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source: tags/ms_r16q2/NTREE/AP_consensus.cxx

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Last change on this file was 14454, checked in by westram, 8 years ago
remove other unwanted callback casts
Property svn:eol-style set to `native` Property svn:keywords set to `Author Date Id Revision`
File size: 32.5 KB

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1	// ================================================================= //
2	// //
3	// File : AP_consensus.cxx //
4	// Purpose : calculate consensus SAIs //
5	// //
6	// http://www.arb-home.de/ //
7	// //
8	// ================================================================= //
9
10	#include "NT_local.h"
11
12	#include <aw_root.hxx>
13	#include <aw_msg.hxx>
14	#include <aw_awar.hxx>
15
16	#include <arbdbt.h>
17
18	#include <arb_strbuf.h>
19	#include <arb_defs.h>
20	#include <arb_progress.h>
21
22	#include <awt_config_manager.hxx>
23	#include <awt_misc.hxx>
24	#include <awt_sel_boxes.hxx>
25
26
27	#define AWAR_MAX_FREQ_PREFIX "tmp/CON_MAX_FREQ/"
28	#define AWAR_CONSENSUS_PREFIX "consensus/"
29	#define AWAR_CONSENSUS_PREFIX_TMP "tmp/" AWAR_CONSENSUS_PREFIX
30
31	#define AWAR_MAX_FREQ_IGNORE_GAPS AWAR_MAX_FREQ_PREFIX "no_gaps"
32	#define AWAR_MAX_FREQ_SAI_NAME AWAR_MAX_FREQ_PREFIX "sai_name"
33
34	#define AWAR_CONSENSUS_MARKED_ONLY AWAR_CONSENSUS_PREFIX_TMP "marked_only"
35	#define AWAR_CONSENSUS_ALIGNMENT AWAR_CONSENSUS_PREFIX_TMP "alignment"
36	#define AWAR_CONSENSUS_COUNTGAPS AWAR_CONSENSUS_PREFIX "countgaps"
37	#define AWAR_CONSENSUS_GAPBOUND AWAR_CONSENSUS_PREFIX "gapbound"
38	#define AWAR_CONSENSUS_GROUP AWAR_CONSENSUS_PREFIX "group"
39	#define AWAR_CONSENSUS_CONSIDBOUND AWAR_CONSENSUS_PREFIX "considbound"
40	#define AWAR_CONSENSUS_UPPER AWAR_CONSENSUS_PREFIX "upper"
41	#define AWAR_CONSENSUS_LOWER AWAR_CONSENSUS_PREFIX "lower"
42	#define AWAR_CONSENSUS_NAME AWAR_CONSENSUS_PREFIX_TMP "name"
43
44	#define CONSENSUS_AWAR_SOURCE CAS_NTREE
45	#include <consensus.h>
46	#include <consensus_config.h>
47	#include <chartable.h>
48
49	static int CON_insertSequences(GBDATA gb_main, const char aliname, long maxalignlen, bool onlymarked, BaseFrequencies& freqs) {
50	/*! read sequence data and fill into 'freqs'
51	* @param gb_main database
52	* @param aliname name of alignment
53	* @param maxalignlen length of alignment
54	* @param onlymarked true -> marked only
55	* @param freqs sequences are inserted here (has to be empty)
56	* @return number of inserted sequences
57	*/
58	int nrofspecies = onlymarked ? GBT_count_marked_species(gb_main) : GBT_get_species_count(gb_main);
59
60	arb_progress progress(nrofspecies);
61	progress.auto_subtitles("Examining sequence");
62
63	GBDATA *gb_species = onlymarked ? GBT_first_marked_species(gb_main) : GBT_first_species(gb_main);
64	while (gb_species) {
65	GBDATA *alidata = GBT_find_sequence(gb_species, aliname);
66	if (alidata) {
67	const char *data = GB_read_char_pntr(alidata);
68	size_t length = GB_read_string_count(alidata);
69
70	nt_assert(long(length)<=maxalignlen);
71	freqs.add(data, length);
72	}
73	gb_species = onlymarked ? GBT_next_marked_species(gb_species) : GBT_next_species(gb_species);
74	++progress;
75	}
76
77	int inserted = freqs.added_sequences();
78	if (nrofspecies < inserted) {
79	GBT_message(gb_main, GBS_global_string("Only %i of %i %sspecies contain data in alignment '%s'",
80	inserted, nrofspecies, onlymarked ? "marked " : "", aliname));
81	progress.done();
82	}
83
84	return inserted;
85	}
86
87	static GB_ERROR CON_export(GBDATA gb_main, const char savename, const char align, const char result, bool onlymarked, long nrofspecies, const ConsensusBuildParams& BK) {
88	/*! writes consensus SAI to DB
89	* @param gb_main database
90	* @param savename name of SAI to save to
91	* @param align alignment name
92	* @param result SAI data to write
93	* @param onlymarked true -> was calculated on marked only (used for SAI comment)
94	* @param nrofspecies number of used sequences (used for SAI comment; if less than 20 -> add an explicit list to field '_SPECIES')
95	* @param BK parameters used for consensus calculation (used for SAI comment)
96	* @return error if something goes wrong
97	*/
98	const char *off = "off";
99	const char *on = "on";
100
101	char buffer = (char )GB_calloc(2000, sizeof(char));
102
103	GBDATA *gb_extended = GBT_find_or_create_SAI(gb_main, savename);
104	GBDATA *gb_data = GBT_add_data(gb_extended, align, "data", GB_STRING);
105	GB_ERROR err = GB_write_string(gb_data, result);
106	if (!err) {
107	GBDATA *gb_options = GBT_add_data(gb_extended, align, "_TYPE", GB_STRING);
108
109	const char *allvsmarked = onlymarked ? "marked" : "all";
110	const char *countgapsstring = BK.countgaps ? on : off;
111	const char *simplifystring = BK.group ? on : off;
112
113	sprintf(buffer, "CON: [species: %s] [number: %ld] [count gaps: %s] "
114	"[threshold for gaps: %d] [simplify: %s] "
115	"[threshold for group: %d] [upper: %d] [lower: %d]",
116	allvsmarked, nrofspecies, countgapsstring,
117	BK.gapbound, simplifystring,
118	BK.considbound, BK.upper, BK.lower);
119
120	err = GB_write_string(gb_options, buffer);
121	if (!err) {
122	GBDATA *gb_names = GB_search(GB_get_father(gb_options), "_SPECIES", GB_FIND);
123	if (gb_names) err = GB_delete(gb_names); // delete old entry
124	}
125
126	if (!err && nrofspecies<20) {
127	GBDATA *gb_species;
128	GBS_strstruct *strstruct = GBS_stropen(1000);
129
130	if (onlymarked) gb_species = GBT_first_marked_species(gb_main);
131	else gb_species = GBT_first_species(gb_main);
132
133	while (gb_species) {
134	if (GBT_find_sequence(gb_species, align)) {
135	GBDATA *gb_speciesname = GB_search(gb_species, "name", GB_FIND);
136	const char *name = GB_read_char_pntr(gb_speciesname);
137
138	GBS_strcat(strstruct, name);
139	GBS_chrcat(strstruct, ' ');
140	}
141	if (onlymarked) gb_species = GBT_next_marked_species(gb_species);
142	else gb_species = GBT_next_species(gb_species);
143	}
144
145	char *allnames = GBS_strclose(strstruct);
146	err = GBT_write_string(GB_get_father(gb_options), "_SPECIES", allnames);
147	free(allnames);
148	}
149
150	// remove data relicts from "complex consensus" (no longer supported)
151	if (!err) {
152	char buffer2[256];
153	sprintf(buffer2, "%s/FREQUENCIES", align);
154	GBDATA *gb_graph = GB_search(gb_extended, buffer2, GB_FIND);
155	if (gb_graph) err = GB_delete(gb_graph); // delete old entry
156	}
157	}
158
159	free(buffer);
160	if (err) err = GBS_global_string("Failed to store consensus '%s' (Reason: %s)", savename, err);
161	return err;
162	}
163
164	static GB_ERROR CON_calculate(GBDATA gb_main, const ConsensusBuildParams& BK, const char aliname, bool onlymarked, const char *sainame) {
165	/*! calculates the consensus and writes it to SAI 'sainame'
166	* Description how consensus is calculated: ../HELP_SOURCE/oldhelp/consensus_def.hlp
167	* @param gb_main database
168	* @param BK parameters for consensus calculation
169	* @param aliname alignment name
170	* @param onlymarked true -> use marked sequences only
171	* @param sainame name of destination SAI
172	* @return error if something goes wrong
173	*/
174	GB_ERROR error = 0;
175
176	GB_push_transaction(gb_main);
177
178	long maxalignlen = GBT_get_alignment_len(gb_main, aliname);
179	if (maxalignlen <= 0) error = GB_export_errorf("alignment '%s' doesn't exist", aliname);
180
181	if (!error) {
182	arb_progress progress("Calculating consensus");
183
184	GB_alignment_type alitype = GBT_get_alignment_type(gb_main, aliname);
185	BaseFrequencies::setup("-.", alitype);
186
187	BaseFrequencies freqs(maxalignlen);
188	int nrofspecies = CON_insertSequences(gb_main, aliname, maxalignlen, onlymarked, freqs);
189
190	if (BK.lower>BK.upper) {
191	error = "fault: lower greater than upper";
192	}
193	else {
194	char *result = freqs.build_consensus_string(BK);
195	error = CON_export(gb_main, sainame, aliname, result, onlymarked, nrofspecies, BK);
196	free(result);
197	}
198	}
199
200	error = GB_end_transaction(gb_main, error);
201
202	return error;
203	}
204
205	static void CON_calculate_cb(AW_window *aw) {
206	AW_root *awr = aw->get_root();
207	char *aliname = awr->awar(AWAR_CONSENSUS_ALIGNMENT)->read_string();
208	char *sainame = awr->awar(AWAR_CONSENSUS_NAME)->read_string();
209	bool onlymarked = awr->awar(AWAR_CONSENSUS_MARKED_ONLY)->read_int();
210
211	ConsensusBuildParams BK(awr);
212
213	{
214	#if defined(ASSERTION_USED)
215	GB_transaction ta(GLOBAL.gb_main);
216	LocallyModify<bool> denyAwarReads(AW_awar::deny_read, true);
217	LocallyModify<bool> denyAwarWrites(AW_awar::deny_write, true);
218	#endif
219
220	GB_ERROR error = CON_calculate(GLOBAL.gb_main, BK, aliname, onlymarked, sainame);
221	aw_message_if(error);
222	}
223
224	free(sainame);
225	free(aliname);
226	}
227
228	static void consensus_upper_lower_changed_cb(AW_root *awr, bool upper_changed) {
229	AW_awar *awar_lower = awr->awar(AWAR_CONSENSUS_LOWER);
230	AW_awar *awar_upper = awr->awar(AWAR_CONSENSUS_UPPER);
231
232	int lower = awar_lower->read_int();
233	int upper = awar_upper->read_int();
234
235	if (upper<lower) {
236	if (upper_changed) awar_lower->write_int(upper);
237	else awar_upper->write_int(lower);
238	}
239	}
240
241	void AP_create_consensus_var(AW_root *aw_root, AW_default aw_def) {
242	GB_transaction ta(GLOBAL.gb_main);
243	{
244	char *defali = GBT_get_default_alignment(GLOBAL.gb_main);
245	aw_root->awar_string(AWAR_CONSENSUS_ALIGNMENT, defali, aw_def);
246	free(defali);
247	}
248	aw_root->awar_int(AWAR_CONSENSUS_MARKED_ONLY, 1, aw_def);
249	aw_root->awar_int(AWAR_CONSENSUS_GROUP, 0, aw_def);
250	aw_root->awar_int(AWAR_CONSENSUS_COUNTGAPS, 1, aw_def);
251	aw_root->awar_int(AWAR_CONSENSUS_UPPER, 95, aw_def)->set_minmax(0, 100)->add_callback(makeRootCallback(consensus_upper_lower_changed_cb, true));
252	aw_root->awar_int(AWAR_CONSENSUS_LOWER, 70, aw_def)->set_minmax(0, 100)->add_callback(makeRootCallback(consensus_upper_lower_changed_cb, false));
253	aw_root->awar_int(AWAR_CONSENSUS_GAPBOUND, 60, aw_def)->set_minmax(0, 100);
254	aw_root->awar_int(AWAR_CONSENSUS_CONSIDBOUND, 30, aw_def)->set_minmax(0, 100);
255	aw_root->awar_int(AWAR_MAX_FREQ_IGNORE_GAPS, 1, aw_def);
256
257	aw_root->awar_string(AWAR_CONSENSUS_NAME, "CONSENSUS", aw_def);
258	aw_root->awar_string(AWAR_MAX_FREQ_SAI_NAME, "MAX_FREQUENCY", aw_def);
259	}
260
261	static AWT_config_mapping_def consensus_config_mapping[] = {
262	{ AWAR_CONSENSUS_COUNTGAPS, CONSENSUS_CONFIG_COUNTGAPS },
263	{ AWAR_CONSENSUS_GAPBOUND, CONSENSUS_CONFIG_GAPBOUND },
264	{ AWAR_CONSENSUS_GROUP, CONSENSUS_CONFIG_GROUP },
265	{ AWAR_CONSENSUS_CONSIDBOUND, CONSENSUS_CONFIG_CONSIDBOUND },
266	{ AWAR_CONSENSUS_UPPER, CONSENSUS_CONFIG_UPPER },
267	{ AWAR_CONSENSUS_LOWER, CONSENSUS_CONFIG_LOWER },
268
269	// make sure the keywords of the following entries
270	// DIFFER from those defined at ../TEMPLATES/consensus_config.h@CommonEntries
271
272	{ AWAR_CONSENSUS_MARKED_ONLY, "marked_only" },
273	{ AWAR_CONSENSUS_NAME, "name" },
274
275	{ 0, 0 }
276	};
277
278	AW_window AP_create_con_expert_window(AW_root aw_root) {
279	// keep in sync with ../EDIT4/ED4_no_class.cxx@ED4_create_consensus_definition_window
280
281	AW_window_simple *aws = new AW_window_simple;
282	aws->init(aw_root, "CALCULATE_CONSENSUS", "CONSENSUS OF SEQUENCES");
283	aws->load_xfig("consensus/expert.fig");
284
285	aws->auto_space(5, 5);
286
287	const int SCALEDCOLUMNS = 3;
288	const int SCALERSIZE = 150;
289
290	// top part of window:
291	aws->button_length(9);
292
293	aws->at("cancel");
294	aws->callback(AW_POPDOWN);
295	aws->create_button("CLOSE", "CLOSE", "C");
296
297	aws->at("help");
298	aws->callback(makeHelpCallback("consensus.hlp"));
299	aws->create_button("HELP", "HELP", "H");
300
301	// left part of window:
302	aws->at("which_alignment");
303	awt_create_ALI_selection_list(GLOBAL.gb_main, (AW_window )aws, AWAR_CONSENSUS_ALIGNMENT, "=");
304
305	aws->at("which_species");
306	aws->create_toggle_field(AWAR_CONSENSUS_MARKED_ONLY);
307	aws->insert_toggle ("all", "a", 0);
308	aws->insert_default_toggle("marked", "m", 1);
309	aws->update_toggle_field();
310
311	aws->at("save_box");
312	awt_create_SAI_selection_list(GLOBAL.gb_main, aws, AWAR_CONSENSUS_NAME, false);
313
314	aws->at("name");
315	aws->create_input_field(AWAR_CONSENSUS_NAME, 10);
316
317	// right part of window (same as in EDIT4):
318	aws->at("countgaps");
319	aws->create_toggle_field(AWAR_CONSENSUS_COUNTGAPS, NULL, "");
320	aws->insert_toggle ("on", "1", 1);
321	aws->insert_default_toggle("off", "0", 0);
322	aws->update_toggle_field();
323
324	aws->at("gapbound");
325	aws->create_input_field_with_scaler(AWAR_CONSENSUS_GAPBOUND, SCALEDCOLUMNS, SCALERSIZE, AW_SCALER_LINEAR);
326
327	aws->at("group");
328	aws->create_toggle_field(AWAR_CONSENSUS_GROUP, NULL, "");
329	aws->insert_toggle ("on", "1", 1);
330	aws->insert_default_toggle("off", "0", 0);
331	aws->update_toggle_field();
332
333	aws->at("considbound");
334	aws->create_input_field_with_scaler(AWAR_CONSENSUS_CONSIDBOUND, SCALEDCOLUMNS, SCALERSIZE, AW_SCALER_LINEAR);
335
336	aws->at("showgroups");
337	aws->callback(AWT_create_IUPAC_info_window);
338	aws->create_autosize_button("SHOW_IUPAC", "Show IUPAC groups", "s");
339
340	aws->at("upper");
341	aws->create_input_field_with_scaler(AWAR_CONSENSUS_UPPER, SCALEDCOLUMNS, SCALERSIZE, AW_SCALER_LINEAR);
342
343	aws->at("lower");
344	aws->create_input_field_with_scaler(AWAR_CONSENSUS_LOWER, SCALEDCOLUMNS, SCALERSIZE, AW_SCALER_LINEAR);
345
346	// bottom part of window:
347	aws->at("calculate");
348	aws->callback(CON_calculate_cb);
349	aws->create_button("GO", "GO", "G");
350
351	aws->at("config");
352	AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, CONSENSUS_CONFIG_ID, consensus_config_mapping);
353
354	return aws;
355	}
356
357	static GB_ERROR CON_calc_max_freq(GBDATA gb_main, bool ignore_gaps, const char savename, const char *aliname) {
358	/*! calculates the maximum frequency for each column and write to SAI
359	* @param gb_main database
360	* @param ignore_gaps true -> ignore gaps; see ../HELP_SOURCE/oldhelp/max_freq.hlp@Gaps
361	* @param savename name of destination SAI
362	* @param aliname name of alignment to use
363	* @return error if something goes wrong
364	*/
365	arb_assert(!GB_have_error());
366
367	GB_ERROR error = NULL;
368	GB_transaction ta(gb_main);
369
370	long maxalignlen = GBT_get_alignment_len(gb_main, aliname);
371	if (maxalignlen<=0) {
372	GB_clear_error();
373	error = "alignment doesn't exist!";
374	}
375	else {
376	arb_progress progress("Calculating max. frequency");
377
378	GB_alignment_type alitype = GBT_get_alignment_type(gb_main, aliname);
379	BaseFrequencies::setup("-.", alitype);
380
381	const int onlymarked = 1;
382	BaseFrequencies freqs(maxalignlen);
383	long nrofspecies = CON_insertSequences(gb_main, aliname, maxalignlen, onlymarked, freqs);
384
385	char *result1 = new char[maxalignlen+1];
386	char *result2 = new char[maxalignlen+1];
387
388	result1[maxalignlen] = 0;
389	result2[maxalignlen] = 0;
390
391	for (int pos = 0; pos < maxalignlen; pos++) {
392	double mf = freqs.max_frequency_at(pos, ignore_gaps);
393	int mfi = int(mf*100.0+0.01); // frequency -> [0..100]; add 1/100 to reduce incompatibilities caused by 32/64 bit differences
394
395	if (mfi) {
396	if (mfi<10) mfi = 10; // hack: otherwise SAI will contain '0' (meaning 100% frequency)
397
398	int mfh = int(mfi/10);
399	int mfl = mfi-10*mfh;
400
401	result1[pos] = "?1234567890"[mfh];
402	result2[pos] = "0123456789"[mfl];
403	}
404	else {
405	result1[pos] = '=';
406	result2[pos] = '=';
407	}
408	}
409
410	GBDATA *gb_extended = GBT_find_or_create_SAI(gb_main, savename);
411	if (!gb_extended) {
412	error = GB_await_error();
413	}
414	else {
415	GBDATA *gb_data1 = GBT_add_data(gb_extended, aliname, "data", GB_STRING);
416	GBDATA *gb_data2 = GBT_add_data(gb_extended, aliname, "dat2", GB_STRING);
417
418	error = GB_write_string(gb_data1, result1);
419	if (!error) error = GB_write_string(gb_data2, result2);
420
421	GBDATA *gb_options = GBT_add_data(gb_extended, aliname, "_TYPE", GB_STRING);
422
423	if (!error) {
424	const char *type = GBS_global_string("MFQ: [species: %li] [ignore gaps: %s]", nrofspecies, ignore_gaps ? "yes" : "no");
425	error = GB_write_string(gb_options, type);
426	}
427	}
428
429	delete [] result1;
430	delete [] result2;
431	}
432
433	error = ta.close(error);
434	arb_assert(!GB_have_error());
435
436	return error;
437	}
438
439	static void CON_calc_max_freq_cb(AW_window *aw) {
440	AW_root *awr = aw->get_root();
441	bool ignore_gaps = awr->awar(AWAR_MAX_FREQ_IGNORE_GAPS)->read_int();
442	const char *savename = awr->awar(AWAR_MAX_FREQ_SAI_NAME)->read_char_pntr();
443	char *aliname = GBT_get_default_alignment(GLOBAL.gb_main);
444
445	GB_ERROR error = CON_calc_max_freq(GLOBAL.gb_main, ignore_gaps, savename, aliname);
446	if (error) aw_message(error);
447
448	free(aliname);
449	}
450
451	AW_window AP_create_max_freq_window(AW_root aw_root) {
452	AW_window_simple *aws = new AW_window_simple;
453	aws->init(aw_root, "MAX_FREQUENCY", "MAX FREQUENCY");
454	aws->load_xfig("consensus/max_freq.fig");
455
456	GB_push_transaction(GLOBAL.gb_main);
457
458	aws->button_length(6);
459
460	aws->at("cancel");
461	aws->callback(AW_POPDOWN);
462	aws->create_button("CLOSE", "CLOSE", "C");
463
464	aws->at("help"); aws->callback(makeHelpCallback("max_freq.hlp"));
465	aws->create_button("HELP", "HELP", "H");
466
467	// activation of consensus calculation by button ...
468	aws->at("go");
469	aws->callback(CON_calc_max_freq_cb);
470	aws->create_button("GO", "GO", "C");
471
472	aws->at("save");
473	aws->create_input_field(AWAR_MAX_FREQ_SAI_NAME, 1);
474
475	aws->at("sai");
476	awt_create_SAI_selection_list(GLOBAL.gb_main, aws, AWAR_MAX_FREQ_SAI_NAME, false);
477
478	aws->at("gaps");
479	aws->create_toggle(AWAR_MAX_FREQ_IGNORE_GAPS);
480
481	GB_pop_transaction(GLOBAL.gb_main);
482
483	return aws;
484	}
485
486	// --------------------------------------------------------------------------------
487
488	#ifdef UNIT_TESTS
489	#ifndef TEST_UNIT_H
490	#include <test_unit.h>
491	#endif
492
493	static GBDATA create_simple_seq_db(const char aliname, const char alitype, const char *sequence, int sequenceCount, int sequenceLength) {
494	GBDATA *gb_main = GB_open("nosuch.arb", "wc");
495
496	{
497	GB_transaction ta(gb_main);
498	GBDATA *gb_species_data = GBT_get_species_data(gb_main);
499	int specCounter = 0;
500
501	TEST_EXPECT_RESULT__NOERROREXPORTED(GBT_create_alignment(gb_main, aliname, sequenceLength, true, 6, alitype));
502
503	for (int s = 0; s<sequenceCount; ++s) {
504	GBDATA *gb_species = GBT_find_or_create_species_rel_species_data(gb_species_data, GBS_global_string("name%04i", ++specCounter));
505	GBDATA *gb_data = GBT_add_data(gb_species, aliname, "data", GB_STRING);
506
507	TEST_EXPECT_EQUAL(strlen(sequence[s]), sequenceLength);
508	TEST_EXPECT_NO_ERROR(GB_write_string(gb_data, sequence[s]));
509	}
510	}
511
512	#if 0
513	// save DB (to view data; should be inactive when committed)
514	char *dbname = GBS_global_string_copy("cons_%s.arb", alitype);
515	TEST_EXPECT_NO_ERROR(GB_save(gb_main, dbname, "a"));
516	free(dbname);
517	#endif
518
519	return gb_main;
520	}
521
522	static void read_frequency(GBDATA gb_main, const char sainame, const char aliname, const char& data, const char*& dat2) {
523	GB_transaction ta(gb_main);
524
525	GBDATA *gb_maxFreq = GBT_find_SAI(gb_main, sainame);
526	GBDATA *gb_ali = GB_entry(gb_maxFreq, aliname);
527	GBDATA *gb_data = GB_entry(gb_ali, "data");
528	GBDATA *gb_dat2 = GB_entry(gb_ali, "dat2");
529
530	data = GB_read_char_pntr(gb_data);
531	dat2 = GB_read_char_pntr(gb_dat2);
532	}
533
534	void TEST_nucleotide_consensus_and_maxFrequency() {
535	const char *sequence[] = {
536	"-.AAAAAAAAAAcAAAAAAAAATTTTTTTTTTTTTTTTTAAAAAAAAgggggAAAAgAA----m-----yykm-mmmAAAAAAAAAmmmmmmmmmNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNKKKKKKKKKWWWWWWWWW",
537	"-.-AAAAAAAAAccAAAAAAAAggTTgTTTTgTTTTTTTcccAAAAAgggggAAAAgAA----k-----kykr-rrrAAAAAAAAmmmmmmmmmT-NNNNNNNNNANNNNNbNNNNNNNNkNNNNNNNNaNNNNNNNNbKKKKKKKKbWWWWWWWW",
538	"-.--AAAAAAAAcccAAAAAAA-ggTggTTTggTTTTTTccccAAAAgggCCtAAAgAC----m-----sykw-wvsAAAAAAAmmmmmmmmmTT--NNNNNNNNCANNNNbbNNNNNNNkkNNNNNNNaaNNNNNNNbbKKKKKKKbbWWWWWWW",
539	"-.---AAAAAAAccccAAAAAA-ggggggTTgggTTTTTcccccAAAggCCC-tAACtC----k----yyyys-smvAAAAAAmmmmmmmmmTTT---NNNNNNNGCANNNbbbNNNNNNkkkNNNNNNaaaNNNNNNbbbKKKKKKbbbWWWWWW",
540	"-.----AAAAAAcccccAAAAA----ggggTggggTTTTGGGcccAAgCCCt-ttACtG----m---nkkkky-yrmAAAAAmmmmmmmmmTTTT----NNNNNNTGCANNbbbbNNNNNkkkkNNNNNaaaaNNNNNbbbbKKKKKbbbbWWWWW",
541	"-.-----AAAAAccccccAAAA----ggggggggggTTgGGGGcccAcCCtt--tttCG----k--nnssssk-kvrAAAAmmmmmmmmmTTTTT-----NNNNN-TGCANbbbbbNNNNkkkkkNNNNaaaaaNNNNbbbbbKKKKbbbbbWWWW",
542	"-.------AAAAcccccccAAA---------ggggggTgGGGGGccccCt----tt-gT----mydddyyyy-vvmsAAAmmmmmmmmmTTTTTT------NNNN-ATGCAbbbbbbNNNkkkkkkNNNaaaaaaNNNbbbbbbKKKbbbbbbWWW",
543	"-.-------AAAccccccccAA---------ggggggggttGGGGccct------t--T-yykkkbbbkkkk-hhrvAAmmmmmmmmmTTTTTTT-------NNN-C-TGCbbbbbbbNNkkkkkkkNNaaaaaaaNNbbbbbbbKKbbbbbbbWW",
544	"-.--------AAcccccccccA----------------gttGGGGGct-------t----ymmmmnnnssss-ddvmAmmmmmmmmmTTTTTTTT--------NN-G--TGbbbbbbbbNkkkkkkkkNaaaaaaaaNbbbbbbbbKbbbbbbbbW",
545	"-.---------Acccccccccc----------------gtAGGGGGG----------------k---------bbmrmmmmmmmmmTTTTTTTTT---------N-T---Tbbbbbbbbbkkkkkkkkkaaaaaaaaabbbbbbbbbbbbbbbbbb",
546	};
547	const char *expected_frequency[] = {
548	// considering gaps:
549	"0=9876567890098765678986665444576545675336544565434475454320888277654333462439988776654434567899876543222523222333322222444433332987765443333444444333444444",
550	"0=0000000000000000000000000000000000000000000000000000000000000500000055005565050505055050000000000000025050025210098765752075207257025702568013568568013568",
551	// ignoring gaps:
552	"==000000000009876567895757865688765678533654456554536655542=552233223333222439988776654434567892222222222222222333322222444433332987765443333444444333444444",
553	"==000000000000000000000505360637520257000000000502036075025=005530983388555565050505055050000005555555555555555210098765752075207257025702568013568568013568",
554	};
555	const char *expected_consensus[] = {
556	"==----..aaaACccMMMMMaa----.....g.kkk.uKb.ssVVmmss...-.ww...=---.---..byk.-.mVAaaaaMMMMmmHH..uuu----............BBbb.....Kkkkkk...aaaa.....BkkkkkkkKB....wwww", // default settings (see ConsensusBuildParams-ctor), gapbound=60, considbound=30, lower/upper=70/95
557	"==AAAAAAAAAACccMMMMMaaKgKugKKKuggKKKuuKb.ssVVmmssssBWWWWs..=Y.......BByk...mVAaaaaMMMMmmHH..uuu................BBbb.....Kkkkkk...aaaa.....BkkkkkkkKB....wwww", // countgaps=0
558	"==AAAAAAAAAACCCMMMMMAAKGKUGKKKUGGKKKUUKBsSSVVMMSSSSBWWWWSwa=YcaaykkkBBYKaaaMVAAAAAMMMMMMHHuuuUUaaaaaaaaaaaaaaaaBBBBBBBBcKKKKKkkkkAAAaaaaaaBBKKKKKKKBBuuuwWWW", // countgaps=0, considbound=26, lower=0, upper=75 (as described in #663)
559	"==AAAAAAAAAACCCMMMMMAAKKKKGKKKUGKKKKKUKBsSSVVMMSSSSBWWWWSwN=YHNNykkkBBYKNNNVVAAAAMMMMMMMHHHuuUUNNNNNNNNNNNNNNNNBBBBBBBBBKKKKKkkkkAAAaaaaaaBBKKKKKKKBBuuwwWWW", // countgaps=0, considbound=25, lower=0, upper=75
560	"==---aaaaAAACCCMMMMMAA-gkugkkkuggKKKuuKBsSSVVMMSsssb-wwWswa=---a--kkbBykaaaMVAAAAAMMMMMMHHuuuUU---aaaaaaaaaaaaaBBBBBBBBcKKKKKkkkkAAAaaaaaaBBKKKKKKKBBuuuwWWW", // countgaps=1, gapbound=70, considbound=26, lower=0, upper=75
561	"==---aaaaAAACCMMMMMMMA-kkkgkkkugKKKKKuKBNSVVVVMSsssb-wwWswN=---N--nnbBBBnnNVVAAAMMMMMMMHHHHHuUU---nnnnNNNnNnNNNBBBBBBBNNKKKKKkkNNAAAaaaaNNBBBBKKKKKBBBNwwWWW", // countgaps=1, gapbound=70, considbound=20, lower=0, upper=75
562	"==---aaaaAAACMMMMMMMMM-kkkkkkkkKKKKKKKKNNVVVVVVBBbbb-wwWbnN=---N--nnbBBBnnNVVMMMMMMMMMHHHHHHHHH---nnnnNNNnNnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNBBBBBBBBBNNNNNNNNN", // countgaps=1, gapbound=70, considbound= 1, lower=0, upper=75
563	"==---aaaaAAACMMMMMMMMM-kkkkkkkkKKKKKKKKNNVVVVVVBBbbb-wwWbnN=---N--nnbBBBnnNVVMMMMMMMMMHHHHHHHHH---nnnnNNNnNnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNBBBBBBBBBNNNNNNNNN", // countgaps=1, gapbound=70, considbound= 0, lower=0, upper=75
564	"==AAAAAAAAAACMMMMMMMMMKKKKKKKKKKKKKKKKKNNVVVVVVBBBBBWWWWBNN=YHNNNNNNBBBBNNNVVMMMMMMMMMHHHHHHHHHNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNBBBBBBBBBNNNNNNNNN", // countgaps=0, considbound= 0, lower=0, upper=75
565	};
566	const size_t seqlen = strlen(sequence[0]);
567	const int sequenceCount = ARRAY_ELEMS(sequence);
568	const int consensusCount = ARRAY_ELEMS(expected_consensus);
569
570	// create DB
571	GB_shell shell;
572	const char *aliname = "ali_nuc";
573	GBDATA *gb_main = create_simple_seq_db(aliname, "rna", sequence, sequenceCount, seqlen);
574
575	ConsensusBuildParams BK;
576	for (int c = 0; c<consensusCount; ++c) {
577	TEST_ANNOTATE(GBS_global_string("c=%i", c));
578	switch (c) {
579	case 0: break; // use default settings
580	case 1: BK.countgaps = false; break; // dont count gaps
581	case 2: BK.considbound = 26; BK.lower = 0; BK.upper = 75; break; // settings from #663
582	case 3: BK.considbound = 25; break;
583	case 4: BK.considbound = 26; BK.countgaps = true; BK.gapbound = 70; break;
584	case 5: BK.considbound = 20; break;
585	case 6: BK.considbound = 1; break;
586	case 7: BK.considbound = 0; break;
587	case 8: BK.countgaps = false; break;
588	default: arb_assert(0); break; // missing
589	}
590
591	{
592	GB_transaction ta(gb_main);
593	const char *sainame = "CONSENSUS";
594	TEST_EXPECT_NO_ERROR(CON_calculate(gb_main, BK, aliname, false, sainame));
595
596	GBDATA *gb_consensus = GBT_find_SAI(gb_main, sainame);
597	GBDATA *gb_seq = GBT_find_sequence(gb_consensus, aliname);
598	const char *consensus = GB_read_char_pntr(gb_seq);
599
600	TEST_EXPECT_EQUAL(consensus, expected_consensus[c]);
601	}
602	}
603
604	// test max.frequency
605	const char *sainame = "MAXFREQ";
606	for (int ignore_gaps = 0; ignore_gaps<=1; ++ignore_gaps) {
607	TEST_ANNOTATE(GBS_global_string("ignore_gaps=%i", ignore_gaps));
608	TEST_EXPECT_NO_ERROR(CON_calc_max_freq(gb_main, ignore_gaps, sainame, aliname));
609	const char data, dat2;
610	read_frequency(gb_main, sainame, aliname, data, dat2);
611	TEST_EXPECT_EQUAL(data, expected_frequency[ignore_gaps*2]);
612	TEST_EXPECT_EQUAL(dat2, expected_frequency[ignore_gaps*2+1]);
613	}
614
615	GB_close(gb_main);
616	}
617
618	void TEST_amino_consensus_and_maxFrequency() {
619	const char *sequence[] = {
620	"-.ppppppppppQQQQQQQQQDDDDDELLLLLwwwwwwwwwwwwwwwwgggggggggggSSSe-PPP-DELp",
621	"-.-pppppppppkQQQQQQQQnDDDDELLLLLVVwwVwwwwVwwwwwwSgggggggggSSSee-QPP-DELa",
622	"-.--ppppppppkkQQQQQQQnnDDDELLLLL-VVwVVwwwVVwwwwwSSgggggggSSSeee-KQP-DEIg",
623	"-.---pppppppkkkQQQQQQnnnDDELLLLL-VVVVVVwwVVVwwwwSSSgggggSSSeee--LQQ-DQIs",
624	"-.----ppppppkkkkQQQQQnnnnDELLLLL----VVVVwVVVVwwweSSSgggSSSeee---WKQ-NQJt",
625	"-.-----pppppkkkkkQQQQnnnnnqiLLLL----VVVVVVVVVVwweeSSSggSSeee-----KQ-NQJq",
626	"-.------ppppkkkkkkQQQnnnnnqiiLLL---------VVVVVVweeeSSSgSeee------LK-NZJn",
627	"-.-------pppkkkkkkkQQnnnnnqiiiLL---------VVVVVVVeeeeSSSeee-------LK-NZJe",
628	"-.--------ppkkkkkkkkQnnnnnqiiiiL----------------eeeeeSSee--------WK-BZJd",
629	"-.---------pkkkkkkkkknnnnnqiiiii----------------eeeeeeSe---------WK-BZJb",
630	"-.ppppppppppQQQQQQQQQDDDDDELLLLLwwwwwwwwwwwwwwwwgggggggggggSSSe-PPP-DELz",
631	"-.-pppppppppkQQQQQQQQnDDDDELLLLLVVwwVwwwwVwwwwwwSgggggggggSSSee-QPP-DELh",
632	"-.--ppppppppkkQQQQQQQnnDDDELLLLL-VVwVVwwwVVwwwwwSSgggggggSSSeee-KQP-DEIk",
633	"-.---pppppppkkkQQQQQQnnnDDELLLLL-VVVVVVwwVVVwwwwSSSgggggSSSeee--LQQ-DQIr",
634	"-.----ppppppkkkkQQQQQnnnnDELLLLL----VVVVwVVVVwwweSSSgggSSSeee---WKQ-NQJl",
635	"-.-----pppppkkkkkQQQQnnnnnqiLLLL----VVVVVVVVVVwweeSSSggSSeee-----KQ-NQJi",
636	"-.------ppppkkkkkkQQQnnnnnqiiLLL---------VVVVVVweeeSSSgSeee------LK-NZJv",
637	"-.-------pppkkkkkkkQQnnnnnqiiiLL---------VVVVVVVeeeeSSSeee-------LK-NZJm",
638	"-.--------ppkkkkkkkkQnnnnnqiiiiL----------------eeeeeSSee--------WK-BZJf",
639	"-.---------pkkkkkkkkknnnnnqiiiii----------------eeeeeeSe---------WK-BZJy",
640	};
641	const char *expected_frequency[] = {
642	// considering gaps:
643	"0=9876567890987656789987655567898666544457654567654456743334567052404451",
644	"0=0000000000000000000000000000000000000000000000000000000000000000000000",
645	// ignoring gaps:
646	"==0000000000987656789987655567895757865688765678654456743345670=224=4451",
647	"==0000000000000000000000000000000505360637520257000000003720050=000=0000",
648	};
649	const char *expected_consensus[] = {
650	"==----..aaaAhhh...dddDDDDDDIIIII----.....i.....f...aaaAa.....--=.X.=DD-.", // default settings (see ConsensusBuildParams-ctor), gapbound=60, considbound=30, lower/upper=70/95
651	"==AAAAAAAAAAhhh...dddDDDDDDIIIII.i.fi...fii...ff...aaaAa.....dD=XX.=DDI.", // countgaps=0
652	"==AAAAAAAAAAHHhhdddDDDDDDDDIIIIIiIiFIiifFIIiifFFdaaaAAAaaaaadDD=XXh=DDId", // countgaps=0, considbound= 26, lower=0, upper=75
653	"==---aaaaAAAHHhhdddDDDDDDDDIIIII-iifiiiffiiiifffdaaaAAAaaaaadd-=xXh=DDid", // countgaps=1, gapbound=70, considbound= 26, lower=0, upper=75
654	"==---aaaaAAAHHhhdddDDDDDDDDIIIII-iifiiiffiiiifffdaaaAAAaaaaadd-=aah=DDid", // countgaps=1, gapbound=70, considbound= 20, lower=0, upper=75
655	"==---aaaaAAAHHhhXddDDDDDDDDIIIII-ixfiixffiiiXfffdXaaAAAaaaaxdd-=xXX=DDiX", // countgaps=1, gapbound=70, considbound= 51, lower=0, upper=75
656	"==---aaaaAAAHXXXXXXXDDDDDDDIIIII-xxxxxxxxXXXXXXXXXXXXAAXXXxxxx-=xXX=DDiX", // countgaps=1, gapbound=70, considbound= 90, lower=0, upper=75
657	"==---aaaaAAAXXXXXXXXXDDDDDDIIIII-xxxxxxxxXXXXXXXXXXXXXAXXXxxxx-=xXX=DDiX", // countgaps=1, gapbound=70, considbound=100, lower=0, upper=75
658	"==---aaaaAAAHHhhdddDDDDDDDDIIIII-iifiiiffiiiifffdaaaAAAaaaaadd-=aah=DDid", // countgaps=1, gapbound=70, considbound= 0, lower=0, upper=75
659	};
660	const size_t seqlen = strlen(sequence[0]);
661	const int sequenceCount = ARRAY_ELEMS(sequence);
662	const int consensusCount = ARRAY_ELEMS(expected_consensus);
663
664	// create DB
665	GB_shell shell;
666	const char *aliname = "ali_ami";
667	GBDATA *gb_main = create_simple_seq_db(aliname, "ami", sequence, sequenceCount, seqlen);
668
669	ConsensusBuildParams BK;
670	for (int c = 0; c<consensusCount; ++c) {
671	TEST_ANNOTATE(GBS_global_string("c=%i", c));
672	switch (c) {
673	case 0: break; // use default settings
674	case 1: BK.countgaps = false; break; // dont count gaps
675	case 2: BK.considbound = 26; BK.lower = 0; BK.upper = 75; break; // settings from #663
676	case 3: BK.countgaps = true; BK.gapbound = 70; break;
677	case 4: BK.considbound = 20; break;
678	case 5: BK.considbound = 51; break;
679	case 6: BK.considbound = 90; break;
680	case 7: BK.considbound = 100; break;
681	case 8: BK.considbound = 0; break;
682	default: arb_assert(0); break; // missing
683	}
684
685	{
686	GB_transaction ta(gb_main);
687	const char *sainame = "CONSENSUS";
688	TEST_EXPECT_NO_ERROR(CON_calculate(gb_main, BK, aliname, false, sainame));
689
690	GBDATA *gb_consensus = GBT_find_SAI(gb_main, sainame);
691	GBDATA *gb_seq = GBT_find_sequence(gb_consensus, aliname);
692	const char *consensus = GB_read_char_pntr(gb_seq);
693
694	TEST_EXPECT_EQUAL(consensus, expected_consensus[c]);
695	}
696	}
697
698	// test max.frequency
699	const char *sainame = "MAXFREQ";
700	for (int ignore_gaps = 0; ignore_gaps<=1; ++ignore_gaps) {
701	TEST_ANNOTATE(GBS_global_string("ignore_gaps=%i", ignore_gaps));
702	TEST_EXPECT_NO_ERROR(CON_calc_max_freq(gb_main, ignore_gaps, sainame, aliname));
703	const char data, dat2;
704	read_frequency(gb_main, sainame, aliname, data, dat2);
705	TEST_EXPECT_EQUAL(data, expected_frequency[ignore_gaps*2]);
706	TEST_EXPECT_EQUAL(dat2, expected_frequency[ignore_gaps*2+1]);
707	}
708
709	GB_close(gb_main);
710	}
711
712	#endif // UNIT_TESTS
713

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