NCBI C++ ToolKit
GC_AssemblyDesc_.hpp
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27 
28 /// @file GC_AssemblyDesc_.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/genomecoll/genome_collection.asn">genome_collection.asn</a>
34 /// and additional tune-up parameters:
35 /// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/genomecoll/genome_collection.def">genome_collection.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_GENOMECOLL_GC_ASSEMBLYDESC_BASE_HPP
42 #define OBJECTS_GENOMECOLL_GC_ASSEMBLYDESC_BASE_HPP
43 
44 // standard includes
45 #include <serial/serialbase.hpp>
46 
47 // generated includes
48 #include <list>
49 #include <string>
50 
52 
53 #ifndef BEGIN_objects_SCOPE
54 # define BEGIN_objects_SCOPE BEGIN_SCOPE(objects)
55 # define END_objects_SCOPE END_SCOPE(objects)
56 #endif
57 BEGIN_objects_SCOPE // namespace ncbi::objects::
58 
59 
60 // forward declarations
61 class CDate;
62 class CGC_DbTagAlias;
63 class CGC_Project;
64 class CSeq_annot;
65 class CSeq_descr;
66 
67 
68 // generated classes
69 
70 
71 /** @addtogroup dataspec_NCBI_GenomeCollection
72  *
73  * @{
74  */
75 
76 /////////////////////////////////////////////////////////////////////////////
77 ///
78 /// CGC_AssemblyDesc_Base --
79 ///
80 
82 {
84 public:
85  // constructor
87  // destructor
88  virtual ~CGC_AssemblyDesc_Base(void);
89 
90  // type info
92 
93  /// release type: RefSeq / GenBank.
95  eRelease_type_genbank = 1,
96  eRelease_type_refseq = 2
97  };
98 
99  /// Access to ERelease_type's attributes (values, names) as defined in spec
100  static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(ERelease_type)(void);
101 
102  /// release status (numeric values have gaps for possible additional states
104  eRelease_status_new = 0,
105  eRelease_status_gpipe = 5,
106  eRelease_status_public = 10,
107  eRelease_status_suppressed = 15,
108  eRelease_status_hup = 100,
109  eRelease_status_withdrawn = 105
110  };
111 
112  /// Access to ERelease_status's attributes (values, names) as defined in spec
113  static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(ERelease_status)(void);
114 
115  /// release level: Most of releases are major
117  eRelease_level_major = 0,
118  eRelease_level_patch = 1,
119  eRelease_level_minor = 2,
120  eRelease_level_other = 255 ///< stopper
121  };
122 
123  /// Access to ERelease_level's attributes (values, names) as defined in spec
124  static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(ERelease_level)(void);
125 
126  // types
127  typedef list< CRef< CGC_Project > > TProjects;
128  typedef string TName;
129  typedef string TSubmitter_name;
130  typedef string TDisplay_name;
132  typedef string TFilesafe_name;
133  typedef string TWgs_acc_prefix;
134  typedef int TWgs_acc_number;
135  typedef int TRelease_type;
136  typedef int TRelease_status;
137  typedef list< CRef< CSeq_annot > > TAnnot;
138  typedef list< CRef< CGC_DbTagAlias > > TSynonyms;
141  typedef bool TPartial;
142  typedef double TCoverage;
143  typedef int TRelease_level;
145 
146  // member index
147  enum class E_memberIndex {
148  e__allMandatory = 0,
149  e_projects,
150  e_name,
151  e_submitter_name,
152  e_display_name,
153  e_long_name,
154  e_filesafe_name,
155  e_wgs_acc_prefix,
156  e_wgs_acc_number,
157  e_release_type,
158  e_release_status,
159  e_annot,
160  e_synonyms,
161  e_submitter_date,
162  e_descr,
163  e_partial,
164  e_coverage,
165  e_release_level,
166  e_submitter_organization
167  };
169 
170  // getters
171  // setters
172 
173  /// project ID for this genome
174  /// this is the ID for this asssembly and may reflect the submitter/source
175  /// Check if a value has been assigned to Projects data member.
176  ///
177  /// Data member Projects is optional;
178  /// its type is defined as 'typedef list< CRef< CGC_Project > > TProjects'
179  /// @return
180  /// - true, if a value has been assigned.
181  /// - false, otherwise.
182  bool IsSetProjects(void) const;
183 
184  /// Check if it is safe to call GetProjects method.
185  ///
186  /// @return
187  /// - true, if the data member is getatable.
188  /// - false, otherwise.
189  bool CanGetProjects(void) const;
190 
191  /// Reset Projects data member.
192  void ResetProjects(void);
193 
194  /// Get the Projects member data.
195  ///
196  /// @return
197  /// Reference to the member data.
198  const TProjects& GetProjects(void) const;
199 
200  /// Assign a value to Projects data member.
201  ///
202  /// @return
203  /// Reference to the data value.
204  TProjects& SetProjects(void);
205 
206  /// Names of the assembly
207  /// Check if a value has been assigned to Name data member.
208  ///
209  /// Data member Name is optional;
210  /// its type is defined as 'typedef string TName'
211  /// @return
212  /// - true, if a value has been assigned.
213  /// - false, otherwise.
214  bool IsSetName(void) const;
215 
216  /// Check if it is safe to call GetName method.
217  ///
218  /// @return
219  /// - true, if the data member is getatable.
220  /// - false, otherwise.
221  bool CanGetName(void) const;
222 
223  /// Reset Name data member.
224  void ResetName(void);
225 
226  /// Get the Name member data.
227  ///
228  /// @return
229  /// Reference to the member data.
230  const TName& GetName(void) const;
231 
232  /// Assign a value to Name data member.
233  ///
234  /// @param value
235  /// Value to assign
236  void SetName(const TName& value);
237  void SetName(TName&& value);
238 
239  /// Assign a value to Name data member.
240  ///
241  /// @return
242  /// Reference to the data value.
243  TName& SetName(void);
244 
245  /// Check if a value has been assigned to Submitter_name data member.
246  ///
247  /// Data member Submitter_name is optional;
248  /// its type is defined as 'typedef string TSubmitter_name'
249  /// @return
250  /// - true, if a value has been assigned.
251  /// - false, otherwise.
252  bool IsSetSubmitter_name(void) const;
253 
254  /// Check if it is safe to call GetSubmitter_name method.
255  ///
256  /// @return
257  /// - true, if the data member is getatable.
258  /// - false, otherwise.
259  bool CanGetSubmitter_name(void) const;
260 
261  /// Reset Submitter_name data member.
262  void ResetSubmitter_name(void);
263 
264  /// Get the Submitter_name member data.
265  ///
266  /// @return
267  /// Reference to the member data.
268  const TSubmitter_name& GetSubmitter_name(void) const;
269 
270  /// Assign a value to Submitter_name data member.
271  ///
272  /// @param value
273  /// Value to assign
274  void SetSubmitter_name(const TSubmitter_name& value);
275  void SetSubmitter_name(TSubmitter_name&& value);
276 
277  /// Assign a value to Submitter_name data member.
278  ///
279  /// @return
280  /// Reference to the data value.
281  TSubmitter_name& SetSubmitter_name(void);
282 
283  /// Check if a value has been assigned to Display_name data member.
284  ///
285  /// Data member Display_name is optional;
286  /// its type is defined as 'typedef string TDisplay_name'
287  /// @return
288  /// - true, if a value has been assigned.
289  /// - false, otherwise.
290  bool IsSetDisplay_name(void) const;
291 
292  /// Check if it is safe to call GetDisplay_name method.
293  ///
294  /// @return
295  /// - true, if the data member is getatable.
296  /// - false, otherwise.
297  bool CanGetDisplay_name(void) const;
298 
299  /// Reset Display_name data member.
300  void ResetDisplay_name(void);
301 
302  /// Get the Display_name member data.
303  ///
304  /// @return
305  /// Reference to the member data.
306  const TDisplay_name& GetDisplay_name(void) const;
307 
308  /// Assign a value to Display_name data member.
309  ///
310  /// @param value
311  /// Value to assign
312  void SetDisplay_name(const TDisplay_name& value);
313  void SetDisplay_name(TDisplay_name&& value);
314 
315  /// Assign a value to Display_name data member.
316  ///
317  /// @return
318  /// Reference to the data value.
319  TDisplay_name& SetDisplay_name(void);
320 
321  /// Check if a value has been assigned to Long_name data member.
322  ///
323  /// Data member Long_name is optional;
324  /// its type is defined as 'typedef CStringUTF8 TLong_name'
325  /// @return
326  /// - true, if a value has been assigned.
327  /// - false, otherwise.
328  bool IsSetLong_name(void) const;
329 
330  /// Check if it is safe to call GetLong_name method.
331  ///
332  /// @return
333  /// - true, if the data member is getatable.
334  /// - false, otherwise.
335  bool CanGetLong_name(void) const;
336 
337  /// Reset Long_name data member.
338  void ResetLong_name(void);
339 
340  /// Get the Long_name member data.
341  ///
342  /// @return
343  /// Reference to the member data.
344  const TLong_name& GetLong_name(void) const;
345 
346  /// Assign a value to Long_name data member.
347  ///
348  /// @param value
349  /// Value to assign
350  void SetLong_name(const TLong_name& value);
351  void SetLong_name(TLong_name&& value);
352 
353  /// Assign a value to Long_name data member.
354  ///
355  /// @return
356  /// Reference to the data value.
357  TLong_name& SetLong_name(void);
358 
359  /// Check if a value has been assigned to Filesafe_name data member.
360  ///
361  /// Data member Filesafe_name is optional;
362  /// its type is defined as 'typedef string TFilesafe_name'
363  /// @return
364  /// - true, if a value has been assigned.
365  /// - false, otherwise.
366  bool IsSetFilesafe_name(void) const;
367 
368  /// Check if it is safe to call GetFilesafe_name method.
369  ///
370  /// @return
371  /// - true, if the data member is getatable.
372  /// - false, otherwise.
373  bool CanGetFilesafe_name(void) const;
374 
375  /// Reset Filesafe_name data member.
376  void ResetFilesafe_name(void);
377 
378  /// Get the Filesafe_name member data.
379  ///
380  /// @return
381  /// Reference to the member data.
382  const TFilesafe_name& GetFilesafe_name(void) const;
383 
384  /// Assign a value to Filesafe_name data member.
385  ///
386  /// @param value
387  /// Value to assign
388  void SetFilesafe_name(const TFilesafe_name& value);
389  void SetFilesafe_name(TFilesafe_name&& value);
390 
391  /// Assign a value to Filesafe_name data member.
392  ///
393  /// @return
394  /// Reference to the data value.
395  TFilesafe_name& SetFilesafe_name(void);
396 
397  /// Check if a value has been assigned to Wgs_acc_prefix data member.
398  ///
399  /// Data member Wgs_acc_prefix is optional;
400  /// its type is defined as 'typedef string TWgs_acc_prefix'
401  /// @return
402  /// - true, if a value has been assigned.
403  /// - false, otherwise.
404  bool IsSetWgs_acc_prefix(void) const;
405 
406  /// Check if it is safe to call GetWgs_acc_prefix method.
407  ///
408  /// @return
409  /// - true, if the data member is getatable.
410  /// - false, otherwise.
411  bool CanGetWgs_acc_prefix(void) const;
412 
413  /// Reset Wgs_acc_prefix data member.
414  void ResetWgs_acc_prefix(void);
415 
416  /// Get the Wgs_acc_prefix member data.
417  ///
418  /// @return
419  /// Reference to the member data.
420  const TWgs_acc_prefix& GetWgs_acc_prefix(void) const;
421 
422  /// Assign a value to Wgs_acc_prefix data member.
423  ///
424  /// @param value
425  /// Value to assign
426  void SetWgs_acc_prefix(const TWgs_acc_prefix& value);
427  void SetWgs_acc_prefix(TWgs_acc_prefix&& value);
428 
429  /// Assign a value to Wgs_acc_prefix data member.
430  ///
431  /// @return
432  /// Reference to the data value.
433  TWgs_acc_prefix& SetWgs_acc_prefix(void);
434 
435  /// Check if a value has been assigned to Wgs_acc_number data member.
436  ///
437  /// Data member Wgs_acc_number is optional;
438  /// its type is defined as 'typedef int TWgs_acc_number'
439  /// @return
440  /// - true, if a value has been assigned.
441  /// - false, otherwise.
442  bool IsSetWgs_acc_number(void) const;
443 
444  /// Check if it is safe to call GetWgs_acc_number method.
445  ///
446  /// @return
447  /// - true, if the data member is getatable.
448  /// - false, otherwise.
449  bool CanGetWgs_acc_number(void) const;
450 
451  /// Reset Wgs_acc_number data member.
452  void ResetWgs_acc_number(void);
453 
454  /// Get the Wgs_acc_number member data.
455  ///
456  /// @return
457  /// Copy of the member data.
458  TWgs_acc_number GetWgs_acc_number(void) const;
459 
460  /// Assign a value to Wgs_acc_number data member.
461  ///
462  /// @param value
463  /// Value to assign
464  void SetWgs_acc_number(TWgs_acc_number value);
465 
466  /// Assign a value to Wgs_acc_number data member.
467  ///
468  /// @return
469  /// Reference to the data value.
470  TWgs_acc_number& SetWgs_acc_number(void);
471 
472  /// Check if a value has been assigned to Release_type data member.
473  ///
474  /// Data member Release_type is optional;
475  /// its type is defined as 'typedef int TRelease_type'
476  /// @return
477  /// - true, if a value has been assigned.
478  /// - false, otherwise.
479  bool IsSetRelease_type(void) const;
480 
481  /// Check if it is safe to call GetRelease_type method.
482  ///
483  /// @return
484  /// - true, if the data member is getatable.
485  /// - false, otherwise.
486  bool CanGetRelease_type(void) const;
487 
488  /// Reset Release_type data member.
489  void ResetRelease_type(void);
490 
491  /// Get the Release_type member data.
492  ///
493  /// @return
494  /// Copy of the member data.
495  TRelease_type GetRelease_type(void) const;
496 
497  /// Assign a value to Release_type data member.
498  ///
499  /// @param value
500  /// Value to assign
501  void SetRelease_type(TRelease_type value);
502 
503  /// Assign a value to Release_type data member.
504  ///
505  /// @return
506  /// Reference to the data value.
507  TRelease_type& SetRelease_type(void);
508 
509  /// Check if a value has been assigned to Release_status data member.
510  ///
511  /// Data member Release_status is optional;
512  /// its type is defined as 'typedef int TRelease_status'
513  /// @return
514  /// - true, if a value has been assigned.
515  /// - false, otherwise.
516  bool IsSetRelease_status(void) const;
517 
518  /// Check if it is safe to call GetRelease_status method.
519  ///
520  /// @return
521  /// - true, if the data member is getatable.
522  /// - false, otherwise.
523  bool CanGetRelease_status(void) const;
524 
525  /// Reset Release_status data member.
526  void ResetRelease_status(void);
527 
528  /// Get the Release_status member data.
529  ///
530  /// @return
531  /// Copy of the member data.
532  TRelease_status GetRelease_status(void) const;
533 
534  /// Assign a value to Release_status data member.
535  ///
536  /// @param value
537  /// Value to assign
538  void SetRelease_status(TRelease_status value);
539 
540  /// Assign a value to Release_status data member.
541  ///
542  /// @return
543  /// Reference to the data value.
544  TRelease_status& SetRelease_status(void);
545 
546  /// in alt-loci units - contain alignment of this sequence to the primary
547  /// unit
548  /// Check if a value has been assigned to Annot data member.
549  ///
550  /// Data member Annot is optional;
551  /// its type is defined as 'typedef list< CRef< CSeq_annot > > TAnnot'
552  /// @return
553  /// - true, if a value has been assigned.
554  /// - false, otherwise.
555  bool IsSetAnnot(void) const;
556 
557  /// Check if it is safe to call GetAnnot method.
558  ///
559  /// @return
560  /// - true, if the data member is getatable.
561  /// - false, otherwise.
562  bool CanGetAnnot(void) const;
563 
564  /// Reset Annot data member.
565  void ResetAnnot(void);
566 
567  /// Get the Annot member data.
568  ///
569  /// @return
570  /// Reference to the member data.
571  const TAnnot& GetAnnot(void) const;
572 
573  /// Assign a value to Annot data member.
574  ///
575  /// @return
576  /// Reference to the data value.
577  TAnnot& SetAnnot(void);
578 
579  /// Synonyms: Other releases of same assembly
580  /// Check if a value has been assigned to Synonyms data member.
581  ///
582  /// Data member Synonyms is optional;
583  /// its type is defined as 'typedef list< CRef< CGC_DbTagAlias > > TSynonyms'
584  /// @return
585  /// - true, if a value has been assigned.
586  /// - false, otherwise.
587  bool IsSetSynonyms(void) const;
588 
589  /// Check if it is safe to call GetSynonyms method.
590  ///
591  /// @return
592  /// - true, if the data member is getatable.
593  /// - false, otherwise.
594  bool CanGetSynonyms(void) const;
595 
596  /// Reset Synonyms data member.
597  void ResetSynonyms(void);
598 
599  /// Get the Synonyms member data.
600  ///
601  /// @return
602  /// Reference to the member data.
603  const TSynonyms& GetSynonyms(void) const;
604 
605  /// Assign a value to Synonyms data member.
606  ///
607  /// @return
608  /// Reference to the data value.
609  TSynonyms& SetSynonyms(void);
610 
611  /// Submitter release date
612  /// Check if a value has been assigned to Submitter_date data member.
613  ///
614  /// Data member Submitter_date is optional;
615  /// its type is defined as 'typedef CDate TSubmitter_date'
616  /// @return
617  /// - true, if a value has been assigned.
618  /// - false, otherwise.
619  bool IsSetSubmitter_date(void) const;
620 
621  /// Check if it is safe to call GetSubmitter_date method.
622  ///
623  /// @return
624  /// - true, if the data member is getatable.
625  /// - false, otherwise.
626  bool CanGetSubmitter_date(void) const;
627 
628  /// Reset Submitter_date data member.
629  void ResetSubmitter_date(void);
630 
631  /// Get the Submitter_date member data.
632  ///
633  /// @return
634  /// Reference to the member data.
635  const TSubmitter_date& GetSubmitter_date(void) const;
636 
637  /// Assign a value to Submitter_date data member.
638  ///
639  /// @param value
640  /// Reference to value.
641  void SetSubmitter_date(TSubmitter_date& value);
642 
643  /// Assign a value to Submitter_date data member.
644  ///
645  /// @return
646  /// Reference to the data value.
647  TSubmitter_date& SetSubmitter_date(void);
648 
649  /// Various attributes assigned at this level:
650  /// biosrc, comments, publications...
651  ///
652  /// Special user-objects:
653  /// Internal identifiers (GCOL-1178): type str ="gencoll-misc"
654  /// data : 2 user fields :
655  /// label str "asm-name" str <contents of asm_name field>
656  /// label str "asm-id" int <contents of asm_id field>
657  /// ftp-sites: type str ="ftp-sites"
658  /// data : one or 2 fields, depending if both GB and RS have ftp-sites
659  /// label str : "genbank" or "refseq" str : path to ftp-site
660  /// diffs between GB / RS assemblies: type str "diff-from-synonym",
661  /// data label id <incrementing int> str <description of diff>
662  /// Check if a value has been assigned to Descr data member.
663  ///
664  /// Data member Descr is optional;
665  /// its type is defined as 'typedef CSeq_descr TDescr'
666  /// @return
667  /// - true, if a value has been assigned.
668  /// - false, otherwise.
669  bool IsSetDescr(void) const;
670 
671  /// Check if it is safe to call GetDescr method.
672  ///
673  /// @return
674  /// - true, if the data member is getatable.
675  /// - false, otherwise.
676  bool CanGetDescr(void) const;
677 
678  /// Reset Descr data member.
679  void ResetDescr(void);
680 
681  /// Get the Descr member data.
682  ///
683  /// @return
684  /// Reference to the member data.
685  const TDescr& GetDescr(void) const;
686 
687  /// Assign a value to Descr data member.
688  ///
689  /// @param value
690  /// Reference to value.
691  void SetDescr(TDescr& value);
692 
693  /// Assign a value to Descr data member.
694  ///
695  /// @return
696  /// Reference to the data value.
697  TDescr& SetDescr(void);
698 
699  /// flag: is this assembly partial?
700  /// **NOTE: not set = not known!!
701  /// Check if a value has been assigned to Partial data member.
702  ///
703  /// Data member Partial is optional;
704  /// its type is defined as 'typedef bool TPartial'
705  /// @return
706  /// - true, if a value has been assigned.
707  /// - false, otherwise.
708  bool IsSetPartial(void) const;
709 
710  /// Check if it is safe to call GetPartial method.
711  ///
712  /// @return
713  /// - true, if the data member is getatable.
714  /// - false, otherwise.
715  bool CanGetPartial(void) const;
716 
717  /// Reset Partial data member.
718  void ResetPartial(void);
719 
720  /// Get the Partial member data.
721  ///
722  /// @return
723  /// Copy of the member data.
724  TPartial GetPartial(void) const;
725 
726  /// Assign a value to Partial data member.
727  ///
728  /// @param value
729  /// Value to assign
730  void SetPartial(TPartial value);
731 
732  /// Assign a value to Partial data member.
733  ///
734  /// @return
735  /// Reference to the data value.
736  TPartial& SetPartial(void);
737 
738  /// level of coverage for this assembly
739  /// **NOTE: not set = not known!!
740  /// Check if a value has been assigned to Coverage data member.
741  ///
742  /// Data member Coverage is optional;
743  /// its type is defined as 'typedef double TCoverage'
744  /// @return
745  /// - true, if a value has been assigned.
746  /// - false, otherwise.
747  bool IsSetCoverage(void) const;
748 
749  /// Check if it is safe to call GetCoverage method.
750  ///
751  /// @return
752  /// - true, if the data member is getatable.
753  /// - false, otherwise.
754  bool CanGetCoverage(void) const;
755 
756  /// Reset Coverage data member.
757  void ResetCoverage(void);
758 
759  /// Get the Coverage member data.
760  ///
761  /// @return
762  /// Copy of the member data.
763  TCoverage GetCoverage(void) const;
764 
765  /// Assign a value to Coverage data member.
766  ///
767  /// @param value
768  /// Value to assign
769  void SetCoverage(TCoverage value);
770 
771  /// Assign a value to Coverage data member.
772  ///
773  /// @return
774  /// Reference to the data value.
775  TCoverage& SetCoverage(void);
776 
777  /// Check if a value has been assigned to Release_level data member.
778  ///
779  /// Data member Release_level is optional with default eRelease_level_major;
780  /// its type is defined as 'typedef int TRelease_level'
781  /// @return
782  /// - true, if a value has been assigned.
783  /// - false, otherwise.
784  bool IsSetRelease_level(void) const;
785 
786  /// Check if it is safe to call GetRelease_level method.
787  ///
788  /// @return
789  /// - true, if the data member is getatable.
790  /// - false, otherwise.
791  bool CanGetRelease_level(void) const;
792 
793  /// Reset Release_level data member.
794  void ResetRelease_level(void);
795 
796  /// Assign default value to Release_level data member.
797  void SetDefaultRelease_level(void);
798 
799  /// Get the Release_level member data.
800  ///
801  /// @return
802  /// Copy of the member data.
803  TRelease_level GetRelease_level(void) const;
804 
805  /// Assign a value to Release_level data member.
806  ///
807  /// @param value
808  /// Value to assign
809  void SetRelease_level(TRelease_level value);
810 
811  /// Assign a value to Release_level data member.
812  ///
813  /// @return
814  /// Reference to the data value.
815  TRelease_level& SetRelease_level(void);
816 
817  /// organization which submitted this assembly.
818  /// populated from BioProject
819  /// Check if a value has been assigned to Submitter_organization data member.
820  ///
821  /// Data member Submitter_organization is optional;
822  /// its type is defined as 'typedef CStringUTF8 TSubmitter_organization'
823  /// @return
824  /// - true, if a value has been assigned.
825  /// - false, otherwise.
826  bool IsSetSubmitter_organization(void) const;
827 
828  /// Check if it is safe to call GetSubmitter_organization method.
829  ///
830  /// @return
831  /// - true, if the data member is getatable.
832  /// - false, otherwise.
833  bool CanGetSubmitter_organization(void) const;
834 
835  /// Reset Submitter_organization data member.
836  void ResetSubmitter_organization(void);
837 
838  /// Get the Submitter_organization member data.
839  ///
840  /// @return
841  /// Reference to the member data.
842  const TSubmitter_organization& GetSubmitter_organization(void) const;
843 
844  /// Assign a value to Submitter_organization data member.
845  ///
846  /// @param value
847  /// Value to assign
848  void SetSubmitter_organization(const TSubmitter_organization& value);
849  void SetSubmitter_organization(TSubmitter_organization&& value);
850 
851  /// Assign a value to Submitter_organization data member.
852  ///
853  /// @return
854  /// Reference to the data value.
855  TSubmitter_organization& SetSubmitter_organization(void);
856 
857  /// Reset the whole object
858  virtual void Reset(void);
859 
860 
861 private:
862  // Prohibit copy constructor and assignment operator
865 
866  // data
867  Uint4 m_set_State[2];
868  list< CRef< CGC_Project > > m_Projects;
869  string m_Name;
878  list< CRef< CSeq_annot > > m_Annot;
879  list< CRef< CGC_DbTagAlias > > m_Synonyms;
882  bool m_Partial;
883  double m_Coverage;
886 };
887 
888 /* @} */
889 
890 
891 
892 
893 
894 ///////////////////////////////////////////////////////////
895 ///////////////////// inline methods //////////////////////
896 ///////////////////////////////////////////////////////////
897 inline
899 {
900  return ((m_set_State[0] & 0x3) != 0);
901 }
902 
903 inline
905 {
906  return true;
907 }
908 
909 inline
911 {
912  return m_Projects;
913 }
914 
915 inline
917 {
918  m_set_State[0] |= 0x1;
919  return m_Projects;
920 }
921 
922 inline
924 {
925  return ((m_set_State[0] & 0xc) != 0);
926 }
927 
928 inline
930 {
931  return IsSetName();
932 }
933 
934 inline
936 {
937  if (!CanGetName()) {
938  ThrowUnassigned(1);
939  }
940  return m_Name;
941 }
942 
943 inline
945 {
946  m_Name = value;
947  m_set_State[0] |= 0xc;
948 }
949 
950 inline
952 {
953  m_Name = std::forward<CGC_AssemblyDesc_Base::TName>(value);
954  m_set_State[0] |= 0xc;
955 }
956 
957 inline
959 {
960 #ifdef _DEBUG
961  if (!IsSetName()) {
963  }
964 #endif
965  m_set_State[0] |= 0x4;
966  return m_Name;
967 }
968 
969 inline
971 {
972  return ((m_set_State[0] & 0x30) != 0);
973 }
974 
975 inline
977 {
978  return IsSetSubmitter_name();
979 }
980 
981 inline
983 {
984  if (!CanGetSubmitter_name()) {
985  ThrowUnassigned(2);
986  }
987  return m_Submitter_name;
988 }
989 
990 inline
992 {
994  m_set_State[0] |= 0x30;
995 }
996 
997 inline
999 {
1000  m_Submitter_name = std::forward<CGC_AssemblyDesc_Base::TSubmitter_name>(value);
1001  m_set_State[0] |= 0x30;
1002 }
1003 
1004 inline
1006 {
1007 #ifdef _DEBUG
1008  if (!IsSetSubmitter_name()) {
1010  }
1011 #endif
1012  m_set_State[0] |= 0x10;
1013  return m_Submitter_name;
1014 }
1015 
1016 inline
1018 {
1019  return ((m_set_State[0] & 0xc0) != 0);
1020 }
1021 
1022 inline
1024 {
1025  return IsSetDisplay_name();
1026 }
1027 
1028 inline
1030 {
1031  if (!CanGetDisplay_name()) {
1032  ThrowUnassigned(3);
1033  }
1034  return m_Display_name;
1035 }
1036 
1037 inline
1039 {
1041  m_set_State[0] |= 0xc0;
1042 }
1043 
1044 inline
1046 {
1047  m_Display_name = std::forward<CGC_AssemblyDesc_Base::TDisplay_name>(value);
1048  m_set_State[0] |= 0xc0;
1049 }
1050 
1051 inline
1053 {
1054 #ifdef _DEBUG
1055  if (!IsSetDisplay_name()) {
1057  }
1058 #endif
1059  m_set_State[0] |= 0x40;
1060  return m_Display_name;
1061 }
1062 
1063 inline
1065 {
1066  return ((m_set_State[0] & 0x300) != 0);
1067 }
1068 
1069 inline
1071 {
1072  return IsSetLong_name();
1073 }
1074 
1075 inline
1077 {
1078  if (!CanGetLong_name()) {
1079  ThrowUnassigned(4);
1080  }
1081  return m_Long_name;
1082 }
1083 
1084 inline
1086 {
1087  m_Long_name = value;
1088  m_set_State[0] |= 0x300;
1089 }
1090 
1091 inline
1093 {
1094  m_Long_name = std::forward<CGC_AssemblyDesc_Base::TLong_name>(value);
1095  m_set_State[0] |= 0x300;
1096 }
1097 
1098 inline
1100 {
1101 #ifdef _DEBUG
1102  if (!IsSetLong_name()) {
1104  }
1105 #endif
1106  m_set_State[0] |= 0x100;
1107  return m_Long_name;
1108 }
1109 
1110 inline
1112 {
1113  return ((m_set_State[0] & 0xc00) != 0);
1114 }
1115 
1116 inline
1118 {
1119  return IsSetFilesafe_name();
1120 }
1121 
1122 inline
1124 {
1125  if (!CanGetFilesafe_name()) {
1126  ThrowUnassigned(5);
1127  }
1128  return m_Filesafe_name;
1129 }
1130 
1131 inline
1133 {
1135  m_set_State[0] |= 0xc00;
1136 }
1137 
1138 inline
1140 {
1141  m_Filesafe_name = std::forward<CGC_AssemblyDesc_Base::TFilesafe_name>(value);
1142  m_set_State[0] |= 0xc00;
1143 }
1144 
1145 inline
1147 {
1148 #ifdef _DEBUG
1149  if (!IsSetFilesafe_name()) {
1151  }
1152 #endif
1153  m_set_State[0] |= 0x400;
1154  return m_Filesafe_name;
1155 }
1156 
1157 inline
1159 {
1160  return ((m_set_State[0] & 0x3000) != 0);
1161 }
1162 
1163 inline
1165 {
1166  return IsSetWgs_acc_prefix();
1167 }
1168 
1169 inline
1171 {
1172  if (!CanGetWgs_acc_prefix()) {
1173  ThrowUnassigned(6);
1174  }
1175  return m_Wgs_acc_prefix;
1176 }
1177 
1178 inline
1180 {
1182  m_set_State[0] |= 0x3000;
1183 }
1184 
1185 inline
1187 {
1188  m_Wgs_acc_prefix = std::forward<CGC_AssemblyDesc_Base::TWgs_acc_prefix>(value);
1189  m_set_State[0] |= 0x3000;
1190 }
1191 
1192 inline
1194 {
1195 #ifdef _DEBUG
1196  if (!IsSetWgs_acc_prefix()) {
1198  }
1199 #endif
1200  m_set_State[0] |= 0x1000;
1201  return m_Wgs_acc_prefix;
1202 }
1203 
1204 inline
1206 {
1207  return ((m_set_State[0] & 0xc000) != 0);
1208 }
1209 
1210 inline
1212 {
1213  return IsSetWgs_acc_number();
1214 }
1215 
1216 inline
1218 {
1219  m_Wgs_acc_number = 0;
1220  m_set_State[0] &= ~0xc000;
1221 }
1222 
1223 inline
1225 {
1226  if (!CanGetWgs_acc_number()) {
1227  ThrowUnassigned(7);
1228  }
1229  return m_Wgs_acc_number;
1230 }
1231 
1232 inline
1234 {
1236  m_set_State[0] |= 0xc000;
1237 }
1238 
1239 inline
1241 {
1242 #ifdef _DEBUG
1243  if (!IsSetWgs_acc_number()) {
1245  }
1246 #endif
1247  m_set_State[0] |= 0x4000;
1248  return m_Wgs_acc_number;
1249 }
1250 
1251 inline
1253 {
1254  return ((m_set_State[0] & 0x30000) != 0);
1255 }
1256 
1257 inline
1259 {
1260  return IsSetRelease_type();
1261 }
1262 
1263 inline
1265 {
1267  m_set_State[0] &= ~0x30000;
1268 }
1269 
1270 inline
1272 {
1273  if (!CanGetRelease_type()) {
1274  ThrowUnassigned(8);
1275  }
1276  return m_Release_type;
1277 }
1278 
1279 inline
1281 {
1283  m_set_State[0] |= 0x30000;
1284 }
1285 
1286 inline
1288 {
1289 #ifdef _DEBUG
1290  if (!IsSetRelease_type()) {
1291  memset(&m_Release_type,UnassignedByte(),sizeof(m_Release_type));
1292  }
1293 #endif
1294  m_set_State[0] |= 0x10000;
1295  return m_Release_type;
1296 }
1297 
1298 inline
1300 {
1301  return ((m_set_State[0] & 0xc0000) != 0);
1302 }
1303 
1304 inline
1306 {
1307  return IsSetRelease_status();
1308 }
1309 
1310 inline
1312 {
1314  m_set_State[0] &= ~0xc0000;
1315 }
1316 
1317 inline
1319 {
1320  if (!CanGetRelease_status()) {
1321  ThrowUnassigned(9);
1322  }
1323  return m_Release_status;
1324 }
1325 
1326 inline
1328 {
1330  m_set_State[0] |= 0xc0000;
1331 }
1332 
1333 inline
1335 {
1336 #ifdef _DEBUG
1337  if (!IsSetRelease_status()) {
1339  }
1340 #endif
1341  m_set_State[0] |= 0x40000;
1342  return m_Release_status;
1343 }
1344 
1345 inline
1347 {
1348  return ((m_set_State[0] & 0x300000) != 0);
1349 }
1350 
1351 inline
1353 {
1354  return true;
1355 }
1356 
1357 inline
1359 {
1360  return m_Annot;
1361 }
1362 
1363 inline
1365 {
1366  m_set_State[0] |= 0x100000;
1367  return m_Annot;
1368 }
1369 
1370 inline
1372 {
1373  return ((m_set_State[0] & 0xc00000) != 0);
1374 }
1375 
1376 inline
1378 {
1379  return true;
1380 }
1381 
1382 inline
1384 {
1385  return m_Synonyms;
1386 }
1387 
1388 inline
1390 {
1391  m_set_State[0] |= 0x400000;
1392  return m_Synonyms;
1393 }
1394 
1395 inline
1397 {
1398  return m_Submitter_date.NotEmpty();
1399 }
1400 
1401 inline
1403 {
1404  return IsSetSubmitter_date();
1405 }
1406 
1407 inline
1409 {
1410  if (!CanGetSubmitter_date()) {
1411  ThrowUnassigned(12);
1412  }
1413  return (*m_Submitter_date);
1414 }
1415 
1416 inline
1418 {
1419  return m_Descr.NotEmpty();
1420 }
1421 
1422 inline
1424 {
1425  return IsSetDescr();
1426 }
1427 
1428 inline
1430 {
1431  if (!CanGetDescr()) {
1432  ThrowUnassigned(13);
1433  }
1434  return (*m_Descr);
1435 }
1436 
1437 inline
1439 {
1440  return ((m_set_State[0] & 0x30000000) != 0);
1441 }
1442 
1443 inline
1445 {
1446  return IsSetPartial();
1447 }
1448 
1449 inline
1451 {
1452  m_Partial = 0;
1453  m_set_State[0] &= ~0x30000000;
1454 }
1455 
1456 inline
1458 {
1459  if (!CanGetPartial()) {
1460  ThrowUnassigned(14);
1461  }
1462  return m_Partial;
1463 }
1464 
1465 inline
1467 {
1468  m_Partial = value;
1469  m_set_State[0] |= 0x30000000;
1470 }
1471 
1472 inline
1474 {
1475 #ifdef _DEBUG
1476  if (!IsSetPartial()) {
1477  memset(&m_Partial,UnassignedByte(),sizeof(m_Partial));
1478  }
1479 #endif
1480  m_set_State[0] |= 0x10000000;
1481  return m_Partial;
1482 }
1483 
1484 inline
1486 {
1487  return ((m_set_State[0] & 0xc0000000) != 0);
1488 }
1489 
1490 inline
1492 {
1493  return IsSetCoverage();
1494 }
1495 
1496 inline
1498 {
1499  m_Coverage = 0;
1500  m_set_State[0] &= ~0xc0000000;
1501 }
1502 
1503 inline
1505 {
1506  if (!CanGetCoverage()) {
1507  ThrowUnassigned(15);
1508  }
1509  return m_Coverage;
1510 }
1511 
1512 inline
1514 {
1515  m_Coverage = value;
1516  m_set_State[0] |= 0xc0000000;
1517 }
1518 
1519 inline
1521 {
1522 #ifdef _DEBUG
1523  if (!IsSetCoverage()) {
1524  memset(&m_Coverage,UnassignedByte(),sizeof(m_Coverage));
1525  }
1526 #endif
1527  m_set_State[0] |= 0x40000000;
1528  return m_Coverage;
1529 }
1530 
1531 inline
1533 {
1534  return ((m_set_State[1] & 0x3) != 0);
1535 }
1536 
1537 inline
1539 {
1540  return true;
1541 }
1542 
1543 inline
1545 {
1547  m_set_State[1] &= ~0x3;
1548 }
1549 
1550 inline
1552 {
1554 }
1555 
1556 inline
1558 {
1559  return m_Release_level;
1560 }
1561 
1562 inline
1564 {
1566  m_set_State[1] |= 0x3;
1567 }
1568 
1569 inline
1571 {
1572 #ifdef _DEBUG
1573  if (!IsSetRelease_level()) {
1574  memset(&m_Release_level,UnassignedByte(),sizeof(m_Release_level));
1575  }
1576 #endif
1577  m_set_State[1] |= 0x1;
1578  return m_Release_level;
1579 }
1580 
1581 inline
1583 {
1584  return ((m_set_State[1] & 0xc) != 0);
1585 }
1586 
1587 inline
1589 {
1590  return IsSetSubmitter_organization();
1591 }
1592 
1593 inline
1595 {
1597  ThrowUnassigned(17);
1598  }
1599  return m_Submitter_organization;
1600 }
1601 
1602 inline
1604 {
1606  m_set_State[1] |= 0xc;
1607 }
1608 
1609 inline
1611 {
1612  m_Submitter_organization = std::forward<CGC_AssemblyDesc_Base::TSubmitter_organization>(value);
1613  m_set_State[1] |= 0xc;
1614 }
1615 
1616 inline
1618 {
1619 #ifdef _DEBUG
1620  if (!IsSetSubmitter_organization()) {
1622  }
1623 #endif
1624  m_set_State[1] |= 0x4;
1625  return m_Submitter_organization;
1626 }
1627 
1628 ///////////////////////////////////////////////////////////
1629 ////////////////// end of inline methods //////////////////
1630 ///////////////////////////////////////////////////////////
1631 
1632 
1633 
1634 
1635 
1636 END_objects_SCOPE // namespace ncbi::objects::
1637 
1639 
1640 
1641 #endif // OBJECTS_GENOMECOLL_GC_ASSEMBLYDESC_BASE_HPP
Definition: Date.hpp:53
CGC_AssemblyDesc_Base –.
CGC_DbTagAlias –.
CGC_Project –.
Definition: GC_Project.hpp:66
CRef –.
Definition: ncbiobj.hpp:618
@Seq_descr.hpp User-defined methods of the data storage class.
Definition: Seq_descr.hpp:55
Base class for all serializable objects.
Definition: serialbase.hpp:150
char value[7]
Definition: config.c:431
static CStringUTF8 UnassignedStringUTF8(void)
Definition: serialbase.hpp:178
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
TSeqPos GetCoverage(const CSeq_loc &loc, CScope *scope)
Get number of unique bases in the location.
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
std::string CStringUTF8
Definition: ncbistl.hpp:254
#define NCBI_GENOME_COLLECTION_EXPORT
Definition: ncbi_export.h:528
list< CRef< CSeq_annot > > TAnnot
bool CanGetSubmitter_date(void) const
Check if it is safe to call GetSubmitter_date method.
CStringUTF8 TSubmitter_organization
ERelease_level
release level: Most of releases are major
TPartial & SetPartial(void)
Assign a value to Partial data member.
const TName & GetName(void) const
Get the Name member data.
TCoverage & SetCoverage(void)
Assign a value to Coverage data member.
bool IsSetRelease_status(void) const
Check if a value has been assigned to Release_status data member.
const TSubmitter_name & GetSubmitter_name(void) const
Get the Submitter_name member data.
bool CanGetPartial(void) const
Check if it is safe to call GetPartial method.
void ResetPartial(void)
Reset Partial data member.
bool IsSetPartial(void) const
flag: is this assembly partial? **NOTE: not set = not known!! Check if a value has been assigned to P...
CGC_AssemblyDesc_Base(const CGC_AssemblyDesc_Base &)
TDisplay_name & SetDisplay_name(void)
Assign a value to Display_name data member.
bool CanGetName(void) const
Check if it is safe to call GetName method.
TCoverage GetCoverage(void) const
Get the Coverage member data.
bool CanGetRelease_type(void) const
Check if it is safe to call GetRelease_type method.
ERelease_type
release type: RefSeq / GenBank.
bool CanGetSubmitter_organization(void) const
Check if it is safe to call GetSubmitter_organization method.
TRelease_type GetRelease_type(void) const
Get the Release_type member data.
TFilesafe_name & SetFilesafe_name(void)
Assign a value to Filesafe_name data member.
bool IsSetAnnot(void) const
in alt-loci units - contain alignment of this sequence to the primary unit Check if a value has been ...
TRelease_level GetRelease_level(void) const
Get the Release_level member data.
TName & SetName(void)
Assign a value to Name data member.
list< CRef< CGC_DbTagAlias > > m_Synonyms
bool IsSetProjects(void) const
project ID for this genome this is the ID for this asssembly and may reflect the submitter/source Che...
TPartial GetPartial(void) const
Get the Partial member data.
list< CRef< CGC_DbTagAlias > > TSynonyms
void ResetRelease_type(void)
Reset Release_type data member.
list< CRef< CSeq_annot > > m_Annot
const TSynonyms & GetSynonyms(void) const
Get the Synonyms member data.
void ResetWgs_acc_number(void)
Reset Wgs_acc_number data member.
bool CanGetDescr(void) const
Check if it is safe to call GetDescr method.
CGC_AssemblyDesc_Base & operator=(const CGC_AssemblyDesc_Base &)
const TDisplay_name & GetDisplay_name(void) const
Get the Display_name member data.
bool CanGetAnnot(void) const
Check if it is safe to call GetAnnot method.
const TFilesafe_name & GetFilesafe_name(void) const
Get the Filesafe_name member data.
const TLong_name & GetLong_name(void) const
Get the Long_name member data.
TRelease_status & SetRelease_status(void)
Assign a value to Release_status data member.
TAnnot & SetAnnot(void)
Assign a value to Annot data member.
bool IsSetFilesafe_name(void) const
Check if a value has been assigned to Filesafe_name data member.
bool CanGetDisplay_name(void) const
Check if it is safe to call GetDisplay_name method.
bool IsSetWgs_acc_number(void) const
Check if a value has been assigned to Wgs_acc_number data member.
CStringUTF8 m_Submitter_organization
bool CanGetRelease_status(void) const
Check if it is safe to call GetRelease_status method.
ERelease_status
release status (numeric values have gaps for possible additional states
TProjects & SetProjects(void)
Assign a value to Projects data member.
const TSubmitter_date & GetSubmitter_date(void) const
Get the Submitter_date member data.
TWgs_acc_number GetWgs_acc_number(void) const
Get the Wgs_acc_number member data.
bool CanGetRelease_level(void) const
Check if it is safe to call GetRelease_level method.
bool IsSetSubmitter_organization(void) const
organization which submitted this assembly.
TSubmitter_organization & SetSubmitter_organization(void)
Assign a value to Submitter_organization data member.
bool IsSetDescr(void) const
Various attributes assigned at this level: biosrc, comments, publications...
bool IsSetRelease_type(void) const
Check if a value has been assigned to Release_type data member.
bool CanGetFilesafe_name(void) const
Check if it is safe to call GetFilesafe_name method.
const TDescr & GetDescr(void) const
Get the Descr member data.
Tparent::CMemberIndex< E_memberIndex, 19 > TmemberIndex
void ResetRelease_status(void)
Reset Release_status data member.
bool CanGetWgs_acc_prefix(void) const
Check if it is safe to call GetWgs_acc_prefix method.
void ResetRelease_level(void)
Reset Release_level data member.
TLong_name & SetLong_name(void)
Assign a value to Long_name data member.
bool CanGetCoverage(void) const
Check if it is safe to call GetCoverage method.
bool IsSetSynonyms(void) const
Synonyms: Other releases of same assembly Check if a value has been assigned to Synonyms data member.
TRelease_type & SetRelease_type(void)
Assign a value to Release_type data member.
bool IsSetRelease_level(void) const
Check if a value has been assigned to Release_level data member.
TRelease_status GetRelease_status(void) const
Get the Release_status member data.
bool IsSetLong_name(void) const
Check if a value has been assigned to Long_name data member.
bool IsSetName(void) const
Names of the assembly Check if a value has been assigned to Name data member.
void SetDefaultRelease_level(void)
Assign default value to Release_level data member.
CRef< TSubmitter_date > m_Submitter_date
const TProjects & GetProjects(void) const
Get the Projects member data.
const TSubmitter_organization & GetSubmitter_organization(void) const
Get the Submitter_organization member data.
bool IsSetWgs_acc_prefix(void) const
Check if a value has been assigned to Wgs_acc_prefix data member.
bool IsSetSubmitter_name(void) const
Check if a value has been assigned to Submitter_name data member.
bool CanGetLong_name(void) const
Check if it is safe to call GetLong_name method.
void ResetCoverage(void)
Reset Coverage data member.
TWgs_acc_number & SetWgs_acc_number(void)
Assign a value to Wgs_acc_number data member.
const TWgs_acc_prefix & GetWgs_acc_prefix(void) const
Get the Wgs_acc_prefix member data.
TSynonyms & SetSynonyms(void)
Assign a value to Synonyms data member.
bool CanGetSynonyms(void) const
Check if it is safe to call GetSynonyms method.
const TAnnot & GetAnnot(void) const
Get the Annot member data.
TRelease_level & SetRelease_level(void)
Assign a value to Release_level data member.
bool CanGetProjects(void) const
Check if it is safe to call GetProjects method.
bool CanGetWgs_acc_number(void) const
Check if it is safe to call GetWgs_acc_number method.
list< CRef< CGC_Project > > TProjects
TWgs_acc_prefix & SetWgs_acc_prefix(void)
Assign a value to Wgs_acc_prefix data member.
TSubmitter_name & SetSubmitter_name(void)
Assign a value to Submitter_name data member.
list< CRef< CGC_Project > > m_Projects
bool IsSetDisplay_name(void) const
Check if a value has been assigned to Display_name data member.
bool IsSetSubmitter_date(void) const
Submitter release date Check if a value has been assigned to Submitter_date data member.
bool IsSetCoverage(void) const
level of coverage for this assembly **NOTE: not set = not known!! Check if a value has been assigned ...
bool CanGetSubmitter_name(void) const
Check if it is safe to call GetSubmitter_name method.
void SetPartial(CSeq_loc &loc, CRef< CSeq_feat > feat, CSeq_loc::TStrand strand, bool partial_start, bool partial_stop)
Modified on Thu Mar 28 17:08:12 2024 by modify_doxy.py rev. 669887