ARB
adali.cxx
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1 // =============================================================== //
2 // //
3 // File : adali.cxx //
4 // Purpose : alignments //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // =============================================================== //
10 
11 #include <arbdbt.h>
12 #include <adGene.h>
13 
14 #include "gb_local.h"
15 
16 #include <arb_strarray.h>
17 #include <arb_str.h>
18 #include <arb_global_defs.h>
19 
20 static void check_for_species_without_data(const char *species_name, long value, void *counterPtr) {
21  if (value == 1) {
22  long cnt = *((long*)counterPtr);
23  if (cnt<40) {
24  GB_warningf("Species '%s' has no data in any alignment", species_name);
25  }
26  *((long*)counterPtr) = cnt+1;
27  }
28 }
29 
31  return GBT_find_or_create(gb_main, "presets", 7);
32 }
33 
35  int count = 0;
36  GBDATA *gb_presets = GBT_get_presets(gb_main);
37  for (GBDATA *gb_ali = GB_entry(gb_presets, "alignment");
38  gb_ali;
39  gb_ali = GB_nextEntry(gb_ali))
40  {
41  ++count;
42  }
43  return count;
44 }
45 
46 static GB_ERROR GBT_check_alignment(GBDATA *gb_main, GBDATA *preset_alignment, GB_HASH *species_name_hash) {
47  /* check
48  * - whether alignment has correct size and
49  * - whether all data is present.
50  *
51  * Sets the security deletes and writes.
52  *
53  * If 'species_name_hash' is not NULp,
54  * - it initially has to contain value == 1 for each existing species.
55  * - afterwards it will contain value == 2 for each species where an alignment has been found.
56  */
57 
59  GBDATA *gb_extended_data = GBT_get_SAI_data(gb_main);
60 
62  char *ali_name = GBT_read_string(preset_alignment, "alignment_name");
63  if (!ali_name) error = "Alignment w/o 'alignment_name'";
64 
65  if (!error) {
66  long security_write = -1;
67  long stored_ali_len = -1;
68  long found_ali_len = -1;
69  long aligned = 1;
70  GBDATA *gb_ali_len = NULp;
71 
72  {
73  GBDATA *gb_ali_wsec = GB_entry(preset_alignment, "alignment_write_security");
74  if (!gb_ali_wsec) {
75  error = "has no 'alignment_write_security' entry";
76  }
77  else {
78  security_write = GB_read_int(gb_ali_wsec);
79  }
80  }
81 
82 
83  if (!error) {
84  gb_ali_len = GB_entry(preset_alignment, "alignment_len");
85  if (!gb_ali_len) {
86  error = "has no 'alignment_len' entry";
87  }
88  else {
89  stored_ali_len = GB_read_int(gb_ali_len);
90  }
91  }
92 
93  if (!error) {
94  GBDATA *gb_species;
95  for (gb_species = GBT_first_species_rel_species_data(gb_species_data);
96  gb_species && !error;
97  gb_species = GBT_next_species(gb_species))
98  {
99  GBDATA *gb_name = GB_entry(gb_species, "name");
100  const char *name = NULp;
101  int alignment_seen = 0;
102 
103  if (!gb_name) {
104  // fatal: name is missing -> create a unique name
105  char *unique = GBT_create_unique_species_name(gb_main, "autoname.");
106  error = GBT_write_string(gb_species, "name", unique);
107 
108  if (!error) {
109  gb_name = GB_entry(gb_species, "name");
110  GBS_write_hash(species_name_hash, unique, 1); // not seen before
111  GB_warningf("Seen unnamed species (gave name '%s')", unique);
112  }
113  free(unique);
114  }
115 
116  if (!error) {
117  name = GB_read_char_pntr(gb_name);
118  if (species_name_hash) {
119  int seen = GBS_read_hash(species_name_hash, name);
120 
121  gb_assert(seen != 0); // species_name_hash not initialized correctly
122  if (seen == 2) alignment_seen = 1; // already seen an alignment
123  }
124  }
125 
126  if (!error) {
127  GB_topSecurityLevel unsecured(gb_name);
128 
129  error = GB_write_security_delete(gb_name, 7);
130  if (!error) error = GB_write_security_write(gb_name, 6);
131 
132  if (!error) {
133  GBDATA *gb_ali = GB_entry(gb_species, ali_name);
134  if (gb_ali) {
135  GBDATA *gb_data = GB_entry(gb_ali, "data");
136  if (!gb_data) {
137  error = GBT_write_string(gb_ali, "data", "Error: entry 'data' was missing and therefore was filled with this text.");
138  GB_warningf("No '%s/data' entry for species '%s' (has been filled with dummy data)", ali_name, name);
139  }
140  else {
141  if (GB_read_type(gb_data) != GB_STRING) {
142  GB_delete(gb_data);
143  error = GBS_global_string("'%s/data' of species '%s' had wrong DB-type (%s) and has been deleted!",
144  ali_name, name, GB_read_key_pntr(gb_data));
145  }
146  else {
147  long data_len = GB_read_string_count(gb_data);
148  if (found_ali_len != data_len) {
149  if (found_ali_len>0) aligned = 0;
150  if (found_ali_len<data_len) found_ali_len = data_len;
151  }
152 
153  error = GB_write_security_delete(gb_data, 7);
154 
155  if (!alignment_seen && species_name_hash) { // mark as seen
156  GBS_write_hash(species_name_hash, name, 2); // 2 means "species has data in at least 1 alignment"
157  }
158  }
159  }
160  }
161  }
162 
163  if (!error) error = GB_write_security_delete(gb_species, security_write);
164  }
165  }
166  }
167 
168  if (!error) {
169  GBDATA *gb_sai;
170  for (gb_sai = GBT_first_SAI_rel_SAI_data(gb_extended_data);
171  gb_sai && !error;
172  gb_sai = GBT_next_SAI(gb_sai))
173  {
174  GBDATA *gb_sai_name = GB_entry(gb_sai, "name");
175  GBDATA *gb_ali;
176 
177  if (!gb_sai_name) continue;
178 
179  GB_write_security_delete(gb_sai_name, 7);
180 
181  gb_ali = GB_entry(gb_sai, ali_name);
182  if (gb_ali) {
183  GBDATA *gb_sai_data;
184  for (gb_sai_data = GB_child(gb_ali);
185  gb_sai_data;
186  gb_sai_data = GB_nextChild(gb_sai_data))
187  {
188  long type = GB_read_type(gb_sai_data);
189  long data_len;
190 
191  if (type == GB_DB || type < GB_BITS) continue;
192  if (GB_read_key_pntr(gb_sai_data)[0] == '_') continue; // e.g. _STRUCT (of secondary structure)
193 
194  data_len = GB_read_count(gb_sai_data);
195 
196  if (found_ali_len != data_len) {
197  if (found_ali_len>0) aligned = 0;
198  if (found_ali_len<data_len) found_ali_len = data_len;
199  }
200  }
201  }
202  }
203  }
204 
205  if (!error && stored_ali_len != found_ali_len) error = GB_write_int(gb_ali_len, found_ali_len);
206  if (!error) error = GBT_write_int(preset_alignment, "aligned", aligned);
207 
208  if (error) {
209  error = GBS_global_string("Error checking alignment '%s':\n%s\n", ali_name, error);
210  }
211  }
212 
213  free(ali_name);
214 
215  return error;
216 }
217 
219  /* alignment_name
220  * == 0 -> check all existing alignments
221  * otherwise -> check only one alignment
222  */
223 
224  GB_ERROR error = NULp;
225  GBDATA *gb_sd = GBT_get_species_data(Main);
226  GBDATA *gb_presets = GBT_get_presets(Main);
227  GB_HASH *species_name_hash = NULp;
228 
229  // create rest of main containers
230  GBT_get_SAI_data(Main);
231  GBT_get_tree_data(Main);
232 
233  if (alignment_name) {
234  GBDATA *gb_ali_name = GB_find_string(gb_presets, "alignment_name", alignment_name, GB_IGNORE_CASE, SEARCH_GRANDCHILD);
235  if (!gb_ali_name) {
236  error = GBS_global_string("Alignment '%s' does not exist - it can't be checked.", alignment_name);
237  }
238  }
239 
240  if (!error) {
241  // check whether we have an default alignment
242  GBDATA *gb_use = GB_entry(gb_presets, "use");
243  if (!gb_use) {
244  // if we have no default alignment -> look for any alignment
245  GBDATA *gb_ali_name = GB_find_string(gb_presets, "alignment_name", alignment_name, GB_IGNORE_CASE, SEARCH_GRANDCHILD);
246 
247  error = gb_ali_name ?
248  GBT_write_string(gb_presets, "use", GB_read_char_pntr(gb_ali_name)) :
249  "No alignment defined";
250  }
251  }
252 
253  if (!alignment_name && !error) {
254  // if all alignments are checked -> use species_name_hash to detect duplicated species and species w/o data
255  long duplicates = 0;
256  long unnamed = 0;
257 
258  species_name_hash = GBS_create_hash(GBT_get_species_count(Main), GB_IGNORE_CASE);
259 
260  if (!error) {
261  for (GBDATA *gb_species = GBT_first_species_rel_species_data(gb_sd);
262  gb_species;
263  gb_species = GBT_next_species(gb_species))
264  {
265  const char *name = GBT_get_name(gb_species);
266  if (name) {
267  if (GBS_read_hash(species_name_hash, name)) duplicates++;
268  GBS_incr_hash(species_name_hash, name);
269  }
270  else {
271  unnamed++;
272  }
273  }
274  }
275 
276  if (duplicates) {
277  error = GBS_global_string("Database is corrupted:\n"
278  "Found %li duplicated species with identical names!\n"
279  "Fix the problem using\n"
280  " 'Search For Equal Fields and Mark Duplicates'\n"
281  "in ARB_NTREE search tool, save DB and restart ARB.",
282  duplicates);
283  }
284  else if (unnamed) {
285  error = GBS_global_string("Database is corrupted:\n"
286  "Found %li species without IDs ('name')!\n"
287  "This is a sewere problem!\n"
288  "ARB will not work as expected!",
289  unnamed);
290  }
291  }
292 
293  if (!error) {
294  for (GBDATA *gb_ali = GB_entry(gb_presets, "alignment");
295  gb_ali && !error;
296  gb_ali = GB_nextEntry(gb_ali))
297  {
298  error = GBT_check_alignment(Main, gb_ali, species_name_hash);
299  }
300  }
301 
302  if (species_name_hash) {
303  if (!error) {
304  long counter = 0;
305  GBS_hash_do_const_loop(species_name_hash, check_for_species_without_data, &counter);
306  if (counter>0) {
307  GB_warningf("Found %li species without alignment data (only some were listed)", counter);
308  }
309  }
310 
311  GBS_free_hash(species_name_hash);
312  }
313 
314  return error;
315 }
316 
318  /* Get names of existing alignments from database.
319  *
320  * Returns: array of strings, the last element is NULp
321  */
322 
323  GBDATA *presets = GBT_get_presets(gbd);
324  for (GBDATA *ali = GB_entry(presets, "alignment"); ali; ali = GB_nextEntry(ali)) {
325  GBDATA *name = GB_entry(ali, "alignment_name");
326  names.put(name ? GB_read_char_pntr(name) : "<unnamed alignment>");
327  }
328 }
329 
330 static char *gbt_nonexisting_alignment(GBDATA *gbMain) {
331  char *ali_other = NULp;
332  int counter;
333 
334  for (counter = 1; !ali_other; ++counter) {
335  ali_other = GBS_global_string_copy("ali_x%i", counter);
336  if (GBT_get_alignment(gbMain, ali_other)) freenull(ali_other); // exists -> continue
337  }
338 
339  GB_clear_error(); // from GBT_get_alignment
340  return ali_other;
341 }
342 
344  GB_ERROR error = GB_check_key(alignment_name);
345  if (!error && !ARB_strBeginsWith(alignment_name, "ali_")) {
346  error = GBS_global_string("alignment name '%s' has to start with 'ali_'", alignment_name);
347  }
348  return error;
349 }
350 
351 static GB_ERROR create_ali_strEntry(GBDATA *gb_ali, const char *field, const char *strval, long write_protection) {
352  GB_ERROR error = NULp;
353  GBDATA *gb_sub = GB_create(gb_ali, field, GB_STRING);
354 
355  if (!gb_sub) error = GB_await_error();
356  else {
357  error = GB_write_string(gb_sub, strval);
358  if (!error) error = GB_write_security_delete(gb_sub, 7);
359  if (!error) error = GB_write_security_write(gb_sub, write_protection);
360  }
361 
362  if (error) {
363  error = GBS_global_string("failed to create alignment subentry '%s'\n"
364  "(Reason: %s)", field, error);
365  }
366 
367  return error;
368 }
369 static GB_ERROR create_ali_intEntry(GBDATA *gb_ali, const char *field, int intval, long write_protection) {
370  GB_ERROR error = NULp;
371  GBDATA *gb_sub = GB_create(gb_ali, field, GB_INT);
372 
373  if (!gb_sub) error = GB_await_error();
374  else {
375  error = GB_write_int(gb_sub, intval);
376  if (!error) error = GB_write_security_delete(gb_sub, 7);
377  if (!error) error = GB_write_security_write(gb_sub, write_protection);
378  }
379 
380  if (error) {
381  error = GBS_global_string("failed to create alignment subentry '%s'\n"
382  "(Reason: %s)", field, error);
383  }
384 
385  return error;
386 }
387 
388 GBDATA *GBT_create_alignment(GBDATA *gb_main, const char *name, long len, long aligned, long security, const char *type, const char *why_created) {
389  /* create alignment
390  *
391  * returns pointer to alignment or
392  * NULp (in this case an error has been exported)
393  */
394  GB_ERROR error = NULp;
395  GBDATA *gb_presets = GBT_get_presets(gb_main);
396  GBDATA *result = NULp;
397 
398  if (!gb_presets) {
399  error = GBS_global_string("can't find/create 'presets' (Reason: %s)", GB_await_error());
400  }
401  else {
402  error = GBT_check_alignment_name(name);
403  if (!error && (security<0 || security>6)) {
404  error = GBS_global_string("Illegal security value %li (allowed 0..6)", security);
405  }
406  if (!error) {
407  const char *allowed_types = ":dna:rna:ami:usr:";
408  int tlen = strlen(type);
409  const char *found = strstr(allowed_types, type);
410  if (!found || found == allowed_types || found[-1] != ':' || found[tlen] != ':') {
411  error = GBS_global_string("Invalid alignment type '%s'", type);
412  }
413  }
414 
415  if (!error) {
416  GBDATA *gb_name = GB_find_string(gb_presets, "alignment_name", name, GB_IGNORE_CASE, SEARCH_GRANDCHILD);
417 
418  if (gb_name) error = GBS_global_string("Alignment '%s' already exists", name);
419  else {
420  GBDATA *gb_ali = GB_create_container(gb_presets, "alignment");
421  if (!gb_ali) error = GB_await_error();
422  else {
423  char *remark = GBS_global_string_copy("%s: alignment created %s", ARB_date_string(), why_created);
424 
425  error = GB_write_security_delete(gb_ali, 6);
426  if (!error) error = create_ali_strEntry(gb_ali, "alignment_name", name, 6);
427  if (!error) error = create_ali_intEntry(gb_ali, "alignment_len", len, 0);
428  if (!error) error = create_ali_intEntry(gb_ali, "aligned", aligned <= 0 ? 0 : 1, 0);
429  if (!error) error = create_ali_intEntry(gb_ali, "alignment_write_security", security, 6);
430  if (!error) error = create_ali_strEntry(gb_ali, "alignment_type", type, 0);
431  if (!error) error = create_ali_strEntry(gb_ali, "alignment_rem", remark, 0);
432 
433  free(remark);
434  }
435 
436  if (!error) result = gb_ali;
437  }
438  }
439  }
440 
441  if (!result) {
442  gb_assert(error);
443  GB_export_errorf("in GBT_create_alignment: %s", error);
444  }
445 #if defined(DEBUG)
446  else gb_assert(!error);
447 #endif // DEBUG
448 
449  return result;
450 }
451 
453 
454 static GB_ERROR gbt_rename_alignment_of_item(GBDATA *gb_item_container, const char *item_name, const char *item_entry_name,
455  const char *source, const char *dest, CopyMoveDelMode mode)
456 {
457  GB_ERROR error = NULp;
458  GBDATA *gb_item;
459 
460  for (gb_item = GB_entry(gb_item_container, item_entry_name);
461  gb_item && !error;
462  gb_item = GB_nextEntry(gb_item))
463  {
464  GBDATA *gb_ali = GB_entry(gb_item, source);
465  if (!gb_ali) continue;
466 
467  if (mode != DELETE) {
468  GBDATA *gb_new = GB_entry(gb_item, dest);
469  if (gb_new) {
470  error = GBS_global_string("Entry '%s' already exists", dest);
471  }
472  else {
473  gb_new = GB_create_container(gb_item, dest);
474  if (!gb_new) error = GB_await_error();
475  else error = GB_copy_dropProtectMarksAndTempstate(gb_new, gb_ali);
476  }
477  }
478  if (mode != COPY) error = GB_delete(gb_ali);
479  }
480 
481  if (error && gb_item) {
482  UNCOVERED();
483  error = GBS_global_string("%s\n(while renaming alignment for %s '%s')", error, item_name, GBT_get_name_or_description(gb_item));
484  }
485 
486  return error;
487 }
488 
489 static GB_ERROR copy_move_del_alignment(GBDATA *gbMain, const char *source, const char *dest, CopyMoveDelMode mode) {
490  // copies, moves or deletes alignments.
491  // affects all data of that alignment in species and SAIs.
492 
493  gb_assert(!GB_have_error()); // illegal to enter this function when an error is exported!
494 
495  GB_ERROR error = NULp;
496  bool is_case_error = false;
497 
498  GB_transaction ta(gbMain);
499 
500  gb_assert(correlated(mode == DELETE, dest == NULp)); // dest shall be NULp for DELETE + !NULp otherwise.
501 
502  GBDATA *gb_presets = GBT_get_presets(gbMain);
503  GBDATA *gb_species_data = gb_presets ? GBT_get_species_data(gbMain) : NULp;
504  GBDATA *gb_extended_data = gb_species_data ? GBT_get_SAI_data(gbMain) : NULp;
505 
506  if (!gb_extended_data) error = GB_await_error();
507 
508  // create copy and/or delete old alignment description
509  if (!error) {
510  GBDATA *gb_old_alignment = GBT_get_alignment(gbMain, source);
511 
512  if (!gb_old_alignment) {
513  error = GB_await_error();
514  }
515  else {
516  if (mode != DELETE) {
517  // copy source -> dest
518  GBDATA *gbh = GBT_get_alignment(gbMain, dest);
519  if (gbh) {
520  error = GBS_global_string("destination alignment '%s' already exists", dest);
521  is_case_error = (strcasecmp(source, dest) == 0); // test for case-only difference
522  }
523  else {
524  GB_clear_error(); // from GBT_get_alignment
525  error = GBT_check_alignment_name(dest);
526  if (!error) {
527  GBDATA *gb_new_alignment = GB_create_container(gb_presets, "alignment");
528  error = GB_copy_dropProtectMarksAndTempstate(gb_new_alignment, gb_old_alignment);
529  if (!error) error = GBT_write_string(gb_new_alignment, "alignment_name", dest);
530  }
531  }
532  }
533 
534  if (mode != COPY && !error) {
535  // delete source
536  error = GB_delete(gb_old_alignment);
537  }
538  }
539  }
540 
541  // change default alignment
542  if (!error && mode == MOVE) {
543  error = GBT_write_string(gb_presets, "use", dest);
544  }
545 
546  // copy and/or delete alignment entries in species
547  if (!error) {
548  error = gbt_rename_alignment_of_item(gb_species_data, "Species", "species", source, dest, mode);
549  }
550 
551  // copy and/or delete alignment entries in SAIs
552  if (!error) {
553  error = gbt_rename_alignment_of_item(gb_extended_data, "SAI", "extended", source, dest, mode);
554  }
555 
556  if (is_case_error) {
557  gb_assert(mode != DELETE);
558  if (mode==COPY) {
559  error = "Cannot copy alignment if destination name only differs in case.";
560  }
561  else {
563 
564  // alignments source and dest only differ in case
565  char *ali_other = gbt_nonexisting_alignment(gbMain);
566 
567  gb_assert(mode==MOVE);
569 
570  printf("Renaming alignment '%s' -> '%s' -> '%s' (to avoid case-problem)\n", source, ali_other, dest);
571 
572  error = copy_move_del_alignment(gbMain, source, ali_other, MOVE);
573  if (!error) error = copy_move_del_alignment(gbMain, ali_other, dest, MOVE);
574 
575  free(ali_other);
576  }
577  }
578 
579  error = ta.close(error);
580 
581  return error;
582 }
583 
584 GB_ERROR GBT_copy_alignment(GBDATA *gbMain, const char *source, const char *dest) {
585  return copy_move_del_alignment(gbMain, source, dest, COPY);
586 }
587 GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest) {
588  return copy_move_del_alignment(gbMain, source, dest, MOVE);
589 }
590 GB_ERROR GBT_delete_alignment(GBDATA *gbMain, const char *source) {
591  return copy_move_del_alignment(gbMain, source, NULp, DELETE);
592 }
593 
594 // -----------------------------------------
595 // alignment related item functions
596 
597 NOT4PERL GBDATA *GBT_add_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type) {
598  // goes to header: __ATTR__DEPRECATED_TODO("better use GBT_create_sequence_data()")
599 
600  /* replace this function by GBT_create_sequence_data
601  * the same as GB_search(species, 'ali_name/key', GB_CREATE)
602  *
603  * Note: The behavior is weird, cause it does sth special for GB_STRING (write default content "...")
604  *
605  * returns create database entry (or NULp; exports an error in this case)
606  */
607 
608  GB_ERROR error = GB_check_key(ali_name);
609  if (error) {
610  error = GBS_global_string("Invalid alignment name '%s' (Reason: %s)", ali_name, error);
611  }
612  else {
613  error = GB_check_hkey(key);
614  if (error) {
615  error = GBS_global_string("Invalid field name '%s' (Reason: %s)", key, error);
616  }
617  }
618 
619  GBDATA *gb_data = NULp;
620  if (error) {
621  GB_export_error(error);
622  }
623  else {
624  GBDATA *gb_gb = GB_entry(species, ali_name);
625  if (!gb_gb) gb_gb = GB_create_container(species, ali_name);
626 
627  if (gb_gb) {
628  if (type == GB_STRING) {
629  gb_data = GB_search(gb_gb, key, GB_FIND);
630  if (!gb_data) {
631  gb_data = GB_search(gb_gb, key, GB_STRING);
632  GB_write_string(gb_data, "...");
633  }
634  }
635  else {
636  gb_data = GB_search(gb_gb, key, type);
637  }
638  }
639  }
640  return gb_data;
641 }
642 
643 NOT4PERL GBDATA *GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write) {
644  GBDATA *gb_data = GBT_add_data(species, ali_name, key, type);
645  if (gb_data) {
646  GB_ERROR error = GB_write_security_write(gb_data, security_write);
647  if (error) {
648  GB_export_error(error);
649  gb_data = NULp;
650  }
651  }
652  return gb_data;
653 }
654 
655 GBDATA *GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name) {
656  GBDATA *gb_acc = GB_entry(gb_species, "acc");
657  if (!gb_acc) {
658  GBDATA *gb_data = GBT_find_sequence(gb_species, ali_name);
659  if (gb_data) { // found a valid alignment
660  GB_CSTR sequence = GB_read_char_pntr(gb_data);
661  long id = GBS_checksum(sequence, 1, ".-");
662  const char *acc = GBS_global_string("ARB_%lX", id);
663  GB_ERROR error = GBT_write_string(gb_species, "acc", acc);
664 
665  if (error) GB_export_error(error);
666  }
667  }
668  return gb_acc;
669 }
670 
671 
672 int GBT_is_partial(GBDATA *gb_species, int default_value, bool define_if_undef) {
673  // checks whether a species has a partial or full sequence
674  //
675  // Note: partial sequences should not be used for tree calculations
676  //
677  // returns: 0 if sequence is full
678  // 1 if sequence is partial
679  // -1 in case of error (which is exported in this case)
680  //
681  // if the sequence has no 'ARB_partial' entry it returns 'default_value'
682  // if 'define_if_undef' is true then create an 'ARB_partial'-entry with the default value
683 
684  int result = -1;
685  GB_ERROR error = NULp;
686  GBDATA *gb_partial = GB_entry(gb_species, "ARB_partial");
687 
688  if (gb_partial) {
689  result = GB_read_int(gb_partial);
690  if (result != 0 && result != 1) {
691  error = "Illegal value for 'ARB_partial' (only 1 or 0 allowed)";
692  }
693  }
694  else {
695  if (define_if_undef) {
696  error = GBT_write_int(gb_species, "ARB_partial", default_value);
697  }
698  result = default_value;
699  }
700 
701  if (error) {
702  GB_export_error(error);
703  return -1;
704  }
705  return result;
706 }
707 
708 GBDATA *GBT_find_sequence(GBDATA *gb_species, const char *aliname) {
709  GBDATA *gb_ali = GB_entry(gb_species, aliname);
710  return gb_ali ? GB_entry(gb_ali, "data") : NULp;
711 }
712 
713 static char *get_default_alignment(GBDATA *gb_main, bool use_startup_ali) {
719  gb_assert(!GB_have_error()); // illegal to enter this function when an error is exported!
720 
721  static SmartCharPtr startup_ali_name; // set once (when function is first called with 'use_startup_ali'==true)
722 
723  char *ali_name = NULp;
724  if (startup_ali_name.isSet()) {
725  ali_name = ARB_strdup(&*startup_ali_name);
726  }
727  else {
728  ali_name = GBT_read_string(gb_main, GB_DEFAULT_ALIGNMENT);
729  if (ali_name) {
730  if (strcmp(ali_name, NO_ALI_SELECTED) == 0) {
731  GB_export_error("No alignment is selected.");
732  freenull(ali_name);
733  }
734  else if (!ARB_strBeginsWith(ali_name, "ali_")) {
735  GB_export_errorf("Selected alignment '%s' is not valid!", ali_name);
736  freenull(ali_name);
737  }
738  }
739  if (ali_name && use_startup_ali) {
740  // first sucessful call with 'use_startup_ali==true'
741  startup_ali_name = ARB_strdup(ali_name); // this will remain default until program terminates
742  }
743  }
744  gb_assert(contradicted(ali_name, GB_have_error())); // either result or error!
745  return ali_name;
746 }
755  return get_default_alignment(gb_main, false);
756 }
762  return get_default_alignment(gb_main, true);
763 }
764 
766  return GBT_write_string(gb_main, GB_DEFAULT_ALIGNMENT, alignment_name);
767 }
769  // Similar to GBT_set_default_alignment, but does not change database default alignment.
770  // Instead it changes the application-local alignment which is derived from default
771  // alignment and "freezed" on first request (by using GBT_get_startup_alignment).
772  //
773  // Warning: GBT_set_startup_alignment fails if GBT_get_startup_alignment was already called!
774 
775  GB_ERROR error = NULp;
776  char *default_ali = GBT_get_default_alignment(gb_main);
777 
778  bool freeze_and_reset = false;
779  if (!default_ali) {
780  GB_clear_error();
781  default_ali = ARB_strdup(NO_ALI_SELECTED);
782  freeze_and_reset = true;
783  }
784  else {
785  freeze_and_reset = strcmp(default_ali, alignment_name) != 0;
786  }
787  if (freeze_and_reset) {
788  error = GBT_set_default_alignment(gb_main, alignment_name);
789  if (!error) {
790  char *startup_ali = GBT_get_startup_alignment(gb_main);
791  if (!startup_ali) error = GB_await_error(); // most unlikely
792  else {
793  if (strcmp(startup_ali, alignment_name) != 0) {
794  error = GBS_global_string("Cannot freeze alignment to '%s' (already was frozen to '%s' before)", alignment_name, startup_ali);
795  }
796  // fine, the correct alignment is freezed!
797  free(startup_ali);
798  }
799  }
800  // undo (tmp) change to default alignment:
801  GB_ERROR minerr = GBT_set_default_alignment(gb_main, default_ali);
802  error = error ? error : minerr;
803  }
804  free(default_ali);
805  return error;
806 }
807 
808 GBDATA *GBT_get_alignment(GBDATA *gb_main, const char *aliname) {
813  GBDATA *gb_ali = NULp;
814  if (!aliname || strcmp(aliname, NO_ALI_SELECTED) == 0) {
815  GB_export_error("no alignment selected");
816  }
817  else {
818  GBDATA *gb_presets = GBT_get_presets(gb_main);
819  GBDATA *gb_alignment_name = GB_find_string(gb_presets, "alignment_name", aliname, GB_IGNORE_CASE, SEARCH_GRANDCHILD);
820 
821  if (!gb_alignment_name) {
822  GB_export_errorf("alignment '%s' not found", aliname);
823  }
824  else {
825  gb_ali = GB_get_father(gb_alignment_name);
826  }
827  }
828  gb_assert(contradicted(gb_ali, GB_have_error())); // either result or error!
829  return gb_ali;
830 }
831 
832 // @@@ recode and change result type to long* ?
833 long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname) {
837  GBDATA *gb_alignment = GBT_get_alignment(gb_main, aliname);
838  long len = gb_alignment ? *GBT_read_int(gb_alignment, "alignment_len") : -1;
839  gb_assert(contradicted(len != -1, GB_have_error())); // either valid result or error!
840  return len;
841 }
842 
843 GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len) {
844  GB_ERROR error = NULp;
845  GBDATA *gb_alignment = GBT_get_alignment(gb_main, aliname);
846 
847  if (!gb_alignment) {
848  error = GB_await_error();
849  }
850  else {
851  GB_topSecurityLevel unsecured(gb_main);
852  error = GBT_write_int(gb_alignment, "alignment_len", new_len); // write new len
853  if (!error) error = GBT_write_int(gb_alignment, "aligned", 0); // mark as unaligned
854  }
855  return error;
856 }
857 
858 char *GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname) {
862  GBDATA *gb_alignment = GBT_get_alignment(gb_main, aliname);
863  char *result = gb_alignment ? GBT_read_string(gb_alignment, "alignment_type") : NULp;
864 
865  if (!result && !GB_have_error()) {
866  GB_export_errorf("Alignment '%s' has no alignment_type defined", aliname);
867  }
868 
869  gb_assert(contradicted(result, GB_have_error())); // either result or error!
870  return result;
871 }
872 
877  char *ali_type = GBT_get_alignment_type_string(gb_main, aliname);
879 
880  if (ali_type) {
881  switch (ali_type[0]) {
882  case 'r': if (strcmp(ali_type, "rna")==0) at = GB_AT_RNA; break;
883  case 'd': if (strcmp(ali_type, "dna")==0) at = GB_AT_DNA; break;
884  case 'a': if (strcmp(ali_type, "ami")==0) at = GB_AT_AA; break;
885  case 'p': if (strcmp(ali_type, "pro")==0) at = GB_AT_AA; break;
886  default: gb_assert(0); break;
887  }
888  free(ali_type);
889  }
890  return at;
891 }
892 
894  GB_alignment_type ali_type = GBT_get_alignment_type(gb_main, alignment_name);
895  gb_assert(ali_type != GB_AT_UNKNOWN);
896  return ali_type == GB_AT_AA;
897 }
898 
899 // -----------------------
900 // gene sequence
901 
902 static const char *gb_cache_genome(GBDATA *gb_genome) {
903  static GBDATA *gb_last_genome = NULp;
904  static char *last_genome = NULp;
905 
906  if (gb_genome != gb_last_genome) {
907  free(last_genome);
908 
909  last_genome = GB_read_string(gb_genome);
910  gb_last_genome = gb_genome;
911  }
912 
913  return last_genome;
914 }
915 
917  int parts; // initialized for parts
918  unsigned char *certain; // contains parts "=" chars
919  char offset[256];
920 };
921 
923 
924 static void init_gpp(int parts) {
925  if (!gpp) {
926  int i;
927  ARB_alloc(gpp, 1);
928  gpp->certain = NULp;
929 
930  for (i = 0; i<256; ++i) gpp->offset[i] = 0;
931 
932  gpp->offset[(int)'+'] = 1;
933  gpp->offset[(int)'-'] = -1;
934  }
935  else {
936  if (parts>gpp->parts) freenull(gpp->certain);
937  }
938 
939  if (!gpp->certain) {
940  int forParts = parts+10;
941  ARB_alloc(gpp->certain, forParts+1);
942  memset(gpp->certain, '=', forParts);
943  gpp->certain[forParts] = 0;
944  gpp->parts = forParts;
945  }
946 }
947 
948 static void getPartPositions(const GEN_position *pos, int part, size_t *startPos, size_t *stopPos) {
949  // returns 'startPos' and 'stopPos' of one part of a gene
950  gb_assert(part<pos->parts);
951  *startPos = pos->start_pos[part]+gpp->offset[(pos->start_uncertain ? pos->start_uncertain : gpp->certain)[part]];
952  *stopPos = pos->stop_pos [part]+gpp->offset[(pos->stop_uncertain ? pos->stop_uncertain : gpp->certain)[part]];
953 }
954 
955 NOT4PERL char *GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length) {
956  // return the sequence data of a gene
957  //
958  // if use_revComplement is true -> use data from complementary strand (if complement is set for gene)
959  // otherwise -> use data from primary strand (sort+merge parts by position)
960  //
961  // if partSeparator not is 0 -> insert partSeparator between single (non-merged) parts
962  //
963  // returns sequence as result (and length of sequence if 'gene_length' points to something)
964  //
965  // if 'pos_certain' contains '+', start behind position (or end at position)
966  // '-', start at position (or end before position)
967  //
968  // For zero-length genes (e.g. "711^712") this function returns an empty string.
969 
970  GB_ERROR error = NULp;
971  char *result = NULp;
972  GBDATA *gb_species = GB_get_grandfather(gb_gene);
973  GEN_position *pos = GEN_read_position(gb_gene);
974 
975  if (!pos) error = GB_await_error();
976  else {
977  GBDATA *gb_seq = GBT_find_sequence(gb_species, "ali_genom");
978  unsigned long seq_length = GB_read_count(gb_seq);
979  int p;
980  int parts = pos->parts;
981  int resultlen = 0;
982  int separatorSize = partSeparator ? 1 : 0;
983 
984  init_gpp(parts);
985 
986  // test positions and calculate overall result length
987  for (p = 0; p<parts && !error; p++) {
988  size_t start;
989  size_t stop;
990  getPartPositions(pos, p, &start, &stop);
991 
992  if (start<1 || start>(stop+1) || stop > seq_length) { // do not reject zero-length genes (start == stop+1)
993  error = GBS_global_string("Illegal gene position(s): start=%zu, end=%zu, seq.length=%li",
994  start, stop, seq_length);
995  }
996  else {
997  resultlen += stop-start+1;
998  }
999  }
1000 
1001  if (separatorSize) resultlen += (parts-1)*separatorSize;
1002 
1003  if (!error) {
1004  char T_or_U = 0;
1005  if (use_revComplement) {
1006  error = GBT_determine_T_or_U(GB_AT_DNA, &T_or_U, "reverse-complement");
1007  }
1008  else if (parts>1) {
1010  parts = pos->parts; // may have changed
1011  }
1012 
1013  if (!error) {
1014  const char *seq_data = gb_cache_genome(gb_seq);
1015  char *resultpos;
1016 
1017  ARB_alloc(result, resultlen+1);
1018  resultpos = result;
1019 
1020  if (gene_length) *gene_length = resultlen;
1021 
1022  for (p = 0; p<parts; ++p) {
1023  size_t start;
1024  size_t stop;
1025  getPartPositions(pos, p, &start, &stop);
1026 
1027  int len = stop-start+1;
1028 
1029  if (separatorSize && p>0) *resultpos++ = partSeparator;
1030 
1031  memcpy(resultpos, seq_data+start-1, len);
1032  if (T_or_U && pos->complement[p]) {
1033  GBT_reverseComplementNucSequence(resultpos, len, T_or_U);
1034  }
1035  resultpos += len;
1036  }
1037 
1038  resultpos[0] = 0;
1039  }
1040  }
1041  GEN_free_position(pos);
1042  }
1043 
1044  gb_assert(contradicted(result, error)); // either result or error!
1045 
1046  if (error) {
1047  char *id = GEN_global_gene_identifier(gb_gene, gb_species);
1048  error = GB_export_errorf("Can't read sequence of '%s' (Reason: %s)", id, error);
1049  free(id);
1050  free(result);
1051  result = NULp;
1052  }
1053 
1054  return result;
1055 }
1056 
1057 char *GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator) {
1058  return GBT_read_gene_sequence_and_length(gb_gene, use_revComplement, partSeparator, NULp);
1059 }
1060 
1061 // --------------------------------------------------------------------------------
1062 
1063 #ifdef UNIT_TESTS
1064 #include <test_unit.h>
1065 
1066 #define TEST_EXPECT_EXISTING_ALIGNMENTS(expected) do{ \
1067  names.erase(); \
1068  GBT_get_alignment_names(names, gb_main); \
1069  TEST_EXPECT_STRARRAY_CONTAINS(names, '*', expected); \
1070  }while(0)
1071 
1072 
1073 #define TEST_EXPECT_EXISTING_ALIGNMENTS__BROKEN(want,got) do{ \
1074  names.erase(); \
1075  GBT_get_alignment_names(names, gb_main); \
1076  TEST_EXPECT_STRARRAY_CONTAINS__BROKEN(names, '*', want,got); \
1077  }while(0)
1078 
1079 
1080 
1081 #define TEST_EXPECT_DEFAULT_ALIGNMENT(expected) \
1082  TEST_EXPECT_EQUAL_STRINGCOPY__NOERROREXPORTED(GBT_get_default_alignment(gb_main), expected);
1083 
1084 
1085 #define TEST_EXPECT_ALIGNMENT_STATE(expected_default,expected_existing) do{ \
1086  GB_initial_transaction ta(gb_main); \
1087  TEST_EXPECT_DEFAULT_ALIGNMENT(expected_default); \
1088  TEST_EXPECT_EXISTING_ALIGNMENTS(expected_existing); \
1089  }while(0)
1090 
1091 void TEST_alignment() {
1092  GB_shell shell;
1093  GBDATA *gb_main = GB_open("TEST_prot.arb", "r"); // ../UNIT_TESTER/run/TEST_prot.arb
1094 
1096  {
1097  GB_transaction ta(gb_main);
1098 
1100 
1101  TEST_EXPECT_DEFAULT_ALIGNMENT("ali_tuf_dna");
1102  TEST_EXPECT_EXISTING_ALIGNMENTS("ali_tuf_pro*ali_tuf_dna");
1103 
1104  for (int i = 0; names[i]; ++i) {
1105  long len = GBT_get_alignment_len(gb_main, names[i]);
1106  TEST_EXPECT_EQUAL(len, i ? 1462 : 487);
1107 
1108  char *type_name = GBT_get_alignment_type_string(gb_main, names[i]);
1109  TEST_EXPECT_EQUAL(type_name, i ? "dna" : "ami");
1110  free(type_name);
1111 
1112  GB_alignment_type type = GBT_get_alignment_type(gb_main, names[i]);
1113  TEST_EXPECT_EQUAL(type, i ? GB_AT_DNA : GB_AT_AA);
1114  TEST_EXPECT_EQUAL(GBT_is_alignment_protein(gb_main, names[i]), !i);
1115  }
1116 
1117  // test functions called with aliname == NULp
1118  TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GBT_get_alignment(gb_main, NULp), "no alignment");
1120  TEST_EXPECT_CONTAINS(GB_await_error(), "no alignment");
1121  TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GBT_get_alignment_type_string(gb_main, NULp), "no alignment");
1122 
1123  // test functions called with aliname == NO_ALI_SELECTED
1124  TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GBT_get_alignment(gb_main, NO_ALI_SELECTED), "no alignment");
1126  TEST_EXPECT_CONTAINS(GB_await_error(), "no alignment");
1127  TEST_EXPECT_NORESULT__ERROREXPORTED_CONTAINS(GBT_get_alignment_type_string(gb_main, NO_ALI_SELECTED), "no alignment");
1128  }
1129 
1130  // test copy, move(rename), delete alignments
1131  TEST_EXPECT_ALIGNMENT_STATE("ali_tuf_dna", "ali_tuf_pro*ali_tuf_dna");
1132 
1133  // copy ali + test names:
1134  {
1135  GB_transaction ta(gb_main);
1136 
1137  TEST_EXPECT_NO_ERROR(GBT_copy_alignment(gb_main, "ali_tuf_pro", "ali_copied_pro"));
1138  TEST_EXPECT_NO_ERROR(GBT_copy_alignment(gb_main, "ali_tuf_dna", "ali_copied_dna"));
1139  }
1140  TEST_EXPECT_ALIGNMENT_STATE("ali_tuf_dna", "ali_tuf_pro*ali_tuf_dna*ali_copied_pro*ali_copied_dna");
1141 
1142  // rename ali + test names:
1143  {
1144  GB_transaction ta(gb_main);
1145  TEST_EXPECT_ERROR_CONTAINS(GBT_rename_alignment(gb_main, "ali_tuf_pro", "ali_moved_pro"), "Security error: deleting entry 'alignment' not permitted");
1146  }
1147  TEST_EXPECT_ALIGNMENT_STATE("ali_tuf_dna", "ali_tuf_pro*ali_tuf_dna*ali_copied_pro*ali_copied_dna");
1148 
1149  {
1150  GB_transaction ta(gb_main);
1151  GB_securityLevel raise(gb_main, 6);
1152  TEST_EXPECT_NO_ERROR(GBT_rename_alignment(gb_main, "ali_tuf_pro", "ali_moved_pro"));
1153  TEST_EXPECT_NO_ERROR(GBT_rename_alignment(gb_main, "ali_tuf_dna", "ali_moved_dna"));
1154  }
1155  TEST_EXPECT_ALIGNMENT_STATE("ali_moved_dna", "ali_copied_pro*ali_copied_dna*ali_moved_pro*ali_moved_dna");
1156 
1157  // delete ali + test names:
1158  {
1159  GB_transaction ta(gb_main);
1160  TEST_EXPECT_NO_ERROR(GBT_delete_alignment(gb_main, "ali_copied_pro"));
1161  TEST_EXPECT_NO_ERROR(GBT_delete_alignment(gb_main, "ali_moved_dna")); // @@@ the rename-test (above) lowered the security of 'ali_tuf_dna' (from 6 to 0?). unwanted behavior!
1162  }
1163  TEST_EXPECT_ALIGNMENT_STATE("ali_moved_dna", // @@@ unwanted behavior (deleted alignment is selected as default)
1164  "ali_copied_dna*ali_moved_pro");
1165 
1166  // trigger error cases:
1167  {
1168  GB_transaction ta(gb_main);
1169  TEST_EXPECT_ERROR_CONTAINS(GBT_rename_alignment(gb_main, "ali_copied_dna", "ali_moved_pro"), "destination alignment 'ali_moved_pro' already exists");
1170  TEST_EXPECT_ERROR_CONTAINS(GBT_copy_alignment(gb_main, "ali_copied_dna", "ali_copied_DNA"), "Cannot copy alignment if destination name only differs in case.");
1171  }
1172 
1173  // test case-only rename
1174  {
1175  GB_transaction ta(gb_main);
1176  TEST_EXPECT_NO_ERROR(GBT_rename_alignment(gb_main, "ali_copied_dna", "ali_copied_DNA"));
1177  }
1178  TEST_EXPECT_ALIGNMENT_STATE("ali_copied_DNA", "ali_moved_pro*ali_copied_DNA");
1179 
1180  GB_close(gb_main);
1181 }
1182 TEST_PUBLISH(TEST_alignment);
1183 
1184 #endif // UNIT_TESTS
GB_ERROR GB_check_key(const char *key) __ATTR__USERESULT
Definition: adstring.cxx:85
GB_ERROR GB_copy_dropProtectMarksAndTempstate(GBDATA *dest, GBDATA *source)
Definition: arbdb.cxx:2152
GB_ERROR GBT_rename_alignment(GBDATA *gbMain, const char *source, const char *dest)
Definition: adali.cxx:587
long GBT_get_alignment_len(GBDATA *gb_main, const char *aliname)
Definition: adali.cxx:833
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
unsigned char * complement
Definition: adGene.h:41
void put(const char *elem)
Definition: arb_strarray.h:199
long GB_read_int(GBDATA *gbd)
Definition: arbdb.cxx:729
static GB_ERROR copy_move_del_alignment(GBDATA *gbMain, const char *source, const char *dest, CopyMoveDelMode mode)
Definition: adali.cxx:489
GBDATA * GB_child(GBDATA *father)
Definition: adquery.cxx:322
CopyMoveDelMode
Definition: adali.cxx:452
static void init_gpp(int parts)
Definition: adali.cxx:924
long GBS_write_hash(GB_HASH *hs, const char *key, long val)
Definition: adhash.cxx:454
Definition: arbdb.h:69
#define GB_DEFAULT_ALIGNMENT
Definition: arbdb.h:30
GB_ERROR GB_write_string(GBDATA *gbd, const char *s)
Definition: arbdb.cxx:1387
char * GBT_read_gene_sequence(GBDATA *gb_gene, bool use_revComplement, char partSeparator)
Definition: adali.cxx:1057
void GEN_free_position(GEN_position *pos)
Definition: adGene.cxx:195
long GBS_incr_hash(GB_HASH *hs, const char *key)
Definition: adhash.cxx:467
static void getPartPositions(const GEN_position *pos, int part, size_t *startPos, size_t *stopPos)
Definition: adali.cxx:948
GBDATA * GB_nextEntry(GBDATA *entry)
Definition: adquery.cxx:339
static const char * gb_cache_genome(GBDATA *gb_genome)
Definition: adali.cxx:902
int parts
Definition: adGene.h:37
static GB_ERROR create_ali_strEntry(GBDATA *gb_ali, const char *field, const char *strval, long write_protection)
Definition: adali.cxx:351
char * ARB_strdup(const char *str)
Definition: arb_string.h:27
const char * ARB_date_string()
Definition: arb_string.cxx:35
const char * GBS_global_string(const char *templat,...)
Definition: arb_msg.cxx:203
static char * alignment_name
bool GB_have_error()
Definition: arb_msg.cxx:338
void GEN_sortAndMergeLocationParts(GEN_position *location)
Definition: adGene.cxx:487
void GBS_free_hash(GB_HASH *hs)
Definition: adhash.cxx:538
GBDATA * GBT_get_tree_data(GBDATA *gb_main)
Definition: adtree.cxx:27
static char * get_default_alignment(GBDATA *gb_main, bool use_startup_ali)
Definition: adali.cxx:713
GBDATA * GB_get_grandfather(GBDATA *gbd)
Definition: arbdb.cxx:1728
GBDATA * GB_get_father(GBDATA *gbd)
Definition: arbdb.cxx:1722
static char * gbt_nonexisting_alignment(GBDATA *gbMain)
Definition: adali.cxx:330
GBDATA * GBT_get_alignment(GBDATA *gb_main, const char *aliname)
Definition: adali.cxx:808
#define NOT4PERL
Definition: arbdb_base.h:23
GB_ERROR GBT_delete_alignment(GBDATA *gbMain, const char *source)
Definition: adali.cxx:590
GB_ERROR GB_delete(GBDATA *&source)
Definition: arbdb.cxx:1916
GBDATA * GBT_first_species_rel_species_data(GBDATA *gb_species_data)
Definition: aditem.cxx:121
static HelixNrInfo * start
GB_ERROR GB_check_hkey(const char *key) __ATTR__USERESULT
Definition: adstring.cxx:92
static FullNameMap names
#define TEST_PUBLISH(testfunction)
Definition: test_unit.h:1517
#define TEST_EXPECT_CONTAINS(str, part)
Definition: test_unit.h:1316
GB_ERROR GB_export_error(const char *error)
Definition: arb_msg.cxx:257
size_t GB_read_string_count(GBDATA *gbd)
Definition: arbdb.cxx:916
GB_ERROR GB_await_error()
Definition: arb_msg.cxx:342
GB_alignment_type GBT_get_alignment_type(GBDATA *gb_main, const char *aliname)
Definition: adali.cxx:873
NOT4PERL long * GBT_read_int(GBDATA *gb_container, const char *fieldpath)
Definition: adtools.cxx:327
GBDATA * GB_create_container(GBDATA *father, const char *key)
Definition: arbdb.cxx:1829
long GB_read_count(GBDATA *gbd)
Definition: arbdb.cxx:758
char * GBT_read_string(GBDATA *gb_container, const char *fieldpath)
Definition: adtools.cxx:267
Definition: arbdb.h:78
GB_TYPES GB_read_type(GBDATA *gbd)
Definition: arbdb.cxx:1643
void GB_warningf(const char *templat,...)
Definition: arb_msg.cxx:536
TYPE * ARB_alloc(size_t nelem)
Definition: arb_mem.h:56
GB_CSTR GB_read_key_pntr(GBDATA *gbd)
Definition: arbdb.cxx:1656
NOT4PERL void GBT_reverseComplementNucSequence(char *seq, long length, char T_or_U)
Definition: adRevCompl.cxx:102
GB_ERROR GBT_copy_alignment(GBDATA *gbMain, const char *source, const char *dest)
Definition: adali.cxx:584
GBDATA * GB_create(GBDATA *father, const char *key, GB_TYPES type)
Definition: arbdb.cxx:1781
GBDATA * GBT_get_presets(GBDATA *gb_main)
Definition: adali.cxx:30
GBDATA * gb_species_data
Definition: adname.cxx:33
unsigned char * start_uncertain
Definition: adGene.h:53
void GBS_hash_do_const_loop(const GB_HASH *hs, gb_hash_const_loop_type func, void *client_data)
Definition: adhash.cxx:559
void GB_clear_error()
Definition: arb_msg.cxx:354
NOT4PERL char * GBT_read_gene_sequence_and_length(GBDATA *gb_gene, bool use_revComplement, char partSeparator, size_t *gene_length)
Definition: adali.cxx:955
static void check_for_species_without_data(const char *species_name, long value, void *counterPtr)
Definition: adali.cxx:20
char * GBT_create_unique_species_name(GBDATA *gb_main, const char *default_name)
Definition: aditem.cxx:287
size_t * stop_pos
Definition: adGene.h:40
static void error(const char *msg)
Definition: mkptypes.cxx:96
char * GBT_get_alignment_type_string(GBDATA *gb_main, const char *aliname)
Definition: adali.cxx:858
GBDATA * GBT_first_SAI_rel_SAI_data(GBDATA *gb_sai_data)
Definition: aditem.cxx:159
char * GBT_get_default_alignment(GBDATA *gb_main)
Definition: adali.cxx:747
GB_ERROR GB_write_security_write(GBDATA *gbd, unsigned long level)
Definition: arbdb.cxx:1584
Definition: arbdb.h:86
NOT4PERL GBDATA * GBT_add_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type)
Definition: adali.cxx:597
GB_ERROR GB_write_int(GBDATA *gbd, long i)
Definition: arbdb.cxx:1250
GB_alignment_type
Definition: arbdb_base.h:61
GB_ERROR GBT_set_alignment_len(GBDATA *gb_main, const char *aliname, long new_len)
Definition: adali.cxx:843
int GBT_count_alignments(GBDATA *gb_main)
Definition: adali.cxx:34
int GBT_is_partial(GBDATA *gb_species, int default_value, bool define_if_undef)
Definition: adali.cxx:672
GBDATA * GBT_next_SAI(GBDATA *gb_sai)
Definition: aditem.cxx:166
static GB_ERROR GBT_check_alignment(GBDATA *gb_main, GBDATA *preset_alignment, GB_HASH *species_name_hash)
Definition: adali.cxx:46
GB_ERROR GB_export_errorf(const char *templat,...)
Definition: arb_msg.cxx:262
bool GBT_is_alignment_protein(GBDATA *gb_main, const char *alignment_name)
Definition: adali.cxx:893
char * GEN_global_gene_identifier(GBDATA *gb_gene, GBDATA *gb_organism)
Definition: adGene.cxx:783
#define gb_assert(cond)
Definition: arbdbt.h:11
GB_ERROR close(GB_ERROR error)
Definition: arbdbpp.cxx:35
static gene_part_pos * gpp
Definition: adali.cxx:922
GB_ERROR GBT_set_default_alignment(GBDATA *gb_main, const char *alignment_name)
Definition: adali.cxx:765
unsigned char * certain
Definition: adali.cxx:918
GB_ERROR GBT_write_string(GBDATA *gb_container, const char *fieldpath, const char *content)
Definition: adtools.cxx:451
static GB_ERROR gbt_rename_alignment_of_item(GBDATA *gb_item_container, const char *item_name, const char *item_entry_name, const char *source, const char *dest, CopyMoveDelMode mode)
Definition: adali.cxx:454
GBDATA * GBT_create_alignment(GBDATA *gb_main, const char *name, long len, long aligned, long security, const char *type, const char *why_created)
Definition: adali.cxx:388
Definition: adali.cxx:452
char * GB_read_string(GBDATA *gbd)
Definition: arbdb.cxx:909
GBDATA * GBT_find_or_create(GBDATA *father, const char *key, long delete_level)
Definition: adtools.cxx:42
char * GBT_get_startup_alignment(GBDATA *gb_main)
Definition: adali.cxx:757
void GBT_get_alignment_names(ConstStrArray &names, GBDATA *gbd)
Definition: adali.cxx:317
GB_ERROR GB_write_security_delete(GBDATA *gbd, unsigned long level)
Definition: arbdb.cxx:1605
uint32_t GBS_checksum(const char *seq, int ignore_case, const char *exclude)
Definition: adstring.cxx:352
#define TEST_EXPECT_NO_ERROR(call)
Definition: test_unit.h:1118
GBDATA * GBT_find_sequence(GBDATA *gb_species, const char *aliname)
Definition: adali.cxx:708
size_t * start_pos
Definition: adGene.h:39
GBDATA * GB_find_string(GBDATA *gbd, const char *key, const char *str, GB_CASE case_sens, GB_SEARCH_TYPE gbs)
Definition: adquery.cxx:302
GB_ERROR GBT_check_alignment_name(const char *alignment_name)
Definition: adali.cxx:343
GBDATA * GBT_next_species(GBDATA *gb_species)
Definition: aditem.cxx:128
#define NULp
Definition: cxxforward.h:114
#define TEST_EXPECT_ERROR_CONTAINS(call, part)
Definition: test_unit.h:1114
#define NO_ALI_SELECTED
GB_ERROR GBT_check_data(GBDATA *Main, const char *alignment_name)
Definition: adali.cxx:218
Definition: adali.cxx:452
bool ARB_strBeginsWith(const char *str, const char *with)
Definition: arb_str.h:42
const char * GBT_get_name(GBDATA *gb_item)
Definition: aditem.cxx:468
GB_TYPES
Definition: arbdb.h:62
GBDATA * GB_nextChild(GBDATA *child)
Definition: adquery.cxx:326
char offset[256]
Definition: adali.cxx:919
long GBT_get_species_count(GBDATA *gb_main)
Definition: aditem.cxx:207
GB_transaction ta(gb_var)
GB_ERROR GBT_write_int(GBDATA *gb_container, const char *fieldpath, long content)
Definition: adtools.cxx:471
GB_CSTR GB_read_char_pntr(GBDATA *gbd)
Definition: arbdb.cxx:904
GBDATA * gb_main
Definition: adname.cxx:32
GBDATA * GBT_get_SAI_data(GBDATA *gb_main)
Definition: aditem.cxx:154
GBDATA * GB_search(GBDATA *gbd, const char *fieldpath, GB_TYPES create)
Definition: adquery.cxx:531
GB_ERROR GBT_set_startup_alignment(GBDATA *gb_main, const char *alignment_name)
Definition: adali.cxx:768
GB_CSTR GBT_get_name_or_description(GBDATA *gb_item)
Definition: aditem.cxx:459
NOT4PERL GBDATA * GBT_create_sequence_data(GBDATA *species, const char *ali_name, const char *key, GB_TYPES type, int security_write)
Definition: adali.cxx:643
GEN_position * GEN_read_position(GBDATA *gb_gene)
Definition: adGene.cxx:250
const char * GB_CSTR
Definition: arbdb_base.h:25
#define TEST_EXPECT_EQUAL(expr, want)
Definition: test_unit.h:1294
GBDATA * GBT_gen_accession_number(GBDATA *gb_species, const char *ali_name)
Definition: adali.cxx:655
long GBS_read_hash(const GB_HASH *hs, const char *key)
Definition: adhash.cxx:392
GBDATA * GB_entry(GBDATA *father, const char *key)
Definition: adquery.cxx:334
static GB_ERROR create_ali_intEntry(GBDATA *gb_ali, const char *field, int intval, long write_protection)
Definition: adali.cxx:369
char * GBS_global_string_copy(const char *templat,...)
Definition: arb_msg.cxx:194
void GB_close(GBDATA *gbd)
Definition: arbdb.cxx:655
NOT4PERL GB_ERROR GBT_determine_T_or_U(GB_alignment_type alignment_type, char *T_or_U, const char *supposed_target)
Definition: adRevCompl.cxx:90
GB_HASH * GBS_create_hash(long estimated_elements, GB_CASE case_sens)
Definition: adhash.cxx:253
unsigned char * stop_uncertain
Definition: adGene.h:54
#define UNCOVERED()
Definition: arb_assert.h:380
Definition: arbdb.h:66
GBDATA * GBT_get_species_data(GBDATA *gb_main)
Definition: aditem.cxx:105