NCBI C++ ToolKit
Variation_.cpp
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1 /* $Id$
2  * ===========================================================================
3  *
4  * PUBLIC DOMAIN NOTICE
5  * National Center for Biotechnology Information
6  *
7  * This software/database is a "United States Government Work" under the
8  * terms of the United States Copyright Act. It was written as part of
9  * the author's official duties as a United States Government employee and
10  * thus cannot be copyrighted. This software/database is freely available
11  * to the public for use. The National Library of Medicine and the U.S.
12  * Government have not placed any restriction on its use or reproduction.
13  *
14  * Although all reasonable efforts have been taken to ensure the accuracy
15  * and reliability of the software and data, the NLM and the U.S.
16  * Government do not and cannot warrant the performance or results that
17  * may be obtained by using this software or data. The NLM and the U.S.
18  * Government disclaim all warranties, express or implied, including
19  * warranties of performance, merchantability or fitness for any particular
20  * purpose.
21  *
22  * Please cite the author in any work or product based on this material.
23  *
24  * ===========================================================================
25  *
26  * File Description:
27  * This code was generated by application DATATOOL
28  * using the following specifications:
29  * 'variation.asn'.
30  *
31  * ATTENTION:
32  * Don't edit or commit this file into CVS as this file will
33  * be overridden (by DATATOOL) without warning!
34  * ===========================================================================
35  */
36 
37 // standard includes
38 #include <ncbi_pch.hpp>
39 #include <serial/serialimpl.hpp>
40 
41 // generated includes
46 #include <objects/pub/Pub_set.hpp>
47 #include <objects/seq/Bioseq.hpp>
57 
58 BEGIN_objects_SCOPE // namespace ncbi::objects::
59 
60 
61 // generated classes
62 
64 {
65  SET_ENUM_INTERNAL_NAME("Variation.data.set", "type");
66  SET_ENUM_MODULE("NCBI-VariationPackage");
67  ADD_ENUM_VALUE("unknown", eData_set_type_unknown);
68  ADD_ENUM_VALUE("compound", eData_set_type_compound);
69  ADD_ENUM_VALUE("products", eData_set_type_products);
70  ADD_ENUM_VALUE("haplotype", eData_set_type_haplotype);
71  ADD_ENUM_VALUE("genotype", eData_set_type_genotype);
72  ADD_ENUM_VALUE("mosaic", eData_set_type_mosaic);
73  ADD_ENUM_VALUE("individual", eData_set_type_individual);
74  ADD_ENUM_VALUE("population", eData_set_type_population);
75  ADD_ENUM_VALUE("alleles", eData_set_type_alleles);
76  ADD_ENUM_VALUE("package", eData_set_type_package);
77  ADD_ENUM_VALUE("chimeric", eData_set_type_chimeric);
78  ADD_ENUM_VALUE("other", eData_set_type_other);
79 }
81 
83 {
84  m_Variations.clear();
85  m_set_State[0] &= ~0xc;
86 }
87 
89 {
90  m_Name.erase();
91  m_set_State[0] &= ~0x30;
92 }
93 
95 {
96  ResetType();
97  ResetVariations();
98  ResetName();
99 }
100 
102 {
103  SET_INTERNAL_NAME("Variation.data", "set");
104  SET_CLASS_MODULE("NCBI-VariationPackage");
105  ADD_NAMED_ENUM_MEMBER("type", m_Type, EData_set_type)->SetSetFlag(MEMBER_PTR(m_set_State[0]));
106  ADD_NAMED_MEMBER("variations", m_Variations, STL_list_set, (STL_CRef, (CLASS, (CVariation))))->SetSetFlag(MEMBER_PTR(m_set_State[0]));
107  ADD_NAMED_STD_MEMBER("name", m_Name)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
108  info->RandomOrder();
109  info->CodeVersion(22301);
110  info->DataSpec(ncbi::EDataSpec::eASN);
111 }
113 
114 // constructor
116  : m_Type((EData_set_type)(0))
117 {
118  memset(m_set_State,0,sizeof(m_set_State));
119 }
120 
121 // destructor
123 {
124 }
125 
126 
128 {
129  if ( m_choice != e_not_set )
130  ResetSelection();
131 }
132 
134 {
135  switch ( m_choice ) {
136  case e_Note:
137  m_string.Destruct();
138  break;
139  case e_Instance:
140  case e_Set:
141  case e_Seq:
142  m_object->RemoveReference();
143  break;
144  default:
145  break;
146  }
148 }
149 
150 void CVariation_Base::C_Data::DoSelect(E_Choice index, NCBI_NS_NCBI::CObjectMemoryPool* pool)
151 {
152  switch ( index ) {
153  case e_Instance:
154  (m_object = new(pool) ncbi::objects::CVariation_inst())->AddReference();
155  break;
156  case e_Set:
157  (m_object = new(pool) C_Set())->AddReference();
158  break;
159  case e_Seq:
160  (m_object = new(pool) ncbi::objects::CBioseq())->AddReference();
161  break;
162  case e_Note:
163  m_string.Construct();
164  break;
165  default:
166  break;
167  }
168  m_choice = index;
169 }
170 
171 const char* const CVariation_Base::C_Data::sm_SelectionNames[] = {
172  "not set",
173  "unknown",
174  "note",
175  "uniparental-disomy",
176  "instance",
177  "set",
178  "complex",
179  "seq"
180 };
181 
183 {
184  return NCBI_NS_NCBI::CInvalidChoiceSelection::GetName(index, sm_SelectionNames, sizeof(sm_SelectionNames)/sizeof(sm_SelectionNames[0]));
185 }
186 
188 {
189  throw NCBI_NS_NCBI::CInvalidChoiceSelection(DIAG_COMPILE_INFO, this, m_choice, index, sm_SelectionNames, sizeof(sm_SelectionNames)/sizeof(sm_SelectionNames[0]));
190 }
191 
193 {
195  *m_string = value;
196 }
197 
199 {
201  return *static_cast<const TInstance*>(m_object);
202 }
203 
205 {
207  return *static_cast<TInstance*>(m_object);
208 }
209 
211 {
212  TInstance* ptr = &value;
213  if ( m_choice != e_Instance || m_object != ptr ) {
214  ResetSelection();
215  (m_object = ptr)->AddReference();
217  }
218 }
219 
221 {
223  return *static_cast<const TSet*>(m_object);
224 }
225 
227 {
229  return *static_cast<TSet*>(m_object);
230 }
231 
233 {
234  TSet* ptr = &value;
235  if ( m_choice != e_Set || m_object != ptr ) {
236  ResetSelection();
237  (m_object = ptr)->AddReference();
238  m_choice = e_Set;
239  }
240 }
241 
243 {
245  return *static_cast<const TSeq*>(m_object);
246 }
247 
249 {
251  return *static_cast<TSeq*>(m_object);
252 }
253 
255 {
256  TSeq* ptr = &value;
257  if ( m_choice != e_Seq || m_object != ptr ) {
258  ResetSelection();
259  (m_object = ptr)->AddReference();
260  m_choice = e_Seq;
261  }
262 }
263 
264 // helper methods
265 
266 // type info
268 {
269  SET_INTERNAL_NAME("Variation", "data");
270  SET_CHOICE_MODULE("NCBI-VariationPackage");
271  ADD_NAMED_NULL_CHOICE_VARIANT("unknown", null, ());
272  ADD_NAMED_BUF_CHOICE_VARIANT("note", m_string, STD, (string));
273  ADD_NAMED_NULL_CHOICE_VARIANT("uniparental-disomy", null, ());
275  ADD_NAMED_REF_CHOICE_VARIANT("set", m_object, C_Set);
276  ADD_NAMED_NULL_CHOICE_VARIANT("complex", null, ());
278  info->CodeVersion(22301);
279  info->DataSpec(ncbi::EDataSpec::eASN);
280 }
282 
283 // constructor
286 {
287 }
288 
289 // destructor
291 {
292  Reset();
293 }
294 
295 
297 {
298  m_Reference.erase();
299  m_set_State[0] &= ~0x3;
300 }
301 
303 {
304  m_Test.erase();
305  m_set_State[0] &= ~0xc;
306 }
307 
309 {
310  ResetReference();
311  ResetTest();
312 }
313 
315 {
316  SET_INTERNAL_NAME("Variation.consequence.E", "loss-of-heterozygosity");
317  SET_CLASS_MODULE("NCBI-VariationPackage");
318  ADD_NAMED_STD_MEMBER("reference", m_Reference)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
319  ADD_NAMED_STD_MEMBER("test", m_Test)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
320  info->RandomOrder();
321  info->CodeVersion(22301);
322  info->DataSpec(ncbi::EDataSpec::eASN);
323 }
325 
326 // constructor
328 {
329  memset(m_set_State,0,sizeof(m_set_State));
330 }
331 
332 // destructor
334 {
335 }
336 
337 
339 {
340  if ( m_choice != e_not_set )
341  ResetSelection();
342 }
343 
345 {
346  switch ( m_choice ) {
347  case e_Note:
348  m_string.Destruct();
349  break;
350  case e_Variation:
351  case e_Loss_of_heterozygosity:
352  m_object->RemoveReference();
353  break;
354  default:
355  break;
356  }
357  m_choice = e_not_set;
358 }
359 
360 void CVariation_Base::C_E_Consequence::DoSelect(E_Choice index, NCBI_NS_NCBI::CObjectMemoryPool* pool)
361 {
362  switch ( index ) {
363  case e_Variation:
364  (m_object = new(pool) ncbi::objects::CVariation())->AddReference();
365  break;
366  case e_Loss_of_heterozygosity:
367  (m_object = new(pool) C_Loss_of_heterozygosity())->AddReference();
368  break;
369  case e_Note:
370  m_string.Construct();
371  break;
372  default:
373  break;
374  }
375  m_choice = index;
376 }
377 
379  "not set",
380  "unknown",
381  "splicing",
382  "note",
383  "variation",
384  "loss-of-heterozygosity"
385 };
386 
388 {
389  return NCBI_NS_NCBI::CInvalidChoiceSelection::GetName(index, sm_SelectionNames, sizeof(sm_SelectionNames)/sizeof(sm_SelectionNames[0]));
390 }
391 
393 {
394  throw NCBI_NS_NCBI::CInvalidChoiceSelection(DIAG_COMPILE_INFO, this, m_choice, index, sm_SelectionNames, sizeof(sm_SelectionNames)/sizeof(sm_SelectionNames[0]));
395 }
396 
398 {
399  Select(e_Note, NCBI_NS_NCBI::eDoNotResetVariant);
400  *m_string = value;
401 }
402 
404 {
405  CheckSelected(e_Variation);
406  return *static_cast<const TVariation*>(m_object);
407 }
408 
410 {
411  Select(e_Variation, NCBI_NS_NCBI::eDoNotResetVariant);
412  return *static_cast<TVariation*>(m_object);
413 }
414 
416 {
417  TVariation* ptr = &value;
418  if ( m_choice != e_Variation || m_object != ptr ) {
419  ResetSelection();
420  (m_object = ptr)->AddReference();
421  m_choice = e_Variation;
422  }
423 }
424 
426 {
427  CheckSelected(e_Loss_of_heterozygosity);
428  return *static_cast<const TLoss_of_heterozygosity*>(m_object);
429 }
430 
432 {
433  Select(e_Loss_of_heterozygosity, NCBI_NS_NCBI::eDoNotResetVariant);
434  return *static_cast<TLoss_of_heterozygosity*>(m_object);
435 }
436 
438 {
440  if ( m_choice != e_Loss_of_heterozygosity || m_object != ptr ) {
441  ResetSelection();
442  (m_object = ptr)->AddReference();
443  m_choice = e_Loss_of_heterozygosity;
444  }
445 }
446 
447 // helper methods
448 
449 // type info
451 {
452  SET_INTERNAL_NAME("Variation.consequence", "E");
453  SET_CHOICE_MODULE("NCBI-VariationPackage");
454  ADD_NAMED_NULL_CHOICE_VARIANT("unknown", null, ());
455  ADD_NAMED_NULL_CHOICE_VARIANT("splicing", null, ());
456  ADD_NAMED_BUF_CHOICE_VARIANT("note", m_string, STD, (string));
457  ADD_NAMED_REF_CHOICE_VARIANT("variation", m_object, CVariation);
458  ADD_NAMED_REF_CHOICE_VARIANT("loss-of-heterozygosity", m_object, C_Loss_of_heterozygosity);
459  info->CodeVersion(22301);
460  info->DataSpec(ncbi::EDataSpec::eASN);
461 }
463 
464 // constructor
466  : m_choice(e_not_set)
467 {
468 }
469 
470 // destructor
472 {
473  Reset();
474 }
475 
476 
478 {
479  ResetPhase();
480  ResetX_length();
481 }
482 
484 {
485  SET_INTERNAL_NAME("Variation", "frameshift");
486  SET_CLASS_MODULE("NCBI-VariationPackage");
487  ADD_NAMED_STD_MEMBER("phase", m_Phase)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
488  ADD_NAMED_STD_MEMBER("x-length", m_X_length)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
489  info->RandomOrder();
490  info->CodeVersion(22301);
491  info->DataSpec(ncbi::EDataSpec::eASN);
492 }
494 
495 // constructor
497  : m_Phase(0), m_X_length(0)
498 {
499  memset(m_set_State,0,sizeof(m_set_State));
500 }
501 
502 // destructor
504 {
505 }
506 
507 
509 {
510  m_Description.erase();
511  m_set_State[0] &= ~0x3;
512 }
513 
515 {
516  m_Object_id.clear();
517  m_set_State[0] &= ~0xc;
518 }
519 
521 {
523  ResetObject_id();
524 }
525 
527 {
528  SET_INTERNAL_NAME("Variation.somatic-origin.E", "condition");
529  SET_CLASS_MODULE("NCBI-VariationPackage");
530  ADD_NAMED_STD_MEMBER("description", m_Description)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
531  ADD_NAMED_MEMBER("object-id", m_Object_id, STL_list_set, (STL_CRef, (CLASS, (CDbtag))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
532  info->RandomOrder();
533  info->CodeVersion(22301);
534  info->DataSpec(ncbi::EDataSpec::eASN);
535 }
537 
538 // constructor
540 {
541  memset(m_set_State,0,sizeof(m_set_State));
542 }
543 
544 // destructor
546 {
547 }
548 
549 
551 {
552  m_Source.Reset();
553 }
554 
556 {
557  m_Source.Reset(&value);
558 }
559 
561 {
562  if ( !m_Source )
563  m_Source.Reset(new TSource());
564  return (*m_Source);
565 }
566 
568 {
569  m_Condition.Reset();
570 }
571 
573 {
574  m_Condition.Reset(&value);
575 }
576 
578 {
579  if ( !m_Condition )
580  m_Condition.Reset(new TCondition());
581  return (*m_Condition);
582 }
583 
585 {
586  ResetSource();
587  ResetCondition();
588 }
589 
591 {
592  SET_INTERNAL_NAME("Variation.somatic-origin", "E");
593  SET_CLASS_MODULE("NCBI-VariationPackage");
594  ADD_NAMED_REF_MEMBER("source", m_Source, CSubSource)->SetOptional();
595  ADD_NAMED_REF_MEMBER("condition", m_Condition, C_Condition)->SetOptional();
596  info->RandomOrder();
597  info->CodeVersion(22301);
598  info->DataSpec(ncbi::EDataSpec::eASN);
599 }
601 
602 // constructor
604 {
605  memset(m_set_State,0,sizeof(m_set_State));
606 }
607 
608 // destructor
610 {
611 }
612 
613 
615 {
616  m_Id.Reset();
617 }
618 
620 {
621  m_Id.Reset(&value);
622 }
623 
625 {
626  if ( !m_Id )
627  m_Id.Reset(new TId());
628  return (*m_Id);
629 }
630 
632 {
633  m_Parent_id.Reset();
634 }
635 
637 {
638  m_Parent_id.Reset(&value);
639 }
640 
642 {
643  if ( !m_Parent_id )
644  m_Parent_id.Reset(new TParent_id());
645  return (*m_Parent_id);
646 }
647 
649 {
650  m_Sample_id.clear();
651  m_set_State[0] &= ~0x30;
652 }
653 
655 {
656  m_Other_ids.clear();
657  m_set_State[0] &= ~0xc0;
658 }
659 
661 {
662  m_Name.erase();
663  m_set_State[0] &= ~0x300;
664 }
665 
667 {
668  m_Synonyms.clear();
669  m_set_State[0] &= ~0xc00;
670 }
671 
673 {
674  m_Description.erase();
675  m_set_State[0] &= ~0x3000;
676 }
677 
679 {
680  m_Placements.clear();
681  m_set_State[0] &= ~0xc000;
682 }
683 
685 {
686  m_Phenotype.clear();
687  m_set_State[0] &= ~0x30000;
688 }
689 
691 {
692  m_Method.Reset();
693 }
694 
696 {
697  m_Method.Reset(&value);
698 }
699 
701 {
702  if ( !m_Method )
703  m_Method.Reset(new TMethod());
704  return (*m_Method);
705 }
706 
708 {
709  m_Population_data.clear();
710  m_set_State[0] &= ~0x300000;
711 }
712 
714 {
715  m_Variant_prop.Reset();
716 }
717 
719 {
720  m_Variant_prop.Reset(&value);
721 }
722 
724 {
725  if ( !m_Variant_prop )
726  m_Variant_prop.Reset(new TVariant_prop());
727  return (*m_Variant_prop);
728 }
729 
731 {
732  m_Pub.Reset();
733 }
734 
736 {
737  m_Pub.Reset(&value);
738 }
739 
741 {
742  if ( !m_Pub )
743  m_Pub.Reset(new TPub());
744  return (*m_Pub);
745 }
746 
748 {
749  m_Clinical_test.Reset();
750 }
751 
753 {
754  m_Clinical_test.Reset(&value);
755 }
756 
758 {
759  if ( !m_Clinical_test )
760  m_Clinical_test.Reset(new TClinical_test());
761  return (*m_Clinical_test);
762 }
763 
765 {
766  if ( !m_Data ) {
767  m_Data.Reset(new TData());
768  return;
769  }
770  (*m_Data).Reset();
771 }
772 
774 {
775  m_Data.Reset(&value);
776 }
777 
779 {
780  m_Consequence.clear();
781  m_set_State[0] &= ~0xc0000000;
782 }
783 
785 {
786  m_Frameshift.Reset();
787 }
788 
790 {
791  m_Frameshift.Reset(&value);
792 }
793 
795 {
796  if ( !m_Frameshift )
797  m_Frameshift.Reset(new TFrameshift());
798  return (*m_Frameshift);
799 }
800 
802 {
803  m_Ext.clear();
804  m_set_State[1] &= ~0xc;
805 }
806 
808 {
809  m_Somatic_origin.clear();
810  m_set_State[1] &= ~0x30;
811 }
812 
814 {
815  m_Exceptions.clear();
816  m_set_State[1] &= ~0xc0;
817 }
818 
820 {
821  m_So_terms.clear();
822  m_set_State[1] &= ~0x300;
823 }
824 
826 {
827  ResetId();
828  ResetParent_id();
829  ResetSample_id();
830  ResetOther_ids();
831  ResetName();
832  ResetSynonyms();
834  ResetPlacements();
835  ResetPhenotype();
836  ResetMethod();
839  ResetPub();
841  ResetData();
843  ResetFrameshift();
844  ResetExt();
846  ResetExceptions();
847  ResetSo_terms();
848 }
849 
851 {
852  SET_CLASS_MODULE("NCBI-VariationPackage");
853  ADD_NAMED_REF_MEMBER("id", m_Id, CDbtag)->SetOptional();
854  ADD_NAMED_REF_MEMBER("parent-id", m_Parent_id, CDbtag)->SetOptional();
855  ADD_NAMED_MEMBER("sample-id", m_Sample_id, STL_list_set, (STL_CRef, (CLASS, (CObject_id))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
856  ADD_NAMED_MEMBER("other-ids", m_Other_ids, STL_list_set, (STL_CRef, (CLASS, (CDbtag))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
857  ADD_NAMED_STD_MEMBER("name", m_Name)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
858  ADD_NAMED_MEMBER("synonyms", m_Synonyms, STL_list_set, (STD, (string)))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
859  ADD_NAMED_STD_MEMBER("description", m_Description)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
860  ADD_NAMED_MEMBER("placements", m_Placements, STL_list, (STL_CRef, (CLASS, (CVariantPlacement))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
861  ADD_NAMED_MEMBER("phenotype", m_Phenotype, STL_list_set, (STL_CRef, (CLASS, (CPhenotype))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
862  ADD_NAMED_REF_MEMBER("method", m_Method, CVariationMethod)->SetOptional();
863  ADD_NAMED_MEMBER("population-data", m_Population_data, STL_list_set, (STL_CRef, (CLASS, (CPopulation_data))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
864  ADD_NAMED_REF_MEMBER("variant-prop", m_Variant_prop, CVariantProperties)->SetOptional();
865  ADD_NAMED_REF_MEMBER("pub", m_Pub, CPub_set)->SetOptional();
866  ADD_NAMED_REF_MEMBER("clinical-test", m_Clinical_test, CDbtag)->SetOptional();
867  ADD_NAMED_REF_MEMBER("data", m_Data, C_Data);
868  ADD_NAMED_MEMBER("consequence", m_Consequence, STL_list_set, (STL_CRef, (CLASS, (C_E_Consequence))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
869  ADD_NAMED_REF_MEMBER("frameshift", m_Frameshift, C_Frameshift)->SetOptional();
870  ADD_NAMED_MEMBER("ext", m_Ext, STL_list_set, (STL_CRef, (CLASS, (CUser_object))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
871  ADD_NAMED_MEMBER("somatic-origin", m_Somatic_origin, STL_list_set, (STL_CRef, (CLASS, (C_E_Somatic_origin))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
872  ADD_NAMED_MEMBER("exceptions", m_Exceptions, STL_list_set, (STL_CRef, (CLASS, (CVariationException))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
873  ADD_NAMED_MEMBER("so-terms", m_So_terms, STL_list_set, (STD, (int)))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
874  info->RandomOrder();
875  info->CodeVersion(22301);
876  info->DataSpec(ncbi::EDataSpec::eASN);
877 }
879 
880 // constructor
882 {
883  memset(m_set_State,0,sizeof(m_set_State));
884  if ( !IsAllocatedInPool() ) {
885  ResetData();
886  }
887 }
888 
889 // destructor
891 {
892 }
893 
894 
895 
896 END_objects_SCOPE // namespace ncbi::objects::
897 
899 
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
BEGIN_NAMED_CHOICE_INFO("", CVariation_Base::C_Data)
Definition: Variation_.cpp:267
BEGIN_NAMED_BASE_CLASS_INFO("Variation", CVariation)
Definition: Variation_.cpp:850
BEGIN_NAMED_ENUM_IN_INFO("", CVariation_Base::C_Data::C_Set::, EData_set_type, true)
Definition: Variation_.cpp:63
BEGIN_NAMED_CLASS_INFO("", CVariation_Base::C_Data::C_Set)
Definition: Variation_.cpp:101
User-defined methods of the data storage class.
END_ENUM_INFO
Definition: aln_errors.cpp:58
Definition: Dbtag.hpp:53
CPhenotype –.
Definition: Phenotype.hpp:66
CPopulation_data –.
CVariantPlacement –.
CVariationException –.
CVariationMethod –.
Set of related Variations.
Definition: Variation_.hpp:127
condition related to this origin's type
Definition: Variation_.hpp:999
Frameshift-related info.
Definition: Variation_.hpp:861
CVariation_inst –.
char value[7]
Definition: config.c:431
string
Definition: cgiapp.hpp:687
#define DIAG_COMPILE_INFO
Make compile time diagnostic information object to use in CNcbiDiag and CException.
Definition: ncbidiag.hpp:170
#define MEMBER_PTR(MemberName)
Definition: serialimpl.hpp:284
#define SET_ENUM_INTERNAL_NAME(OwnerName, MemberName)
Definition: serialimpl.hpp:559
#define ADD_NAMED_MEMBER(MemberAlias, MemberName, TypeMacro, TypeMacroArgs)
Definition: serialimpl.hpp:342
#define ADD_NAMED_REF_MEMBER(MemberAlias, MemberName, ClassName)
Definition: serialimpl.hpp:357
#define SET_ENUM_MODULE(ModuleName)
Definition: serialimpl.hpp:553
#define END_CLASS_INFO
Definition: serialimpl.hpp:456
#define ADD_NAMED_REF_CHOICE_VARIANT(MemberAlias, MemberName, ClassName)
Definition: serialimpl.hpp:400
#define ADD_NAMED_STD_MEMBER(MemberAlias, MemberName)
Definition: serialimpl.hpp:345
#define SET_CLASS_MODULE(ModuleName)
Definition: serialimpl.hpp:444
#define ADD_NAMED_ENUM_MEMBER(MemberAlias, MemberName, EnumName)
Definition: serialimpl.hpp:351
#define ADD_ENUM_VALUE(EnumValueName, EnumValueValue)
Definition: serialimpl.hpp:562
#define END_CHOICE_INFO
Definition: serialimpl.hpp:506
#define SET_INTERNAL_NAME(OwnerName, MemberName)
Definition: serialimpl.hpp:447
#define SET_CHOICE_MODULE(ModuleName)
Definition: serialimpl.hpp:500
#define ADD_NAMED_NULL_CHOICE_VARIANT(MemberAlias, TypeMacro, TypeMacroArgs)
Definition: serialimpl.hpp:379
#define ADD_NAMED_BUF_CHOICE_VARIANT(MemberAlias, MemberName, TypeMacro, TypeMacroArgs)
Definition: serialimpl.hpp:385
@ eDoNotResetVariant
Definition: serialbase.hpp:78
void AddReference(void) const
Add reference to object.
Definition: ncbiobj.hpp:489
void Reset(void)
Reset reference object.
Definition: ncbiobj.hpp:773
bool IsAllocatedInPool(void) const THROWS_NONE
Check if object is allocated in memory pool (not system heap)
Definition: ncbiobj.hpp:461
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
virtual void Reset(void)
Reset the whole object.
Definition: SubSource_.cpp:113
CRef< TId > m_Id
void ResetSelection(void)
Reset the selection (set it to e_not_set).
Definition: Variation_.cpp:133
void ResetDescription(void)
Reset Description data member.
Definition: Variation_.cpp:508
TInstance & SetInstance(void)
Select the variant.
Definition: Variation_.cpp:204
void ResetId(void)
Reset Id data member.
Definition: Variation_.cpp:614
void ResetOther_ids(void)
Reset Other_ids data member.
Definition: Variation_.cpp:654
void ResetPub(void)
Reset Pub data member.
Definition: Variation_.cpp:730
static string SelectionName(E_Choice index)
Retrieve selection name (for diagnostic purposes).
Definition: Variation_.cpp:182
TVariation & SetVariation(void)
Select the variant.
Definition: Variation_.cpp:409
CRef< TFrameshift > m_Frameshift
list< CRef< C_E_Consequence > > m_Consequence
void ResetExceptions(void)
Reset Exceptions data member.
Definition: Variation_.cpp:813
TPub & SetPub(void)
Assign a value to Pub data member.
Definition: Variation_.cpp:740
void ResetMethod(void)
Reset Method data member.
Definition: Variation_.cpp:690
const TSeq & GetSeq(void) const
Get the variant data.
Definition: Variation_.cpp:242
void ResetFrameshift(void)
Reset Frameshift data member.
Definition: Variation_.cpp:784
TSeq & SetSeq(void)
Select the variant.
Definition: Variation_.cpp:248
TSet & SetSet(void)
Select the variant.
Definition: Variation_.cpp:226
NCBI_NS_NCBI::CSerialObject * m_object
Definition: Variation_.hpp:519
void ThrowInvalidSelection(E_Choice index) const
Throw 'InvalidSelection' exception.
Definition: Variation_.cpp:392
list< CRef< CDbtag > > m_Other_ids
static const char *const sm_SelectionNames[]
Definition: Variation_.hpp:515
list< CRef< CPopulation_data > > m_Population_data
list< string > m_Synonyms
CRef< TPub > m_Pub
void ResetClinical_test(void)
Reset Clinical_test data member.
Definition: Variation_.cpp:747
void ResetSelection(void)
Reset the selection (set it to e_not_set).
Definition: Variation_.cpp:344
void ResetConsequence(void)
Reset Consequence data member.
Definition: Variation_.cpp:778
CRef< TData > m_Data
static const char *const sm_SelectionNames[]
Definition: Variation_.hpp:846
list< CRef< CObject_id > > m_Sample_id
list< CRef< CPhenotype > > m_Phenotype
list< CRef< CVariantPlacement > > m_Placements
CRef< TClinical_test > m_Clinical_test
const TSet & GetSet(void) const
Get the variant data.
Definition: Variation_.cpp:220
void Reset(void)
Reset the whole object.
Definition: Variation_.cpp:94
TVariant_prop & SetVariant_prop(void)
Assign a value to Variant_prop data member.
Definition: Variation_.cpp:723
void ResetSource(void)
Reset Source data member.
Definition: Variation_.cpp:550
TFrameshift & SetFrameshift(void)
Assign a value to Frameshift data member.
Definition: Variation_.cpp:794
CVariationMethod TMethod
CVariantProperties TVariant_prop
NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string > m_string
Definition: Variation_.hpp:518
void ResetSomatic_origin(void)
Reset Somatic_origin data member.
Definition: Variation_.cpp:807
CRef< TVariant_prop > m_Variant_prop
const TLoss_of_heterozygosity & GetLoss_of_heterozygosity(void) const
Get the variant data.
Definition: Variation_.cpp:425
void ResetSynonyms(void)
Reset Synonyms data member.
Definition: Variation_.cpp:666
void ResetPhenotype(void)
Reset Phenotype data member.
Definition: Variation_.cpp:684
const TInstance & GetInstance(void) const
Get the variant data.
Definition: Variation_.cpp:198
TCondition & SetCondition(void)
Assign a value to Condition data member.
Definition: Variation_.cpp:577
void Reset(void)
Reset the whole object.
Definition: Variation_.cpp:584
void ResetVariant_prop(void)
Reset Variant_prop data member.
Definition: Variation_.cpp:713
C_Frameshift TFrameshift
TLoss_of_heterozygosity & SetLoss_of_heterozygosity(void)
Select the variant.
Definition: Variation_.cpp:431
list< int > m_So_terms
TClinical_test & SetClinical_test(void)
Assign a value to Clinical_test data member.
Definition: Variation_.cpp:757
TMethod & SetMethod(void)
Assign a value to Method data member.
Definition: Variation_.cpp:700
void Reset(void)
Reset the whole object.
Definition: Variation_.cpp:520
void ResetName(void)
Reset Name data member.
Definition: Variation_.cpp:88
void ResetObject_id(void)
Reset Object_id data member.
Definition: Variation_.cpp:514
void ResetPopulation_data(void)
Reset Population_data data member.
Definition: Variation_.cpp:707
list< CRef< CVariation > > m_Variations
Definition: Variation_.hpp:291
static string SelectionName(E_Choice index)
Retrieve selection name (for diagnostic purposes).
Definition: Variation_.cpp:387
void ResetVariations(void)
Reset Variations data member.
Definition: Variation_.cpp:82
void Reset(void)
Reset the whole object.
Definition: Variation_.cpp:127
virtual ~CVariation_Base(void)
Definition: Variation_.cpp:890
void ResetName(void)
Reset Name data member.
Definition: Variation_.cpp:660
void ResetPlacements(void)
Reset Placements data member.
Definition: Variation_.cpp:678
void DoSelect(E_Choice index, CObjectMemoryPool *pool=0)
Definition: Variation_.cpp:360
const TVariation & GetVariation(void) const
Get the variant data.
Definition: Variation_.cpp:403
TData & SetData(void)
Assign a value to Data data member.
TSource & SetSource(void)
Assign a value to Source data member.
Definition: Variation_.cpp:560
TParent_id & SetParent_id(void)
Assign a value to Parent_id data member.
Definition: Variation_.cpp:641
void ResetData(void)
Reset Data data member.
Definition: Variation_.cpp:764
Uint4 m_set_State[2]
void Select(E_Choice index, EResetVariant reset=eDoResetVariant)
Select the requested variant if needed.
TNote & SetNote(void)
Select the variant.
list< CRef< CVariationException > > m_Exceptions
list< CRef< C_E_Somatic_origin > > m_Somatic_origin
virtual void Reset(void)
Reset the whole object.
Definition: Variation_.cpp:825
void CheckSelected(E_Choice index) const
Verify selection, throw exception if it differs from the expected.
TNote & SetNote(void)
Select the variant.
void Reset(void)
Reset the whole object.
Definition: Variation_.cpp:477
CRef< TMethod > m_Method
void ResetSample_id(void)
Reset Sample_id data member.
Definition: Variation_.cpp:648
void DoSelect(E_Choice index, CObjectMemoryPool *pool=0)
Definition: Variation_.cpp:150
void ResetParent_id(void)
Reset Parent_id data member.
Definition: Variation_.cpp:631
TId & SetId(void)
Assign a value to Id data member.
Definition: Variation_.cpp:624
void ThrowInvalidSelection(E_Choice index) const
Throw 'InvalidSelection' exception.
Definition: Variation_.cpp:187
void ResetDescription(void)
Reset Description data member.
Definition: Variation_.cpp:672
void Reset(void)
Reset the whole object.
Definition: Variation_.cpp:338
void ResetCondition(void)
Reset Condition data member.
Definition: Variation_.cpp:567
E_Choice
Choice variants.
Definition: Variation_.hpp:296
void ResetReference(void)
Reset Reference data member.
Definition: Variation_.cpp:296
list< CRef< CUser_object > > m_Ext
void ResetSo_terms(void)
Reset So_terms data member.
Definition: Variation_.cpp:819
void ResetExt(void)
Reset Ext data member.
Definition: Variation_.cpp:801
CRef< TParent_id > m_Parent_id
@ e_Instance
actual sequence-edit at feat.location
Definition: Variation_.hpp:301
@ e_not_set
No variant selected.
Definition: Variation_.hpp:297
@ e_Seq
Sequnece as it exists post-alteration.
Definition: Variation_.hpp:304
@ e_not_set
static MDB_envinfo info
Definition: mdb_load.c:37
Modified on Tue Dec 05 02:17:56 2023 by modify_doxy.py rev. 669887