NCBI C++ ToolKit
INSDReference_.hpp
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27 
28 /// @file INSDReference_.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/insdseq/insdseq.asn">insdseq.asn</a>
34 /// and additional tune-up parameters:
35 /// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/insdseq/insdseq.def">insdseq.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_INSDSEQ_INSDREFERENCE_BASE_HPP
42 #define OBJECTS_INSDSEQ_INSDREFERENCE_BASE_HPP
43 
44 // standard includes
45 #include <serial/serialbase.hpp>
46 
47 // generated includes
48 #include <list>
49 #include <string>
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 CINSDXref;
63 
64 
65 // generated classes
66 
67 
68 /** @addtogroup dataspec_INSD_INSDSeq
69  *
70  * @{
71  */
72 
73 /////////////////////////////////////////////////////////////////////////////
74 /// INSDReference_position contains a string value indicating the
75 /// basepair span(s) to which a reference applies. The allowable
76 /// formats are:
77 ///
78 /// X..Y : Where X and Y are integers separated by two periods,
79 /// X >= 1 , Y <= sequence length, and X <= Y
80 ///
81 /// Multiple basepair spans can exist, separated by a
82 /// semi-colon and a space. For example : 10..20; 100..500
83 ///
84 /// sites : The string literal 'sites', indicating that a reference
85 /// provides sequence annotation information, but the specific
86 /// basepair spans are either not captured, or were too numerous
87 /// to record.
88 ///
89 /// The 'sites' literal string is singly occuring, and
90 /// cannot be used in conjunction with any X..Y basepair spans.
91 ///
92 /// 'sites' is a convention utilized by GenBank, and might
93 /// not be presented in XML provided by EMBL and DDBJ.
94 ///
95 /// References that lack an INSDReference_position element are not
96 /// attributed to any particular region of the sequence.
97 ///
98 /// CINSDReference_Base --
99 ///
100 
102 {
104 public:
105  // constructor
106  CINSDReference_Base(void);
107  // destructor
108  virtual ~CINSDReference_Base(void);
109 
110  // type info
112 
113  // types
114  typedef string TReference;
115  typedef string TPosition;
116  typedef list< CINSDAuthor > TAuthors;
117  typedef string TConsortium;
118  typedef string TTitle;
119  typedef string TJournal;
120  typedef list< CRef< CINSDXref > > TXref;
121  typedef int TPubmed;
122  typedef string TRemark;
123 
124  // member index
125  enum class E_memberIndex {
126  e__allMandatory = 0,
127  e_reference,
128  e_position,
129  e_authors,
130  e_consortium,
131  e_title,
132  e_journal,
133  e_xref,
134  e_pubmed,
135  e_remark
136  };
138 
139  // getters
140  // setters
141 
142  /// Check if a value has been assigned to Reference data member.
143  ///
144  /// Data member Reference is mandatory;
145  /// its type is defined as 'typedef string TReference'
146  /// @return
147  /// - true, if a value has been assigned.
148  /// - false, otherwise.
149  bool IsSetReference(void) const;
150 
151  /// Check if it is safe to call GetReference method.
152  ///
153  /// @return
154  /// - true, if the data member is getatable.
155  /// - false, otherwise.
156  bool CanGetReference(void) const;
157 
158  /// Reset Reference data member.
159  void ResetReference(void);
160 
161  /// Get the Reference member data.
162  ///
163  /// @return
164  /// Reference to the member data.
165  const TReference& GetReference(void) const;
166 
167  /// Assign a value to Reference data member.
168  ///
169  /// @param value
170  /// Value to assign
171  void SetReference(const TReference& value);
172  void SetReference(TReference&& value);
173 
174  /// Assign a value to Reference data member.
175  ///
176  /// @return
177  /// Reference to the data value.
178  TReference& SetReference(void);
179 
180  /// Check if a value has been assigned to Position data member.
181  ///
182  /// Data member Position is optional;
183  /// its type is defined as 'typedef string TPosition'
184  /// @return
185  /// - true, if a value has been assigned.
186  /// - false, otherwise.
187  bool IsSetPosition(void) const;
188 
189  /// Check if it is safe to call GetPosition method.
190  ///
191  /// @return
192  /// - true, if the data member is getatable.
193  /// - false, otherwise.
194  bool CanGetPosition(void) const;
195 
196  /// Reset Position data member.
197  void ResetPosition(void);
198 
199  /// Get the Position member data.
200  ///
201  /// @return
202  /// Reference to the member data.
203  const TPosition& GetPosition(void) const;
204 
205  /// Assign a value to Position data member.
206  ///
207  /// @param value
208  /// Value to assign
209  void SetPosition(const TPosition& value);
210  void SetPosition(TPosition&& value);
211 
212  /// Assign a value to Position data member.
213  ///
214  /// @return
215  /// Reference to the data value.
216  TPosition& SetPosition(void);
217 
218  /// Check if a value has been assigned to Authors data member.
219  ///
220  /// Data member Authors is optional;
221  /// its type is defined as 'typedef list< CINSDAuthor > TAuthors'
222  /// @return
223  /// - true, if a value has been assigned.
224  /// - false, otherwise.
225  bool IsSetAuthors(void) const;
226 
227  /// Check if it is safe to call GetAuthors method.
228  ///
229  /// @return
230  /// - true, if the data member is getatable.
231  /// - false, otherwise.
232  bool CanGetAuthors(void) const;
233 
234  /// Reset Authors data member.
235  void ResetAuthors(void);
236 
237  /// Get the Authors member data.
238  ///
239  /// @return
240  /// Reference to the member data.
241  const TAuthors& GetAuthors(void) const;
242 
243  /// Assign a value to Authors data member.
244  ///
245  /// @return
246  /// Reference to the data value.
247  TAuthors& SetAuthors(void);
248 
249  /// Check if a value has been assigned to Consortium data member.
250  ///
251  /// Data member Consortium is optional;
252  /// its type is defined as 'typedef string TConsortium'
253  /// @return
254  /// - true, if a value has been assigned.
255  /// - false, otherwise.
256  bool IsSetConsortium(void) const;
257 
258  /// Check if it is safe to call GetConsortium method.
259  ///
260  /// @return
261  /// - true, if the data member is getatable.
262  /// - false, otherwise.
263  bool CanGetConsortium(void) const;
264 
265  /// Reset Consortium data member.
266  void ResetConsortium(void);
267 
268  /// Get the Consortium member data.
269  ///
270  /// @return
271  /// Reference to the member data.
272  const TConsortium& GetConsortium(void) const;
273 
274  /// Assign a value to Consortium data member.
275  ///
276  /// @param value
277  /// Value to assign
278  void SetConsortium(const TConsortium& value);
279  void SetConsortium(TConsortium&& value);
280 
281  /// Assign a value to Consortium data member.
282  ///
283  /// @return
284  /// Reference to the data value.
285  TConsortium& SetConsortium(void);
286 
287  /// Check if a value has been assigned to Title data member.
288  ///
289  /// Data member Title is optional;
290  /// its type is defined as 'typedef string TTitle'
291  /// @return
292  /// - true, if a value has been assigned.
293  /// - false, otherwise.
294  bool IsSetTitle(void) const;
295 
296  /// Check if it is safe to call GetTitle method.
297  ///
298  /// @return
299  /// - true, if the data member is getatable.
300  /// - false, otherwise.
301  bool CanGetTitle(void) const;
302 
303  /// Reset Title data member.
304  void ResetTitle(void);
305 
306  /// Get the Title member data.
307  ///
308  /// @return
309  /// Reference to the member data.
310  const TTitle& GetTitle(void) const;
311 
312  /// Assign a value to Title data member.
313  ///
314  /// @param value
315  /// Value to assign
316  void SetTitle(const TTitle& value);
317  void SetTitle(TTitle&& value);
318 
319  /// Assign a value to Title data member.
320  ///
321  /// @return
322  /// Reference to the data value.
323  TTitle& SetTitle(void);
324 
325  /// Check if a value has been assigned to Journal data member.
326  ///
327  /// Data member Journal is mandatory;
328  /// its type is defined as 'typedef string TJournal'
329  /// @return
330  /// - true, if a value has been assigned.
331  /// - false, otherwise.
332  bool IsSetJournal(void) const;
333 
334  /// Check if it is safe to call GetJournal method.
335  ///
336  /// @return
337  /// - true, if the data member is getatable.
338  /// - false, otherwise.
339  bool CanGetJournal(void) const;
340 
341  /// Reset Journal data member.
342  void ResetJournal(void);
343 
344  /// Get the Journal member data.
345  ///
346  /// @return
347  /// Reference to the member data.
348  const TJournal& GetJournal(void) const;
349 
350  /// Assign a value to Journal data member.
351  ///
352  /// @param value
353  /// Value to assign
354  void SetJournal(const TJournal& value);
355  void SetJournal(TJournal&& value);
356 
357  /// Assign a value to Journal data member.
358  ///
359  /// @return
360  /// Reference to the data value.
361  TJournal& SetJournal(void);
362 
363  /// Check if a value has been assigned to Xref data member.
364  ///
365  /// Data member Xref is optional;
366  /// its type is defined as 'typedef list< CRef< CINSDXref > > TXref'
367  /// @return
368  /// - true, if a value has been assigned.
369  /// - false, otherwise.
370  bool IsSetXref(void) const;
371 
372  /// Check if it is safe to call GetXref method.
373  ///
374  /// @return
375  /// - true, if the data member is getatable.
376  /// - false, otherwise.
377  bool CanGetXref(void) const;
378 
379  /// Reset Xref data member.
380  void ResetXref(void);
381 
382  /// Get the Xref member data.
383  ///
384  /// @return
385  /// Reference to the member data.
386  const TXref& GetXref(void) const;
387 
388  /// Assign a value to Xref data member.
389  ///
390  /// @return
391  /// Reference to the data value.
392  TXref& SetXref(void);
393 
394  /// Check if a value has been assigned to Pubmed data member.
395  ///
396  /// Data member Pubmed is optional;
397  /// its type is defined as 'typedef int TPubmed'
398  /// @return
399  /// - true, if a value has been assigned.
400  /// - false, otherwise.
401  bool IsSetPubmed(void) const;
402 
403  /// Check if it is safe to call GetPubmed method.
404  ///
405  /// @return
406  /// - true, if the data member is getatable.
407  /// - false, otherwise.
408  bool CanGetPubmed(void) const;
409 
410  /// Reset Pubmed data member.
411  void ResetPubmed(void);
412 
413  /// Get the Pubmed member data.
414  ///
415  /// @return
416  /// Copy of the member data.
417  TPubmed GetPubmed(void) const;
418 
419  /// Assign a value to Pubmed data member.
420  ///
421  /// @param value
422  /// Value to assign
423  void SetPubmed(TPubmed value);
424 
425  /// Assign a value to Pubmed data member.
426  ///
427  /// @return
428  /// Reference to the data value.
429  TPubmed& SetPubmed(void);
430 
431  /// Check if a value has been assigned to Remark data member.
432  ///
433  /// Data member Remark is optional;
434  /// its type is defined as 'typedef string TRemark'
435  /// @return
436  /// - true, if a value has been assigned.
437  /// - false, otherwise.
438  bool IsSetRemark(void) const;
439 
440  /// Check if it is safe to call GetRemark method.
441  ///
442  /// @return
443  /// - true, if the data member is getatable.
444  /// - false, otherwise.
445  bool CanGetRemark(void) const;
446 
447  /// Reset Remark data member.
448  void ResetRemark(void);
449 
450  /// Get the Remark member data.
451  ///
452  /// @return
453  /// Reference to the member data.
454  const TRemark& GetRemark(void) const;
455 
456  /// Assign a value to Remark data member.
457  ///
458  /// @param value
459  /// Value to assign
460  void SetRemark(const TRemark& value);
461  void SetRemark(TRemark&& value);
462 
463  /// Assign a value to Remark data member.
464  ///
465  /// @return
466  /// Reference to the data value.
467  TRemark& SetRemark(void);
468 
469  /// Reset the whole object
470  virtual void Reset(void);
471 
472 
473 private:
474  // Prohibit copy constructor and assignment operator
477 
478  // data
479  Uint4 m_set_State[1];
480  string m_Reference;
481  string m_Position;
482  list< CINSDAuthor > m_Authors;
483  string m_Consortium;
484  string m_Title;
485  string m_Journal;
486  list< CRef< CINSDXref > > m_Xref;
487  int m_Pubmed;
488  string m_Remark;
489 };
490 
491 /* @} */
492 
493 
494 
495 
496 
497 ///////////////////////////////////////////////////////////
498 ///////////////////// inline methods //////////////////////
499 ///////////////////////////////////////////////////////////
500 inline
502 {
503  return ((m_set_State[0] & 0x3) != 0);
504 }
505 
506 inline
508 {
509  return IsSetReference();
510 }
511 
512 inline
514 {
515  if (!CanGetReference()) {
516  ThrowUnassigned(0);
517  }
518  return m_Reference;
519 }
520 
521 inline
523 {
524  m_Reference = value;
525  m_set_State[0] |= 0x3;
526 }
527 
528 inline
530 {
531  m_Reference = std::forward<CINSDReference_Base::TReference>(value);
532  m_set_State[0] |= 0x3;
533 }
534 
535 inline
537 {
538 #ifdef _DEBUG
539  if (!IsSetReference()) {
541  }
542 #endif
543  m_set_State[0] |= 0x1;
544  return m_Reference;
545 }
546 
547 inline
549 {
550  return ((m_set_State[0] & 0xc) != 0);
551 }
552 
553 inline
555 {
556  return IsSetPosition();
557 }
558 
559 inline
561 {
562  if (!CanGetPosition()) {
563  ThrowUnassigned(1);
564  }
565  return m_Position;
566 }
567 
568 inline
570 {
571  m_Position = value;
572  m_set_State[0] |= 0xc;
573 }
574 
575 inline
577 {
578  m_Position = std::forward<CINSDReference_Base::TPosition>(value);
579  m_set_State[0] |= 0xc;
580 }
581 
582 inline
584 {
585 #ifdef _DEBUG
586  if (!IsSetPosition()) {
588  }
589 #endif
590  m_set_State[0] |= 0x4;
591  return m_Position;
592 }
593 
594 inline
596 {
597  return ((m_set_State[0] & 0x30) != 0);
598 }
599 
600 inline
602 {
603  return true;
604 }
605 
606 inline
608 {
609  return m_Authors;
610 }
611 
612 inline
614 {
615  m_set_State[0] |= 0x10;
616  return m_Authors;
617 }
618 
619 inline
621 {
622  return ((m_set_State[0] & 0xc0) != 0);
623 }
624 
625 inline
627 {
628  return IsSetConsortium();
629 }
630 
631 inline
633 {
634  if (!CanGetConsortium()) {
635  ThrowUnassigned(3);
636  }
637  return m_Consortium;
638 }
639 
640 inline
642 {
644  m_set_State[0] |= 0xc0;
645 }
646 
647 inline
649 {
650  m_Consortium = std::forward<CINSDReference_Base::TConsortium>(value);
651  m_set_State[0] |= 0xc0;
652 }
653 
654 inline
656 {
657 #ifdef _DEBUG
658  if (!IsSetConsortium()) {
660  }
661 #endif
662  m_set_State[0] |= 0x40;
663  return m_Consortium;
664 }
665 
666 inline
668 {
669  return ((m_set_State[0] & 0x300) != 0);
670 }
671 
672 inline
674 {
675  return IsSetTitle();
676 }
677 
678 inline
680 {
681  if (!CanGetTitle()) {
682  ThrowUnassigned(4);
683  }
684  return m_Title;
685 }
686 
687 inline
689 {
690  m_Title = value;
691  m_set_State[0] |= 0x300;
692 }
693 
694 inline
696 {
697  m_Title = std::forward<CINSDReference_Base::TTitle>(value);
698  m_set_State[0] |= 0x300;
699 }
700 
701 inline
703 {
704 #ifdef _DEBUG
705  if (!IsSetTitle()) {
707  }
708 #endif
709  m_set_State[0] |= 0x100;
710  return m_Title;
711 }
712 
713 inline
715 {
716  return ((m_set_State[0] & 0xc00) != 0);
717 }
718 
719 inline
721 {
722  return IsSetJournal();
723 }
724 
725 inline
727 {
728  if (!CanGetJournal()) {
729  ThrowUnassigned(5);
730  }
731  return m_Journal;
732 }
733 
734 inline
736 {
737  m_Journal = value;
738  m_set_State[0] |= 0xc00;
739 }
740 
741 inline
743 {
744  m_Journal = std::forward<CINSDReference_Base::TJournal>(value);
745  m_set_State[0] |= 0xc00;
746 }
747 
748 inline
750 {
751 #ifdef _DEBUG
752  if (!IsSetJournal()) {
754  }
755 #endif
756  m_set_State[0] |= 0x400;
757  return m_Journal;
758 }
759 
760 inline
762 {
763  return ((m_set_State[0] & 0x3000) != 0);
764 }
765 
766 inline
768 {
769  return true;
770 }
771 
772 inline
774 {
775  return m_Xref;
776 }
777 
778 inline
780 {
781  m_set_State[0] |= 0x1000;
782  return m_Xref;
783 }
784 
785 inline
787 {
788  return ((m_set_State[0] & 0xc000) != 0);
789 }
790 
791 inline
793 {
794  return IsSetPubmed();
795 }
796 
797 inline
799 {
800  m_Pubmed = 0;
801  m_set_State[0] &= ~0xc000;
802 }
803 
804 inline
806 {
807  if (!CanGetPubmed()) {
808  ThrowUnassigned(7);
809  }
810  return m_Pubmed;
811 }
812 
813 inline
815 {
816  m_Pubmed = value;
817  m_set_State[0] |= 0xc000;
818 }
819 
820 inline
822 {
823 #ifdef _DEBUG
824  if (!IsSetPubmed()) {
825  memset(&m_Pubmed,UnassignedByte(),sizeof(m_Pubmed));
826  }
827 #endif
828  m_set_State[0] |= 0x4000;
829  return m_Pubmed;
830 }
831 
832 inline
834 {
835  return ((m_set_State[0] & 0x30000) != 0);
836 }
837 
838 inline
840 {
841  return IsSetRemark();
842 }
843 
844 inline
846 {
847  if (!CanGetRemark()) {
848  ThrowUnassigned(8);
849  }
850  return m_Remark;
851 }
852 
853 inline
855 {
856  m_Remark = value;
857  m_set_State[0] |= 0x30000;
858 }
859 
860 inline
862 {
863  m_Remark = std::forward<CINSDReference_Base::TRemark>(value);
864  m_set_State[0] |= 0x30000;
865 }
866 
867 inline
869 {
870 #ifdef _DEBUG
871  if (!IsSetRemark()) {
873  }
874 #endif
875  m_set_State[0] |= 0x10000;
876  return m_Remark;
877 }
878 
879 ///////////////////////////////////////////////////////////
880 ////////////////// end of inline methods //////////////////
881 ///////////////////////////////////////////////////////////
882 
883 
884 
885 
886 
887 END_objects_SCOPE // namespace ncbi::objects::
888 
890 
891 
892 #endif // OBJECTS_INSDSEQ_INSDREFERENCE_BASE_HPP
User-defined methods of the data storage class.
INSDReference_position contains a string value indicating the basepair span(s) to which a reference a...
CINSDXref –.
Definition: INSDXref.hpp:66
Base class for all serializable objects.
Definition: serialbase.hpp:150
static char UnassignedByte(void)
Definition: serialbase.hpp:181
void ThrowUnassigned(TMemberIndex index) const
static string UnassignedString(void)
Definition: serialbase.hpp:175
NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)
Definition: seqtitle.cpp:106
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_INSDSEQ_EXPORT
Definition: ncbi_export.h:568
bool IsSetJournal(void) const
Check if a value has been assigned to Journal data member.
bool CanGetPosition(void) const
Check if it is safe to call GetPosition method.
TPubmed & SetPubmed(void)
Assign a value to Pubmed data member.
TRemark & SetRemark(void)
Assign a value to Remark data member.
TPubmed GetPubmed(void) const
Get the Pubmed member data.
bool IsSetPosition(void) const
Check if a value has been assigned to Position data member.
TXref & SetXref(void)
Assign a value to Xref data member.
bool CanGetConsortium(void) const
Check if it is safe to call GetConsortium method.
TReference & SetReference(void)
Assign a value to Reference data member.
bool IsSetReference(void) const
Check if a value has been assigned to Reference data member.
bool CanGetRemark(void) const
Check if it is safe to call GetRemark method.
void ResetPubmed(void)
Reset Pubmed data member.
bool IsSetTitle(void) const
Check if a value has been assigned to Title data member.
list< CINSDAuthor > m_Authors
TTitle & SetTitle(void)
Assign a value to Title data member.
bool CanGetJournal(void) const
Check if it is safe to call GetJournal method.
const TConsortium & GetConsortium(void) const
Get the Consortium member data.
bool IsSetConsortium(void) const
Check if a value has been assigned to Consortium data member.
const TAuthors & GetAuthors(void) const
Get the Authors member data.
TPosition & SetPosition(void)
Assign a value to Position data member.
bool IsSetAuthors(void) const
Check if a value has been assigned to Authors data member.
TAuthors & SetAuthors(void)
Assign a value to Authors data member.
const TJournal & GetJournal(void) const
Get the Journal member data.
const TRemark & GetRemark(void) const
Get the Remark member data.
const TPosition & GetPosition(void) const
Get the Position member data.
bool CanGetXref(void) const
Check if it is safe to call GetXref method.
list< CINSDAuthor > TAuthors
bool CanGetPubmed(void) const
Check if it is safe to call GetPubmed method.
CINSDReference_Base & operator=(const CINSDReference_Base &)
bool IsSetPubmed(void) const
Check if a value has been assigned to Pubmed data member.
bool IsSetRemark(void) const
Check if a value has been assigned to Remark data member.
TJournal & SetJournal(void)
Assign a value to Journal data member.
const TXref & GetXref(void) const
Get the Xref member data.
bool CanGetTitle(void) const
Check if it is safe to call GetTitle method.
list< CRef< CINSDXref > > m_Xref
const TTitle & GetTitle(void) const
Get the Title member data.
TConsortium & SetConsortium(void)
Assign a value to Consortium data member.
bool CanGetAuthors(void) const
Check if it is safe to call GetAuthors method.
bool CanGetReference(void) const
Check if it is safe to call GetReference method.
list< CRef< CINSDXref > > TXref
const TReference & GetReference(void) const
Get the Reference member data.
bool IsSetXref(void) const
Check if a value has been assigned to Xref data member.
Tparent::CMemberIndex< E_memberIndex, 10 > TmemberIndex
CINSDReference_Base(const CINSDReference_Base &)
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
static void SetTitle(CRef< CSeq_entry > entry, string title)
Modified on Mon May 27 04:40:50 2024 by modify_doxy.py rev. 669887