NCBI C++ ToolKit
Seq_feat_.hpp
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27 
28 /// @file Seq_feat_.hpp
29 /// Data storage class.
30 ///
31 /// This file was generated by application DATATOOL
32 /// using the following specifications:
33 /// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/seqfeat/seqfeat.asn">seqfeat.asn</a>
34 /// and additional tune-up parameters:
35 /// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/seqfeat/seqfeat.def">seqfeat.def</a>
36 ///
37 /// ATTENTION:
38 /// Don't edit or commit this file into CVS as this file will
39 /// be overridden (by DATATOOL) without warning!
40 
41 #ifndef OBJECTS_SEQFEAT_SEQ_FEAT_BASE_HPP
42 #define OBJECTS_SEQFEAT_SEQ_FEAT_BASE_HPP
43 
44 // standard includes
45 #include <serial/serialbase.hpp>
46 
47 // generated includes
48 #include <list>
49 #include <string>
50 #include <vector>
51 
53 
54 #ifndef BEGIN_objects_SCOPE
55 # define BEGIN_objects_SCOPE BEGIN_SCOPE(objects)
56 # define END_objects_SCOPE END_SCOPE(objects)
57 #endif
58 BEGIN_objects_SCOPE // namespace ncbi::objects::
59 
60 
61 // forward declarations
62 class CDbtag;
63 class CFeat_id;
64 class CGb_qual;
65 class CPub_set;
66 class CSeqFeatData;
67 class CSeqFeatSupport;
68 class CSeqFeatXref;
69 class CSeq_loc;
70 class CUser_object;
71 
72 
73 // generated classes
74 
75 
76 /** @addtogroup dataspec_NCBI_Seqfeat
77  *
78  * @{
79  */
80 
81 /////////////////////////////////////////////////////////////////////////////
82 ///*** Seq-feat *******************************************
83 ///* sequence feature generalization
84 ///
85 /// CSeq_feat_Base --
86 ///
87 
89 {
91 public:
92  // constructor
93  CSeq_feat_Base(void);
94  // destructor
95  virtual ~CSeq_feat_Base(void);
96 
97  // type info
99 
100  /// evidence for existence of feature
101  enum EExp_ev {
102  eExp_ev_experimental = 1, ///< any reasonable experimental check
103  eExp_ev_not_experimental = 2 ///< similarity, pattern, etc
104  };
105 
106  /// Access to EExp_ev's attributes (values, names) as defined in spec
107  static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(EExp_ev)(void);
108 
109  // types
110  typedef CFeat_id TId;
112  typedef bool TPartial;
113  typedef bool TExcept;
114  typedef string TComment;
117  typedef vector< CRef< CGb_qual > > TQual;
118  typedef string TTitle;
120  typedef CPub_set TCit;
121  typedef EExp_ev TExp_ev;
122  typedef vector< CRef< CSeqFeatXref > > TXref;
123  typedef vector< CRef< CDbtag > > TDbxref;
124  typedef bool TPseudo;
125  typedef string TExcept_text;
126  typedef list< CRef< CFeat_id > > TIds;
127  typedef list< CRef< CUser_object > > TExts;
129 
130  // member index
131  enum class E_memberIndex {
132  e__allMandatory = 0,
133  e_id,
134  e_data,
135  e_partial,
136  e_except,
137  e_comment,
138  e_product,
139  e_location,
140  e_qual,
141  e_title,
142  e_ext,
143  e_cit,
144  e_exp_ev,
145  e_xref,
146  e_dbxref,
147  e_pseudo,
148  e_except_text,
149  e_ids,
150  e_exts,
151  e_support
152  };
154 
155  // getters
156  // setters
157 
158  /// Check if a value has been assigned to Id data member.
159  ///
160  /// Data member Id is optional;
161  /// its type is defined as 'typedef CFeat_id TId'
162  /// @return
163  /// - true, if a value has been assigned.
164  /// - false, otherwise.
165  bool IsSetId(void) const;
166 
167  /// Check if it is safe to call GetId method.
168  ///
169  /// @return
170  /// - true, if the data member is getatable.
171  /// - false, otherwise.
172  bool CanGetId(void) const;
173 
174  /// Reset Id data member.
175  void ResetId(void);
176 
177  /// Get the Id member data.
178  ///
179  /// @return
180  /// Reference to the member data.
181  const TId& GetId(void) const;
182 
183  /// Assign a value to Id data member.
184  ///
185  /// @param value
186  /// Reference to value.
187  void SetId(TId& value);
188 
189  /// Assign a value to Id data member.
190  ///
191  /// @return
192  /// Reference to the data value.
193  TId& SetId(void);
194 
195  /// the specific data
196  /// Check if a value has been assigned to Data data member.
197  ///
198  /// Data member Data is mandatory;
199  /// its type is defined as 'typedef CSeqFeatData TData'
200  /// @return
201  /// - true, if a value has been assigned.
202  /// - false, otherwise.
203  bool IsSetData(void) const;
204 
205  /// Check if it is safe to call GetData method.
206  ///
207  /// @return
208  /// - true, if the data member is getatable.
209  /// - false, otherwise.
210  bool CanGetData(void) const;
211 
212  /// Reset Data data member.
213  void ResetData(void);
214 
215  /// Get the Data member data.
216  ///
217  /// @return
218  /// Reference to the member data.
219  const TData& GetData(void) const;
220 
221  /// Assign a value to Data data member.
222  ///
223  /// @param value
224  /// Reference to value.
225  void SetData(TData& value);
226 
227  /// Assign a value to Data data member.
228  ///
229  /// @return
230  /// Reference to the data value.
231  TData& SetData(void);
232 
233  /// incomplete in some way?
234  /// Check if a value has been assigned to Partial data member.
235  ///
236  /// Data member Partial is optional;
237  /// its type is defined as 'typedef bool TPartial'
238  /// @return
239  /// - true, if a value has been assigned.
240  /// - false, otherwise.
241  bool IsSetPartial(void) const;
242 
243  /// Check if it is safe to call GetPartial method.
244  ///
245  /// @return
246  /// - true, if the data member is getatable.
247  /// - false, otherwise.
248  bool CanGetPartial(void) const;
249 
250  /// Reset Partial data member.
251  void ResetPartial(void);
252 
253  /// Get the Partial member data.
254  ///
255  /// @return
256  /// Copy of the member data.
257  TPartial GetPartial(void) const;
258 
259  /// Assign a value to Partial data member.
260  ///
261  /// @param value
262  /// Value to assign
263  void SetPartial(TPartial value);
264 
265  /// Assign a value to Partial data member.
266  ///
267  /// @return
268  /// Reference to the data value.
269  TPartial& SetPartial(void);
270 
271  /// something funny about this?
272  /// Check if a value has been assigned to Except data member.
273  ///
274  /// Data member Except is optional;
275  /// its type is defined as 'typedef bool TExcept'
276  /// @return
277  /// - true, if a value has been assigned.
278  /// - false, otherwise.
279  bool IsSetExcept(void) const;
280 
281  /// Check if it is safe to call GetExcept method.
282  ///
283  /// @return
284  /// - true, if the data member is getatable.
285  /// - false, otherwise.
286  bool CanGetExcept(void) const;
287 
288  /// Reset Except data member.
289  void ResetExcept(void);
290 
291  /// Get the Except member data.
292  ///
293  /// @return
294  /// Copy of the member data.
295  TExcept GetExcept(void) const;
296 
297  /// Assign a value to Except data member.
298  ///
299  /// @param value
300  /// Value to assign
301  void SetExcept(TExcept value);
302 
303  /// Assign a value to Except data member.
304  ///
305  /// @return
306  /// Reference to the data value.
307  TExcept& SetExcept(void);
308 
309  /// Check if a value has been assigned to Comment data member.
310  ///
311  /// Data member Comment is optional;
312  /// its type is defined as 'typedef string TComment'
313  /// @return
314  /// - true, if a value has been assigned.
315  /// - false, otherwise.
316  bool IsSetComment(void) const;
317 
318  /// Check if it is safe to call GetComment method.
319  ///
320  /// @return
321  /// - true, if the data member is getatable.
322  /// - false, otherwise.
323  bool CanGetComment(void) const;
324 
325  /// Reset Comment data member.
326  void ResetComment(void);
327 
328  /// Get the Comment member data.
329  ///
330  /// @return
331  /// Reference to the member data.
332  const TComment& GetComment(void) const;
333 
334  /// Assign a value to Comment data member.
335  ///
336  /// @param value
337  /// Value to assign
338  void SetComment(const TComment& value);
339  void SetComment(TComment&& value);
340 
341  /// Assign a value to Comment data member.
342  ///
343  /// @return
344  /// Reference to the data value.
345  TComment& SetComment(void);
346 
347  /// product of process
348  /// Check if a value has been assigned to Product data member.
349  ///
350  /// Data member Product is optional;
351  /// its type is defined as 'typedef CSeq_loc TProduct'
352  /// @return
353  /// - true, if a value has been assigned.
354  /// - false, otherwise.
355  bool IsSetProduct(void) const;
356 
357  /// Check if it is safe to call GetProduct method.
358  ///
359  /// @return
360  /// - true, if the data member is getatable.
361  /// - false, otherwise.
362  bool CanGetProduct(void) const;
363 
364  /// Reset Product data member.
365  void ResetProduct(void);
366 
367  /// Get the Product member data.
368  ///
369  /// @return
370  /// Reference to the member data.
371  const TProduct& GetProduct(void) const;
372 
373  /// Assign a value to Product data member.
374  ///
375  /// @param value
376  /// Reference to value.
377  void SetProduct(TProduct& value);
378 
379  /// Assign a value to Product data member.
380  ///
381  /// @return
382  /// Reference to the data value.
383  TProduct& SetProduct(void);
384 
385  /// feature made from
386  /// Check if a value has been assigned to Location data member.
387  ///
388  /// Data member Location is mandatory;
389  /// its type is defined as 'typedef CSeq_loc TLocation'
390  /// @return
391  /// - true, if a value has been assigned.
392  /// - false, otherwise.
393  bool IsSetLocation(void) const;
394 
395  /// Check if it is safe to call GetLocation method.
396  ///
397  /// @return
398  /// - true, if the data member is getatable.
399  /// - false, otherwise.
400  bool CanGetLocation(void) const;
401 
402  /// Reset Location data member.
403  void ResetLocation(void);
404 
405  /// Get the Location member data.
406  ///
407  /// @return
408  /// Reference to the member data.
409  const TLocation& GetLocation(void) const;
410 
411  /// Assign a value to Location data member.
412  ///
413  /// @param value
414  /// Reference to value.
415  void SetLocation(TLocation& value);
416 
417  /// Assign a value to Location data member.
418  ///
419  /// @return
420  /// Reference to the data value.
421  TLocation& SetLocation(void);
422 
423  /// qualifiers
424  /// Check if a value has been assigned to Qual data member.
425  ///
426  /// Data member Qual is optional;
427  /// its type is defined as 'typedef vector< CRef< CGb_qual > > TQual'
428  /// @return
429  /// - true, if a value has been assigned.
430  /// - false, otherwise.
431  bool IsSetQual(void) const;
432 
433  /// Check if it is safe to call GetQual method.
434  ///
435  /// @return
436  /// - true, if the data member is getatable.
437  /// - false, otherwise.
438  bool CanGetQual(void) const;
439 
440  /// Reset Qual data member.
441  void ResetQual(void);
442 
443  /// Get the Qual member data.
444  ///
445  /// @return
446  /// Reference to the member data.
447  const TQual& GetQual(void) const;
448 
449  /// Assign a value to Qual data member.
450  ///
451  /// @return
452  /// Reference to the data value.
453  TQual& SetQual(void);
454 
455  /// for user defined label
456  /// Check if a value has been assigned to Title data member.
457  ///
458  /// Data member Title is optional;
459  /// its type is defined as 'typedef string TTitle'
460  /// @return
461  /// - true, if a value has been assigned.
462  /// - false, otherwise.
463  bool IsSetTitle(void) const;
464 
465  /// Check if it is safe to call GetTitle method.
466  ///
467  /// @return
468  /// - true, if the data member is getatable.
469  /// - false, otherwise.
470  bool CanGetTitle(void) const;
471 
472  /// Reset Title data member.
473  void ResetTitle(void);
474 
475  /// Get the Title member data.
476  ///
477  /// @return
478  /// Reference to the member data.
479  const TTitle& GetTitle(void) const;
480 
481  /// Assign a value to Title data member.
482  ///
483  /// @param value
484  /// Value to assign
485  void SetTitle(const TTitle& value);
486  void SetTitle(TTitle&& value);
487 
488  /// Assign a value to Title data member.
489  ///
490  /// @return
491  /// Reference to the data value.
492  TTitle& SetTitle(void);
493 
494  /// user defined structure extension
495  /// Check if a value has been assigned to Ext data member.
496  ///
497  /// Data member Ext is optional;
498  /// its type is defined as 'typedef CUser_object TExt'
499  /// @return
500  /// - true, if a value has been assigned.
501  /// - false, otherwise.
502  bool IsSetExt(void) const;
503 
504  /// Check if it is safe to call GetExt method.
505  ///
506  /// @return
507  /// - true, if the data member is getatable.
508  /// - false, otherwise.
509  bool CanGetExt(void) const;
510 
511  /// Reset Ext data member.
512  void ResetExt(void);
513 
514  /// Get the Ext member data.
515  ///
516  /// @return
517  /// Reference to the member data.
518  const TExt& GetExt(void) const;
519 
520  /// Assign a value to Ext data member.
521  ///
522  /// @param value
523  /// Reference to value.
524  void SetExt(TExt& value);
525 
526  /// Assign a value to Ext data member.
527  ///
528  /// @return
529  /// Reference to the data value.
530  TExt& SetExt(void);
531 
532  /// citations for this feature
533  /// Check if a value has been assigned to Cit data member.
534  ///
535  /// Data member Cit is optional;
536  /// its type is defined as 'typedef CPub_set TCit'
537  /// @return
538  /// - true, if a value has been assigned.
539  /// - false, otherwise.
540  bool IsSetCit(void) const;
541 
542  /// Check if it is safe to call GetCit method.
543  ///
544  /// @return
545  /// - true, if the data member is getatable.
546  /// - false, otherwise.
547  bool CanGetCit(void) const;
548 
549  /// Reset Cit data member.
550  void ResetCit(void);
551 
552  /// Get the Cit member data.
553  ///
554  /// @return
555  /// Reference to the member data.
556  const TCit& GetCit(void) const;
557 
558  /// Assign a value to Cit data member.
559  ///
560  /// @param value
561  /// Reference to value.
562  void SetCit(TCit& value);
563 
564  /// Assign a value to Cit data member.
565  ///
566  /// @return
567  /// Reference to the data value.
568  TCit& SetCit(void);
569 
570  /// Check if a value has been assigned to Exp_ev data member.
571  ///
572  /// Data member Exp_ev is optional;
573  /// its type is defined as 'typedef EExp_ev TExp_ev'
574  /// @return
575  /// - true, if a value has been assigned.
576  /// - false, otherwise.
577  bool IsSetExp_ev(void) const;
578 
579  /// Check if it is safe to call GetExp_ev method.
580  ///
581  /// @return
582  /// - true, if the data member is getatable.
583  /// - false, otherwise.
584  bool CanGetExp_ev(void) const;
585 
586  /// Reset Exp_ev data member.
587  void ResetExp_ev(void);
588 
589  /// Get the Exp_ev member data.
590  ///
591  /// @return
592  /// Copy of the member data.
593  TExp_ev GetExp_ev(void) const;
594 
595  /// Assign a value to Exp_ev data member.
596  ///
597  /// @param value
598  /// Value to assign
599  void SetExp_ev(TExp_ev value);
600 
601  /// Assign a value to Exp_ev data member.
602  ///
603  /// @return
604  /// Reference to the data value.
605  TExp_ev& SetExp_ev(void);
606 
607  /// cite other relevant features
608  /// Check if a value has been assigned to Xref data member.
609  ///
610  /// Data member Xref is optional;
611  /// its type is defined as 'typedef vector< CRef< CSeqFeatXref > > TXref'
612  /// @return
613  /// - true, if a value has been assigned.
614  /// - false, otherwise.
615  bool IsSetXref(void) const;
616 
617  /// Check if it is safe to call GetXref method.
618  ///
619  /// @return
620  /// - true, if the data member is getatable.
621  /// - false, otherwise.
622  bool CanGetXref(void) const;
623 
624  /// Reset Xref data member.
625  void ResetXref(void);
626 
627  /// Get the Xref member data.
628  ///
629  /// @return
630  /// Reference to the member data.
631  const TXref& GetXref(void) const;
632 
633  /// Assign a value to Xref data member.
634  ///
635  /// @return
636  /// Reference to the data value.
637  TXref& SetXref(void);
638 
639  /// support for xref to other databases
640  /// Check if a value has been assigned to Dbxref data member.
641  ///
642  /// Data member Dbxref is optional;
643  /// its type is defined as 'typedef vector< CRef< CDbtag > > TDbxref'
644  /// @return
645  /// - true, if a value has been assigned.
646  /// - false, otherwise.
647  bool IsSetDbxref(void) const;
648 
649  /// Check if it is safe to call GetDbxref method.
650  ///
651  /// @return
652  /// - true, if the data member is getatable.
653  /// - false, otherwise.
654  bool CanGetDbxref(void) const;
655 
656  /// Reset Dbxref data member.
657  void ResetDbxref(void);
658 
659  /// Get the Dbxref member data.
660  ///
661  /// @return
662  /// Reference to the member data.
663  const TDbxref& GetDbxref(void) const;
664 
665  /// Assign a value to Dbxref data member.
666  ///
667  /// @return
668  /// Reference to the data value.
669  TDbxref& SetDbxref(void);
670 
671  /// annotated on pseudogene?
672  /// Check if a value has been assigned to Pseudo data member.
673  ///
674  /// Data member Pseudo is optional;
675  /// its type is defined as 'typedef bool TPseudo'
676  /// @return
677  /// - true, if a value has been assigned.
678  /// - false, otherwise.
679  bool IsSetPseudo(void) const;
680 
681  /// Check if it is safe to call GetPseudo method.
682  ///
683  /// @return
684  /// - true, if the data member is getatable.
685  /// - false, otherwise.
686  bool CanGetPseudo(void) const;
687 
688  /// Reset Pseudo data member.
689  void ResetPseudo(void);
690 
691  /// Get the Pseudo member data.
692  ///
693  /// @return
694  /// Copy of the member data.
695  TPseudo GetPseudo(void) const;
696 
697  /// Assign a value to Pseudo data member.
698  ///
699  /// @param value
700  /// Value to assign
701  void SetPseudo(TPseudo value);
702 
703  /// Assign a value to Pseudo data member.
704  ///
705  /// @return
706  /// Reference to the data value.
707  TPseudo& SetPseudo(void);
708 
709  /// explain if except=TRUE
710  /// Check if a value has been assigned to Except_text data member.
711  ///
712  /// Data member Except_text is optional;
713  /// its type is defined as 'typedef string TExcept_text'
714  /// @return
715  /// - true, if a value has been assigned.
716  /// - false, otherwise.
717  bool IsSetExcept_text(void) const;
718 
719  /// Check if it is safe to call GetExcept_text method.
720  ///
721  /// @return
722  /// - true, if the data member is getatable.
723  /// - false, otherwise.
724  bool CanGetExcept_text(void) const;
725 
726  /// Reset Except_text data member.
727  void ResetExcept_text(void);
728 
729  /// Get the Except_text member data.
730  ///
731  /// @return
732  /// Reference to the member data.
733  const TExcept_text& GetExcept_text(void) const;
734 
735  /// Assign a value to Except_text data member.
736  ///
737  /// @param value
738  /// Value to assign
739  void SetExcept_text(const TExcept_text& value);
740  void SetExcept_text(TExcept_text&& value);
741 
742  /// Assign a value to Except_text data member.
743  ///
744  /// @return
745  /// Reference to the data value.
746  TExcept_text& SetExcept_text(void);
747 
748  /// set of Ids; will replace 'id' field
749  /// Check if a value has been assigned to Ids data member.
750  ///
751  /// Data member Ids is optional;
752  /// its type is defined as 'typedef list< CRef< CFeat_id > > TIds'
753  /// @return
754  /// - true, if a value has been assigned.
755  /// - false, otherwise.
756  bool IsSetIds(void) const;
757 
758  /// Check if it is safe to call GetIds method.
759  ///
760  /// @return
761  /// - true, if the data member is getatable.
762  /// - false, otherwise.
763  bool CanGetIds(void) const;
764 
765  /// Reset Ids data member.
766  void ResetIds(void);
767 
768  /// Get the Ids member data.
769  ///
770  /// @return
771  /// Reference to the member data.
772  const TIds& GetIds(void) const;
773 
774  /// Assign a value to Ids data member.
775  ///
776  /// @return
777  /// Reference to the data value.
778  TIds& SetIds(void);
779 
780  /// set of extensions; will replace 'ext' field
781  /// Check if a value has been assigned to Exts data member.
782  ///
783  /// Data member Exts is optional;
784  /// its type is defined as 'typedef list< CRef< CUser_object > > TExts'
785  /// @return
786  /// - true, if a value has been assigned.
787  /// - false, otherwise.
788  bool IsSetExts(void) const;
789 
790  /// Check if it is safe to call GetExts method.
791  ///
792  /// @return
793  /// - true, if the data member is getatable.
794  /// - false, otherwise.
795  bool CanGetExts(void) const;
796 
797  /// Reset Exts data member.
798  void ResetExts(void);
799 
800  /// Get the Exts member data.
801  ///
802  /// @return
803  /// Reference to the member data.
804  const TExts& GetExts(void) const;
805 
806  /// Assign a value to Exts data member.
807  ///
808  /// @return
809  /// Reference to the data value.
810  TExts& SetExts(void);
811 
812  /// will replace /experiment, /inference, model-evidence
813  /// Check if a value has been assigned to Support data member.
814  ///
815  /// Data member Support is optional;
816  /// its type is defined as 'typedef CSeqFeatSupport TSupport'
817  /// @return
818  /// - true, if a value has been assigned.
819  /// - false, otherwise.
820  bool IsSetSupport(void) const;
821 
822  /// Check if it is safe to call GetSupport method.
823  ///
824  /// @return
825  /// - true, if the data member is getatable.
826  /// - false, otherwise.
827  bool CanGetSupport(void) const;
828 
829  /// Reset Support data member.
830  void ResetSupport(void);
831 
832  /// Get the Support member data.
833  ///
834  /// @return
835  /// Reference to the member data.
836  const TSupport& GetSupport(void) const;
837 
838  /// Assign a value to Support data member.
839  ///
840  /// @param value
841  /// Reference to value.
842  void SetSupport(TSupport& value);
843 
844  /// Assign a value to Support data member.
845  ///
846  /// @return
847  /// Reference to the data value.
848  TSupport& SetSupport(void);
849 
850  /// Reset the whole object
851  virtual void Reset(void);
852 
853 
854 private:
855  // Prohibit copy constructor and assignment operator
858 
859  // data
860  Uint4 m_set_State[2];
863  bool m_Partial;
864  bool m_Except;
865  string m_Comment;
868  vector< CRef< CGb_qual > > m_Qual;
869  string m_Title;
873  vector< CRef< CSeqFeatXref > > m_Xref;
874  vector< CRef< CDbtag > > m_Dbxref;
875  bool m_Pseudo;
877  list< CRef< CFeat_id > > m_Ids;
878  list< CRef< CUser_object > > m_Exts;
880 };
881 
882 /* @} */
883 
884 
885 
886 
887 
888 ///////////////////////////////////////////////////////////
889 ///////////////////// inline methods //////////////////////
890 ///////////////////////////////////////////////////////////
891 inline
892 bool CSeq_feat_Base::IsSetId(void) const
893 {
894  return m_Id.NotEmpty();
895 }
896 
897 inline
898 bool CSeq_feat_Base::CanGetId(void) const
899 {
900  return IsSetId();
901 }
902 
903 inline
905 {
906  if (!CanGetId()) {
907  ThrowUnassigned(0);
908  }
909  return (*m_Id);
910 }
911 
912 inline
914 {
915  return m_Data.NotEmpty();
916 }
917 
918 inline
920 {
921  return true;
922 }
923 
924 inline
926 {
927  if ( !m_Data ) {
928  const_cast<CSeq_feat_Base*>(this)->ResetData();
929  }
930  return (*m_Data);
931 }
932 
933 inline
935 {
936  if ( !m_Data ) {
937  ResetData();
938  }
939  return (*m_Data);
940 }
941 
942 inline
944 {
945  return ((m_set_State[0] & 0x30) != 0);
946 }
947 
948 inline
950 {
951  return IsSetPartial();
952 }
953 
954 inline
956 {
957  m_Partial = 0;
958  m_set_State[0] &= ~0x30;
959 }
960 
961 inline
963 {
964  if (!CanGetPartial()) {
965  ThrowUnassigned(2);
966  }
967  return m_Partial;
968 }
969 
970 inline
972 {
973  m_Partial = value;
974  m_set_State[0] |= 0x30;
975 }
976 
977 inline
979 {
980 #ifdef _DEBUG
981  if (!IsSetPartial()) {
982  memset(&m_Partial,UnassignedByte(),sizeof(m_Partial));
983  }
984 #endif
985  m_set_State[0] |= 0x10;
986  return m_Partial;
987 }
988 
989 inline
991 {
992  return ((m_set_State[0] & 0xc0) != 0);
993 }
994 
995 inline
997 {
998  return IsSetExcept();
999 }
1000 
1001 inline
1003 {
1004  m_Except = 0;
1005  m_set_State[0] &= ~0xc0;
1006 }
1007 
1008 inline
1010 {
1011  if (!CanGetExcept()) {
1012  ThrowUnassigned(3);
1013  }
1014  return m_Except;
1015 }
1016 
1017 inline
1019 {
1020  m_Except = value;
1021  m_set_State[0] |= 0xc0;
1022 }
1023 
1024 inline
1026 {
1027 #ifdef _DEBUG
1028  if (!IsSetExcept()) {
1029  memset(&m_Except,UnassignedByte(),sizeof(m_Except));
1030  }
1031 #endif
1032  m_set_State[0] |= 0x40;
1033  return m_Except;
1034 }
1035 
1036 inline
1038 {
1039  return ((m_set_State[0] & 0x300) != 0);
1040 }
1041 
1042 inline
1044 {
1045  return IsSetComment();
1046 }
1047 
1048 inline
1050 {
1051  if (!CanGetComment()) {
1052  ThrowUnassigned(4);
1053  }
1054  return m_Comment;
1055 }
1056 
1057 inline
1059 {
1060  m_Comment = value;
1061  m_set_State[0] |= 0x300;
1062 }
1063 
1064 inline
1066 {
1067  m_Comment = std::forward<CSeq_feat_Base::TComment>(value);
1068  m_set_State[0] |= 0x300;
1069 }
1070 
1071 inline
1073 {
1074 #ifdef _DEBUG
1075  if (!IsSetComment()) {
1077  }
1078 #endif
1079  m_set_State[0] |= 0x100;
1080  return m_Comment;
1081 }
1082 
1083 inline
1085 {
1086  return m_Product.NotEmpty();
1087 }
1088 
1089 inline
1091 {
1092  return IsSetProduct();
1093 }
1094 
1095 inline
1097 {
1098  if (!CanGetProduct()) {
1099  ThrowUnassigned(5);
1100  }
1101  return (*m_Product);
1102 }
1103 
1104 inline
1106 {
1107  return m_Location.NotEmpty();
1108 }
1109 
1110 inline
1112 {
1113  return true;
1114 }
1115 
1116 inline
1118 {
1119  if ( !m_Location ) {
1120  const_cast<CSeq_feat_Base*>(this)->ResetLocation();
1121  }
1122  return (*m_Location);
1123 }
1124 
1125 inline
1127 {
1128  if ( !m_Location ) {
1129  ResetLocation();
1130  }
1131  return (*m_Location);
1132 }
1133 
1134 inline
1136 {
1137  return ((m_set_State[0] & 0xc000) != 0);
1138 }
1139 
1140 inline
1142 {
1143  return true;
1144 }
1145 
1146 inline
1148 {
1149  return m_Qual;
1150 }
1151 
1152 inline
1154 {
1155  m_set_State[0] |= 0x4000;
1156  return m_Qual;
1157 }
1158 
1159 inline
1161 {
1162  return ((m_set_State[0] & 0x30000) != 0);
1163 }
1164 
1165 inline
1167 {
1168  return IsSetTitle();
1169 }
1170 
1171 inline
1173 {
1174  if (!CanGetTitle()) {
1175  ThrowUnassigned(8);
1176  }
1177  return m_Title;
1178 }
1179 
1180 inline
1182 {
1183  m_Title = value;
1184  m_set_State[0] |= 0x30000;
1185 }
1186 
1187 inline
1189 {
1190  m_Title = std::forward<CSeq_feat_Base::TTitle>(value);
1191  m_set_State[0] |= 0x30000;
1192 }
1193 
1194 inline
1196 {
1197 #ifdef _DEBUG
1198  if (!IsSetTitle()) {
1200  }
1201 #endif
1202  m_set_State[0] |= 0x10000;
1203  return m_Title;
1204 }
1205 
1206 inline
1208 {
1209  return m_Ext.NotEmpty();
1210 }
1211 
1212 inline
1214 {
1215  return IsSetExt();
1216 }
1217 
1218 inline
1220 {
1221  if (!CanGetExt()) {
1222  ThrowUnassigned(9);
1223  }
1224  return (*m_Ext);
1225 }
1226 
1227 inline
1229 {
1230  return m_Cit.NotEmpty();
1231 }
1232 
1233 inline
1235 {
1236  return IsSetCit();
1237 }
1238 
1239 inline
1241 {
1242  if (!CanGetCit()) {
1243  ThrowUnassigned(10);
1244  }
1245  return (*m_Cit);
1246 }
1247 
1248 inline
1250 {
1251  return ((m_set_State[0] & 0xc00000) != 0);
1252 }
1253 
1254 inline
1256 {
1257  return IsSetExp_ev();
1258 }
1259 
1260 inline
1262 {
1263  m_Exp_ev = (EExp_ev)(0);
1264  m_set_State[0] &= ~0xc00000;
1265 }
1266 
1267 inline
1269 {
1270  if (!CanGetExp_ev()) {
1271  ThrowUnassigned(11);
1272  }
1273  return m_Exp_ev;
1274 }
1275 
1276 inline
1278 {
1279  m_Exp_ev = value;
1280  m_set_State[0] |= 0xc00000;
1281 }
1282 
1283 inline
1285 {
1286 #ifdef _DEBUG
1287  if (!IsSetExp_ev()) {
1288  memset(&m_Exp_ev,UnassignedByte(),sizeof(m_Exp_ev));
1289  }
1290 #endif
1291  m_set_State[0] |= 0x400000;
1292  return m_Exp_ev;
1293 }
1294 
1295 inline
1297 {
1298  return ((m_set_State[0] & 0x3000000) != 0);
1299 }
1300 
1301 inline
1303 {
1304  return true;
1305 }
1306 
1307 inline
1309 {
1310  return m_Xref;
1311 }
1312 
1313 inline
1315 {
1316  m_set_State[0] |= 0x1000000;
1317  return m_Xref;
1318 }
1319 
1320 inline
1322 {
1323  return ((m_set_State[0] & 0xc000000) != 0);
1324 }
1325 
1326 inline
1328 {
1329  return true;
1330 }
1331 
1332 inline
1334 {
1335  return m_Dbxref;
1336 }
1337 
1338 inline
1340 {
1341  m_set_State[0] |= 0x4000000;
1342  return m_Dbxref;
1343 }
1344 
1345 inline
1347 {
1348  return ((m_set_State[0] & 0x30000000) != 0);
1349 }
1350 
1351 inline
1353 {
1354  return IsSetPseudo();
1355 }
1356 
1357 inline
1359 {
1360  m_Pseudo = 0;
1361  m_set_State[0] &= ~0x30000000;
1362 }
1363 
1364 inline
1366 {
1367  if (!CanGetPseudo()) {
1368  ThrowUnassigned(14);
1369  }
1370  return m_Pseudo;
1371 }
1372 
1373 inline
1375 {
1376  m_Pseudo = value;
1377  m_set_State[0] |= 0x30000000;
1378 }
1379 
1380 inline
1382 {
1383 #ifdef _DEBUG
1384  if (!IsSetPseudo()) {
1385  memset(&m_Pseudo,UnassignedByte(),sizeof(m_Pseudo));
1386  }
1387 #endif
1388  m_set_State[0] |= 0x10000000;
1389  return m_Pseudo;
1390 }
1391 
1392 inline
1394 {
1395  return ((m_set_State[0] & 0xc0000000) != 0);
1396 }
1397 
1398 inline
1400 {
1401  return IsSetExcept_text();
1402 }
1403 
1404 inline
1406 {
1407  if (!CanGetExcept_text()) {
1408  ThrowUnassigned(15);
1409  }
1410  return m_Except_text;
1411 }
1412 
1413 inline
1415 {
1416  m_Except_text = value;
1417  m_set_State[0] |= 0xc0000000;
1418 }
1419 
1420 inline
1422 {
1423  m_Except_text = std::forward<CSeq_feat_Base::TExcept_text>(value);
1424  m_set_State[0] |= 0xc0000000;
1425 }
1426 
1427 inline
1429 {
1430 #ifdef _DEBUG
1431  if (!IsSetExcept_text()) {
1433  }
1434 #endif
1435  m_set_State[0] |= 0x40000000;
1436  return m_Except_text;
1437 }
1438 
1439 inline
1441 {
1442  return ((m_set_State[1] & 0x3) != 0);
1443 }
1444 
1445 inline
1447 {
1448  return true;
1449 }
1450 
1451 inline
1453 {
1454  return m_Ids;
1455 }
1456 
1457 inline
1459 {
1460  m_set_State[1] |= 0x1;
1461  return m_Ids;
1462 }
1463 
1464 inline
1466 {
1467  return ((m_set_State[1] & 0xc) != 0);
1468 }
1469 
1470 inline
1472 {
1473  return true;
1474 }
1475 
1476 inline
1478 {
1479  return m_Exts;
1480 }
1481 
1482 inline
1484 {
1485  m_set_State[1] |= 0x4;
1486  return m_Exts;
1487 }
1488 
1489 inline
1491 {
1492  return m_Support.NotEmpty();
1493 }
1494 
1495 inline
1497 {
1498  return IsSetSupport();
1499 }
1500 
1501 inline
1503 {
1504  if (!CanGetSupport()) {
1505  ThrowUnassigned(18);
1506  }
1507  return (*m_Support);
1508 }
1509 
1510 ///////////////////////////////////////////////////////////
1511 ////////////////// end of inline methods //////////////////
1512 ///////////////////////////////////////////////////////////
1513 
1514 
1515 
1516 
1517 
1518 END_objects_SCOPE // namespace ncbi::objects::
1519 
1521 
1522 
1523 #endif // OBJECTS_SEQFEAT_SEQ_FEAT_BASE_HPP
Definition: Dbtag.hpp:53
CFeat_id –.
Definition: Feat_id.hpp:66
@Gb_qual.hpp User-defined methods of the data storage class.
Definition: Gb_qual.hpp:61
CRef –.
Definition: ncbiobj.hpp:618
CSeqFeatSupport –.
CSeqFeatXref –.
Definition: SeqFeatXref.hpp:66
*** Seq-feat ******************************************* * sequence feature generalization
Definition: Seq_feat_.hpp:89
Base class for all serializable objects.
Definition: serialbase.hpp:150
static char UnassignedByte(void)
Definition: serialbase.hpp:181
void ThrowUnassigned(TMemberIndex index) const
#define ENUM_METHOD_NAME(EnumName)
Definition: serialbase.hpp:994
static string UnassignedString(void)
Definition: serialbase.hpp:175
const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)
If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...
NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)
Definition: seqtitle.cpp:106
bool NotEmpty(void) const THROWS_NONE
Check if CRef is not empty – pointing to an object and has a non-null value.
Definition: ncbiobj.hpp:726
uint32_t Uint4
4-byte (32-bit) unsigned integer
Definition: ncbitype.h:103
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define NCBI_SEQFEAT_EXPORT
Definition: ncbi_export.h:768
bool IsSetTitle(void) const
for user defined label Check if a value has been assigned to Title data member.
Definition: Seq_feat_.hpp:1160
bool CanGetDbxref(void) const
Check if it is safe to call GetDbxref method.
Definition: Seq_feat_.hpp:1327
bool CanGetExp_ev(void) const
Check if it is safe to call GetExp_ev method.
Definition: Seq_feat_.hpp:1255
CRef< TCit > m_Cit
Definition: Seq_feat_.hpp:871
string m_Except_text
Definition: Seq_feat_.hpp:876
bool CanGetExts(void) const
Check if it is safe to call GetExts method.
Definition: Seq_feat_.hpp:1471
TXref & SetXref(void)
Assign a value to Xref data member.
Definition: Seq_feat_.hpp:1314
CUser_object TExt
Definition: Seq_feat_.hpp:119
bool IsSetComment(void) const
Check if a value has been assigned to Comment data member.
Definition: Seq_feat_.hpp:1037
EExp_ev m_Exp_ev
Definition: Seq_feat_.hpp:872
bool CanGetCit(void) const
Check if it is safe to call GetCit method.
Definition: Seq_feat_.hpp:1234
CFeat_id TId
Definition: Seq_feat_.hpp:110
bool CanGetSupport(void) const
Check if it is safe to call GetSupport method.
Definition: Seq_feat_.hpp:1496
vector< CRef< CDbtag > > TDbxref
Definition: Seq_feat_.hpp:123
TDbxref & SetDbxref(void)
Assign a value to Dbxref data member.
Definition: Seq_feat_.hpp:1339
void ResetPartial(void)
Reset Partial data member.
Definition: Seq_feat_.hpp:955
bool CanGetXref(void) const
Check if it is safe to call GetXref method.
Definition: Seq_feat_.hpp:1302
TPartial & SetPartial(void)
Assign a value to Partial data member.
Definition: Seq_feat_.hpp:978
bool IsSetData(void) const
the specific data Check if a value has been assigned to Data data member.
Definition: Seq_feat_.hpp:913
bool IsSetQual(void) const
qualifiers Check if a value has been assigned to Qual data member.
Definition: Seq_feat_.hpp:1135
const TExts & GetExts(void) const
Get the Exts member data.
Definition: Seq_feat_.hpp:1477
bool CanGetQual(void) const
Check if it is safe to call GetQual method.
Definition: Seq_feat_.hpp:1141
vector< CRef< CGb_qual > > m_Qual
Definition: Seq_feat_.hpp:868
string m_Comment
Definition: Seq_feat_.hpp:865
bool IsSetExt(void) const
user defined structure extension Check if a value has been assigned to Ext data member.
Definition: Seq_feat_.hpp:1207
TExcept & SetExcept(void)
Assign a value to Except data member.
Definition: Seq_feat_.hpp:1025
const TIds & GetIds(void) const
Get the Ids member data.
Definition: Seq_feat_.hpp:1452
Uint4 m_set_State[2]
Definition: Seq_feat_.hpp:860
TIds & SetIds(void)
Assign a value to Ids data member.
Definition: Seq_feat_.hpp:1458
bool IsSetSupport(void) const
will replace /experiment, /inference, model-evidence Check if a value has been assigned to Support da...
Definition: Seq_feat_.hpp:1490
list< CRef< CUser_object > > TExts
Definition: Seq_feat_.hpp:127
const TTitle & GetTitle(void) const
Get the Title member data.
Definition: Seq_feat_.hpp:1172
const TCit & GetCit(void) const
Get the Cit member data.
Definition: Seq_feat_.hpp:1240
void ResetExcept(void)
Reset Except data member.
Definition: Seq_feat_.hpp:1002
list< CRef< CFeat_id > > m_Ids
Definition: Seq_feat_.hpp:877
void ResetExp_ev(void)
Reset Exp_ev data member.
Definition: Seq_feat_.hpp:1261
const TQual & GetQual(void) const
Get the Qual member data.
Definition: Seq_feat_.hpp:1147
bool IsSetPartial(void) const
incomplete in some way? Check if a value has been assigned to Partial data member.
Definition: Seq_feat_.hpp:943
list< CRef< CUser_object > > m_Exts
Definition: Seq_feat_.hpp:878
const TId & GetId(void) const
Get the Id member data.
Definition: Seq_feat_.hpp:904
bool IsSetXref(void) const
cite other relevant features Check if a value has been assigned to Xref data member.
Definition: Seq_feat_.hpp:1296
TExts & SetExts(void)
Assign a value to Exts data member.
Definition: Seq_feat_.hpp:1483
const TLocation & GetLocation(void) const
Get the Location member data.
Definition: Seq_feat_.hpp:1117
vector< CRef< CDbtag > > m_Dbxref
Definition: Seq_feat_.hpp:874
TData & SetData(void)
Assign a value to Data data member.
Definition: Seq_feat_.hpp:934
CRef< TProduct > m_Product
Definition: Seq_feat_.hpp:866
EExp_ev
evidence for existence of feature
Definition: Seq_feat_.hpp:101
void ResetPseudo(void)
Reset Pseudo data member.
Definition: Seq_feat_.hpp:1358
EExp_ev TExp_ev
Definition: Seq_feat_.hpp:121
CSeq_feat_Base & operator=(const CSeq_feat_Base &)
CRef< TData > m_Data
Definition: Seq_feat_.hpp:862
const TData & GetData(void) const
Get the Data member data.
Definition: Seq_feat_.hpp:925
bool CanGetData(void) const
Check if it is safe to call GetData method.
Definition: Seq_feat_.hpp:919
bool IsSetExcept(void) const
something funny about this? Check if a value has been assigned to Except data member.
Definition: Seq_feat_.hpp:990
TLocation & SetLocation(void)
Assign a value to Location data member.
Definition: Seq_feat_.hpp:1126
const TExcept_text & GetExcept_text(void) const
Get the Except_text member data.
Definition: Seq_feat_.hpp:1405
vector< CRef< CSeqFeatXref > > m_Xref
Definition: Seq_feat_.hpp:873
void ResetData(void)
Reset Data data member.
Definition: Seq_feat_.cpp:85
CPub_set TCit
Definition: Seq_feat_.hpp:120
TPseudo & SetPseudo(void)
Assign a value to Pseudo data member.
Definition: Seq_feat_.hpp:1381
bool IsSetExcept_text(void) const
explain if except=TRUE Check if a value has been assigned to Except_text data member.
Definition: Seq_feat_.hpp:1393
bool CanGetPartial(void) const
Check if it is safe to call GetPartial method.
Definition: Seq_feat_.hpp:949
const TDbxref & GetDbxref(void) const
Get the Dbxref member data.
Definition: Seq_feat_.hpp:1333
CRef< TLocation > m_Location
Definition: Seq_feat_.hpp:867
bool CanGetId(void) const
Check if it is safe to call GetId method.
Definition: Seq_feat_.hpp:898
CRef< TSupport > m_Support
Definition: Seq_feat_.hpp:879
CRef< TId > m_Id
Definition: Seq_feat_.hpp:861
list< CRef< CFeat_id > > TIds
Definition: Seq_feat_.hpp:126
bool IsSetExp_ev(void) const
Check if a value has been assigned to Exp_ev data member.
Definition: Seq_feat_.hpp:1249
bool CanGetLocation(void) const
Check if it is safe to call GetLocation method.
Definition: Seq_feat_.hpp:1111
bool IsSetIds(void) const
set of Ids; will replace 'id' field Check if a value has been assigned to Ids data member.
Definition: Seq_feat_.hpp:1440
bool CanGetExcept_text(void) const
Check if it is safe to call GetExcept_text method.
Definition: Seq_feat_.hpp:1399
bool IsSetId(void) const
Check if a value has been assigned to Id data member.
Definition: Seq_feat_.hpp:892
TPseudo GetPseudo(void) const
Get the Pseudo member data.
Definition: Seq_feat_.hpp:1365
const TProduct & GetProduct(void) const
Get the Product member data.
Definition: Seq_feat_.hpp:1096
bool CanGetExcept(void) const
Check if it is safe to call GetExcept method.
Definition: Seq_feat_.hpp:996
bool IsSetPseudo(void) const
annotated on pseudogene? Check if a value has been assigned to Pseudo data member.
Definition: Seq_feat_.hpp:1346
const TComment & GetComment(void) const
Get the Comment member data.
Definition: Seq_feat_.hpp:1049
bool CanGetExt(void) const
Check if it is safe to call GetExt method.
Definition: Seq_feat_.hpp:1213
CSerialObject Tparent
Definition: Seq_feat_.hpp:90
CSeqFeatData TData
Definition: Seq_feat_.hpp:111
bool IsSetExts(void) const
set of extensions; will replace 'ext' field Check if a value has been assigned to Exts data member.
Definition: Seq_feat_.hpp:1465
bool IsSetCit(void) const
citations for this feature Check if a value has been assigned to Cit data member.
Definition: Seq_feat_.hpp:1228
TTitle & SetTitle(void)
Assign a value to Title data member.
Definition: Seq_feat_.hpp:1195
CRef< TExt > m_Ext
Definition: Seq_feat_.hpp:870
TPartial GetPartial(void) const
Get the Partial member data.
Definition: Seq_feat_.hpp:962
const TSupport & GetSupport(void) const
Get the Support member data.
Definition: Seq_feat_.hpp:1502
void ResetLocation(void)
Reset Location data member.
Definition: Seq_feat_.cpp:122
TExcept GetExcept(void) const
Get the Except member data.
Definition: Seq_feat_.hpp:1009
CSeq_loc TLocation
Definition: Seq_feat_.hpp:116
TComment & SetComment(void)
Assign a value to Comment data member.
Definition: Seq_feat_.hpp:1072
const TXref & GetXref(void) const
Get the Xref member data.
Definition: Seq_feat_.hpp:1308
vector< CRef< CSeqFeatXref > > TXref
Definition: Seq_feat_.hpp:122
DECLARE_INTERNAL_TYPE_INFO()
vector< CRef< CGb_qual > > TQual
Definition: Seq_feat_.hpp:117
bool CanGetProduct(void) const
Check if it is safe to call GetProduct method.
Definition: Seq_feat_.hpp:1090
bool CanGetIds(void) const
Check if it is safe to call GetIds method.
Definition: Seq_feat_.hpp:1446
TExp_ev & SetExp_ev(void)
Assign a value to Exp_ev data member.
Definition: Seq_feat_.hpp:1284
bool IsSetDbxref(void) const
support for xref to other databases Check if a value has been assigned to Dbxref data member.
Definition: Seq_feat_.hpp:1321
Tparent::CMemberIndex< E_memberIndex, 20 > TmemberIndex
Definition: Seq_feat_.hpp:153
TQual & SetQual(void)
Assign a value to Qual data member.
Definition: Seq_feat_.hpp:1153
string TExcept_text
Definition: Seq_feat_.hpp:125
bool IsSetProduct(void) const
product of process Check if a value has been assigned to Product data member.
Definition: Seq_feat_.hpp:1084
const TExt & GetExt(void) const
Get the Ext member data.
Definition: Seq_feat_.hpp:1219
CSeq_loc TProduct
Definition: Seq_feat_.hpp:115
CSeqFeatSupport TSupport
Definition: Seq_feat_.hpp:128
TExcept_text & SetExcept_text(void)
Assign a value to Except_text data member.
Definition: Seq_feat_.hpp:1428
CSeq_feat_Base(const CSeq_feat_Base &)
TExp_ev GetExp_ev(void) const
Get the Exp_ev member data.
Definition: Seq_feat_.hpp:1268
bool CanGetTitle(void) const
Check if it is safe to call GetTitle method.
Definition: Seq_feat_.hpp:1166
bool CanGetPseudo(void) const
Check if it is safe to call GetPseudo method.
Definition: Seq_feat_.hpp:1352
bool IsSetLocation(void) const
feature made from Check if a value has been assigned to Location data member.
Definition: Seq_feat_.hpp:1105
bool CanGetComment(void) const
Check if it is safe to call GetComment method.
Definition: Seq_feat_.hpp:1043
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)
string GetProduct(const CProt_ref &prot_ref)
void SetPartial(CSeq_loc &loc, CRef< CSeq_feat > feat, CSeq_loc::TStrand strand, bool partial_start, bool partial_stop)
void SetDbxref(objects::CBioSource &src, string db, objects::CObject_id::TId id)
static void SetTitle(CRef< CSeq_entry > entry, string title)
Modified on Mon Apr 22 04:07:33 2024 by modify_doxy.py rev. 669887