLytic 2 5 0.0 101 89 0 GGGGAAACU-==AGCUAA=A=-CGCAUAAUC\1"
775	"ClfPerfr\1" " ClfPerfr 2 5 0.0 172 158 0 AGGAAGAUU-A=UAC=CC=C=-UUUCU\1"; // many hits are truncated here
776
777	arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0);
778	arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1);
779	arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2);
780	}
781	}
782
783	static char extract_locations(const char probe_design_result) {
784	const char *Target = strstr(probe_design_result, "\nTarget");
785	if (Target) {
786	const char *designed = strchr(Target+7, '\n');
787	if (designed) {
788	++designed;
789	char *result = strdup("");
790
791	while (designed) {
792	const char *eol = strchr(designed, '\n');
793	const char *space1 = strchr(designed, ' '); if (!space1) break; // 1st space between probe and len
794	const char *nonspace = space1+strspn(space1, " "); if (!nonspace) break;
795	const char *space2 = strchr(nonspace, ' '); if (!space2) break; // 1st space between len and "X="
796	const char *nonspace2 = space2+strspn(space2, " "); if (!nonspace2) break;
797	const char *space3 = strchr(nonspace2, ' '); if (!space3) break; // 1st space between "X=" and abs
798	const char *nonspace3 = space3+strspn(space3, " "); if (!nonspace3) break;
799	const char *space4 = strchr(nonspace3, ' '); if (!space4) break; // 1st space between abs and rest
800
801	char *abs = GB_strpartdup(nonspace3, space4-1);
802
803	freeset(result, GBS_global_string_copy("%s%c%c%s", result, space2[1], space2[2], abs));
804	free(abs);
805
806	designed = eol ? eol+1 : NULL;
807	}
808
809	return result;
810	}
811	}
812	return strdup("can't extract");
813	}
814
815	void TEST_SLOW_design_probe() {
816	bool use_gene_ptserver = false;
817	const char *arguments[] = {
818	"prgnamefake",
819	"designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr",
820	"designmintargets=100",
821	};
822	const char *expected =
823	"Probe design Parameters:\n"
824	"Length of probe 18\n"
825	"Temperature [ 0.0 -400.0]\n"
826	"GC-Content [30.0 -80.0]\n"
827	"E.Coli Position [any]\n"
828	"Max Non Group Hits 0\n"
829	"Min Group Hits 100%\n"
830	"Target le apos ecol grps G+C 4GC+2AT Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
831	"CGAAAGGAAGAUUAAUAC 18 A= 94 82 4 33.3 48.0 GUAUUAAUCUUCCUUUCG \| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,\n"
832	"GAAAGGAAGAUUAAUACC 18 A+ 1 83 4 33.3 48.0 GGUAUUAAUCUUCCUUUC \| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,\n"
833	"UCAAGUCGAGCGAUGAAG 18 B= 18 17 4 50.0 54.0 CUUCAUCGCUCGACUUGA \| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,\n"
834	"AUCAAGUCGAGCGAUGAA 18 B- 1 16 4 44.4 52.0 UUCAUCGCUCGACUUGAU \| 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 2, 3,\n";
835
836	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
837
838	// ------------------------------------------------------
839	// design MANY probes to test location specifier
840
841	{
842	char *positions = extract_locations(expected);
843	TEST_ASSERT_EQUAL(positions, "A=94A+1B=18B-1");
844	free(positions);
845	}
846
847	const char *arguments_loc[] = {
848	"prgnamefake",
849	// "designnames=Stsssola#Stsssola", // @@@ crashes the ptserver
850	"designnames=CPPParap#PsAAAA00",
851	"designmintargets=50", // hit at least 1 of the 2 targets
852	"designmingc=0", "designmaxgc=100", // allow all GCs
853	"designmishit=99999", // allow enough outgroup hits
854	"designmaxhits=99999", // do not limit results
855	"designprobelength=3",
856	};
857
858	const char *expected_loc =
859	"A=96B=141C=20D=107B+1E=110F=84G=9H=150I=145C+1D+1J=17K=122L=72C-1M=33N=114E+1O=163"
860	"P=24E+2F+1Q=138R=54O+1S=49A-1T=87G+1J-1N-1U=79F+2U-1V=129I+2H-2C+2W=12D-1D+2C-2R+1"
861	"P-1J-2O+2V-2X=92W+2W+1Y=125Z=176D-2H+1a=104H-1L+1";
862
863	TEST_ARB_PROBE_FILT(ARRAY_ELEMS(arguments_loc), arguments_loc, extract_locations, expected_loc);
864	}
865
866	void TEST_SLOW_match_designed_probe() {
867	bool use_gene_ptserver = false;
868	const char *arguments[] = {
869	"prgnamefake",
870	"matchsequence=UCAAGUCGAGCGAUGAAG",
871	};
872	CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UCAAGUCGAGCGAUGAAG'\1"
873	"ClnCorin\1" " ClnCorin 0 0 0.0 18 17 0 .GAGUUUGA-==================-UUCCUUCGG\1"
874	"CltBotul\1" " CltBotul 0 0 0.0 18 17 0 ........A-==================-CUUCUUCGG\1"
875	"CPPParap\1" " CPPParap 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUCCUUCGG\1"
876	"ClfPerfr\1" " ClfPerfr 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUUCCUUCG\1";
877
878	TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected);
879	}
880
881	void TEST_SLOW_variable_defaults_in_server() {
882	test_setup(false);
883
884	const char *server_tag = GBS_ptserver_tag(TEST_SERVER_ID);
885	TEST_ASSERT_NO_ERROR(arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag));
886
887	const char *servername = GBS_read_arb_tcp(server_tag);;
888	TEST_ASSERT_EQUAL(servername, "localhost:3200"); // as defined in ../lib/arb_tcp.dat@ARB_TEST_PT_SERVER
889
890	long com;
891	long locs;
892	aisc_com *link = aisc_open(servername, &com, AISC_MAGIC_NUMBER);
893	TEST_ASSERT(link);
894
895	TEST_ASSERT_ZERO(aisc_create(link, PT_MAIN, com,
896	MAIN_LOCS, PT_LOCS, &locs,
897	NULL));
898
899	{
900	#define LOCAL(rvar) (prev_read_##rvar)
901
902
903	#define FREE_LOCAL_long(rvar)
904	#define FREE_LOCAL_charp(rvar) free(LOCAL(rvar))
905	#define FREE_LOCAL(type,rvar) FREE_LOCAL_##type(rvar)
906
907	#define TEST__READ(type,rvar,expected) \
908	do { \
909	TEST_ASSERT_ZERO(aisc_get(link, PT_LOCS, locs, rvar, &(LOCAL(rvar)), NULL)); \
910	TEST_ASSERT_EQUAL(LOCAL(rvar), expected); \
911	FREE_LOCAL(type,rvar); \
912	} while(0)
913	#define TEST_WRITE(type,rvar,val) \
914	TEST_ASSERT_ZERO(aisc_put(link, PT_LOCS, locs, rvar, (type)val, NULL))
915	#define TEST_CHANGE(type,rvar,val) \
916	do { \
917	TEST_WRITE(type, rvar, val); \
918	TEST__READ(type, rvar, val); \
919	} while(0)
920	#define TEST_DEFAULT_CHANGE(ctype,type,remote_variable,default_value,other_value) \
921	do { \
922	ctype DEFAULT_VALUE = default_value; \
923	ctype OTHER_VALUE = other_value; \
924	type LOCAL(remote_variable); \
925	TEST__READ(type, remote_variable, DEFAULT_VALUE); \
926	TEST_CHANGE(type, remote_variable, OTHER_VALUE); \
927	TEST_CHANGE(type, remote_variable, DEFAULT_VALUE); \
928	} while(0)
929
930	TEST_DEFAULT_CHANGE(const long, long, LOCS_MATCH_REVERSED, 1, 67);
931	typedef char *charp;
932	typedef const char *ccharp;
933	TEST_DEFAULT_CHANGE(ccharp, charp, LOCS_LOGINTIME, "notime", "sometime");
934	}
935
936	TEST_ASSERT_ZERO(aisc_close(link));
937	}
938
939	#endif

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