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source: tags/ms_r16q3/MULTI_PROBE/MP_Window.cxx

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Last change on this file was 15176, checked in by westram, 8 years ago
reintegrates 'fixres' into 'trunk' fixes #715 adds: log:branches/fixres@15127:15175
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1	// ================================================================ //
2	// //
3	// File : MP_Window.cxx //
4	// Purpose : //
5	// //
6	// Institute of Microbiology (Technical University Munich) //
7	// http://www.arb-home.de/ //
8	// //
9	// ================================================================ //
10
11	#include "MP_externs.hxx"
12	#include "MultiProbe.hxx"
13	#include "mp_proto.hxx"
14
15	#include <awt_sel_boxes.hxx>
16	#include <awt_modules.hxx>
17	#include <aw_select.hxx>
18	#include <aw_file.hxx>
19	#include <aw_msg.hxx>
20	#include <aw_root.hxx>
21	#include <aw_awar_defs.hxx>
22
23	#include <arb_strarray.h>
24	#include <arb_defs.h>
25	#include <arb_strbuf.h>
26	#include <arbdbt.h>
27	#include <ad_cb.h>
28	#include <RegExpr.hxx>
29
30	// **************************************************************************
31
32	struct mp_gl_struct mp_pd_gl; // global link
33
34	AW_selection_list *selected_list;
35	AW_selection_list *probelist;
36	AW_selection_list *result_probes_list;
37
38
39	AW_window_simple MP_Window::create_result_window(AW_root aw_root) {
40	if (!result_window) {
41	result_window = new AW_window_simple;
42	result_window->init(aw_root, "MULTIPROBE_RESULTS", "MultiProbe combination results");
43	result_window->load_xfig("mp_results.fig");
44
45	result_window->auto_space(5, 5);
46
47	result_window->button_length(7);
48	result_window->at("close");
49	result_window->callback(AW_POPDOWN);
50	result_window->create_button("CLOSE", "CLOSE");
51
52	result_window->at("Help");
53	result_window->callback(makeHelpCallback("multiproberesults.hlp"));
54	result_window->create_button("HELP", "HELP");
55
56	result_window->at("Comment");
57	result_window->callback(makeWindowCallback(MP_Comment, (const char *)NULL));
58	result_window->create_input_field(MP_AWAR_RESULTPROBESCOMMENT);
59
60	result_window->at("box");
61	aw_root->awar(MP_AWAR_RESULTPROBES)->add_callback(MP_result_combination_chosen);
62	result_probes_list = result_window->create_selection_list(MP_AWAR_RESULTPROBES, true);
63	result_probes_list->set_file_suffix("mpr");
64	result_probes_list->insert_default("", "");
65
66	const StorableSelectionList *storable_probes_list = new StorableSelectionList(TypedSelectionList("mpr", result_probes_list, "multiprobes", "multi_probes"));
67
68	result_window->at("buttons");
69	result_window->callback(makeCreateWindowCallback(create_load_box_for_selection_lists, storable_probes_list));
70	result_window->create_button("LOAD_RPL", "LOAD");
71
72	result_window->callback(makeCreateWindowCallback(create_save_box_for_selection_lists, storable_probes_list));
73	result_window->create_button("SAVE_RPL", "SAVE");
74
75	result_window->callback(makeWindowCallback(awt_clear_selection_list_cb, result_probes_list));
76	result_window->create_button("CLEAR", "CLEAR");
77
78	result_window->callback(makeWindowCallback(MP_delete_selected, result_probes_list));
79	result_window->create_button("DELETE", "DELETE");
80
81	// change comment :
82
83	result_window->button_length(8);
84
85	result_window->at("comment");
86	result_window->callback(makeWindowCallback(MP_Comment, "Bad"));
87	result_window->create_button("MARK_AS_BAD", "BAD");
88
89	result_window->callback(makeWindowCallback(MP_Comment, "???"));
90	result_window->create_button("MARK_AS_GOOD", "???");
91
92	result_window->callback(makeWindowCallback(MP_Comment, "Good"));
93	result_window->create_button("MARK_AS_BEST", "Good");
94
95	result_window->at("auto");
96	result_window->create_toggle(MP_AWAR_AUTOADVANCE);
97
98	// tree actions :
99
100	result_window->button_length(3);
101
102	result_window->at("ct_back");
103	result_window->callback(makeWindowCallback(MP_show_probes_in_tree_move, true, result_probes_list));
104	result_window->create_button("COLOR_TREE_BACKWARD", "#rightleft_small.xpm");
105
106	result_window->at("ct_fwd");
107	result_window->callback(makeWindowCallback(MP_show_probes_in_tree_move, false, result_probes_list));
108	result_window->create_button("COLOR_TREE_FORWARD", "#leftright_small.xpm");
109
110	result_window->button_length(8);
111
112	result_window->at("ColorTree");
113	result_window->button_length(4);
114	result_window->callback(MP_show_probes_in_tree);
115	result_window->create_button("COLOR_TREE", "GO");
116
117	result_window->at("MarkTree");
118	result_window->callback(MP_mark_probes_in_tree);
119	result_window->create_button("MARK_TREE", "GO");
120
121	result_window->at("GroupAll");
122	result_window->callback(MP_group_all_except_marked);
123	result_window->create_button("GROUP_UNMARKED", "GO");
124
125	result_window->at("StandardColor");
126	result_window->callback(MP_normal_colors_in_tree);
127	result_window->create_button("RESET_COLORS", "GO");
128	}
129	return result_window;
130	}
131
132	// --------------------------------------------------------------------------------
133	// Format of probe-list for multi-probes:
134	//
135	// The saved format is identical to the internal format (of sellist entries; where value always equals displayed!)
136	// "quality#singlemismatch#ecolipos#target"
137	//
138	// When loading input probes, several other formats are accepted:
139	//
140	// "quality,singlemismatch#ecolipos#probe" (old save format)
141	// "target le pos apos ecol grps GC 4gc2at probe \| ..." (save of probe design; old format)
142	// "target le pos apos ecol grps GC 4gc2at probe \| ...,target" (save of probe design)
143	//
144	// above
145	// 'target' is the target-string of the 'probe'. Internally MP works with target strings,
146	// so when loading the old save-format, 'probe' gets reverse-complemented into 'target'
147
148
149	#define SPACED(expr) "[[:space:]]" expr "[[:space:]]"
150
151	inline char gen_display(int quality, int singleMis, int ecoliPos, const char probe) {
152	return GBS_global_string_copy("%i#%i#%5i#%s", quality, singleMis, ecoliPos, probe);
153	}
154
155	static GB_ERROR mp_list2file(const CharPtrArray& display, const CharPtrArray& value, StrArray& line) {
156	GB_ERROR error = NULL;
157
158	if (value.empty()) error = "nothing to save";
159
160	for (size_t i = 0; i<display.size() && !error; ++i) {
161	line.put(ARB_strdup(display[i]));
162	}
163
164	return error;
165	}
166
167	static char T_or_U_for_load = 0;
168
169	static GB_ERROR mp_file2list(const CharPtrArray& line, StrArray& display, StrArray& value) {
170	GB_ERROR error = NULL;
171
172	if (line.empty()) error = "empty file";
173
174	// detect format
175	if (!error) {
176	// 1. try to read probes saved from multiprobes inputlist
177	RegExpr reg_saved("^" SPACED("([0-9]+)") "([,#])" SPACED("([0-9])+") "#" SPACED("([0-9]+)") "#" SPACED("([A-Z]+)") "$", true);
178	bool isSavedFormat = true;
179
180	for (size_t i = 0; i<line.size() && isSavedFormat; ++i) {
181	const RegMatch *match = reg_saved.match(line[i]);
182	if (!match \|\| reg_saved.subexpr_count() != 5) {
183	isSavedFormat = false;
184	}
185	else {
186	char T_or_U = T_or_U_for_load ? T_or_U_for_load : 'U';
187
188	std::string sep = reg_saved.subexpr_match(2)->extract(line[i]);
189
190	int quality = atoi(reg_saved.subexpr_match(1)->extract(line[i]).c_str());
191	int singlemis = atoi(reg_saved.subexpr_match(3)->extract(line[i]).c_str());
192	int ecoli = atoi(reg_saved.subexpr_match(4)->extract(line[i]).c_str());
193
194	std::string probe = reg_saved.subexpr_match(5)->extract(line[i]);
195
196	if (sep[0] == ',') { // old format (saved probe instead of probe-target)
197	size_t plen = probe.length();
198	char *dprobe = ARB_strndup(probe.c_str(), plen);
199
200	GBT_reverseComplementNucSequence(dprobe, plen, T_or_U);
201	probe = dprobe;
202	free(dprobe);
203	}
204
205	char *entry = gen_display(quality, singlemis, ecoli, probe.c_str());
206	display.put(entry); // transfers ownership - dont free!
207	value.put(ARB_strdup(entry));
208	}
209	}
210
211	if (!isSavedFormat) {
212	// delete attempt to read saved format:
213	display.clear();
214	value.clear();
215
216	// try to read designed list
217	RegExpr reg_designed("^([A-Z]+)" // subexpr #1 (target)
218	"[[:space:]]+[0-9]+"
219	"[[:space:]]+[A-Z][=+-]"
220	"[[:space:]]*[0-9]+"
221	"[[:space:]]+([0-9]+)" // subexpr #2 (ecoli pos)
222	"([[:space:]]+[0-9]+){1,2}" // accept with and without quality entry
223	"([[:space:]]+[0-9.]+){2}"
224	"[[:space:]]+[A-Z]+"
225	"[[:space:]]+[\|]", true);
226
227	for (size_t i = 0; i<line.size() && !error; ++i) {
228	char *probe = NULL;
229	char *description = NULL;
230	bool new_format = false;
231
232	const char *comma = strchr(line[i], ',');
233	if (comma) {
234	description = ARB_strpartdup(line[i], comma-1);
235
236	const char *cprobe = comma+1;
237	while (cprobe[0] == ' ') ++cprobe;
238	probe = ARB_strdup(cprobe);
239
240	new_format = true;
241	}
242	else {
243	description = ARB_strdup(line[i]);
244	}
245
246	const RegMatch *match = reg_designed.match(description);
247	if (match) { // line from probe design (old + new format)
248	mp_assert(match->didMatch());
249
250	match = reg_designed.subexpr_match(1);
251	mp_assert(match->didMatch());
252	std::string parsed_probe = match->extract(description);
253
254	if (new_format) { // already got probe value -> compare
255	if (strcmp(probe, parsed_probe.c_str()) != 0) {
256	error = GBS_global_string("probe string mismatch (probe='%s', parsed_probe='%s', parsed from='%s')",
257	probe, parsed_probe.c_str(), line[i]);
258	}
259	}
260	else {
261	probe = ARB_strdup(parsed_probe.c_str());
262	}
263
264	if (!error) {
265	int quality, ecoli;
266
267	match = reg_designed.subexpr_match(2);
268	mp_assert(match->didMatch());
269	ecoli = atoi(match->extract(description).c_str());
270	quality = 3;
271
272	char *entry = gen_display(quality, 0, ecoli, probe);
273	display.put(entry); // transfers ownership - dont free!
274	value.put(ARB_strdup(entry));
275	}
276	}
277	else if (new_format && probe[0]) {
278	error = GBS_global_string("can't parse line '%s'", line[i]);
279	}
280	// (when loading old format -> silently ignore non-matching lines)
281
282	free(probe);
283	free(description);
284	}
285	}
286	}
287
288	return error;
289	}
290
291	static void track_ali_change_cb(AW_root, GBDATA gb_main) {
292	GB_transaction ta(gb_main);
293	char *aliname = GBT_get_default_alignment(gb_main);
294	GB_alignment_type alitype = GBT_get_alignment_type(gb_main, aliname);
295
296	GBT_determine_T_or_U(alitype, &T_or_U_for_load, "reverse-complement"); // T_or_U_for_load is set to 0 in error-case
297	GB_clear_error();
298
299	free(aliname);
300	}
301
302	static void MP_collect_probes(AW_window*, awt_collect_mode mode) {
303	switch (mode) {
304	case ACM_ADD:
305	if (!probelist->default_is_selected()) {
306	int idx = probelist->get_index_of_selected();
307	AW_selection_list_iterator sel(probelist, idx);
308	selected_list->insert(sel.get_displayed(), sel.get_value());
309	MP_delete_selected(NULL, probelist);
310	}
311	break;
312
313	case ACM_REMOVE:
314	if (!selected_list->default_is_selected()) {
315	int idx = selected_list->get_index_of_selected();
316	AW_selection_list_iterator sel(selected_list, idx);
317	probelist->insert(sel.get_displayed(), sel.get_value());
318	MP_delete_selected(NULL, selected_list);
319	}
320	break;
321
322	case ACM_FILL:
323	probelist->move_content_to(selected_list);
324	break;
325
326	case ACM_EMPTY:
327	selected_list->move_content_to(probelist);
328	break;
329	}
330
331	selected_list->sort(false, true);
332
333	probelist->update();
334	selected_list->update();
335	}
336
337	MP_Window::MP_Window(AW_root aw_root, GBDATA gb_main) {
338	int max_seq_col = 35;
339	int max_seq_hgt = 15;
340
341	#if defined(DEBUG)
342	static bool initialized = false;
343	mp_assert(!initialized); // this function may only be called once!
344	initialized = true;
345	#endif
346
347	aw_root->awar(AWAR_DEFAULT_ALIGNMENT)->add_callback(makeRootCallback(track_ali_change_cb, gb_main));
348	track_ali_change_cb(aw_root, gb_main);
349
350	result_window = NULL;
351
352	aws = new AW_window_simple;
353	aws->init(aw_root, "MULTIPROBE", "MULTI_PROBE");
354	aws->load_xfig("multiprobe.fig");
355
356	aws->at("close");
357	aws->callback(MP_close_main);
358	aws->create_button("CLOSE", "CLOSE");
359
360	aws->at("help");
361	aws->callback(makeHelpCallback("multiprobe.hlp"));
362	aws->create_button("HELP", "HELP");
363
364	aws->button_length(7);
365	aws->at("Selectedprobes");
366	aw_root->awar(MP_AWAR_SELECTEDPROBES)->add_callback(MP_selected_chosen);
367	selected_list = aws->create_selection_list(MP_AWAR_SELECTEDPROBES, max_seq_col, max_seq_hgt, true);
368
369	const StorableSelectionList *storable_selected_list = new StorableSelectionList(TypedSelectionList("prb", selected_list, "probes", "selected_probes"), mp_list2file, mp_file2list);
370
371	selected_list->insert_default("", "");
372
373	aws->at("Probelist");
374	probelist = aws->create_selection_list(MP_AWAR_PROBELIST, true);
375	const StorableSelectionList *storable_probelist = new StorableSelectionList(TypedSelectionList("prb", probelist, "probes", "all_probes"), mp_list2file, mp_file2list);
376	probelist->insert_default("", "");
377
378	aws->at("collect");
379	awt_create_collect_buttons(aws, true, MP_collect_probes);
380
381	aws->auto_space(5, 5);
382	aws->button_length(7);
383
384	for (int rightSide = 0; rightSide <= 1; ++rightSide) {
385	const StorableSelectionList *storableList = rightSide ? storable_selected_list : storable_probelist;
386	const char *id_suffix = rightSide ? "SELECTED_PROBES" : "PROBES";
387
388	AW_selection_list *sellist = storableList->get_typedsellist().get_sellist();
389
390	aws->at(rightSide ? "RightButtons" : "LeftButtons");
391
392	aws->callback(makeCreateWindowCallback(create_load_box_for_selection_lists, storableList));
393	aws->create_button(GBS_global_string("LOAD_%s", id_suffix), "LOAD");
394
395	aws->callback(makeCreateWindowCallback(create_save_box_for_selection_lists, storableList));
396	aws->create_button(GBS_global_string("SAVE_%s", id_suffix), "SAVE");
397
398	aws->callback(makeWindowCallback(awt_clear_selection_list_cb, sellist));
399	aws->create_button(GBS_global_string("CLEAR_%s", id_suffix), "CLEAR");
400
401	aws->callback(makeWindowCallback(MP_delete_selected, sellist));
402	aws->create_button(GBS_global_string("DELETE_%s", id_suffix), "DELETE");
403	}
404
405	aws->at("Quality");
406	aws->callback(MP_cache_sonden); // @@@ used as OPTIONMENU_SELECT_CB (see #559)
407	aws->create_option_menu(MP_AWAR_QUALITY, true);
408	aws->insert_option("High Priority", "", 5);
409	aws->insert_option(" 4", "", 4);
410	aws->insert_option("Normal 3", "", 3);
411	aws->insert_option(" 2", "", 2);
412	aws->insert_option("Low Prio. 1", "", 1);
413	aws->update_option_menu();
414
415	aws->at("add");
416	aws->callback(MP_new_sequence);
417	aws->create_autosize_button("ADD_PROBE", "ADD");
418	aws->at("seqin");
419	aws->create_input_field(MP_AWAR_SEQIN, 25);
420
421	// --------------------------------
422	// multi probe parameters
423
424	aws->at("PTServer");
425	awt_create_PTSERVER_selection_button(aws, MP_AWAR_PTSERVER);
426	aw_root->awar(MP_AWAR_PTSERVER)->add_callback(MP_cache_sonden2); // remove cached probes when changing pt-server
427
428	aws->at("NoOfProbes");
429	aws->create_option_menu(MP_AWAR_NOOFPROBES, true);
430	aws->callback(MP_cache_sonden); // @@@ used as OPTIONMENU_SELECT_CB (see #559)
431	aws->insert_option("Compute 1 probe ", "", 1);
432	char str[50];
433	for (int i=2; i<=MAXPROBECOMBIS; i++) {
434	sprintf(str, "%2d-probe-combinations", i);
435	aws->insert_option(str, "", i);
436	}
437	aws->update_option_menu();
438
439	aws->button_length(10);
440	aws->at("Compute");
441	aws->callback(makeWindowCallback(MP_compute, gb_main));
442	aws->highlight();
443	aws->help_text("Compute possible Solutions");
444	aws->create_button("GO", "GO");
445
446	aws->button_length(20);
447	aws->at("Results");
448	aws->callback(MP_popup_result_window);
449	aws->create_button("OPEN_RESULT_WIN", "Open result window");
450
451	aws->at("Komplement");
452	aws->callback(MP_cache_sonden); // @@@ used as TOGGLE_CLICK_CB (see #559)
453	aws->create_toggle(MP_AWAR_COMPLEMENT);
454
455	aws->at("WeightedMismatches");
456	aws->callback(MP_cache_sonden); // @@@ used as TOGGLE_CLICK_CB (see #559)
457	aws->create_toggle(MP_AWAR_WEIGHTEDMISMATCHES);
458
459	// max non group hits
460	aws->at("Border1");
461	aws->callback(MP_cache_sonden); // @@@ used as INPUTFIELD_CB (see #559)
462	aws->create_input_field(MP_AWAR_QUALITYBORDER1, 6);
463
464	aws->at("OutsideMismatches");
465	aws->callback(MP_cache_sonden); // @@@ used as OPTIONMENU_SELECT_CB (see #559)
466	aws->create_option_menu(MP_AWAR_OUTSIDEMISMATCHES, true);
467	aws->insert_option("3.0", "", (float)3.0);
468	aws->insert_option("2.5", "", (float)2.5);
469	aws->insert_option("2.0", "", (float)2.0);
470	aws->insert_option("1.5", "", (float)1.5);
471	aws->insert_option("1.0", "", (float)1.0);
472	aws->update_option_menu();
473
474	// max mismatches for group
475	aws->at("Greyzone");
476	aws->callback(MP_cache_sonden); // @@@ used as OPTIONMENU_SELECT_CB (see #559)
477	aws->create_option_menu(MP_AWAR_GREYZONE, true);
478	aws->insert_default_option("0.0", "", (float)0.0);
479	for (float lauf=0.1; lauf<(float)1.0; lauf+=0.1) {
480	char strs[20];
481	sprintf(strs, "%.1f", lauf);
482	aws->insert_option(strs, "", lauf);
483	}
484	aws->update_option_menu();
485
486	}
487
488
489	MP_Window::~MP_Window()
490	{
491	if (result_window) result_window->hide();
492	if (aws) aws->hide();
493
494	delete result_window;
495	delete aws;
496	}
497
498	// --------------------------------------------------------------------------------
499
500	#ifdef UNIT_TESTS
501	#ifndef TEST_UNIT_H
502	#include <test_unit.h>
503	#endif
504	#include <command_output.h>
505
506	inline void array2cpa(const char **content, int count, ConstStrArray& array) {
507	array.erase();
508	for (int i = 0; i<count; ++i) {
509	array.put(content[i]);
510	}
511	}
512
513	inline char *array2string(const CharPtrArray& array) {
514	GBS_strstruct out(1000);
515
516	for (size_t i = 0; i<array.size(); ++i) {
517	out.cat(array[i]);
518	out.put('\n');
519	}
520
521	return out.release();
522	}
523
524	static arb_test::match_expectation inputConvertsInto(const char input, const char expected_result) {
525	ConstStrArray lines;
526	GBT_split_string(lines, input, "\n", true);
527
528	using namespace arb_test;
529	expectation_group expected;
530
531	StrArray display, value;
532	expected.add(doesnt_report_error(mp_file2list(lines, display, value)));
533
534	char *displ_as_string = array2string(display);
535	char *value_as_string = array2string(value);
536
537	expected.add(that(displ_as_string).is_equal_to(expected_result));
538	expected.add(that(value_as_string).is_equal_to(expected_result));
539
540	free(value_as_string);
541	free(displ_as_string);
542
543	return all().ofgroup(expected);
544	}
545
546	#define TEST_EXPECT_LOADS_INTO_MULTIPROBE_AS(input,expected) TEST_EXPECTATION(inputConvertsInto(input, expected))
547	#define TEST_EXPECT_LOADS_INTO_MULTIPROBE_AS__BROKEN(input,expected) TEST_EXPECTATION__BROKEN(inputConvertsInto(input, expected))
548
549	void TEST_load_probe_design_results() {
550	{
551	const char *expected =
552	"3#0# 521#GCAGCCGCGGUAAUACGG\n"
553	"3#0# 510#ACUCCGUGCCAGCAGCCG\n"
554	"3#0# 511#CUCCGUGCCAGCAGCCGC\n"
555	"3#0# 512#UCCGUGCCAGCAGCCGCG\n"
556	"3#0# 513#CCGUGCCAGCAGCCGCGG\n"
557	"3#0# 509#AACUCCGUGCCAGCAGCC\n";
558
559	const char *old_probeDesignSave =
560	"Probe design Parameters:\n"
561	"Length of probe 18\n"
562	"Temperature [30.0 -100.0]\n"
563	"GC-Content [50.0 -100.0]\n"
564	"E.Coli Position [any]\n"
565	"Max Non Group Hits 0\n"
566	"Min Group Hits 50%\n"
567	"Target le apos ecol grps G+C 4GC+2AT Probe sequence \| Decrease T by n*.3C -> probe matches n non group species\n"
568	"GCAGCCGCGGUAAUACGG 18 A= 4398 521 23 66.7 60.0 CCGUAUUACCGCGGCUGC \| 0; 0; 0; 0; 0; 0; 0; 0; 35; 35; 35; 38; 74; 74; 74; 77;113;113;113;148;\n"
569	"ACUCCGUGCCAGCAGCCG 18 B= 3852 510 23 72.2 62.0 CGGCUGCUGGCACGGAGU \| 0; 0; 0; 0; 0; 40; 40; 40; 80; 80; 80; 80;120;120;120;200;200;200;200;201;\n"
570	"CUCCGUGCCAGCAGCCGC 18 B+ 4 511 23 77.8 64.0 GCGGCUGCUGGCACGGAG \| 0; 0; 0; 0; 0; 40; 40; 40; 40; 80; 80; 80;160;160;160;160;201;201;201;201;\n"
571	"UCCGUGCCAGCAGCCGCG 18 B+ 7 512 23 77.8 64.0 CGCGGCUGCUGGCACGGA \| 0; 0; 0; 0; 0; 40; 40; 40;120;120;120;120;160;160;161;201;201;201;202;202;\n"
572	"CCGUGCCAGCAGCCGCGG 18 B+ 9 513 23 83.3 66.0 CCGCGGCUGCUGGCACGG \| 0; 0; 0; 0; 0; 80; 80; 80; 80;120;120;121;161;161;161;162;203;203;204;204;\n"
573	"AACUCCGUGCCAGCAGCC 18 B- 1 509 22 66.7 60.0 GGCUGCUGGCACGGAGUU \| 0; 0; 0; 0; 0; 40; 40; 40; 80; 80; 80;120;120;120;120;160;160;160;240;240;\n";
574
575	TEST_EXPECT_LOADS_INTO_MULTIPROBE_AS(old_probeDesignSave, expected);
576
577
578	const char *old_multiprobeInputSave = // old multi-probe saved probe (i.e. not target) sequences -> load shall correct that
579	"3,0# 521#CCGUAUUACCGCGGCUGC\n"
580	"3,0# 510#CGGCUGCUGGCACGGAGU\n"
581	"3,0# 511#GCGGCUGCUGGCACGGAG\n"
582	"3,0# 512#CGCGGCUGCUGGCACGGA\n"
583	"3,0# 513#CCGCGGCUGCUGGCACGG\n"
584	"3,0# 509#GGCUGCUGGCACGGAGUU\n";
585
586	{
587	LocallyModify<char> TorU(T_or_U_for_load, 'U');
588	TEST_EXPECT_LOADS_INTO_MULTIPROBE_AS(old_multiprobeInputSave, expected);
589	}
590
591	const char *new_probeDesignSave_v1 =
592	"Probe design Parameters:,\n"
593	"Length of probe 18,\n"
594	"Temperature [30.0 -100.0],\n"
595	"GC-Content [50.0 -100.0],\n"
596	"E.Coli Position [any],\n"
597	"Max Non Group Hits 0,\n"
598	"Min Group Hits 50%,\n"
599	"Target le apos ecol grps G+C 4GC+2AT Probe sequence \| Decrease T by n*.3C -> probe matches n non group species,\n"
600	"GCAGCCGCGGUAAUACGG 18 A= 4398 521 23 66.7 60.0 CCGUAUUACCGCGGCUGC \| 0; 0; 0; 0; 0; 0; 0; 0; 35; 35; 35; 38; 74; 74; 74; 77;113;113;113;148;,GCAGCCGCGGUAAUACGG\n"
601	"ACUCCGUGCCAGCAGCCG 18 B= 3852 510 23 72.2 62.0 CGGCUGCUGGCACGGAGU \| 0; 0; 0; 0; 0; 40; 40; 40; 80; 80; 80; 80;120;120;120;200;200;200;200;201;,ACUCCGUGCCAGCAGCCG\n"
602	"CUCCGUGCCAGCAGCCGC 18 B+ 4 511 23 77.8 64.0 GCGGCUGCUGGCACGGAG \| 0; 0; 0; 0; 0; 40; 40; 40; 40; 80; 80; 80;160;160;160;160;201;201;201;201;,CUCCGUGCCAGCAGCCGC\n"
603	"UCCGUGCCAGCAGCCGCG 18 B+ 7 512 23 77.8 64.0 CGCGGCUGCUGGCACGGA \| 0; 0; 0; 0; 0; 40; 40; 40;120;120;120;120;160;160;161;201;201;201;202;202;,UCCGUGCCAGCAGCCGCG\n"
604	"CCGUGCCAGCAGCCGCGG 18 B+ 9 513 23 83.3 66.0 CCGCGGCUGCUGGCACGG \| 0; 0; 0; 0; 0; 80; 80; 80; 80;120;120;121;161;161;161;162;203;203;204;204;,CCGUGCCAGCAGCCGCGG\n"
605	"AACUCCGUGCCAGCAGCC 18 B- 1 509 22 66.7 60.0 GGCUGCUGGCACGGAGUU \| 0; 0; 0; 0; 0; 40; 40; 40; 80; 80; 80;120;120;120;120;160;160;160;240;240;,AACUCCGUGCCAGCAGCC\n";
606
607	TEST_EXPECT_LOADS_INTO_MULTIPROBE_AS(new_probeDesignSave_v1, expected);
608
609
610	const char *new_multiprobeInputSave =
611	"3#0# 521#GCAGCCGCGGUAAUACGG\n"
612	"3#0# 510#ACUCCGUGCCAGCAGCCG\n"
613	"3#0# 511#CUCCGUGCCAGCAGCCGC\n"
614	"3#0# 512#UCCGUGCCAGCAGCCGCG\n"
615	"3#0# 513#CCGUGCCAGCAGCCGCGG\n"
616	"3#0# 509#AACUCCGUGCCAGCAGCC\n";
617
618	TEST_EXPECT_LOADS_INTO_MULTIPROBE_AS(new_multiprobeInputSave, expected);
619	}
620	}
621
622	static const char *recent_expected =
623	"3#0# 82#CGAAAGGAAGAUUA\n"
624	"3#0# 82#CGAAAGGAAGAUUAA\n"
625	"3#0# 86#AGGAAGAUUAAUACC\n"
626	"3#0# 87#GGAAGAUUAAUACC\n"
627	"3#0# 21#GUCGAGCGAUGAAG\n"
628	"3#0# 20#AGUCGAGCGAUGAAG\n"
629	"3#0# 20#AGUCGAGCGAUGAA\n"
630	"3#0# 19#AAGUCGAGCGAUGAA\n"
631	"3#0# 18#CAAGUCGAGCGAUGA\n"
632	"3#0# 19#AAGUCGAGCGAUGA\n"
633	"3#0# 17#UCAAGUCGAGCGAUG\n"
634	"3#0# 18#CAAGUCGAGCGAUG\n"
635	"3#0# 16#AUCAAGUCGAGCGAU\n"
636	"3#0# 17#UCAAGUCGAGCGAU\n"
637	"3#0# 16#AUCAAGUCGAGCGA\n";
638
639	static const char *recent_probeDesignSave =
640	"Probe design parameters:,\n"
641	"Length of probe 14-15,\n"
642	"Temperature [ 0.0 -400.0],\n"
643	"GC-content [30.0 - 80.0],\n"
644	"E.Coli position [any],\n"
645	"Max. nongroup hits 0,\n"
646	"Min. group hits 100% (max. rejected coverage: 75%),\n"
647	"Target le apos ecol qual grps G+C temp Probe sequence \| Decrease T by n*.3C -> probe matches n non group species,\n"
648	"CGAAAGGAAGAUUA 14 A=94 82 77 4 35.7 38.0 UAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -,CGAAAGGAAGAUUA\n"
649	"CGAAAGGAAGAUUAA 15 A+ 0 82 77 4 33.3 40.0 UUAAUCUUCCUUUCG \| - - - - - - - - - - - - - - - - - - - -,CGAAAGGAAGAUUAA\n"
650	"AGGAAGAUUAAUACC 15 A+ 4 86 77 4 33.3 40.0 GGUAUUAAUCUUCCU \| - - - - - - - - - - - - - - - - - - - -,AGGAAGAUUAAUACC\n"
651	"GGAAGAUUAAUACC 14 A+ 5 87 77 4 35.7 38.0 GGUAUUAAUCUUCC \| - - - - - - - - - - - - - - - - - - - -,GGAAGAUUAAUACC\n"
652	"GUCGAGCGAUGAAG 14 B=22 21 77 4 57.1 44.0 CUUCAUCGCUCGAC \| - - - - - - - - - - - - - - - - - - - 2,GUCGAGCGAUGAAG\n"
653	"AGUCGAGCGAUGAAG 15 B- 1 20 73 4 53.3 46.0 CUUCAUCGCUCGACU \| - - - - - - - - - - - - - - - - - - 2 2,AGUCGAGCGAUGAAG\n"
654	"AGUCGAGCGAUGAA 14 B- 1 20 57 4 50.0 42.0 UUCAUCGCUCGACU \| - - - - - - - - - - - - - - 2 2 2 2 2 2,AGUCGAGCGAUGAA\n"
655	"AAGUCGAGCGAUGAA 15 B- 2 19 53 4 46.7 44.0 UUCAUCGCUCGACUU \| - - - - - - - - - - - - - 2 2 2 2 2 2 2,AAGUCGAGCGAUGAA\n"
656	"CAAGUCGAGCGAUGA 15 B- 3 18 41 4 53.3 46.0 UCAUCGCUCGACUUG \| - - - - - - - - - - 2 2 2 2 2 2 2 2 2 2,CAAGUCGAGCGAUGA\n"
657	"AAGUCGAGCGAUGA 14 B- 2 19 41 4 50.0 42.0 UCAUCGCUCGACUU \| - - - - - - - - - - 2 2 2 2 2 2 2 2 2 2,AAGUCGAGCGAUGA\n"
658	"UCAAGUCGAGCGAUG 15 B- 4 17 25 4 53.3 46.0 CAUCGCUCGACUUGA \| - - - - - - 2 2 2 2 2 2 2 2 2 2 2 2 9 9,UCAAGUCGAGCGAUG\n"
659	"CAAGUCGAGCGAUG 14 B- 3 18 25 4 57.1 44.0 CAUCGCUCGACUUG \| - - - - - - 2 2 2 2 2 2 2 2 2 2 2 2 2 2,CAAGUCGAGCGAUG\n"
660	"AUCAAGUCGAGCGAU 15 B- 5 16 5 4 46.7 44.0 AUCGCUCGACUUGAU \| - 2 2 2 2 2 2 2 9 9 9 9 9 9 9 9 9 9 9 9,AUCAAGUCGAGCGAU\n"
661	"UCAAGUCGAGCGAU 14 B- 4 17 5 4 50.0 42.0 AUCGCUCGACUUGA \| - 2 2 2 2 2 2 2 2 9 9 9 9 9 9 9 9 9 9 9,UCAAGUCGAGCGAU\n"
662	"AUCAAGUCGAGCGA 14 B- 5 16 5 4 50.0 42.0 UCGCUCGACUUGAU \| - 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9,AUCAAGUCGAGCGA";
663
664	void TEST_AFTER_SLOW_recent_probe_design_result() {
665	// --------------------------------------------------------------------------------
666	// whenever probe design output changes, copy current 'recent_probeDesignSave' and
667	// 'recent_expected' into TEST_load_probe_design_results, to ensure ARB can load
668	// any saved probe design ever created with ARB.
669
670	TEST_EXPECT_LOADS_INTO_MULTIPROBE_AS(recent_probeDesignSave, recent_expected);
671	}
672
673	void TEST_SLOW_design_probes_and_load_result() {
674	TEST_SETUP_GLOBAL_ENVIRONMENT("ptserver");
675
676	CommandOutput designed_probes("arb_probe serverid=-666 designprobelength=14 designmaxprobelength=15 designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr designmintargets=100", true);
677	TEST_EXPECT_NO_ERROR(designed_probes.get_error());
678
679	// Simulate result of designing probes in ARB_NT and saving the result to a file:
680	char *saved_design_result = NULL; // content of that file
681	{
682	ConstStrArray lines;
683	GBT_split_string(lines, designed_probes.get_stdoutput(), "\n", true);
684
685	StrArray saved_lines;
686
687	for (size_t i = 0; i<lines.size(); ++i) {
688	char *probe; // same as awar-value of probe-design-resultlist in ARB_NT
689	{
690	size_t plen = strspn(lines[i], "acgtuACGTU");
691	if (plen<10) { // no probe at start // @@@ 10 is min. probelen, use a global definition here!
692	probe = ARB_strdup("");
693	}
694	else {
695	probe = ARB_strndup(lines[i], plen);
696	}
697	}
698
699	char *conv4save = GBS_string_eval(lines[i], ":,=;", NULL); // saving selection list converts comma to semicolon
700	arb_assert(conv4save);
701
702	saved_lines.put(GBS_global_string_copy("%s,%s", conv4save, probe));
703
704	free(conv4save);
705	free(probe);
706	}
707
708	saved_design_result = GBT_join_strings(saved_lines, '\n');
709	TEST_EXPECT_EQUAL(saved_design_result, recent_probeDesignSave); // see comment in TEST_LATE_recent_probe_design_result
710	}
711
712	TEST_EXPECT_LOADS_INTO_MULTIPROBE_AS(saved_design_result, recent_expected);
713	free(saved_design_result);
714	}
715
716
717	#endif // UNIT_TESTS
718
719	// --------------------------------------------------------------------------------

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