NCBI C++ ToolKit
Assembly_.hpp
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27 
28 /// @file Assembly_.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/docsum/docsum.asn">docsum.asn</a>
34 /// and additional tune-up parameters:
35 /// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/docsum/docsum.def">docsum.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_DOCSUM_ASSEMBLY_BASE_HPP
42 #define OBJECTS_DOCSUM_ASSEMBLY_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 CComponent;
62 
63 
64 // generated classes
65 
66 
67 /** @addtogroup dataspec_Docsum_3_4
68  *
69  * @{
70  */
71 
72 /////////////////////////////////////////////////////////////////////////////
73 ///A collection of genome sequence records (curated gene regions (NG's),
74 /// contigs (NWNT's) and chromosomes (NC/AC's) produced by a genome sequence project.
75 /// Structure is populated from ContigInfo tables.
76 ///
77 /// CAssembly_Base --
78 ///
79 
81 {
83 public:
84  // constructor
85  CAssembly_Base(void);
86  // destructor
87  virtual ~CAssembly_Base(void);
88 
89  // type info
91 
92  /////////////////////////////////////////////////////////////////////////////
93  ///
94  /// C_Attlist --
95  ///
96 
98  {
100  public:
101  // constructor
102  C_Attlist(void);
103  // destructor
104  ~C_Attlist(void);
105 
106  // type info
108 
109  // types
110  typedef int TDbSnpBuild;
111  typedef string TGenomeBuild;
112  typedef string TGroupLabel;
113  typedef string TAssemblySource;
114  typedef bool TCurrent;
115  typedef bool TReference;
116 
117  // member index
118  enum class E_memberIndex {
119  e__allMandatory = 0,
120  e_dbSnpBuild,
121  e_genomeBuild,
122  e_groupLabel,
123  e_assemblySource,
124  e_current,
125  e_reference
126  };
128 
129  // getters
130  // setters
131 
132  ///dbSNP build number defining the rsid set aligned to this
133  /// assembly
134  /// Check if a value has been assigned to DbSnpBuild data member.
135  ///
136  /// Data member DbSnpBuild is mandatory;
137  /// its type is defined as 'typedef int TDbSnpBuild'
138  /// @return
139  /// - true, if a value has been assigned.
140  /// - false, otherwise.
141  bool IsSetDbSnpBuild(void) const;
142 
143  /// Check if it is safe to call GetDbSnpBuild method.
144  ///
145  /// @return
146  /// - true, if the data member is getatable.
147  /// - false, otherwise.
148  bool CanGetDbSnpBuild(void) const;
149 
150  /// Reset DbSnpBuild data member.
151  void ResetDbSnpBuild(void);
152 
153  /// Get the DbSnpBuild member data.
154  ///
155  /// @return
156  /// Copy of the member data.
157  TDbSnpBuild GetDbSnpBuild(void) const;
158 
159  /// Assign a value to DbSnpBuild data member.
160  ///
161  /// @param value
162  /// Value to assign
163  void SetDbSnpBuild(TDbSnpBuild value);
164 
165  /// Assign a value to DbSnpBuild data member.
166  ///
167  /// @return
168  /// Reference to the data value.
169  TDbSnpBuild& SetDbSnpBuild(void);
170 
171  ///assembly build number with possible 'subbuild' version
172  /// numbers to reflect updates in gene annotation (human e.g. 34_3, 35_1,
173  /// 36_1)
174  /// Check if a value has been assigned to GenomeBuild data member.
175  ///
176  /// Data member GenomeBuild is mandatory;
177  /// its type is defined as 'typedef string TGenomeBuild'
178  /// @return
179  /// - true, if a value has been assigned.
180  /// - false, otherwise.
181  bool IsSetGenomeBuild(void) const;
182 
183  /// Check if it is safe to call GetGenomeBuild method.
184  ///
185  /// @return
186  /// - true, if the data member is getatable.
187  /// - false, otherwise.
188  bool CanGetGenomeBuild(void) const;
189 
190  /// Reset GenomeBuild data member.
191  void ResetGenomeBuild(void);
192 
193  /// Get the GenomeBuild member data.
194  ///
195  /// @return
196  /// Reference to the member data.
197  const TGenomeBuild& GetGenomeBuild(void) const;
198 
199  /// Assign a value to GenomeBuild data member.
200  ///
201  /// @param value
202  /// Value to assign
203  void SetGenomeBuild(const TGenomeBuild& value);
204  void SetGenomeBuild(TGenomeBuild&& value);
205 
206  /// Assign a value to GenomeBuild data member.
207  ///
208  /// @return
209  /// Reference to the data value.
210  TGenomeBuild& SetGenomeBuild(void);
211 
212  ///High-level classification of the assembly to distinguish
213  /// reference projects from alternate solutions. GroupLabel field from
214  /// organism/build-specific ContigInfo tables. "reference" is occasionally used
215  /// as the preferred assembly; standards will converge as additional organism
216  /// genome projects are finished. Note that some organism assembly names include
217  /// extended characters like '~' and '/' that may be incompatible with OS
218  /// filename conventions.
219  /// Check if a value has been assigned to GroupLabel data member.
220  ///
221  /// Data member GroupLabel is optional;
222  /// its type is defined as 'typedef string TGroupLabel'
223  /// @return
224  /// - true, if a value has been assigned.
225  /// - false, otherwise.
226  bool IsSetGroupLabel(void) const;
227 
228  /// Check if it is safe to call GetGroupLabel method.
229  ///
230  /// @return
231  /// - true, if the data member is getatable.
232  /// - false, otherwise.
233  bool CanGetGroupLabel(void) const;
234 
235  /// Reset GroupLabel data member.
236  void ResetGroupLabel(void);
237 
238  /// Get the GroupLabel member data.
239  ///
240  /// @return
241  /// Reference to the member data.
242  const TGroupLabel& GetGroupLabel(void) const;
243 
244  /// Assign a value to GroupLabel data member.
245  ///
246  /// @param value
247  /// Value to assign
248  void SetGroupLabel(const TGroupLabel& value);
249  void SetGroupLabel(TGroupLabel&& value);
250 
251  /// Assign a value to GroupLabel data member.
252  ///
253  /// @return
254  /// Reference to the data value.
255  TGroupLabel& SetGroupLabel(void);
256 
257  ///Name of the group(s) or organization(s) that generated the
258  /// assembly
259  /// Check if a value has been assigned to AssemblySource data member.
260  ///
261  /// Data member AssemblySource is optional;
262  /// its type is defined as 'typedef string TAssemblySource'
263  /// @return
264  /// - true, if a value has been assigned.
265  /// - false, otherwise.
266  bool IsSetAssemblySource(void) const;
267 
268  /// Check if it is safe to call GetAssemblySource method.
269  ///
270  /// @return
271  /// - true, if the data member is getatable.
272  /// - false, otherwise.
273  bool CanGetAssemblySource(void) const;
274 
275  /// Reset AssemblySource data member.
276  void ResetAssemblySource(void);
277 
278  /// Get the AssemblySource member data.
279  ///
280  /// @return
281  /// Reference to the member data.
282  const TAssemblySource& GetAssemblySource(void) const;
283 
284  /// Assign a value to AssemblySource data member.
285  ///
286  /// @param value
287  /// Value to assign
288  void SetAssemblySource(const TAssemblySource& value);
289  void SetAssemblySource(TAssemblySource&& value);
290 
291  /// Assign a value to AssemblySource data member.
292  ///
293  /// @return
294  /// Reference to the data value.
295  TAssemblySource& SetAssemblySource(void);
296 
297  ///Marks the current genomic assembly
298  /// Check if a value has been assigned to Current data member.
299  ///
300  /// Data member Current is optional;
301  /// its type is defined as 'typedef bool TCurrent'
302  /// @return
303  /// - true, if a value has been assigned.
304  /// - false, otherwise.
305  bool IsSetCurrent(void) const;
306 
307  /// Check if it is safe to call GetCurrent method.
308  ///
309  /// @return
310  /// - true, if the data member is getatable.
311  /// - false, otherwise.
312  bool CanGetCurrent(void) const;
313 
314  /// Reset Current data member.
315  void ResetCurrent(void);
316 
317  /// Get the Current member data.
318  ///
319  /// @return
320  /// Copy of the member data.
321  TCurrent GetCurrent(void) const;
322 
323  /// Assign a value to Current data member.
324  ///
325  /// @param value
326  /// Value to assign
327  void SetCurrent(TCurrent value);
328 
329  /// Assign a value to Current data member.
330  ///
331  /// @return
332  /// Reference to the data value.
333  TCurrent& SetCurrent(void);
334 
335  /// Check if a value has been assigned to Reference data member.
336  ///
337  /// Data member Reference is optional;
338  /// its type is defined as 'typedef bool TReference'
339  /// @return
340  /// - true, if a value has been assigned.
341  /// - false, otherwise.
342  bool IsSetReference(void) const;
343 
344  /// Check if it is safe to call GetReference method.
345  ///
346  /// @return
347  /// - true, if the data member is getatable.
348  /// - false, otherwise.
349  bool CanGetReference(void) const;
350 
351  /// Reset Reference data member.
352  void ResetReference(void);
353 
354  /// Get the Reference member data.
355  ///
356  /// @return
357  /// Copy of the member data.
358  TReference GetReference(void) const;
359 
360  /// Assign a value to Reference data member.
361  ///
362  /// @param value
363  /// Value to assign
364  void SetReference(TReference value);
365 
366  /// Assign a value to Reference data member.
367  ///
368  /// @return
369  /// Reference to the data value.
370  TReference& SetReference(void);
371 
372  /// Reset the whole object
373  void Reset(void);
374 
375 
376  private:
377  // Prohibit copy constructor and assignment operator
380 
381  // data
382  Uint4 m_set_State[1];
385  string m_GroupLabel;
387  bool m_Current;
389  };
390  /////////////////////////////////////////////////////////////////////////////
391  ///
392  /// C_SnpStat --
393  ///
394 
396  {
398  public:
399  // constructor
400  C_SnpStat(void);
401  // destructor
402  ~C_SnpStat(void);
403 
404  // type info
406 
407  /////////////////////////////////////////////////////////////////////////////
408  ///
409  /// C_Attlist --
410  ///
411 
413  {
415  public:
416  // constructor
417  C_Attlist(void);
418  // destructor
419  ~C_Attlist(void);
420 
421  // type info
423 
424  ///summary measure of placement precision in the
425  /// assembly
427  eSnpStat_attlist_mapWeight_unmapped = 1,
428  eSnpStat_attlist_mapWeight_unique_in_contig = 2,
429  eSnpStat_attlist_mapWeight_two_hits_in_contig = 3,
430  eSnpStat_attlist_mapWeight_less_10_hits = 4,
431  eSnpStat_attlist_mapWeight_multiple_hits = 5
432  };
433 
434  /// Access to ESnpStat_attlist_mapWeight's attributes (values, names) as defined in spec
435  static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(ESnpStat_attlist_mapWeight)(void);
436 
437  // types
439  typedef int TChromCount;
440  typedef int TPlacedContigCount;
441  typedef int TUnplacedContigCount;
442  typedef int TSeqlocCount;
443  typedef int THapCount;
444 
445  // member index
446  enum class E_memberIndex {
447  e__allMandatory = 0,
448  e_mapWeight,
449  e_chromCount,
450  e_placedContigCount,
451  e_unplacedContigCount,
452  e_seqlocCount,
453  e_hapCount
454  };
456 
457  // getters
458  // setters
459 
460  /// Check if a value has been assigned to MapWeight data member.
461  ///
462  /// Data member MapWeight is mandatory;
463  /// its type is defined as 'typedef ESnpStat_attlist_mapWeight TMapWeight'
464  /// @return
465  /// - true, if a value has been assigned.
466  /// - false, otherwise.
467  bool IsSetMapWeight(void) const;
468 
469  /// Check if it is safe to call GetMapWeight method.
470  ///
471  /// @return
472  /// - true, if the data member is getatable.
473  /// - false, otherwise.
474  bool CanGetMapWeight(void) const;
475 
476  /// Reset MapWeight data member.
477  void ResetMapWeight(void);
478 
479  /// Get the MapWeight member data.
480  ///
481  /// @return
482  /// Copy of the member data.
483  TMapWeight GetMapWeight(void) const;
484 
485  /// Assign a value to MapWeight data member.
486  ///
487  /// @param value
488  /// Value to assign
489  void SetMapWeight(TMapWeight value);
490 
491  /// Assign a value to MapWeight data member.
492  ///
493  /// @return
494  /// Reference to the data value.
495  TMapWeight& SetMapWeight(void);
496 
497  ///number of distinct chromosomes in the
498  /// mapset
499  /// Check if a value has been assigned to ChromCount data member.
500  ///
501  /// Data member ChromCount is optional;
502  /// its type is defined as 'typedef int TChromCount'
503  /// @return
504  /// - true, if a value has been assigned.
505  /// - false, otherwise.
506  bool IsSetChromCount(void) const;
507 
508  /// Check if it is safe to call GetChromCount method.
509  ///
510  /// @return
511  /// - true, if the data member is getatable.
512  /// - false, otherwise.
513  bool CanGetChromCount(void) const;
514 
515  /// Reset ChromCount data member.
516  void ResetChromCount(void);
517 
518  /// Get the ChromCount member data.
519  ///
520  /// @return
521  /// Copy of the member data.
522  TChromCount GetChromCount(void) const;
523 
524  /// Assign a value to ChromCount data member.
525  ///
526  /// @param value
527  /// Value to assign
528  void SetChromCount(TChromCount value);
529 
530  /// Assign a value to ChromCount data member.
531  ///
532  /// @return
533  /// Reference to the data value.
534  TChromCount& SetChromCount(void);
535 
536  ///number of distinct contigs [ gi |
537  /// accession[.version] ] in the mapset
538  /// Check if a value has been assigned to PlacedContigCount data member.
539  ///
540  /// Data member PlacedContigCount is optional;
541  /// its type is defined as 'typedef int TPlacedContigCount'
542  /// @return
543  /// - true, if a value has been assigned.
544  /// - false, otherwise.
545  bool IsSetPlacedContigCount(void) const;
546 
547  /// Check if it is safe to call GetPlacedContigCount method.
548  ///
549  /// @return
550  /// - true, if the data member is getatable.
551  /// - false, otherwise.
552  bool CanGetPlacedContigCount(void) const;
553 
554  /// Reset PlacedContigCount data member.
555  void ResetPlacedContigCount(void);
556 
557  /// Get the PlacedContigCount member data.
558  ///
559  /// @return
560  /// Copy of the member data.
561  TPlacedContigCount GetPlacedContigCount(void) const;
562 
563  /// Assign a value to PlacedContigCount data member.
564  ///
565  /// @param value
566  /// Value to assign
567  void SetPlacedContigCount(TPlacedContigCount value);
568 
569  /// Assign a value to PlacedContigCount data member.
570  ///
571  /// @return
572  /// Reference to the data value.
573  TPlacedContigCount& SetPlacedContigCount(void);
574 
575  ///number of sequence postions to a contig with
576  /// unknown chromosomal assignment
577  /// Check if a value has been assigned to UnplacedContigCount data member.
578  ///
579  /// Data member UnplacedContigCount is optional;
580  /// its type is defined as 'typedef int TUnplacedContigCount'
581  /// @return
582  /// - true, if a value has been assigned.
583  /// - false, otherwise.
584  bool IsSetUnplacedContigCount(void) const;
585 
586  /// Check if it is safe to call GetUnplacedContigCount method.
587  ///
588  /// @return
589  /// - true, if the data member is getatable.
590  /// - false, otherwise.
591  bool CanGetUnplacedContigCount(void) const;
592 
593  /// Reset UnplacedContigCount data member.
594  void ResetUnplacedContigCount(void);
595 
596  /// Get the UnplacedContigCount member data.
597  ///
598  /// @return
599  /// Copy of the member data.
600  TUnplacedContigCount GetUnplacedContigCount(void) const;
601 
602  /// Assign a value to UnplacedContigCount data member.
603  ///
604  /// @param value
605  /// Value to assign
606  void SetUnplacedContigCount(TUnplacedContigCount value);
607 
608  /// Assign a value to UnplacedContigCount data member.
609  ///
610  /// @return
611  /// Reference to the data value.
612  TUnplacedContigCount& SetUnplacedContigCount(void);
613 
614  ///total number of sequence positions in the
615  /// mapset
616  /// Check if a value has been assigned to SeqlocCount data member.
617  ///
618  /// Data member SeqlocCount is optional;
619  /// its type is defined as 'typedef int TSeqlocCount'
620  /// @return
621  /// - true, if a value has been assigned.
622  /// - false, otherwise.
623  bool IsSetSeqlocCount(void) const;
624 
625  /// Check if it is safe to call GetSeqlocCount method.
626  ///
627  /// @return
628  /// - true, if the data member is getatable.
629  /// - false, otherwise.
630  bool CanGetSeqlocCount(void) const;
631 
632  /// Reset SeqlocCount data member.
633  void ResetSeqlocCount(void);
634 
635  /// Get the SeqlocCount member data.
636  ///
637  /// @return
638  /// Copy of the member data.
639  TSeqlocCount GetSeqlocCount(void) const;
640 
641  /// Assign a value to SeqlocCount data member.
642  ///
643  /// @param value
644  /// Value to assign
645  void SetSeqlocCount(TSeqlocCount value);
646 
647  /// Assign a value to SeqlocCount data member.
648  ///
649  /// @return
650  /// Reference to the data value.
651  TSeqlocCount& SetSeqlocCount(void);
652 
653  ///Number of hits to alternative genomic haplotypes
654  /// (e.g. HLA DR region, KIR, or pseudo-autosomal regions like PAR)
655  /// within the assembly mapset. Note that positions on haplotypes
656  /// defined in other assemblies (a different assembly_group_label
657  /// value) will not be counted in this value.
658  /// Check if a value has been assigned to HapCount data member.
659  ///
660  /// Data member HapCount is optional;
661  /// its type is defined as 'typedef int THapCount'
662  /// @return
663  /// - true, if a value has been assigned.
664  /// - false, otherwise.
665  bool IsSetHapCount(void) const;
666 
667  /// Check if it is safe to call GetHapCount method.
668  ///
669  /// @return
670  /// - true, if the data member is getatable.
671  /// - false, otherwise.
672  bool CanGetHapCount(void) const;
673 
674  /// Reset HapCount data member.
675  void ResetHapCount(void);
676 
677  /// Get the HapCount member data.
678  ///
679  /// @return
680  /// Copy of the member data.
681  THapCount GetHapCount(void) const;
682 
683  /// Assign a value to HapCount data member.
684  ///
685  /// @param value
686  /// Value to assign
687  void SetHapCount(THapCount value);
688 
689  /// Assign a value to HapCount data member.
690  ///
691  /// @return
692  /// Reference to the data value.
693  THapCount& SetHapCount(void);
694 
695  /// Reset the whole object
696  void Reset(void);
697 
698 
699  private:
700  // Prohibit copy constructor and assignment operator
703 
704  // data
705  Uint4 m_set_State[1];
712  };
713  // types
715 
716  // member index
717  enum class E_memberIndex {
718  e__allMandatory = 0,
719  e_attlist,
720  e_snpStat
721  };
723 
724  // getters
725  // setters
726 
727  /// Check if a value has been assigned to Attlist data member.
728  ///
729  /// Data member Attlist is mandatory;
730  /// its type is defined as 'typedef C_Attlist TAttlist'
731  /// @return
732  /// - true, if a value has been assigned.
733  /// - false, otherwise.
734  bool IsSetAttlist(void) const;
735 
736  /// Check if it is safe to call GetAttlist method.
737  ///
738  /// @return
739  /// - true, if the data member is getatable.
740  /// - false, otherwise.
741  bool CanGetAttlist(void) const;
742 
743  /// Reset Attlist data member.
744  void ResetAttlist(void);
745 
746  /// Get the Attlist member data.
747  ///
748  /// @return
749  /// Reference to the member data.
750  const TAttlist& GetAttlist(void) const;
751 
752  /// Assign a value to Attlist data member.
753  ///
754  /// @param value
755  /// Reference to value.
756  void SetAttlist(TAttlist& value);
757 
758  /// Assign a value to Attlist data member.
759  ///
760  /// @return
761  /// Reference to the data value.
762  TAttlist& SetAttlist(void);
763 
764  /// Check if a value has been assigned to SnpStat data member.
765  ///
766  /// Data member SnpStat is mandatory
767  /// @return
768  /// - true, if a value has been assigned.
769  /// - false, otherwise.
770  bool IsSetSnpStat(void) const;
771 
772  /// Check if value of SnpStat member is getatable.
773  ///
774  /// @return
775  /// - false; the data member of type 'NULL' has no value.
776  bool CanGetSnpStat(void) const;
777 
778  /// Reset SnpStat data member.
779  void ResetSnpStat(void);
780 
781  /// Set NULL data member (assign 'NULL' value to SnpStat data member).
782  void SetSnpStat(void);
783 
784  /// Reset the whole object
785  void Reset(void);
786 
787 
788  private:
789  // Prohibit copy constructor and assignment operator
792 
793  // data
794  Uint4 m_set_State[1];
796  };
797  // types
799  typedef list< CRef< CComponent > > TComponent;
801 
802  // member index
803  enum class E_memberIndex {
804  e__allMandatory = 0,
805  e_attlist,
806  e_component,
807  e_snpStat
808  };
810 
811  // getters
812  // setters
813 
814  /// Check if a value has been assigned to Attlist data member.
815  ///
816  /// Data member Attlist is mandatory;
817  /// its type is defined as 'typedef C_Attlist TAttlist'
818  /// @return
819  /// - true, if a value has been assigned.
820  /// - false, otherwise.
821  bool IsSetAttlist(void) const;
822 
823  /// Check if it is safe to call GetAttlist method.
824  ///
825  /// @return
826  /// - true, if the data member is getatable.
827  /// - false, otherwise.
828  bool CanGetAttlist(void) const;
829 
830  /// Reset Attlist data member.
831  void ResetAttlist(void);
832 
833  /// Get the Attlist member data.
834  ///
835  /// @return
836  /// Reference to the member data.
837  const TAttlist& GetAttlist(void) const;
838 
839  /// Assign a value to Attlist data member.
840  ///
841  /// @param value
842  /// Reference to value.
843  void SetAttlist(TAttlist& value);
844 
845  /// Assign a value to Attlist data member.
846  ///
847  /// @return
848  /// Reference to the data value.
849  TAttlist& SetAttlist(void);
850 
851  /// Check if a value has been assigned to Component data member.
852  ///
853  /// Data member Component is optional;
854  /// its type is defined as 'typedef list< CRef< CComponent > > TComponent'
855  /// @return
856  /// - true, if a value has been assigned.
857  /// - false, otherwise.
858  bool IsSetComponent(void) const;
859 
860  /// Check if it is safe to call GetComponent method.
861  ///
862  /// @return
863  /// - true, if the data member is getatable.
864  /// - false, otherwise.
865  bool CanGetComponent(void) const;
866 
867  /// Reset Component data member.
868  void ResetComponent(void);
869 
870  /// Get the Component member data.
871  ///
872  /// @return
873  /// Reference to the member data.
874  const TComponent& GetComponent(void) const;
875 
876  /// Assign a value to Component data member.
877  ///
878  /// @return
879  /// Reference to the data value.
880  TComponent& SetComponent(void);
881 
882  /// Check if a value has been assigned to SnpStat data member.
883  ///
884  /// Data member SnpStat is mandatory;
885  /// its type is defined as 'typedef C_SnpStat TSnpStat'
886  /// @return
887  /// - true, if a value has been assigned.
888  /// - false, otherwise.
889  bool IsSetSnpStat(void) const;
890 
891  /// Check if it is safe to call GetSnpStat method.
892  ///
893  /// @return
894  /// - true, if the data member is getatable.
895  /// - false, otherwise.
896  bool CanGetSnpStat(void) const;
897 
898  /// Reset SnpStat data member.
899  void ResetSnpStat(void);
900 
901  /// Get the SnpStat member data.
902  ///
903  /// @return
904  /// Reference to the member data.
905  const TSnpStat& GetSnpStat(void) const;
906 
907  /// Assign a value to SnpStat data member.
908  ///
909  /// @param value
910  /// Reference to value.
911  void SetSnpStat(TSnpStat& value);
912 
913  /// Assign a value to SnpStat data member.
914  ///
915  /// @return
916  /// Reference to the data value.
917  TSnpStat& SetSnpStat(void);
918 
919  /// Reset the whole object
920  virtual void Reset(void);
921 
922 
923 private:
924  // Prohibit copy constructor and assignment operator
927 
928  // data
929  Uint4 m_set_State[1];
931  list< CRef< CComponent > > m_Component;
933 };
934 
935 /* @} */
936 
937 
938 
939 
940 
941 ///////////////////////////////////////////////////////////
942 ///////////////////// inline methods //////////////////////
943 ///////////////////////////////////////////////////////////
944 inline
946 {
947  return ((m_set_State[0] & 0x3) != 0);
948 }
949 
950 inline
952 {
953  return IsSetDbSnpBuild();
954 }
955 
956 inline
958 {
959  m_DbSnpBuild = 0;
960  m_set_State[0] &= ~0x3;
961 }
962 
963 inline
965 {
966  if (!CanGetDbSnpBuild()) {
967  ThrowUnassigned(0);
968  }
969  return m_DbSnpBuild;
970 }
971 
972 inline
974 {
975  m_DbSnpBuild = value;
976  m_set_State[0] |= 0x3;
977 }
978 
979 inline
981 {
982 #ifdef _DEBUG
983  if (!IsSetDbSnpBuild()) {
984  memset(&m_DbSnpBuild,UnassignedByte(),sizeof(m_DbSnpBuild));
985  }
986 #endif
987  m_set_State[0] |= 0x1;
988  return m_DbSnpBuild;
989 }
990 
991 inline
993 {
994  return ((m_set_State[0] & 0xc) != 0);
995 }
996 
997 inline
999 {
1000  return IsSetGenomeBuild();
1001 }
1002 
1003 inline
1005 {
1006  if (!CanGetGenomeBuild()) {
1007  ThrowUnassigned(1);
1008  }
1009  return m_GenomeBuild;
1010 }
1011 
1012 inline
1014 {
1015  m_GenomeBuild = value;
1016  m_set_State[0] |= 0xc;
1017 }
1018 
1019 inline
1021 {
1022  m_GenomeBuild = std::forward<CAssembly_Base::C_Attlist::TGenomeBuild>(value);
1023  m_set_State[0] |= 0xc;
1024 }
1025 
1026 inline
1028 {
1029 #ifdef _DEBUG
1030  if (!IsSetGenomeBuild()) {
1031  m_GenomeBuild = UnassignedString();
1032  }
1033 #endif
1034  m_set_State[0] |= 0x4;
1035  return m_GenomeBuild;
1036 }
1037 
1038 inline
1040 {
1041  return ((m_set_State[0] & 0x30) != 0);
1042 }
1043 
1044 inline
1046 {
1047  return IsSetGroupLabel();
1048 }
1049 
1050 inline
1052 {
1053  if (!CanGetGroupLabel()) {
1054  ThrowUnassigned(2);
1055  }
1056  return m_GroupLabel;
1057 }
1058 
1059 inline
1061 {
1062  m_GroupLabel = value;
1063  m_set_State[0] |= 0x30;
1064 }
1065 
1066 inline
1068 {
1069  m_GroupLabel = std::forward<CAssembly_Base::C_Attlist::TGroupLabel>(value);
1070  m_set_State[0] |= 0x30;
1071 }
1072 
1073 inline
1075 {
1076 #ifdef _DEBUG
1077  if (!IsSetGroupLabel()) {
1078  m_GroupLabel = UnassignedString();
1079  }
1080 #endif
1081  m_set_State[0] |= 0x10;
1082  return m_GroupLabel;
1083 }
1084 
1085 inline
1087 {
1088  return ((m_set_State[0] & 0xc0) != 0);
1089 }
1090 
1091 inline
1093 {
1094  return IsSetAssemblySource();
1095 }
1096 
1097 inline
1099 {
1100  if (!CanGetAssemblySource()) {
1101  ThrowUnassigned(3);
1102  }
1103  return m_AssemblySource;
1104 }
1105 
1106 inline
1108 {
1109  m_AssemblySource = value;
1110  m_set_State[0] |= 0xc0;
1111 }
1112 
1113 inline
1115 {
1116  m_AssemblySource = std::forward<CAssembly_Base::C_Attlist::TAssemblySource>(value);
1117  m_set_State[0] |= 0xc0;
1118 }
1119 
1120 inline
1122 {
1123 #ifdef _DEBUG
1124  if (!IsSetAssemblySource()) {
1125  m_AssemblySource = UnassignedString();
1126  }
1127 #endif
1128  m_set_State[0] |= 0x40;
1129  return m_AssemblySource;
1130 }
1131 
1132 inline
1134 {
1135  return ((m_set_State[0] & 0x300) != 0);
1136 }
1137 
1138 inline
1140 {
1141  return IsSetCurrent();
1142 }
1143 
1144 inline
1146 {
1147  m_Current = 0;
1148  m_set_State[0] &= ~0x300;
1149 }
1150 
1151 inline
1153 {
1154  if (!CanGetCurrent()) {
1155  ThrowUnassigned(4);
1156  }
1157  return m_Current;
1158 }
1159 
1160 inline
1162 {
1163  m_Current = value;
1164  m_set_State[0] |= 0x300;
1165 }
1166 
1167 inline
1169 {
1170 #ifdef _DEBUG
1171  if (!IsSetCurrent()) {
1172  memset(&m_Current,UnassignedByte(),sizeof(m_Current));
1173  }
1174 #endif
1175  m_set_State[0] |= 0x100;
1176  return m_Current;
1177 }
1178 
1179 inline
1181 {
1182  return ((m_set_State[0] & 0xc00) != 0);
1183 }
1184 
1185 inline
1187 {
1188  return IsSetReference();
1189 }
1190 
1191 inline
1193 {
1194  m_Reference = 0;
1195  m_set_State[0] &= ~0xc00;
1196 }
1197 
1198 inline
1200 {
1201  if (!CanGetReference()) {
1202  ThrowUnassigned(5);
1203  }
1204  return m_Reference;
1205 }
1206 
1207 inline
1209 {
1210  m_Reference = value;
1211  m_set_State[0] |= 0xc00;
1212 }
1213 
1214 inline
1216 {
1217 #ifdef _DEBUG
1218  if (!IsSetReference()) {
1219  memset(&m_Reference,UnassignedByte(),sizeof(m_Reference));
1220  }
1221 #endif
1222  m_set_State[0] |= 0x400;
1223  return m_Reference;
1224 }
1225 
1226 inline
1228 {
1229  return ((m_set_State[0] & 0x3) != 0);
1230 }
1231 
1232 inline
1234 {
1235  return IsSetMapWeight();
1236 }
1237 
1238 inline
1240 {
1241  m_MapWeight = (ESnpStat_attlist_mapWeight)(0);
1242  m_set_State[0] &= ~0x3;
1243 }
1244 
1245 inline
1247 {
1248  if (!CanGetMapWeight()) {
1249  ThrowUnassigned(0);
1250  }
1251  return m_MapWeight;
1252 }
1253 
1254 inline
1256 {
1257  m_MapWeight = value;
1258  m_set_State[0] |= 0x3;
1259 }
1260 
1261 inline
1263 {
1264 #ifdef _DEBUG
1265  if (!IsSetMapWeight()) {
1266  memset(&m_MapWeight,UnassignedByte(),sizeof(m_MapWeight));
1267  }
1268 #endif
1269  m_set_State[0] |= 0x1;
1270  return m_MapWeight;
1271 }
1272 
1273 inline
1275 {
1276  return ((m_set_State[0] & 0xc) != 0);
1277 }
1278 
1279 inline
1281 {
1282  return IsSetChromCount();
1283 }
1284 
1285 inline
1287 {
1288  m_ChromCount = 0;
1289  m_set_State[0] &= ~0xc;
1290 }
1291 
1292 inline
1294 {
1295  if (!CanGetChromCount()) {
1296  ThrowUnassigned(1);
1297  }
1298  return m_ChromCount;
1299 }
1300 
1301 inline
1303 {
1304  m_ChromCount = value;
1305  m_set_State[0] |= 0xc;
1306 }
1307 
1308 inline
1310 {
1311 #ifdef _DEBUG
1312  if (!IsSetChromCount()) {
1313  memset(&m_ChromCount,UnassignedByte(),sizeof(m_ChromCount));
1314  }
1315 #endif
1316  m_set_State[0] |= 0x4;
1317  return m_ChromCount;
1318 }
1319 
1320 inline
1322 {
1323  return ((m_set_State[0] & 0x30) != 0);
1324 }
1325 
1326 inline
1328 {
1329  return IsSetPlacedContigCount();
1330 }
1331 
1332 inline
1334 {
1335  m_PlacedContigCount = 0;
1336  m_set_State[0] &= ~0x30;
1337 }
1338 
1339 inline
1341 {
1342  if (!CanGetPlacedContigCount()) {
1343  ThrowUnassigned(2);
1344  }
1345  return m_PlacedContigCount;
1346 }
1347 
1348 inline
1350 {
1351  m_PlacedContigCount = value;
1352  m_set_State[0] |= 0x30;
1353 }
1354 
1355 inline
1357 {
1358 #ifdef _DEBUG
1359  if (!IsSetPlacedContigCount()) {
1360  memset(&m_PlacedContigCount,UnassignedByte(),sizeof(m_PlacedContigCount));
1361  }
1362 #endif
1363  m_set_State[0] |= 0x10;
1364  return m_PlacedContigCount;
1365 }
1366 
1367 inline
1369 {
1370  return ((m_set_State[0] & 0xc0) != 0);
1371 }
1372 
1373 inline
1375 {
1376  return IsSetUnplacedContigCount();
1377 }
1378 
1379 inline
1381 {
1382  m_UnplacedContigCount = 0;
1383  m_set_State[0] &= ~0xc0;
1384 }
1385 
1386 inline
1388 {
1389  if (!CanGetUnplacedContigCount()) {
1390  ThrowUnassigned(3);
1391  }
1392  return m_UnplacedContigCount;
1393 }
1394 
1395 inline
1397 {
1398  m_UnplacedContigCount = value;
1399  m_set_State[0] |= 0xc0;
1400 }
1401 
1402 inline
1404 {
1405 #ifdef _DEBUG
1406  if (!IsSetUnplacedContigCount()) {
1407  memset(&m_UnplacedContigCount,UnassignedByte(),sizeof(m_UnplacedContigCount));
1408  }
1409 #endif
1410  m_set_State[0] |= 0x40;
1411  return m_UnplacedContigCount;
1412 }
1413 
1414 inline
1416 {
1417  return ((m_set_State[0] & 0x300) != 0);
1418 }
1419 
1420 inline
1422 {
1423  return IsSetSeqlocCount();
1424 }
1425 
1426 inline
1428 {
1429  m_SeqlocCount = 0;
1430  m_set_State[0] &= ~0x300;
1431 }
1432 
1433 inline
1435 {
1436  if (!CanGetSeqlocCount()) {
1437  ThrowUnassigned(4);
1438  }
1439  return m_SeqlocCount;
1440 }
1441 
1442 inline
1444 {
1445  m_SeqlocCount = value;
1446  m_set_State[0] |= 0x300;
1447 }
1448 
1449 inline
1451 {
1452 #ifdef _DEBUG
1453  if (!IsSetSeqlocCount()) {
1454  memset(&m_SeqlocCount,UnassignedByte(),sizeof(m_SeqlocCount));
1455  }
1456 #endif
1457  m_set_State[0] |= 0x100;
1458  return m_SeqlocCount;
1459 }
1460 
1461 inline
1463 {
1464  return ((m_set_State[0] & 0xc00) != 0);
1465 }
1466 
1467 inline
1469 {
1470  return IsSetHapCount();
1471 }
1472 
1473 inline
1475 {
1476  m_HapCount = 0;
1477  m_set_State[0] &= ~0xc00;
1478 }
1479 
1480 inline
1482 {
1483  if (!CanGetHapCount()) {
1484  ThrowUnassigned(5);
1485  }
1486  return m_HapCount;
1487 }
1488 
1489 inline
1491 {
1492  m_HapCount = value;
1493  m_set_State[0] |= 0xc00;
1494 }
1495 
1496 inline
1498 {
1499 #ifdef _DEBUG
1500  if (!IsSetHapCount()) {
1501  memset(&m_HapCount,UnassignedByte(),sizeof(m_HapCount));
1502  }
1503 #endif
1504  m_set_State[0] |= 0x400;
1505  return m_HapCount;
1506 }
1507 
1508 inline
1510 {
1511  return m_Attlist.NotEmpty();
1512 }
1513 
1514 inline
1516 {
1517  return true;
1518 }
1519 
1520 inline
1522 {
1523  if ( !m_Attlist ) {
1524  const_cast<C_SnpStat*>(this)->ResetAttlist();
1525  }
1526  return (*m_Attlist);
1527 }
1528 
1529 inline
1531 {
1532  if ( !m_Attlist ) {
1533  ResetAttlist();
1534  }
1535  return (*m_Attlist);
1536 }
1537 
1538 inline
1540 {
1541  return ((m_set_State[0] & 0xc) != 0);
1542 }
1543 
1544 inline
1546 {
1547  return false;
1548 }
1549 
1550 inline
1552 {
1553  m_set_State[0] &= ~0xc;
1554 }
1555 
1556 inline
1558 {
1559  m_set_State[0] |= 0xc;
1560 }
1561 
1562 inline
1564 {
1565  return m_Attlist.NotEmpty();
1566 }
1567 
1568 inline
1570 {
1571  return true;
1572 }
1573 
1574 inline
1576 {
1577  if ( !m_Attlist ) {
1578  const_cast<CAssembly_Base*>(this)->ResetAttlist();
1579  }
1580  return (*m_Attlist);
1581 }
1582 
1583 inline
1585 {
1586  if ( !m_Attlist ) {
1587  ResetAttlist();
1588  }
1589  return (*m_Attlist);
1590 }
1591 
1592 inline
1594 {
1595  return ((m_set_State[0] & 0xc) != 0);
1596 }
1597 
1598 inline
1600 {
1601  return true;
1602 }
1603 
1604 inline
1606 {
1607  return m_Component;
1608 }
1609 
1610 inline
1612 {
1613  m_set_State[0] |= 0x4;
1614  return m_Component;
1615 }
1616 
1617 inline
1619 {
1620  return m_SnpStat.NotEmpty();
1621 }
1622 
1623 inline
1625 {
1626  return true;
1627 }
1628 
1629 inline
1631 {
1632  if ( !m_SnpStat ) {
1633  const_cast<CAssembly_Base*>(this)->ResetSnpStat();
1634  }
1635  return (*m_SnpStat);
1636 }
1637 
1638 inline
1640 {
1641  if ( !m_SnpStat ) {
1642  ResetSnpStat();
1643  }
1644  return (*m_SnpStat);
1645 }
1646 
1647 ///////////////////////////////////////////////////////////
1648 ////////////////// end of inline methods //////////////////
1649 ///////////////////////////////////////////////////////////
1650 
1651 
1652 
1653 
1654 
1655 END_objects_SCOPE // namespace ncbi::objects::
1656 
1658 
1659 
1660 #endif // OBJECTS_DOCSUM_ASSEMBLY_BASE_HPP
A collection of genome sequence records (curated gene regions (NG's), contigs (NWNT's) and chromosome...
Definition: Assembly_.hpp:81
CComponent –.
Definition: Component.hpp:66
CRef –.
Definition: ncbiobj.hpp:618
Base class for all serializable objects.
Definition: serialbase.hpp:150
char value[7]
Definition: config.c:431
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
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_DOCSUM_EXPORT
Definition: ncbi_export.h:456
CAssembly_Base & operator=(const CAssembly_Base &)
bool IsSetReference(void) const
Check if a value has been assigned to Reference data member.
Definition: Assembly_.hpp:1180
bool IsSetDbSnpBuild(void) const
dbSNP build number defining the rsid set aligned to this assembly Check if a value has been assigned ...
Definition: Assembly_.hpp:945
void ResetUnplacedContigCount(void)
Reset UnplacedContigCount data member.
Definition: Assembly_.hpp:1380
bool IsSetComponent(void) const
Check if a value has been assigned to Component data member.
Definition: Assembly_.hpp:1593
Tparent::CMemberIndex< E_memberIndex, 7 > TmemberIndex
Definition: Assembly_.hpp:455
TSeqlocCount GetSeqlocCount(void) const
Get the SeqlocCount member data.
Definition: Assembly_.hpp:1434
const TSnpStat & GetSnpStat(void) const
Get the SnpStat member data.
Definition: Assembly_.hpp:1630
void ResetSnpStat(void)
Reset SnpStat data member.
Definition: Assembly_.hpp:1551
bool IsSetPlacedContigCount(void) const
number of distinct contigs [ gi | accession[.version] ] in the mapset Check if a value has been assig...
Definition: Assembly_.hpp:1321
C_Attlist & operator=(const C_Attlist &)
bool CanGetDbSnpBuild(void) const
Check if it is safe to call GetDbSnpBuild method.
Definition: Assembly_.hpp:951
Uint4 m_set_State[1]
Definition: Assembly_.hpp:929
void ResetPlacedContigCount(void)
Reset PlacedContigCount data member.
Definition: Assembly_.hpp:1333
C_Attlist(const C_Attlist &)
bool CanGetGenomeBuild(void) const
Check if it is safe to call GetGenomeBuild method.
Definition: Assembly_.hpp:998
void ResetHapCount(void)
Reset HapCount data member.
Definition: Assembly_.hpp:1474
TAttlist & SetAttlist(void)
Assign a value to Attlist data member.
Definition: Assembly_.hpp:1530
bool IsSetChromCount(void) const
number of distinct chromosomes in the mapset Check if a value has been assigned to ChromCount data me...
Definition: Assembly_.hpp:1274
Tparent::CMemberIndex< E_memberIndex, 3 > TmemberIndex
Definition: Assembly_.hpp:722
bool CanGetAttlist(void) const
Check if it is safe to call GetAttlist method.
Definition: Assembly_.hpp:1569
C_SnpStat(const C_SnpStat &)
const TComponent & GetComponent(void) const
Get the Component member data.
Definition: Assembly_.hpp:1605
ESnpStat_attlist_mapWeight
summary measure of placement precision in the assembly
Definition: Assembly_.hpp:426
void ResetSnpStat(void)
Reset SnpStat data member.
Definition: Assembly_.cpp:226
CRef< TAttlist > m_Attlist
Definition: Assembly_.hpp:930
C_SnpStat TSnpStat
Definition: Assembly_.hpp:800
bool CanGetCurrent(void) const
Check if it is safe to call GetCurrent method.
Definition: Assembly_.hpp:1139
bool IsSetAssemblySource(void) const
Name of the group(s) or organization(s) that generated the assembly Check if a value has been assigne...
Definition: Assembly_.hpp:1086
TChromCount & SetChromCount(void)
Assign a value to ChromCount data member.
Definition: Assembly_.hpp:1309
bool IsSetSnpStat(void) const
Check if a value has been assigned to SnpStat data member.
Definition: Assembly_.hpp:1539
list< CRef< CComponent > > TComponent
Definition: Assembly_.hpp:799
TSeqlocCount & SetSeqlocCount(void)
Assign a value to SeqlocCount data member.
Definition: Assembly_.hpp:1450
TPlacedContigCount & SetPlacedContigCount(void)
Assign a value to PlacedContigCount data member.
Definition: Assembly_.hpp:1356
bool CanGetMapWeight(void) const
Check if it is safe to call GetMapWeight method.
Definition: Assembly_.hpp:1233
TReference GetReference(void) const
Get the Reference member data.
Definition: Assembly_.hpp:1199
void ResetSeqlocCount(void)
Reset SeqlocCount data member.
Definition: Assembly_.hpp:1427
ESnpStat_attlist_mapWeight TMapWeight
Definition: Assembly_.hpp:438
TSnpStat & SetSnpStat(void)
Assign a value to SnpStat data member.
Definition: Assembly_.hpp:1639
bool CanGetSnpStat(void) const
Check if it is safe to call GetSnpStat method.
Definition: Assembly_.hpp:1624
void ResetDbSnpBuild(void)
Reset DbSnpBuild data member.
Definition: Assembly_.hpp:957
void ResetAttlist(void)
Reset Attlist data member.
Definition: Assembly_.cpp:206
TReference & SetReference(void)
Assign a value to Reference data member.
Definition: Assembly_.hpp:1215
bool IsSetUnplacedContigCount(void) const
number of sequence postions to a contig with unknown chromosomal assignment Check if a value has been...
Definition: Assembly_.hpp:1368
const TGenomeBuild & GetGenomeBuild(void) const
Get the GenomeBuild member data.
Definition: Assembly_.hpp:1004
TUnplacedContigCount GetUnplacedContigCount(void) const
Get the UnplacedContigCount member data.
Definition: Assembly_.hpp:1387
TDbSnpBuild & SetDbSnpBuild(void)
Assign a value to DbSnpBuild data member.
Definition: Assembly_.hpp:980
bool CanGetHapCount(void) const
Check if it is safe to call GetHapCount method.
Definition: Assembly_.hpp:1468
bool CanGetAssemblySource(void) const
Check if it is safe to call GetAssemblySource method.
Definition: Assembly_.hpp:1092
CAssembly_Base(const CAssembly_Base &)
const TAttlist & GetAttlist(void) const
Get the Attlist member data.
Definition: Assembly_.hpp:1521
TComponent & SetComponent(void)
Assign a value to Component data member.
Definition: Assembly_.hpp:1611
bool CanGetComponent(void) const
Check if it is safe to call GetComponent method.
Definition: Assembly_.hpp:1599
C_Attlist & operator=(const C_Attlist &)
TPlacedContigCount GetPlacedContigCount(void) const
Get the PlacedContigCount member data.
Definition: Assembly_.hpp:1340
CSerialObject Tparent
Definition: Assembly_.hpp:82
TCurrent GetCurrent(void) const
Get the Current member data.
Definition: Assembly_.hpp:1152
const TAttlist & GetAttlist(void) const
Get the Attlist member data.
Definition: Assembly_.hpp:1575
Tparent::CMemberIndex< E_memberIndex, 4 > TmemberIndex
Definition: Assembly_.hpp:809
TAssemblySource & SetAssemblySource(void)
Assign a value to AssemblySource data member.
Definition: Assembly_.hpp:1121
void ResetChromCount(void)
Reset ChromCount data member.
Definition: Assembly_.hpp:1286
bool IsSetSeqlocCount(void) const
total number of sequence positions in the mapset Check if a value has been assigned to SeqlocCount da...
Definition: Assembly_.hpp:1415
TDbSnpBuild GetDbSnpBuild(void) const
Get the DbSnpBuild member data.
Definition: Assembly_.hpp:964
bool IsSetAttlist(void) const
Check if a value has been assigned to Attlist data member.
Definition: Assembly_.hpp:1509
const TAssemblySource & GetAssemblySource(void) const
Get the AssemblySource member data.
Definition: Assembly_.hpp:1098
void ResetMapWeight(void)
Reset MapWeight data member.
Definition: Assembly_.hpp:1239
THapCount GetHapCount(void) const
Get the HapCount member data.
Definition: Assembly_.hpp:1481
TMapWeight GetMapWeight(void) const
Get the MapWeight member data.
Definition: Assembly_.hpp:1246
THapCount & SetHapCount(void)
Assign a value to HapCount data member.
Definition: Assembly_.hpp:1497
TGenomeBuild & SetGenomeBuild(void)
Assign a value to GenomeBuild data member.
Definition: Assembly_.hpp:1027
TGroupLabel & SetGroupLabel(void)
Assign a value to GroupLabel data member.
Definition: Assembly_.hpp:1074
bool IsSetGroupLabel(void) const
High-level classification of the assembly to distinguish reference projects from alternate solutions.
Definition: Assembly_.hpp:1039
C_SnpStat & operator=(const C_SnpStat &)
TUnplacedContigCount & SetUnplacedContigCount(void)
Assign a value to UnplacedContigCount data member.
Definition: Assembly_.hpp:1403
C_Attlist TAttlist
Definition: Assembly_.hpp:798
bool IsSetGenomeBuild(void) const
assembly build number with possible 'subbuild' version numbers to reflect updates in gene annotation ...
Definition: Assembly_.hpp:992
bool IsSetAttlist(void) const
Check if a value has been assigned to Attlist data member.
Definition: Assembly_.hpp:1563
bool IsSetHapCount(void) const
Number of hits to alternative genomic haplotypes (e.g.
Definition: Assembly_.hpp:1462
TChromCount GetChromCount(void) const
Get the ChromCount member data.
Definition: Assembly_.hpp:1293
CRef< TSnpStat > m_SnpStat
Definition: Assembly_.hpp:932
bool IsSetCurrent(void) const
Marks the current genomic assembly Check if a value has been assigned to Current data member.
Definition: Assembly_.hpp:1133
bool CanGetSnpStat(void) const
Check if value of SnpStat member is getatable.
Definition: Assembly_.hpp:1545
bool CanGetGroupLabel(void) const
Check if it is safe to call GetGroupLabel method.
Definition: Assembly_.hpp:1045
bool IsSetMapWeight(void) const
Check if a value has been assigned to MapWeight data member.
Definition: Assembly_.hpp:1227
TAttlist & SetAttlist(void)
Assign a value to Attlist data member.
Definition: Assembly_.hpp:1584
CRef< TAttlist > m_Attlist
Definition: Assembly_.hpp:795
void ResetReference(void)
Reset Reference data member.
Definition: Assembly_.hpp:1192
const TGroupLabel & GetGroupLabel(void) const
Get the GroupLabel member data.
Definition: Assembly_.hpp:1051
bool IsSetSnpStat(void) const
Check if a value has been assigned to SnpStat data member.
Definition: Assembly_.hpp:1618
list< CRef< CComponent > > m_Component
Definition: Assembly_.hpp:931
ESnpStat_attlist_mapWeight m_MapWeight
Definition: Assembly_.hpp:706
bool CanGetUnplacedContigCount(void) const
Check if it is safe to call GetUnplacedContigCount method.
Definition: Assembly_.hpp:1374
TMapWeight & SetMapWeight(void)
Assign a value to MapWeight data member.
Definition: Assembly_.hpp:1262
DECLARE_INTERNAL_TYPE_INFO()
bool CanGetPlacedContigCount(void) const
Check if it is safe to call GetPlacedContigCount method.
Definition: Assembly_.hpp:1327
bool CanGetAttlist(void) const
Check if it is safe to call GetAttlist method.
Definition: Assembly_.hpp:1515
Tparent::CMemberIndex< E_memberIndex, 7 > TmemberIndex
Definition: Assembly_.hpp:127
bool CanGetSeqlocCount(void) const
Check if it is safe to call GetSeqlocCount method.
Definition: Assembly_.hpp:1421
bool CanGetChromCount(void) const
Check if it is safe to call GetChromCount method.
Definition: Assembly_.hpp:1280
bool CanGetReference(void) const
Check if it is safe to call GetReference method.
Definition: Assembly_.hpp:1186
void ResetCurrent(void)
Reset Current data member.
Definition: Assembly_.hpp:1145
TCurrent & SetCurrent(void)
Assign a value to Current data member.
Definition: Assembly_.hpp:1168
void SetSnpStat(void)
Set NULL data member (assign 'NULL' value to SnpStat data member).
Definition: Assembly_.hpp:1557
Modified on Mon Feb 26 04:04:05 2024 by modify_doxy.py rev. 669887