NCBI C++ ToolKit
Variation_ref_.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
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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  * 'seqfeat.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.hpp>
55 
56 BEGIN_objects_SCOPE // namespace ncbi::objects::
57 
58 
59 // generated classes
60 
62 {
63  SET_ENUM_INTERNAL_NAME("Variation-ref.method", "E");
64  SET_ENUM_MODULE("NCBI-Variation");
65  ADD_ENUM_VALUE("unknown", eMethod_E_unknown);
66  ADD_ENUM_VALUE("bac-acgh", eMethod_E_bac_acgh);
67  ADD_ENUM_VALUE("computational", eMethod_E_computational);
68  ADD_ENUM_VALUE("curated", eMethod_E_curated);
69  ADD_ENUM_VALUE("digital-array", eMethod_E_digital_array);
70  ADD_ENUM_VALUE("expression-array", eMethod_E_expression_array);
71  ADD_ENUM_VALUE("fish", eMethod_E_fish);
72  ADD_ENUM_VALUE("flanking-sequence", eMethod_E_flanking_sequence);
73  ADD_ENUM_VALUE("maph", eMethod_E_maph);
74  ADD_ENUM_VALUE("mcd-analysis", eMethod_E_mcd_analysis);
75  ADD_ENUM_VALUE("mlpa", eMethod_E_mlpa);
76  ADD_ENUM_VALUE("oea-assembly", eMethod_E_oea_assembly);
77  ADD_ENUM_VALUE("oligo-acgh", eMethod_E_oligo_acgh);
78  ADD_ENUM_VALUE("paired-end", eMethod_E_paired_end);
79  ADD_ENUM_VALUE("pcr", eMethod_E_pcr);
80  ADD_ENUM_VALUE("qpcr", eMethod_E_qpcr);
81  ADD_ENUM_VALUE("read-depth", eMethod_E_read_depth);
82  ADD_ENUM_VALUE("roma", eMethod_E_roma);
83  ADD_ENUM_VALUE("rt-pcr", eMethod_E_rt_pcr);
84  ADD_ENUM_VALUE("sage", eMethod_E_sage);
85  ADD_ENUM_VALUE("sequence-alignment", eMethod_E_sequence_alignment);
86  ADD_ENUM_VALUE("sequencing", eMethod_E_sequencing);
87  ADD_ENUM_VALUE("snp-array", eMethod_E_snp_array);
88  ADD_ENUM_VALUE("snp-genoytyping", eMethod_E_snp_genoytyping);
89  ADD_ENUM_VALUE("southern", eMethod_E_southern);
90  ADD_ENUM_VALUE("western", eMethod_E_western);
91  ADD_ENUM_VALUE("optical-mapping", eMethod_E_optical_mapping);
92  ADD_ENUM_VALUE("other", eMethod_E_other);
93 }
95 
96 BEGIN_NAMED_ENUM_IN_INFO("", CVariation_ref_Base::, EAllele_origin, true)
97 {
98  SET_ENUM_INTERNAL_NAME("Variation-ref", "allele-origin");
99  SET_ENUM_MODULE("NCBI-Variation");
100  ADD_ENUM_VALUE("unknown", eAllele_origin_unknown);
101  ADD_ENUM_VALUE("germline", eAllele_origin_germline);
102  ADD_ENUM_VALUE("somatic", eAllele_origin_somatic);
103  ADD_ENUM_VALUE("inherited", eAllele_origin_inherited);
104  ADD_ENUM_VALUE("paternal", eAllele_origin_paternal);
105  ADD_ENUM_VALUE("maternal", eAllele_origin_maternal);
106  ADD_ENUM_VALUE("de-novo", eAllele_origin_de_novo);
107  ADD_ENUM_VALUE("biparental", eAllele_origin_biparental);
108  ADD_ENUM_VALUE("uniparental", eAllele_origin_uniparental);
109  ADD_ENUM_VALUE("not-tested", eAllele_origin_not_tested);
110  ADD_ENUM_VALUE("tested-inconclusive", eAllele_origin_tested_inconclusive);
111  ADD_ENUM_VALUE("other", eAllele_origin_other);
112 }
114 
116 {
117  SET_ENUM_INTERNAL_NAME("Variation-ref", "allele-state");
118  SET_ENUM_MODULE("NCBI-Variation");
119  ADD_ENUM_VALUE("unknown", eAllele_state_unknown);
120  ADD_ENUM_VALUE("homozygous", eAllele_state_homozygous);
121  ADD_ENUM_VALUE("heterozygous", eAllele_state_heterozygous);
122  ADD_ENUM_VALUE("hemizygous", eAllele_state_hemizygous);
123  ADD_ENUM_VALUE("nullizygous", eAllele_state_nullizygous);
124  ADD_ENUM_VALUE("other", eAllele_state_other);
125 }
127 
129 {
130  SET_ENUM_INTERNAL_NAME("Variation-ref.data.set", "type");
131  SET_ENUM_MODULE("NCBI-Variation");
132  ADD_ENUM_VALUE("unknown", eData_set_type_unknown);
133  ADD_ENUM_VALUE("compound", eData_set_type_compound);
134  ADD_ENUM_VALUE("products", eData_set_type_products);
135  ADD_ENUM_VALUE("haplotype", eData_set_type_haplotype);
136  ADD_ENUM_VALUE("genotype", eData_set_type_genotype);
137  ADD_ENUM_VALUE("mosaic", eData_set_type_mosaic);
138  ADD_ENUM_VALUE("individual", eData_set_type_individual);
139  ADD_ENUM_VALUE("population", eData_set_type_population);
140  ADD_ENUM_VALUE("alleles", eData_set_type_alleles);
141  ADD_ENUM_VALUE("package", eData_set_type_package);
142  ADD_ENUM_VALUE("other", eData_set_type_other);
143 }
145 
147 {
148  m_Variations.clear();
149  m_set_State[0] &= ~0xc;
150 }
151 
153 {
154  m_Name.erase();
155  m_set_State[0] &= ~0x30;
156 }
157 
159 {
160  ResetType();
161  ResetVariations();
162  ResetName();
163 }
164 
166 {
167  SET_INTERNAL_NAME("Variation-ref.data", "set");
168  SET_CLASS_MODULE("NCBI-Variation");
169  ADD_NAMED_ENUM_MEMBER("type", m_Type, EData_set_type)->SetSetFlag(MEMBER_PTR(m_set_State[0]));
170  ADD_NAMED_MEMBER("variations", m_Variations, STL_list_set, (STL_CRef, (CLASS, (CVariation_ref))))->SetSetFlag(MEMBER_PTR(m_set_State[0]));
171  ADD_NAMED_STD_MEMBER("name", m_Name)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
172  info->RandomOrder();
173  info->CodeVersion(22301);
174  info->DataSpec(ncbi::EDataSpec::eASN);
175 }
177 
178 // constructor
180  : m_Type((EData_set_type)(0))
181 {
182  memset(m_set_State,0,sizeof(m_set_State));
183 }
184 
185 // destructor
187 {
188 }
189 
190 
192 {
193  if ( m_choice != e_not_set )
194  ResetSelection();
195 }
196 
198 {
199  switch ( m_choice ) {
200  case e_Note:
201  m_string.Destruct();
202  break;
203  case e_Instance:
204  case e_Set:
205  m_object->RemoveReference();
206  break;
207  default:
208  break;
209  }
211 }
212 
213 void CVariation_ref_Base::C_Data::DoSelect(E_Choice index, NCBI_NS_NCBI::CObjectMemoryPool* pool)
214 {
215  switch ( index ) {
216  case e_Instance:
217  (m_object = new(pool) ncbi::objects::CVariation_inst())->AddReference();
218  break;
219  case e_Set:
220  (m_object = new(pool) C_Set())->AddReference();
221  break;
222  case e_Note:
223  m_string.Construct();
224  break;
225  default:
226  break;
227  }
228  m_choice = index;
229 }
230 
232  "not set",
233  "unknown",
234  "note",
235  "uniparental-disomy",
236  "instance",
237  "set",
238  "complex"
239 };
240 
242 {
243  return NCBI_NS_NCBI::CInvalidChoiceSelection::GetName(index, sm_SelectionNames, sizeof(sm_SelectionNames)/sizeof(sm_SelectionNames[0]));
244 }
245 
247 {
248  throw NCBI_NS_NCBI::CInvalidChoiceSelection(DIAG_COMPILE_INFO, this, m_choice, index, sm_SelectionNames, sizeof(sm_SelectionNames)/sizeof(sm_SelectionNames[0]));
249 }
250 
252 {
254  *m_string = value;
255 }
256 
258 {
260  return *static_cast<const TInstance*>(m_object);
261 }
262 
264 {
266  return *static_cast<TInstance*>(m_object);
267 }
268 
270 {
271  TInstance* ptr = &value;
272  if ( m_choice != e_Instance || m_object != ptr ) {
273  ResetSelection();
274  (m_object = ptr)->AddReference();
276  }
277 }
278 
280 {
282  return *static_cast<const TSet*>(m_object);
283 }
284 
286 {
288  return *static_cast<TSet*>(m_object);
289 }
290 
292 {
293  TSet* ptr = &value;
294  if ( m_choice != e_Set || m_object != ptr ) {
295  ResetSelection();
296  (m_object = ptr)->AddReference();
297  m_choice = e_Set;
298  }
299 }
300 
301 // helper methods
302 
303 // type info
305 {
306  SET_INTERNAL_NAME("Variation-ref", "data");
307  SET_CHOICE_MODULE("NCBI-Variation");
308  ADD_NAMED_NULL_CHOICE_VARIANT("unknown", null, ());
309  ADD_NAMED_BUF_CHOICE_VARIANT("note", m_string, STD, (string));
310  ADD_NAMED_NULL_CHOICE_VARIANT("uniparental-disomy", null, ());
312  ADD_NAMED_REF_CHOICE_VARIANT("set", m_object, C_Set);
313  ADD_NAMED_NULL_CHOICE_VARIANT("complex", null, ());
314  info->CodeVersion(22301);
315  info->DataSpec(ncbi::EDataSpec::eASN);
316 }
318 
319 // constructor
322 {
323 }
324 
325 // destructor
327 {
328  Reset();
329 }
330 
331 
333 {
334  ResetPhase();
335  ResetX_length();
336 }
337 
339 {
340  SET_INTERNAL_NAME("Variation-ref.consequence.E", "frameshift");
341  SET_CLASS_MODULE("NCBI-Variation");
342  ADD_NAMED_STD_MEMBER("phase", m_Phase)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
343  ADD_NAMED_STD_MEMBER("x-length", m_X_length)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
344  info->RandomOrder();
345  info->CodeVersion(22301);
346  info->DataSpec(ncbi::EDataSpec::eASN);
347 }
349 
350 // constructor
352  : m_Phase(0), m_X_length(0)
353 {
354  memset(m_set_State,0,sizeof(m_set_State));
355 }
356 
357 // destructor
359 {
360 }
361 
362 
364 {
365  m_Reference.erase();
366  m_set_State[0] &= ~0x3;
367 }
368 
370 {
371  m_Test.erase();
372  m_set_State[0] &= ~0xc;
373 }
374 
376 {
377  ResetReference();
378  ResetTest();
379 }
380 
382 {
383  SET_INTERNAL_NAME("Variation-ref.consequence.E", "loss-of-heterozygosity");
384  SET_CLASS_MODULE("NCBI-Variation");
385  ADD_NAMED_STD_MEMBER("reference", m_Reference)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
386  ADD_NAMED_STD_MEMBER("test", m_Test)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
387  info->RandomOrder();
388  info->CodeVersion(22301);
389  info->DataSpec(ncbi::EDataSpec::eASN);
390 }
392 
393 // constructor
395 {
396  memset(m_set_State,0,sizeof(m_set_State));
397 }
398 
399 // destructor
401 {
402 }
403 
404 
406 {
407  if ( m_choice != e_not_set )
408  ResetSelection();
409 }
410 
412 {
413  switch ( m_choice ) {
414  case e_Note:
415  m_string.Destruct();
416  break;
417  case e_Variation:
418  case e_Frameshift:
420  m_object->RemoveReference();
421  break;
422  default:
423  break;
424  }
426 }
427 
428 void CVariation_ref_Base::C_E_Consequence::DoSelect(E_Choice index, NCBI_NS_NCBI::CObjectMemoryPool* pool)
429 {
430  switch ( index ) {
431  case e_Variation:
432  (m_object = new(pool) ncbi::objects::CVariation_ref())->AddReference();
433  break;
434  case e_Frameshift:
435  (m_object = new(pool) C_Frameshift())->AddReference();
436  break;
439  break;
440  case e_Note:
441  m_string.Construct();
442  break;
443  default:
444  break;
445  }
446  m_choice = index;
447 }
448 
450  "not set",
451  "unknown",
452  "splicing",
453  "note",
454  "variation",
455  "frameshift",
456  "loss-of-heterozygosity"
457 };
458 
460 {
461  return NCBI_NS_NCBI::CInvalidChoiceSelection::GetName(index, sm_SelectionNames, sizeof(sm_SelectionNames)/sizeof(sm_SelectionNames[0]));
462 }
463 
465 {
466  throw NCBI_NS_NCBI::CInvalidChoiceSelection(DIAG_COMPILE_INFO, this, m_choice, index, sm_SelectionNames, sizeof(sm_SelectionNames)/sizeof(sm_SelectionNames[0]));
467 }
468 
470 {
472  *m_string = value;
473 }
474 
476 {
478  return *static_cast<const TVariation*>(m_object);
479 }
480 
482 {
484  return *static_cast<TVariation*>(m_object);
485 }
486 
488 {
489  TVariation* ptr = &value;
490  if ( m_choice != e_Variation || m_object != ptr ) {
491  ResetSelection();
492  (m_object = ptr)->AddReference();
494  }
495 }
496 
498 {
500  return *static_cast<const TFrameshift*>(m_object);
501 }
502 
504 {
506  return *static_cast<TFrameshift*>(m_object);
507 }
508 
510 {
511  TFrameshift* ptr = &value;
512  if ( m_choice != e_Frameshift || m_object != ptr ) {
513  ResetSelection();
514  (m_object = ptr)->AddReference();
516  }
517 }
518 
520 {
522  return *static_cast<const TLoss_of_heterozygosity*>(m_object);
523 }
524 
526 {
528  return *static_cast<TLoss_of_heterozygosity*>(m_object);
529 }
530 
532 {
534  if ( m_choice != e_Loss_of_heterozygosity || m_object != ptr ) {
535  ResetSelection();
536  (m_object = ptr)->AddReference();
538  }
539 }
540 
541 // helper methods
542 
543 // type info
545 {
546  SET_INTERNAL_NAME("Variation-ref.consequence", "E");
547  SET_CHOICE_MODULE("NCBI-Variation");
548  ADD_NAMED_NULL_CHOICE_VARIANT("unknown", null, ());
549  ADD_NAMED_NULL_CHOICE_VARIANT("splicing", null, ());
550  ADD_NAMED_BUF_CHOICE_VARIANT("note", m_string, STD, (string));
552  ADD_NAMED_REF_CHOICE_VARIANT("frameshift", m_object, C_Frameshift);
553  ADD_NAMED_REF_CHOICE_VARIANT("loss-of-heterozygosity", m_object, C_Loss_of_heterozygosity);
554  info->CodeVersion(22301);
555  info->DataSpec(ncbi::EDataSpec::eASN);
556 }
558 
559 // constructor
562 {
563 }
564 
565 // destructor
567 {
568  Reset();
569 }
570 
571 
573 {
574  m_Description.erase();
575  m_set_State[0] &= ~0x3;
576 }
577 
579 {
580  m_Object_id.clear();
581  m_set_State[0] &= ~0xc;
582 }
583 
585 {
587  ResetObject_id();
588 }
589 
591 {
592  SET_INTERNAL_NAME("Variation-ref.somatic-origin.E", "condition");
593  SET_CLASS_MODULE("NCBI-Variation");
594  ADD_NAMED_STD_MEMBER("description", m_Description)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
595  ADD_NAMED_MEMBER("object-id", m_Object_id, STL_list_set, (STL_CRef, (CLASS, (CDbtag))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->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_Source.Reset();
617 }
618 
620 {
621  m_Source.Reset(&value);
622 }
623 
625 {
626  if ( !m_Source )
627  m_Source.Reset(new TSource());
628  return (*m_Source);
629 }
630 
632 {
633  m_Condition.Reset();
634 }
635 
637 {
638  m_Condition.Reset(&value);
639 }
640 
642 {
643  if ( !m_Condition )
644  m_Condition.Reset(new TCondition());
645  return (*m_Condition);
646 }
647 
649 {
650  ResetSource();
651  ResetCondition();
652 }
653 
655 {
656  SET_INTERNAL_NAME("Variation-ref.somatic-origin", "E");
657  SET_CLASS_MODULE("NCBI-Variation");
658  ADD_NAMED_REF_MEMBER("source", m_Source, CSubSource)->SetOptional();
659  ADD_NAMED_REF_MEMBER("condition", m_Condition, C_Condition)->SetOptional();
660  info->RandomOrder();
661  info->CodeVersion(22301);
662  info->DataSpec(ncbi::EDataSpec::eASN);
663 }
665 
666 // constructor
668 {
669  memset(m_set_State,0,sizeof(m_set_State));
670 }
671 
672 // destructor
674 {
675 }
676 
677 
679 {
680  m_Id.Reset();
681 }
682 
684 {
685  m_Id.Reset(&value);
686 }
687 
689 {
690  if ( !m_Id )
691  m_Id.Reset(new TId());
692  return (*m_Id);
693 }
694 
696 {
697  m_Parent_id.Reset();
698 }
699 
701 {
702  m_Parent_id.Reset(&value);
703 }
704 
706 {
707  if ( !m_Parent_id )
708  m_Parent_id.Reset(new TParent_id());
709  return (*m_Parent_id);
710 }
711 
713 {
714  m_Sample_id.Reset();
715 }
716 
718 {
719  m_Sample_id.Reset(&value);
720 }
721 
723 {
724  if ( !m_Sample_id )
725  m_Sample_id.Reset(new TSample_id());
726  return (*m_Sample_id);
727 }
728 
730 {
731  m_Other_ids.clear();
732  m_set_State[0] &= ~0xc0;
733 }
734 
736 {
737  m_Name.erase();
738  m_set_State[0] &= ~0x300;
739 }
740 
742 {
743  m_Synonyms.clear();
744  m_set_State[0] &= ~0xc00;
745 }
746 
748 {
749  m_Description.erase();
750  m_set_State[0] &= ~0x3000;
751 }
752 
754 {
755  m_Phenotype.clear();
756  m_set_State[0] &= ~0xc000;
757 }
758 
760 {
761  m_Method.clear();
762  m_set_State[0] &= ~0x30000;
763 }
764 
766 {
767  m_Population_data.clear();
768  m_set_State[0] &= ~0xc0000;
769 }
770 
772 {
773  m_Variant_prop.Reset();
774 }
775 
777 {
778  m_Variant_prop.Reset(&value);
779 }
780 
782 {
783  if ( !m_Variant_prop )
784  m_Variant_prop.Reset(new TVariant_prop());
785  return (*m_Variant_prop);
786 }
787 
789 {
790  m_Clinical_test.clear();
791  m_set_State[0] &= ~0x3000000;
792 }
793 
795 {
796  m_Pub.Reset();
797 }
798 
800 {
801  m_Pub.Reset(&value);
802 }
803 
805 {
806  if ( !m_Pub )
807  m_Pub.Reset(new TPub());
808  return (*m_Pub);
809 }
810 
812 {
813  if ( !m_Data ) {
814  m_Data.Reset(new TData());
815  return;
816  }
817  (*m_Data).Reset();
818 }
819 
821 {
822  m_Data.Reset(&value);
823 }
824 
826 {
827  m_Consequence.clear();
828  m_set_State[1] &= ~0xc0;
829 }
830 
832 {
833  m_Location.Reset();
834 }
835 
837 {
838  m_Location.Reset(&value);
839 }
840 
842 {
843  if ( !m_Location )
844  m_Location.Reset(new TLocation());
845  return (*m_Location);
846 }
847 
849 {
850  m_Ext_locs.clear();
851  m_set_State[1] &= ~0xc00;
852 }
853 
855 {
856  m_Ext.Reset();
857 }
858 
860 {
861  m_Ext.Reset(&value);
862 }
863 
865 {
866  if ( !m_Ext )
867  m_Ext.Reset(new TExt());
868  return (*m_Ext);
869 }
870 
872 {
873  m_Somatic_origin.clear();
874  m_set_State[1] &= ~0xc000;
875 }
876 
878 {
879  ResetId();
880  ResetParent_id();
881  ResetSample_id();
882  ResetOther_ids();
883  ResetName();
884  ResetSynonyms();
886  ResetPhenotype();
887  ResetMethod();
890  ResetValidated();
896  ResetPub();
897  ResetData();
899  ResetLocation();
900  ResetExt_locs();
901  ResetExt();
903 }
904 
906 {
907  SET_CLASS_MODULE("NCBI-Variation");
908  ADD_NAMED_REF_MEMBER("id", m_Id, CDbtag)->SetOptional();
909  ADD_NAMED_REF_MEMBER("parent-id", m_Parent_id, CDbtag)->SetOptional();
910  ADD_NAMED_REF_MEMBER("sample-id", m_Sample_id, CObject_id)->SetOptional();
911  ADD_NAMED_MEMBER("other-ids", m_Other_ids, STL_list_set, (STL_CRef, (CLASS, (CDbtag))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
912  ADD_NAMED_STD_MEMBER("name", m_Name)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
913  ADD_NAMED_MEMBER("synonyms", m_Synonyms, STL_list_set, (STD, (string)))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
914  ADD_NAMED_STD_MEMBER("description", m_Description)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
915  ADD_NAMED_MEMBER("phenotype", m_Phenotype, STL_list_set, (STL_CRef, (CLASS, (CPhenotype))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
916  ADD_NAMED_MEMBER("method", m_Method, STL_list_set, (ENUM, (int, EMethod_E)))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
917  ADD_NAMED_MEMBER("population-data", m_Population_data, STL_list_set, (STL_CRef, (CLASS, (CPopulation_data))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
918  ADD_NAMED_REF_MEMBER("variant-prop", m_Variant_prop, CVariantProperties)->SetOptional();
919  ADD_NAMED_STD_MEMBER("validated", m_Validated)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
920  ADD_NAMED_MEMBER("clinical-test", m_Clinical_test, STL_list_set, (STL_CRef, (CLASS, (CDbtag))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
921  ADD_NAMED_ENUM_MEMBER("allele-origin", m_Allele_origin, EAllele_origin)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
922  ADD_NAMED_ENUM_MEMBER("allele-state", m_Allele_state, EAllele_state)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
923  ADD_NAMED_STD_MEMBER("allele-frequency", m_Allele_frequency)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
924  ADD_NAMED_STD_MEMBER("is-ancestral-allele", m_Is_ancestral_allele)->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
925  ADD_NAMED_REF_MEMBER("pub", m_Pub, CPub)->SetOptional();
926  ADD_NAMED_REF_MEMBER("data", m_Data, C_Data);
927  ADD_NAMED_MEMBER("consequence", m_Consequence, STL_list_set, (STL_CRef, (CLASS, (C_E_Consequence))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
928  ADD_NAMED_REF_MEMBER("location", m_Location, CSeq_loc)->SetOptional();
929  ADD_NAMED_MEMBER("ext-locs", m_Ext_locs, STL_list_set, (STL_CRef, (CLASS, (CExt_loc))))->SetSetFlag(MEMBER_PTR(m_set_State[0]))->SetOptional();
930  ADD_NAMED_REF_MEMBER("ext", m_Ext, CUser_object)->SetOptional();
931  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();
932  info->RandomOrder();
933  info->CodeVersion(22301);
934  info->DataSpec(ncbi::EDataSpec::eASN);
935 }
937 
938 // constructor
941 {
942  memset(m_set_State,0,sizeof(m_set_State));
943  if ( !IsAllocatedInPool() ) {
944  ResetData();
945  }
946 }
947 
948 // destructor
950 {
951 }
952 
953 
954 
955 END_objects_SCOPE // namespace ncbi::objects::
956 
958 
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_ref_Base::C_Data)
BEGIN_NAMED_BASE_CLASS_INFO("Variation-ref", CVariation_ref)
BEGIN_NAMED_CLASS_INFO("", CVariation_ref_Base::C_Data::C_Set)
BEGIN_NAMED_ENUM_IN_INFO("", CVariation_ref_Base::, EMethod_E, true)
END_ENUM_INFO
Definition: aln_errors.cpp:58
Definition: Dbtag.hpp:53
CExt_loc –.
Definition: Ext_loc.hpp:66
CPhenotype –.
Definition: Phenotype.hpp:66
CPopulation_data –.
Definition: Pub.hpp:56
CVariation_inst –.
Set of related Variations.
see http://www.hgvs.org/mutnomen/recs-prot.html
condition related to this origin's type
CVariation_ref_Base –.
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
void ResetClinical_test(void)
Reset Clinical_test data member.
static string SelectionName(E_Choice index)
Retrieve selection name (for diagnostic purposes).
TNote & SetNote(void)
Select the variant.
const TInstance & GetInstance(void) const
Get the variant data.
void ResetPopulation_data(void)
Reset Population_data data member.
list< CRef< CDbtag > > m_Clinical_test
void ResetId(void)
Reset Id data member.
TSource & SetSource(void)
Assign a value to Source data member.
void ResetSource(void)
Reset Source data member.
void ResetMethod(void)
Reset Method data member.
void ResetSelection(void)
Reset the selection (set it to e_not_set).
virtual ~CVariation_ref_Base(void)
const TVariation & GetVariation(void) const
Get the variant data.
void ResetValidated(void)
Reset Validated data member.
void Select(E_Choice index, EResetVariant reset=eDoResetVariant)
Select the requested variant if needed.
CRef< TParent_id > m_Parent_id
const TSet & GetSet(void) const
Get the variant data.
void ResetAllele_frequency(void)
Reset Allele_frequency data member.
void ThrowInvalidSelection(E_Choice index) const
Throw 'InvalidSelection' exception.
TFrameshift & SetFrameshift(void)
Select the variant.
list< CRef< CPhenotype > > m_Phenotype
void DoSelect(E_Choice index, CObjectMemoryPool *pool=0)
list< CRef< C_E_Consequence > > m_Consequence
list< CRef< CPopulation_data > > m_Population_data
static const char *const sm_SelectionNames[]
list< CRef< CDbtag > > m_Other_ids
void ThrowInvalidSelection(E_Choice index) const
Throw 'InvalidSelection' exception.
void Reset(void)
Reset the whole object.
TLocation & SetLocation(void)
Assign a value to Location data member.
NCBI_NS_NCBI::CSerialObject * m_object
list< CRef< CVariation_ref > > m_Variations
TVariation & SetVariation(void)
Select the variant.
void ResetLocation(void)
Reset Location data member.
void ResetExt(void)
Reset Ext data member.
void Reset(void)
Reset the whole object.
void ResetAllele_state(void)
Reset Allele_state data member.
const TFrameshift & GetFrameshift(void) const
Get the variant data.
void CheckSelected(E_Choice index) const
Verify selection, throw exception if it differs from the expected.
void ResetName(void)
Reset Name data member.
TData & SetData(void)
Assign a value to Data data member.
TCondition & SetCondition(void)
Assign a value to Condition data member.
void ResetData(void)
Reset Data data member.
TSample_id & SetSample_id(void)
Assign a value to Sample_id data member.
NCBI_NS_NCBI::CSerialObject * m_object
void ResetObject_id(void)
Reset Object_id data member.
void ResetOther_ids(void)
Reset Other_ids data member.
static const char *const sm_SelectionNames[]
TVariant_prop & SetVariant_prop(void)
Assign a value to Variant_prop data member.
void ResetExt_locs(void)
Reset Ext_locs data member.
TLoss_of_heterozygosity & SetLoss_of_heterozygosity(void)
Select the variant.
void ResetConsequence(void)
Reset Consequence data member.
CRef< TLocation > m_Location
void ResetCondition(void)
Reset Condition data member.
const TLoss_of_heterozygosity & GetLoss_of_heterozygosity(void) const
Get the variant data.
EAllele_state
observed allele state, if known DEPRECATED: new field = VariantProperties.allele-state
TNote & SetNote(void)
Select the variant.
void CheckSelected(E_Choice index) const
Verify selection, throw exception if it differs from the expected.
EAllele_origin
origin of this allele, if known note that these are powers-of-two, and represent bits; thus,...
virtual void Reset(void)
Reset the whole object.
list< CRef< CExt_loc > > m_Ext_locs
static string SelectionName(E_Choice index)
Retrieve selection name (for diagnostic purposes).
CRef< TVariant_prop > m_Variant_prop
void ResetSomatic_origin(void)
Reset Somatic_origin data member.
CVariantProperties TVariant_prop
void ResetAllele_origin(void)
Reset Allele_origin data member.
NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string > m_string
TSet & SetSet(void)
Select the variant.
void ResetSynonyms(void)
Reset Synonyms data member.
void ResetPub(void)
Reset Pub data member.
void Reset(void)
Reset the whole object.
CRef< TSample_id > m_Sample_id
void ResetDescription(void)
Reset Description data member.
void ResetParent_id(void)
Reset Parent_id data member.
void ResetIs_ancestral_allele(void)
Reset Is_ancestral_allele data member.
TId & SetId(void)
Assign a value to Id data member.
void DoSelect(E_Choice index, CObjectMemoryPool *pool=0)
TInstance & SetInstance(void)
Select the variant.
void ResetSample_id(void)
Reset Sample_id data member.
TPub & SetPub(void)
Assign a value to Pub data member.
void ResetName(void)
Reset Name data member.
void ResetDescription(void)
Reset Description data member.
void ResetVariations(void)
Reset Variations data member.
void Select(E_Choice index, EResetVariant reset=eDoResetVariant)
Select the requested variant if needed.
void ResetVariant_prop(void)
Reset Variant_prop data member.
list< string > m_Synonyms
NCBI_NS_NCBI::CUnionBuffer< NCBI_NS_STD::string > m_string
TExt & SetExt(void)
Assign a value to Ext data member.
void ResetPhenotype(void)
Reset Phenotype data member.
list< CRef< C_E_Somatic_origin > > m_Somatic_origin
void Reset(void)
Reset the whole object.
TParent_id & SetParent_id(void)
Assign a value to Parent_id data member.
void ResetSelection(void)
Reset the selection (set it to e_not_set).
@ e_Variation
Describe resulting variation in the product, e.g. missense, nonsense, silent, neutral,...
@ e_Instance
actual sequence-edit at feat.location
@ e_not_set
No variant selected.
static MDB_envinfo info
Definition: mdb_load.c:37
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
Modified on Sat Apr 13 11:46:07 2024 by modify_doxy.py rev. 669887