ARB
AP_consensus.cxx
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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 // AISC_MKPT_PROMOTE:#ifndef AW_BASE_HXX
27 // AISC_MKPT_PROMOTE:#include <aw_base.hxx>
28 // AISC_MKPT_PROMOTE:#endif
29 
30 #define AWAR_MAX_FREQ_PREFIX "tmp/CON_MAX_FREQ/"
31 #define AWAR_CONSENSUS_PREFIX "consensus/"
32 #define AWAR_CONSENSUS_PREFIX_TMP "tmp/" AWAR_CONSENSUS_PREFIX
33 
34 #define AWAR_MAX_FREQ_IGNORE_GAPS AWAR_MAX_FREQ_PREFIX "no_gaps"
35 #define AWAR_MAX_FREQ_SAI_NAME AWAR_MAX_FREQ_PREFIX "sai_name"
36 
37 #define AWAR_CONSENSUS_MARKED_ONLY AWAR_CONSENSUS_PREFIX_TMP "marked_only"
38 #define AWAR_CONSENSUS_ALIGNMENT AWAR_CONSENSUS_PREFIX_TMP "alignment"
39 #define AWAR_CONSENSUS_COUNTGAPS AWAR_CONSENSUS_PREFIX "countgaps"
40 #define AWAR_CONSENSUS_GAPBOUND AWAR_CONSENSUS_PREFIX "gapbound"
41 #define AWAR_CONSENSUS_GROUP AWAR_CONSENSUS_PREFIX "group"
42 #define AWAR_CONSENSUS_CONSIDBOUND AWAR_CONSENSUS_PREFIX "considbound"
43 #define AWAR_CONSENSUS_UPPER AWAR_CONSENSUS_PREFIX "upper"
44 #define AWAR_CONSENSUS_LOWER AWAR_CONSENSUS_PREFIX "lower"
45 #define AWAR_CONSENSUS_NAME AWAR_CONSENSUS_PREFIX_TMP "name"
46 
47 #define CONSENSUS_AWAR_SOURCE CAS_NTREE
48 #include <consensus.h>
49 #include <consensus_config.h>
50 #include <chartable.h>
51 
52 static int CON_insertSequences(GBDATA *gb_main, const char *aliname, long IF_ASSERTION_USED(maxalignlen), bool onlymarked, BaseFrequencies& freqs) {
61  long nrofspecies = onlymarked ? GBT_count_marked_species(gb_main) : GBT_get_species_count(gb_main);
62 
63  arb_progress progress(nrofspecies);
64  progress.auto_subtitles("Examining sequence");
65 
66  GBDATA *gb_species = onlymarked ? GBT_first_marked_species(gb_main) : GBT_first_species(gb_main);
67  while (gb_species) {
68  GBDATA *alidata = GBT_find_sequence(gb_species, aliname);
69  if (alidata) {
70  const char *data = GB_read_char_pntr(alidata);
71  size_t length = GB_read_string_count(alidata);
72 
73  nt_assert(long(length)<=maxalignlen);
74  freqs.add(data, length);
75  }
76  gb_species = onlymarked ? GBT_next_marked_species(gb_species) : GBT_next_species(gb_species);
77  ++progress;
78  }
79 
80  int inserted = freqs.added_sequences();
81  if (nrofspecies < inserted) {
82  GBT_message(gb_main, GBS_global_string("Only %i of %li %sspecies contain data in alignment '%s'",
83  inserted, nrofspecies, onlymarked ? "marked " : "", aliname));
84  progress.done();
85  }
86 
87  return inserted;
88 }
89 
90 static GB_ERROR CON_export(GBDATA *gb_main, const char *savename, const char *align, const char *result, bool onlymarked, long nrofspecies, const ConsensusBuildParams& BK) {
101  const char *off = "off";
102  const char *on = "on";
103 
104  GBDATA *gb_extended = GBT_find_or_create_SAI(gb_main, savename);
105  GBDATA *gb_data = GBT_add_data(gb_extended, align, "data", GB_STRING);
106  GB_ERROR err = GB_write_string(gb_data, result);
107  if (!err) {
108  GBDATA *gb_options = GBT_add_data(gb_extended, align, "_TYPE", GB_STRING);
109 
110  const char *allvsmarked = onlymarked ? "marked" : "all";
111  const char *countgapsstring = BK.countgaps ? on : off;
112  const char *simplifystring = BK.group ? on : off;
113 
114  {
115  char *buffer = ARB_alloc<char>(2000);
116  sprintf(buffer, "CON: [species: %s] [number: %ld] [count gaps: %s] "
117  "[threshold for gaps: %d] [simplify: %s] "
118  "[threshold for group: %d] [upper: %d] [lower: %d]",
119  allvsmarked, nrofspecies, countgapsstring,
120  BK.gapbound, simplifystring,
121  BK.considbound, BK.upper, BK.lower);
122 
123  err = GB_write_string(gb_options, buffer);
124  free(buffer);
125  }
126 
127  if (!err) {
128  GBDATA *gb_names = GB_search(GB_get_father(gb_options), "_SPECIES", GB_FIND);
129  if (gb_names) err = GB_delete(gb_names); // delete old entry
130  }
131 
132  if (!err && nrofspecies<20) {
133  GBS_strstruct namelist(1000);
134 
135  GBDATA *gb_species =
136  onlymarked
137  ? GBT_first_marked_species(gb_main)
138  : GBT_first_species(gb_main);
139 
140  while (gb_species) {
141  if (GBT_find_sequence(gb_species, align)) {
142  GBDATA *gb_speciesname = GB_search(gb_species, "name", GB_FIND);
143  const char *name = GB_read_char_pntr(gb_speciesname);
144 
145  namelist.cat(name);
146  namelist.put( ' ');
147  }
148  if (onlymarked) gb_species = GBT_next_marked_species(gb_species);
149  else gb_species = GBT_next_species(gb_species);
150  }
151 
152  err = GBT_write_string(GB_get_father(gb_options), "_SPECIES", namelist.get_data());
153  }
154 
155  // remove data relicts from "complex consensus" (no longer supported)
156  if (!err) {
157  char buffer2[256];
158  sprintf(buffer2, "%s/FREQUENCIES", align);
159  GBDATA *gb_graph = GB_search(gb_extended, buffer2, GB_FIND);
160  if (gb_graph) err = GB_delete(gb_graph); // delete old entry
161  }
162  }
163 
164  if (err) err = GBS_global_string("Failed to store consensus '%s' (Reason: %s)", savename, err);
165  return err;
166 }
167 
168 static GB_ERROR CON_calculate(GBDATA *gb_main, const ConsensusBuildParams& BK, const char *aliname, bool onlymarked, const char *sainame) {
178  GB_ERROR error = NULp;
179 
180  GB_push_transaction(gb_main);
181 
182  long maxalignlen = GBT_get_alignment_len(gb_main, aliname);
183  if (maxalignlen <= 0) error = GB_export_errorf("alignment '%s' doesn't exist", aliname);
184 
185  if (!error) {
186  arb_progress progress("Calculating consensus");
187 
188  GB_alignment_type alitype = GBT_get_alignment_type(gb_main, aliname);
189  BaseFrequencies::setup("-.", alitype);
190 
191  BaseFrequencies freqs(maxalignlen);
192  int nrofspecies = CON_insertSequences(gb_main, aliname, maxalignlen, onlymarked, freqs);
193 
194  if (BK.lower>BK.upper) {
195  error = "fault: lower greater than upper";
196  }
197  else {
198  char *result = freqs.build_consensus_string(BK);
199  error = CON_export(gb_main, sainame, aliname, result, onlymarked, nrofspecies, BK);
200  free(result);
201  }
202  }
203 
204  error = GB_end_transaction(gb_main, error);
205 
206  return error;
207 }
208 
209 static void CON_calculate_cb(AW_window *aw) {
210  AW_root *awr = aw->get_root();
211  char *aliname = awr->awar(AWAR_CONSENSUS_ALIGNMENT)->read_string();
212  char *sainame = awr->awar(AWAR_CONSENSUS_NAME)->read_string();
213  bool onlymarked = awr->awar(AWAR_CONSENSUS_MARKED_ONLY)->read_int();
214 
215  ConsensusBuildParams BK(awr);
216 
217  {
218 #if defined(ASSERTION_USED)
220  LocallyModify<bool> denyAwarReads(AW_awar::deny_read, true);
221  LocallyModify<bool> denyAwarWrites(AW_awar::deny_write, true);
222 #endif
223 
224  GB_ERROR error = CON_calculate(GLOBAL.gb_main, BK, aliname, onlymarked, sainame);
225  aw_message_if(error);
226  }
227 
228  free(sainame);
229  free(aliname);
230 }
231 
232 static void consensus_upper_lower_changed_cb(AW_root *awr, bool upper_changed) {
233  AW_awar *awar_lower = awr->awar(AWAR_CONSENSUS_LOWER);
234  AW_awar *awar_upper = awr->awar(AWAR_CONSENSUS_UPPER);
235 
236  int lower = awar_lower->read_int();
237  int upper = awar_upper->read_int();
238 
239  if (upper<lower) {
240  if (upper_changed) awar_lower->write_int(upper);
241  else awar_upper->write_int(lower);
242  }
243 }
244 
247  {
248  char *defali = GBT_get_default_alignment(GLOBAL.gb_main);
249  aw_root->awar_string(AWAR_CONSENSUS_ALIGNMENT, defali, aw_def);
250  free(defali);
251  }
252  aw_root->awar_int(AWAR_CONSENSUS_MARKED_ONLY, 1, aw_def);
253  aw_root->awar_int(AWAR_CONSENSUS_GROUP, 0, aw_def);
254  aw_root->awar_int(AWAR_CONSENSUS_COUNTGAPS, 1, aw_def);
255  aw_root->awar_int(AWAR_CONSENSUS_UPPER, 95, aw_def)->set_minmax(0, 100)->add_callback(makeRootCallback(consensus_upper_lower_changed_cb, true));
256  aw_root->awar_int(AWAR_CONSENSUS_LOWER, 70, aw_def)->set_minmax(0, 100)->add_callback(makeRootCallback(consensus_upper_lower_changed_cb, false));
257  aw_root->awar_int(AWAR_CONSENSUS_GAPBOUND, 60, aw_def)->set_minmax(0, 100);
258  aw_root->awar_int(AWAR_CONSENSUS_CONSIDBOUND, 30, aw_def)->set_minmax(0, 100);
259  aw_root->awar_int(AWAR_MAX_FREQ_IGNORE_GAPS, 1, aw_def);
260 
261  aw_root->awar_string(AWAR_CONSENSUS_NAME, "CONSENSUS", aw_def);
262  aw_root->awar_string(AWAR_MAX_FREQ_SAI_NAME, "MAX_FREQUENCY", aw_def);
263 }
264 
272 
273  // make sure the keywords of the following entries
274  // DIFFER from those defined at ../TEMPLATES/consensus_config.h@CommonEntries
275 
276  { AWAR_CONSENSUS_MARKED_ONLY, "marked_only" },
277  { AWAR_CONSENSUS_NAME, "name" },
278 
279  { NULp, NULp }
280 };
281 
283  // keep in sync with ../EDIT4/ED4_no_class.cxx@ED4_create_consensus_definition_window
284 
285  AW_window_simple *aws = new AW_window_simple;
286  aws->init(aw_root, "CALCULATE_CONSENSUS", "CONSENSUS OF SEQUENCES");
287  aws->load_xfig("consensus/expert.fig");
288 
289  aws->auto_space(5, 5);
290 
291  const int SCALEDCOLUMNS = 3;
292  const int SCALERSIZE = 150;
293 
294  // top part of window:
295  aws->button_length(9);
296 
297  aws->at("cancel");
298  aws->callback(AW_POPDOWN);
299  aws->create_button("CLOSE", "CLOSE", "C");
300 
301  aws->at("help");
302  aws->callback(makeHelpCallback("consensus.hlp"));
303  aws->create_button("HELP", "HELP", "H");
304 
305  // left part of window:
306  aws->at("which_alignment");
308 
309  aws->at("which_species");
310  aws->create_toggle_field(AWAR_CONSENSUS_MARKED_ONLY);
311  aws->insert_toggle ("all", "a", 0);
312  aws->insert_default_toggle("marked", "m", 1);
313  aws->update_toggle_field();
314 
315  aws->at("save_box");
317 
318  aws->at("name");
319  aws->create_input_field(AWAR_CONSENSUS_NAME, 10);
320 
321  // right part of window (same as in EDIT4):
322  aws->at("countgaps");
323  aws->create_toggle_field(AWAR_CONSENSUS_COUNTGAPS, NULp, "");
324  aws->insert_toggle ("on", "1", 1);
325  aws->insert_default_toggle("off", "0", 0);
326  aws->update_toggle_field();
327 
328  aws->at("gapbound");
329  aws->create_input_field_with_scaler(AWAR_CONSENSUS_GAPBOUND, SCALEDCOLUMNS, SCALERSIZE, AW_SCALER_LINEAR);
330 
331  aws->at("group");
332  aws->create_toggle_field(AWAR_CONSENSUS_GROUP, NULp, "");
333  aws->insert_toggle ("on", "1", 1);
334  aws->insert_default_toggle("off", "0", 0);
335  aws->update_toggle_field();
336 
337  aws->at("considbound");
338  aws->create_input_field_with_scaler(AWAR_CONSENSUS_CONSIDBOUND, SCALEDCOLUMNS, SCALERSIZE, AW_SCALER_LINEAR);
339 
340  aws->at("showgroups");
341  aws->callback(AWT_create_IUPAC_info_window);
342  aws->create_autosize_button("SHOW_IUPAC", "Show IUPAC groups", "s");
343 
344  aws->at("upper");
345  aws->create_input_field_with_scaler(AWAR_CONSENSUS_UPPER, SCALEDCOLUMNS, SCALERSIZE, AW_SCALER_LINEAR);
346 
347  aws->at("lower");
348  aws->create_input_field_with_scaler(AWAR_CONSENSUS_LOWER, SCALEDCOLUMNS, SCALERSIZE, AW_SCALER_LINEAR);
349 
350  // bottom part of window:
351  aws->at("calculate");
352  aws->callback(CON_calculate_cb);
353  aws->create_button("GO", "GO", "G");
354 
355  aws->at("config");
356  AWT_insert_config_manager(aws, AW_ROOT_DEFAULT, CONSENSUS_CONFIG_ID, consensus_config_mapping);
357 
358  return aws;
359 }
360 
361 static GB_ERROR CON_calc_max_freq(GBDATA *gb_main, bool ignore_gaps, const char *savename, const char *aliname) {
370 
371  GB_ERROR error = NULp;
372  GB_transaction ta(gb_main);
373 
374  long maxalignlen = GBT_get_alignment_len(gb_main, aliname);
375  if (maxalignlen<=0) {
376  GB_clear_error();
377  error = "alignment doesn't exist!";
378  }
379  else {
380  arb_progress progress("Calculating max. frequency");
381 
382  GB_alignment_type alitype = GBT_get_alignment_type(gb_main, aliname);
383  BaseFrequencies::setup("-.", alitype);
384 
385  const int onlymarked = 1;
386  BaseFrequencies freqs(maxalignlen);
387  long nrofspecies = CON_insertSequences(gb_main, aliname, maxalignlen, onlymarked, freqs);
388 
389  char *result1 = new char[maxalignlen+1];
390  char *result2 = new char[maxalignlen+1];
391 
392  result1[maxalignlen] = 0;
393  result2[maxalignlen] = 0;
394 
395  for (int pos = 0; pos < maxalignlen; pos++) {
396  double mf = freqs.max_frequency_at(pos, ignore_gaps);
397  int mfi = int(mf*100.0+0.01); // frequency -> [0..100]; add 1/100 to reduce incompatibilities caused by 32/64 bit differences
398 
399  if (mfi) {
400  if (mfi<10) mfi = 10; // hack: otherwise SAI will contain '0' (meaning 100% frequency)
401 
402  int mfh = int(mfi/10);
403  int mfl = mfi-10*mfh;
404 
405  result1[pos] = "?1234567890"[mfh];
406  result2[pos] = "0123456789"[mfl];
407  }
408  else {
409  result1[pos] = '=';
410  result2[pos] = '=';
411  }
412  }
413 
414  GBDATA *gb_extended = GBT_find_or_create_SAI(gb_main, savename);
415  if (!gb_extended) {
416  error = GB_await_error();
417  }
418  else {
419  GBDATA *gb_data1 = GBT_add_data(gb_extended, aliname, "data", GB_STRING);
420  GBDATA *gb_data2 = GBT_add_data(gb_extended, aliname, "dat2", GB_STRING);
421 
422  error = GB_write_string(gb_data1, result1);
423  if (!error) error = GB_write_string(gb_data2, result2);
424 
425  GBDATA *gb_options = GBT_add_data(gb_extended, aliname, "_TYPE", GB_STRING);
426 
427  if (!error) {
428  const char *type = GBS_global_string("MFQ: [species: %li] [ignore gaps: %s]", nrofspecies, ignore_gaps ? "yes" : "no");
429  error = GB_write_string(gb_options, type);
430  }
431  }
432 
433  delete [] result1;
434  delete [] result2;
435  }
436 
437  error = ta.close(error);
439 
440  return error;
441 }
442 
443 static void CON_calc_max_freq_cb(AW_window *aw) {
444  AW_root *awr = aw->get_root();
445  bool ignore_gaps = awr->awar(AWAR_MAX_FREQ_IGNORE_GAPS)->read_int();
446  const char *savename = awr->awar(AWAR_MAX_FREQ_SAI_NAME)->read_char_pntr();
447  char *aliname = GBT_get_default_alignment(GLOBAL.gb_main);
448 
449  GB_ERROR error = CON_calc_max_freq(GLOBAL.gb_main, ignore_gaps, savename, aliname);
450  if (error) aw_message(error);
451 
452  free(aliname);
453 }
454 
456  AW_window_simple *aws = new AW_window_simple;
457  aws->init(aw_root, "MAX_FREQUENCY", "MAX FREQUENCY");
458  aws->load_xfig("consensus/max_freq.fig");
459 
461 
462  aws->button_length(6);
463 
464  aws->at("cancel");
465  aws->callback(AW_POPDOWN);
466  aws->create_button("CLOSE", "CLOSE", "C");
467 
468  aws->at("help"); aws->callback(makeHelpCallback("max_freq.hlp"));
469  aws->create_button("HELP", "HELP", "H");
470 
471  // activation of consensus calculation by button ...
472  aws->at("go");
473  aws->callback(CON_calc_max_freq_cb);
474  aws->create_button("GO", "GO", "C");
475 
476  aws->at("save");
477  aws->create_input_field(AWAR_MAX_FREQ_SAI_NAME, 1);
478 
479  aws->at("sai");
481 
482  aws->at("gaps");
483  aws->create_toggle(AWAR_MAX_FREQ_IGNORE_GAPS);
484 
486 
487  return aws;
488 }
489 
490 // --------------------------------------------------------------------------------
491 
492 #ifdef UNIT_TESTS
493 #ifndef TEST_UNIT_H
494 #include <test_unit.h>
495 #endif
496 
497 static GBDATA *create_simple_seq_db(const char *aliname, const char *alitype, const char **sequence, int sequenceCount, int sequenceLength) {
498  GBDATA *gb_main = GB_open("nosuch.arb", "wc");
499 
500  {
501  GB_transaction ta(gb_main);
503  int specCounter = 0;
504 
505  TEST_EXPECT_RESULT__NOERROREXPORTED(GBT_create_alignment(gb_main, aliname, sequenceLength, true, 6, alitype));
506 
507  for (int s = 0; s<sequenceCount; ++s) {
508  GBDATA *gb_species = GBT_find_or_create_species_rel_species_data(gb_species_data, GBS_global_string("name%04i", ++specCounter), true);
509  GBDATA *gb_data = GBT_add_data(gb_species, aliname, "data", GB_STRING);
510 
511  TEST_EXPECT_EQUAL(strlen(sequence[s]), sequenceLength);
512  TEST_EXPECT_NO_ERROR(GB_write_string(gb_data, sequence[s]));
513  }
514  }
515 
516 #if 0
517  // save DB (to view data; should be inactive when committed)
518  char *dbname = GBS_global_string_copy("cons_%s.arb", alitype);
519  TEST_EXPECT_NO_ERROR(GB_save(gb_main, dbname, "a"));
520  free(dbname);
521 #endif
522 
523  return gb_main;
524 }
525 
526 static void read_frequency(GBDATA *gb_main, const char *sainame, const char *aliname, const char*& data, const char*& dat2) {
527  GB_transaction ta(gb_main);
528 
529  GBDATA *gb_maxFreq = GBT_find_SAI(gb_main, sainame);
530  GBDATA *gb_ali = GB_entry(gb_maxFreq, aliname);
531  GBDATA *gb_data = GB_entry(gb_ali, "data");
532  GBDATA *gb_dat2 = GB_entry(gb_ali, "dat2");
533 
534  data = GB_read_char_pntr(gb_data);
535  dat2 = GB_read_char_pntr(gb_dat2);
536 }
537 
538 void TEST_nucleotide_consensus_and_maxFrequency() {
539  const char *sequence[] = {
540  "-.AAAAAAAAAAcAAAAAAAAATTTTTTTTTTTTTTTTTAAAAAAAAgggggAAAAgAA----m-----yykm-mmmAAAAAAAAAmmmmmmmmmNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNKKKKKKKKKWWWWWWWWW",
541  "-.-AAAAAAAAAccAAAAAAAAggTTgTTTTgTTTTTTTcccAAAAAgggggAAAAgAA----k-----kykr-rrrAAAAAAAAmmmmmmmmmT-NNNNNNNNNANNNNNbNNNNNNNNkNNNNNNNNaNNNNNNNNbKKKKKKKKbWWWWWWWW",
542  "-.--AAAAAAAAcccAAAAAAA-ggTggTTTggTTTTTTccccAAAAgggCCtAAAgAC----m-----sykw-wvsAAAAAAAmmmmmmmmmTT--NNNNNNNNCANNNNbbNNNNNNNkkNNNNNNNaaNNNNNNNbbKKKKKKKbbWWWWWWW",
543  "-.---AAAAAAAccccAAAAAA-ggggggTTgggTTTTTcccccAAAggCCC-tAACtC----k----yyyys-smvAAAAAAmmmmmmmmmTTT---NNNNNNNGCANNNbbbNNNNNNkkkNNNNNNaaaNNNNNNbbbKKKKKKbbbWWWWWW",
544  "-.----AAAAAAcccccAAAAA----ggggTggggTTTTGGGcccAAgCCCt-ttACtG----m---nkkkky-yrmAAAAAmmmmmmmmmTTTT----NNNNNNTGCANNbbbbNNNNNkkkkNNNNNaaaaNNNNNbbbbKKKKKbbbbWWWWW",
545  "-.-----AAAAAccccccAAAA----ggggggggggTTgGGGGcccAcCCtt--tttCG----k--nnssssk-kvrAAAAmmmmmmmmmTTTTT-----NNNNN-TGCANbbbbbNNNNkkkkkNNNNaaaaaNNNNbbbbbKKKKbbbbbWWWW",
546  "-.------AAAAcccccccAAA---------ggggggTgGGGGGccccCt----tt-gT----mydddyyyy-vvmsAAAmmmmmmmmmTTTTTT------NNNN-ATGCAbbbbbbNNNkkkkkkNNNaaaaaaNNNbbbbbbKKKbbbbbbWWW",
547  "-.-------AAAccccccccAA---------ggggggggttGGGGccct------t--T-yykkkbbbkkkk-hhrvAAmmmmmmmmmTTTTTTT-------NNN-C-TGCbbbbbbbNNkkkkkkkNNaaaaaaaNNbbbbbbbKKbbbbbbbWW",
548  "-.--------AAcccccccccA----------------gttGGGGGct-------t----ymmmmnnnssss-ddvmAmmmmmmmmmTTTTTTTT--------NN-G--TGbbbbbbbbNkkkkkkkkNaaaaaaaaNbbbbbbbbKbbbbbbbbW",
549  "-.---------Acccccccccc----------------gtAGGGGGG----------------k---------bbmrmmmmmmmmmTTTTTTTTT---------N-T---Tbbbbbbbbbkkkkkkkkkaaaaaaaaabbbbbbbbbbbbbbbbbb",
550  };
551  const char *expected_frequency[] = {
552  // considering gaps:
553  "0=9876567890098765678986665444576545675336544565434475454320888277654333462439988776654434567899876543222523222333322222444433332987765443333444444333444444",
554  "0=0000000000000000000000000000000000000000000000000000000000000500000055005565050505055050000000000000025050025210098765752075207257025702568013568568013568",
555  // ignoring gaps:
556  "==000000000009876567895757865688765678533654456554536655542=552233223333222439988776654434567892222222222222222333322222444433332987765443333444444333444444",
557  "==000000000000000000000505360637520257000000000502036075025=005530983388555565050505055050000005555555555555555210098765752075207257025702568013568568013568",
558  };
559  const char *expected_consensus[] = {
560  "==----..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
561  "==AAAAAAAAAACccMMMMMaaKgKugKKKuggKKKuuKb.ssVVmmssssBWWWWs..=Y.......BByk...mVAaaaaMMMMmmHH..uuu................BBbb.....Kkkkkk...aaaa.....BkkkkkkkKB....wwww", // countgaps=0
562  "==AAAAAAAAAACCCMMMMMAAKGKUGKKKUGGKKKUUKBsSSVVMMSSSSBWWWWSwa=YcaaykkkBBYKaaaMVAAAAAMMMMMMHHuuuUUaaaaaaaaaaaaaaaaBBBBBBBBcKKKKKkkkkAAAaaaaaaBBKKKKKKKBBuuuwWWW", // countgaps=0, considbound=26, lower=0, upper=75 (as described in #663)
563  "==AAAAAAAAAACCCMMMMMAAKKKKGKKKUGKKKKKUKBsSSVVMMSSSSBWWWWSwN=YHNNykkkBBYKNNNVVAAAAMMMMMMMHHHuuUUNNNNNNNNNNNNNNNNBBBBBBBBBKKKKKkkkkAAAaaaaaaBBKKKKKKKBBuuwwWWW", // countgaps=0, considbound=25, lower=0, upper=75
564  "==---aaaaAAACCCMMMMMAA-gkugkkkuggKKKuuKBsSSVVMMSsssb-wwWswa=---a--kkbBykaaaMVAAAAAMMMMMMHHuuuUU---aaaaaaaaaaaaaBBBBBBBBcKKKKKkkkkAAAaaaaaaBBKKKKKKKBBuuuwWWW", // countgaps=1, gapbound=70, considbound=26, lower=0, upper=75
565  "==---aaaaAAACCMMMMMMMA-kkkgkkkugKKKKKuKBNSVVVVMSsssb-wwWswN=---N--nnbBBBnnNVVAAAMMMMMMMHHHHHuUU---nnnnNNNnNnNNNBBBBBBBNNKKKKKkkNNAAAaaaaNNBBBBKKKKKBBBNwwWWW", // countgaps=1, gapbound=70, considbound=20, lower=0, upper=75
566  "==---aaaaAAACMMMMMMMMM-kkkkkkkkKKKKKKKKNNVVVVVVBBbbb-wwWbnN=---N--nnbBBBnnNVVMMMMMMMMMHHHHHHHHH---nnnnNNNnNnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNBBBBBBBBBNNNNNNNNN", // countgaps=1, gapbound=70, considbound= 1, lower=0, upper=75
567  "==---aaaaAAACMMMMMMMMM-kkkkkkkkKKKKKKKKNNVVVVVVBBbbb-wwWbnN=---N--nnbBBBnnNVVMMMMMMMMMHHHHHHHHH---nnnnNNNnNnNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNBBBBBBBBBNNNNNNNNN", // countgaps=1, gapbound=70, considbound= 0, lower=0, upper=75
568  "==AAAAAAAAAACMMMMMMMMMKKKKKKKKKKKKKKKKKNNVVVVVVBBBBBWWWWBNN=YHNNNNNNBBBBNNNVVMMMMMMMMMHHHHHHHHHNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNBBBBBBBBBNNNNNNNNN", // countgaps=0, considbound= 0, lower=0, upper=75
569  };
570  const size_t seqlen = strlen(sequence[0]);
571  const int sequenceCount = ARRAY_ELEMS(sequence);
572  const int consensusCount = ARRAY_ELEMS(expected_consensus);
573 
574  // create DB
575  GB_shell shell;
576  const char *aliname = "ali_nuc";
577  GBDATA *gb_main = create_simple_seq_db(aliname, "rna", sequence, sequenceCount, seqlen);
578 
580  for (int c = 0; c<consensusCount; ++c) {
581  TEST_ANNOTATE(GBS_global_string("c=%i", c));
582  switch (c) {
583  case 0: break; // use default settings
584  case 1: BK.countgaps = false; break; // dont count gaps
585  case 2: BK.considbound = 26; BK.lower = 0; BK.upper = 75; break; // settings from #663
586  case 3: BK.considbound = 25; break;
587  case 4: BK.considbound = 26; BK.countgaps = true; BK.gapbound = 70; break;
588  case 5: BK.considbound = 20; break;
589  case 6: BK.considbound = 1; break;
590  case 7: BK.considbound = 0; break;
591  case 8: BK.countgaps = false; break;
592  default: arb_assert(0); break; // missing
593  }
594 
595  {
596  GB_transaction ta(gb_main);
597  const char *sainame = "CONSENSUS";
598  TEST_EXPECT_NO_ERROR(CON_calculate(gb_main, BK, aliname, false, sainame));
599 
600  GBDATA *gb_consensus = GBT_find_SAI(gb_main, sainame);
601  GBDATA *gb_seq = GBT_find_sequence(gb_consensus, aliname);
602  const char *consensus = GB_read_char_pntr(gb_seq); // @@@ NOT_ALL_SAI_HAVE_DATA
603 
604  TEST_EXPECT_EQUAL(consensus, expected_consensus[c]);
605  }
606  }
607 
608  // test max.frequency
609  const char *sainame = "MAXFREQ";
610  for (int ignore_gaps = 0; ignore_gaps<=1; ++ignore_gaps) {
611  TEST_ANNOTATE(GBS_global_string("ignore_gaps=%i", ignore_gaps));
612  TEST_EXPECT_NO_ERROR(CON_calc_max_freq(gb_main, ignore_gaps, sainame, aliname));
613  const char *data, *dat2;
614  read_frequency(gb_main, sainame, aliname, data, dat2);
615  TEST_EXPECT_EQUAL(data, expected_frequency[ignore_gaps*2]);
616  TEST_EXPECT_EQUAL(dat2, expected_frequency[ignore_gaps*2+1]);
617  }
618 
619  GB_close(gb_main);
620 }
621 
622 void TEST_amino_consensus_and_maxFrequency() {
623  const char *sequence[] = {
624  "-.ppppppppppQQQQQQQQQDDDDDELLLLLwwwwwwwwwwwwwwwwgggggggggggSSSe-PPP-DELp",
625  "-.-pppppppppkQQQQQQQQnDDDDELLLLLVVwwVwwwwVwwwwwwSgggggggggSSSee-QPP-DELa",
626  "-.--ppppppppkkQQQQQQQnnDDDELLLLL-VVwVVwwwVVwwwwwSSgggggggSSSeee-KQP-DEIg",
627  "-.---pppppppkkkQQQQQQnnnDDELLLLL-VVVVVVwwVVVwwwwSSSgggggSSSeee--LQQ-DQIs",
628  "-.----ppppppkkkkQQQQQnnnnDELLLLL----VVVVwVVVVwwweSSSgggSSSeee---WKQ-NQJt",
629  "-.-----pppppkkkkkQQQQnnnnnqiLLLL----VVVVVVVVVVwweeSSSggSSeee-----KQ-NQJq",
630  "-.------ppppkkkkkkQQQnnnnnqiiLLL---------VVVVVVweeeSSSgSeee------LK-NZJn",
631  "-.-------pppkkkkkkkQQnnnnnqiiiLL---------VVVVVVVeeeeSSSeee-------LK-NZJe",
632  "-.--------ppkkkkkkkkQnnnnnqiiiiL----------------eeeeeSSee--------WK-BZJd",
633  "-.---------pkkkkkkkkknnnnnqiiiii----------------eeeeeeSe---------WK-BZJb",
634  "-.ppppppppppQQQQQQQQQDDDDDELLLLLwwwwwwwwwwwwwwwwgggggggggggSSSe-PPP-DELz",
635  "-.-pppppppppkQQQQQQQQnDDDDELLLLLVVwwVwwwwVwwwwwwSgggggggggSSSee-QPP-DELh",
636  "-.--ppppppppkkQQQQQQQnnDDDELLLLL-VVwVVwwwVVwwwwwSSgggggggSSSeee-KQP-DEIk",
637  "-.---pppppppkkkQQQQQQnnnDDELLLLL-VVVVVVwwVVVwwwwSSSgggggSSSeee--LQQ-DQIr",
638  "-.----ppppppkkkkQQQQQnnnnDELLLLL----VVVVwVVVVwwweSSSgggSSSeee---WKQ-NQJl",
639  "-.-----pppppkkkkkQQQQnnnnnqiLLLL----VVVVVVVVVVwweeSSSggSSeee-----KQ-NQJi",
640  "-.------ppppkkkkkkQQQnnnnnqiiLLL---------VVVVVVweeeSSSgSeee------LK-NZJv",
641  "-.-------pppkkkkkkkQQnnnnnqiiiLL---------VVVVVVVeeeeSSSeee-------LK-NZJm",
642  "-.--------ppkkkkkkkkQnnnnnqiiiiL----------------eeeeeSSee--------WK-BZJf",
643  "-.---------pkkkkkkkkknnnnnqiiiii----------------eeeeeeSe---------WK-BZJy",
644  };
645  const char *expected_frequency[] = {
646  // considering gaps:
647  "0=9876567890987656789987655567898666544457654567654456743334567052404461",
648  "0=0000000000000000000000000000000000000000000000000000000000000000000000",
649  // ignoring gaps:
650  "==0000000000987656789987655567895757865688765678654456743345670=224=4461",
651  "==0000000000000000000000000000000505360637520257000000003720050=000=0000",
652  };
653  const char *expected_consensus[] = {
654  "==----..aaaAhhh...dddDDDDDDIIIII----.....i.....f...aaaAa.....--=.X.=DDI.", // default settings (see ConsensusBuildParams-ctor), gapbound=60, considbound=30, lower/upper=70/95
655  "==AAAAAAAAAAhhh...dddDDDDDDIIIII.i.fi...fii...ff...aaaAa.....dD=XX.=DDI.", // countgaps=0
656  "==AAAAAAAAAAHHhhdddDDDDDDDDIIIIIiIiFIiifFIIiifFFdaaaAAAaaaaadDD=XXh=DDId", // countgaps=0, considbound= 26, lower=0, upper=75
657  "==---aaaaAAAHHhhdddDDDDDDDDIIIII-iifiiiffiiiifffdaaaAAAaaaaadd-=xXh=DDId", // countgaps=1, gapbound=70, considbound= 26, lower=0, upper=75
658  "==---aaaaAAAHHhhdddDDDDDDDDIIIII-iifiiiffiiiifffdaaaAAAaaaaadd-=aah=DDId", // countgaps=1, gapbound=70, considbound= 20, lower=0, upper=75
659  "==---aaaaAAAHHhhXddDDDDDDDDIIIII-ixfiixffiiiXfffdXaaAAAaaaaxdd-=xXX=DDIX", // countgaps=1, gapbound=70, considbound= 51, lower=0, upper=75
660  "==---aaaaAAAHXXXXXXXDDDDDDDIIIII-xxxxxxxxXXXXXXXXXXXXAAXXXxxxx-=xXX=DDIX", // countgaps=1, gapbound=70, considbound= 90, lower=0, upper=75
661  "==---aaaaAAAXXXXXXXXXDDDDDDIIIII-xxxxxxxxXXXXXXXXXXXXXAXXXxxxx-=xXX=DDIX", // countgaps=1, gapbound=70, considbound=100, lower=0, upper=75
662  "==---aaaaAAAHHhhdddDDDDDDDDIIIII-iifiiiffiiiifffdaaaAAAaaaaadd-=aah=DDId", // countgaps=1, gapbound=70, considbound= 0, lower=0, upper=75
663  };
664  const size_t seqlen = strlen(sequence[0]);
665  const int sequenceCount = ARRAY_ELEMS(sequence);
666  const int consensusCount = ARRAY_ELEMS(expected_consensus);
667 
668  // create DB
669  GB_shell shell;
670  const char *aliname = "ali_ami";
671  GBDATA *gb_main = create_simple_seq_db(aliname, "ami", sequence, sequenceCount, seqlen);
672 
674  for (int c = 0; c<consensusCount; ++c) {
675  TEST_ANNOTATE(GBS_global_string("c=%i", c));
676  switch (c) {
677  case 0: break; // use default settings
678  case 1: BK.countgaps = false; break; // dont count gaps
679  case 2: BK.considbound = 26; BK.lower = 0; BK.upper = 75; break; // settings from #663
680  case 3: BK.countgaps = true; BK.gapbound = 70; break;
681  case 4: BK.considbound = 20; break;
682  case 5: BK.considbound = 51; break;
683  case 6: BK.considbound = 90; break;
684  case 7: BK.considbound = 100; break;
685  case 8: BK.considbound = 0; break;
686  default: arb_assert(0); break; // missing
687  }
688 
689  {
690  GB_transaction ta(gb_main);
691  const char *sainame = "CONSENSUS";
692  TEST_EXPECT_NO_ERROR(CON_calculate(gb_main, BK, aliname, false, sainame));
693 
694  GBDATA *gb_consensus = GBT_find_SAI(gb_main, sainame);
695  GBDATA *gb_seq = GBT_find_sequence(gb_consensus, aliname);
696  const char *consensus = GB_read_char_pntr(gb_seq);
697 
698  TEST_EXPECT_EQUAL(consensus, expected_consensus[c]);
699  }
700  }
701 
702  // test max.frequency
703  const char *sainame = "MAXFREQ";
704  for (int ignore_gaps = 0; ignore_gaps<=1; ++ignore_gaps) {
705  TEST_ANNOTATE(GBS_global_string("ignore_gaps=%i", ignore_gaps));
706  TEST_EXPECT_NO_ERROR(CON_calc_max_freq(gb_main, ignore_gaps, sainame, aliname));
707  const char *data, *dat2;
708  read_frequency(gb_main, sainame, aliname, data, dat2);
709  TEST_EXPECT_EQUAL(data, expected_frequency[ignore_gaps*2]);
710  TEST_EXPECT_EQUAL(dat2, expected_frequency[ignore_gaps*2+1]);
711  }
712 
713  GB_close(gb_main);
714 }
715 
716 #endif // UNIT_TESTS
717 
AW_window * AP_create_max_freq_window(AW_root *aw_root)
#define arb_assert(cond)
Definition: arb_assert.h:245
const char * GB_ERROR
Definition: arb_core.h:25
string result
GBDATA * GB_open(const char *path, const char *opent)
Definition: ad_load.cxx:1363
GB_TYPES type
GBDATA * GBT_first_marked_species(GBDATA *gb_main)
Definition: aditem.cxx:113
#define AWAR_CONSENSUS_GAPBOUND
GB_ERROR GB_save(GBDATA *gb, const char *path, const char *savetype)
#define AWAR_CONSENSUS_NAME
GB_ERROR GB_write_string(GBDATA *gbd, const char *s)
Definition: arbdb.cxx:1385
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Definition: AW_window.cxx:717
#define AWAR_CONSENSUS_MARKED_ONLY
static AWT_config_mapping_def consensus_config_mapping[]
#define CONSENSUS_CONFIG_COUNTGAPS
GB_ERROR GB_end_transaction(GBDATA *gbd, GB_ERROR error)
Definition: arbdb.cxx:2549
char * build_consensus_string(PosRange r, const ConsensusBuildParams &cbp) const
Definition: chartable.cxx:370
#define AWAR_CONSENSUS_GROUP
void AWT_insert_config_manager(AW_window *aww, AW_default default_file_, const char *id, const StoreConfigCallback &store_cb, const RestoreConfigCallback &load_or_reset_cb, const char *macro_id, const AWT_predefined_config *predef)
long read_int() const
Definition: AW_awar.cxx:187
double max_frequency_at(int column, bool ignore_gaps) const
Definition: chartable.cxx:763
AW_awar * set_minmax(float min, float max)
Definition: AW_awar.cxx:532
const char * GBS_global_string(const char *templat,...)
Definition: arb_msg.cxx:204
long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname)
Definition: adali.cxx:706
bool GB_have_error()
Definition: arb_msg.cxx:349
void AW_POPDOWN(AW_window *window)
Definition: AW_window.cxx:52
void auto_subtitles(const char *prefix)
Definition: arb_progress.h:286
void cat(const char *from)
Definition: arb_strbuf.h:158
#define CONSENSUS_CONFIG_GROUP
#define ARRAY_ELEMS(array)
Definition: arb_defs.h:19
char buffer[MESSAGE_BUFFERSIZE]
Definition: seq_search.cxx:34
GBDATA * GB_get_father(GBDATA *gbd)
Definition: arbdb.cxx:1720
GB_ERROR GB_push_transaction(GBDATA *gbd)
Definition: arbdb.cxx:2482
AW_awar * add_callback(const RootCallback &cb)
Definition: AW_awar.cxx:234
GB_ERROR GB_delete(GBDATA *&source)
Definition: arbdb.cxx:1904
#define CONSENSUS_CONFIG_GAPBOUND
GBDATA * GBT_find_SAI(GBDATA *gb_main, const char *name)
Definition: aditem.cxx:177
const char * read_char_pntr() const
Definition: AW_awar.cxx:171
#define AWAR_CONSENSUS_CONSIDBOUND
NOT4PERL GBDATA * GBT_add_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type) __ATTR__DEPRECATED_TODO("better use GBT_create_sequence_data()")
Definition: adali.cxx:559
#define CONSENSUS_CONFIG_ID
size_t GB_read_string_count(GBDATA *gbd)
Definition: arbdb.cxx:910
GB_ERROR GB_await_error()
Definition: arb_msg.cxx:353
static bool deny_read
Definition: aw_awar.hxx:106
static void setup(const char *gap_chars, GB_alignment_type ali_type_)
Definition: chartable.cxx:604
WindowCallback makeHelpCallback(const char *helpfile)
Definition: aw_window.hxx:106
GBDATA * GBT_create_alignment(GBDATA *gbd, const char *name, long len, long aligned, long security, const char *type)
Definition: adali.cxx:387
#define CONSENSUS_CONFIG_CONSIDBOUND
AW_window * AWT_create_IUPAC_info_window(AW_root *aw_root)
Definition: AWT_misc.cxx:21
#define AWAR_MAX_FREQ_SAI_NAME
GBDATA * gb_species_data
Definition: adname.cxx:34
void GB_clear_error()
Definition: arb_msg.cxx:365
static void CON_calculate_cb(AW_window *aw)
static void error(const char *msg)
Definition: mkptypes.cxx:96
void AP_create_consensus_var(AW_root *aw_root, AW_default aw_def)
#define CONSENSUS_CONFIG_UPPER
GBDATA * GBT_find_or_create_species_rel_species_data(GBDATA *gb_species_data, const char *name, bool markCreated)
Definition: aditem.cxx:57
#define AWAR_CONSENSUS_LOWER
GBDATA * GBT_next_marked_species(GBDATA *gb_species)
Definition: aditem.cxx:116
GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname)
Definition: adali.cxx:740
static void consensus_upper_lower_changed_cb(AW_root *awr, bool upper_changed)
char * read_string() const
Definition: AW_awar.cxx:201
AW_awar * awar(const char *awar)
Definition: AW_root.cxx:554
GB_ERROR GB_pop_transaction(GBDATA *gbd)
Definition: arbdb.cxx:2512
Definition: arbdb.h:86
GBDATA * GBT_find_sequence(GBDATA *gb_species, const char *aliname)
Definition: adali.cxx:670
#define AWAR_CONSENSUS_UPPER
long GBT_count_marked_species(GBDATA *gb_main)
Definition: aditem.cxx:353
GB_alignment_type
Definition: arbdb_base.h:61
#define nt_assert(cond)
Definition: NT_local.h:27
static int CON_insertSequences(GBDATA *gb_main, const char *aliname, long maxalignlen, bool onlymarked, BaseFrequencies &freqs)
AW_DB_selection * awt_create_ALI_selection_list(GBDATA *gb_main, AW_window *aws, const char *varname, const char *ali_type_match)
GB_ERROR GB_export_errorf(const char *templat,...)
Definition: arb_msg.cxx:264
AW_awar * awar_int(const char *var_name, long default_value=0, AW_default default_file=AW_ROOT_DEFAULT)
Definition: AW_root.cxx:580
#define IF_ASSERTION_USED(x)
Definition: arb_assert.h:308
GB_ERROR close(GB_ERROR error)
Definition: arbdbpp.cxx:32
static void CON_calc_max_freq_cb(AW_window *aw)
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AW_window * AP_create_con_expert_window(AW_root *aw_root)
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Definition: aditem.cxx:124
static GB_ERROR CON_export(GBDATA *gb_main, const char *savename, const char *align, const char *result, bool onlymarked, long nrofspecies, const ConsensusBuildParams &BK)
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size_t length
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static GB_ERROR CON_calculate(GBDATA *gb_main, const ConsensusBuildParams &BK, const char *aliname, bool onlymarked, const char *sainame)
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Definition: arb_msg.cxx:195
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NT_global GLOBAL
Definition: NT_main.cxx:44
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Definition: arb_strbuf.h:138
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Definition: AW_awar.cxx:156