NCBI C++ ToolKit
GC_Sequence_.hpp
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27 
28 /// @file GC_Sequence_.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_SEQUENCE_BASE_HPP
42 #define OBJECTS_GENOMECOLL_GC_SEQUENCE_BASE_HPP
43 
44 // standard includes
45 #include <serial/serialbase.hpp>
46 
47 // generated includes
48 #include <list>
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 CDelta_ext;
62 class CGC_SequenceStats;
64 class CGC_TypedSeqId;
65 class CSeq_annot;
66 class CSeq_descr;
67 class CSeq_id;
68 
69 
70 // generated classes
71 
72 
73 /** @addtogroup dataspec_NCBI_GenomeCollection
74  *
75  * @{
76  */
77 
78 /////////////////////////////////////////////////////////////////////////////
79 /// GC-Sequence:
80 /// Used for scaffolds, scaffold-sets and components in Gencoll terminology.
81 /// Theoretically can support sequences decsribed with more levels than
82 /// Chromosome / scaffold-set/scaffold/component.
83 /// The meaning of the GC-Sequence record - if it is component, scaffold or
84 /// or scaffold-set, is defined by its context.
85 /// ??? DO WE NEED A FIELD TO SPECIFY WHAT LEVEL IT IS???
86 ///
87 /// GC-Sequences are made of GC-Sequences: At the lowest level there is only one
88 /// seq-id of a component with no further structure.
89 ///
90 /// CGC_Sequence_Base --
91 ///
92 
94 {
96 public:
97  // constructor
98  CGC_Sequence_Base(void);
99  // destructor
100  virtual ~CGC_Sequence_Base(void);
101 
102  // type info
104 
105  enum EPatch_type {
106  ePatch_type_novel = 0,
107  ePatch_type_fix = 1,
108  ePatch_type_other = 255 ///< stopper
109  };
110 
111  /// Access to EPatch_type's attributes (values, names) as defined in spec
112  static const NCBI_NS_NCBI::CEnumeratedTypeValues* ENUM_METHOD_NAME(EPatch_type)(void);
113 
114  // types
115  typedef CSeq_id TSeq_id;
116  typedef list< CRef< CGC_TypedSeqId > > TSeq_id_synonyms;
118  typedef list< CRef< CSeq_annot > > TAnnot;
119  typedef list< CRef< CGC_TaggedSequences > > TSequences;
122  typedef int TPatch_type;
123  typedef list< int > TRoles;
124 
125  // member index
126  enum class E_memberIndex {
127  e__allMandatory = 0,
128  e_seq_id,
129  e_seq_id_synonyms,
130  e_descr,
131  e_annot,
132  e_sequences,
133  e_structure,
134  e_stats,
135  e_patch_type,
136  e_roles
137  };
139 
140  // getters
141  // setters
142 
143  /// identifiers are: Local / gpipe-satellite / genbank / refseq
144  /// local is merely local name (or maybe with WGS accession??)
145  /// others are accession/ver/gi
146  ///
147  /// Main identifier:
148  /// we will report the one that matches the context of who asked.
149  /// Check if a value has been assigned to Seq_id data member.
150  ///
151  /// Data member Seq_id is mandatory;
152  /// its type is defined as 'typedef CSeq_id TSeq_id'
153  /// @return
154  /// - true, if a value has been assigned.
155  /// - false, otherwise.
156  bool IsSetSeq_id(void) const;
157 
158  /// Check if it is safe to call GetSeq_id method.
159  ///
160  /// @return
161  /// - true, if the data member is getatable.
162  /// - false, otherwise.
163  bool CanGetSeq_id(void) const;
164 
165  /// Reset Seq_id data member.
166  void ResetSeq_id(void);
167 
168  /// Get the Seq_id member data.
169  ///
170  /// @return
171  /// Reference to the member data.
172  const TSeq_id& GetSeq_id(void) const;
173 
174  /// Assign a value to Seq_id data member.
175  ///
176  /// @param value
177  /// Reference to value.
178  void SetSeq_id(TSeq_id& value);
179 
180  /// Assign a value to Seq_id data member.
181  ///
182  /// @return
183  /// Reference to the data value.
184  TSeq_id& SetSeq_id(void);
185 
186  /// Other known identifiers: Local / gpipe-satellite / genbank / refseq
187  /// Check if a value has been assigned to Seq_id_synonyms data member.
188  ///
189  /// Data member Seq_id_synonyms is optional;
190  /// its type is defined as 'typedef list< CRef< CGC_TypedSeqId > > TSeq_id_synonyms'
191  /// @return
192  /// - true, if a value has been assigned.
193  /// - false, otherwise.
194  bool IsSetSeq_id_synonyms(void) const;
195 
196  /// Check if it is safe to call GetSeq_id_synonyms method.
197  ///
198  /// @return
199  /// - true, if the data member is getatable.
200  /// - false, otherwise.
201  bool CanGetSeq_id_synonyms(void) const;
202 
203  /// Reset Seq_id_synonyms data member.
204  void ResetSeq_id_synonyms(void);
205 
206  /// Get the Seq_id_synonyms member data.
207  ///
208  /// @return
209  /// Reference to the member data.
210  const TSeq_id_synonyms& GetSeq_id_synonyms(void) const;
211 
212  /// Assign a value to Seq_id_synonyms data member.
213  ///
214  /// @return
215  /// Reference to the data value.
216  TSeq_id_synonyms& SetSeq_id_synonyms(void);
217 
218  /// Various attributes assigned at this level:
219  /// biosrc, comments, publications...
220  /// Check if a value has been assigned to Descr data member.
221  ///
222  /// Data member Descr is optional;
223  /// its type is defined as 'typedef CSeq_descr TDescr'
224  /// @return
225  /// - true, if a value has been assigned.
226  /// - false, otherwise.
227  bool IsSetDescr(void) const;
228 
229  /// Check if it is safe to call GetDescr method.
230  ///
231  /// @return
232  /// - true, if the data member is getatable.
233  /// - false, otherwise.
234  bool CanGetDescr(void) const;
235 
236  /// Reset Descr data member.
237  void ResetDescr(void);
238 
239  /// Get the Descr member data.
240  ///
241  /// @return
242  /// Reference to the member data.
243  const TDescr& GetDescr(void) const;
244 
245  /// Assign a value to Descr data member.
246  ///
247  /// @param value
248  /// Reference to value.
249  void SetDescr(TDescr& value);
250 
251  /// Assign a value to Descr data member.
252  ///
253  /// @return
254  /// Reference to the data value.
255  TDescr& SetDescr(void);
256 
257  /// Feature annotation;
258  /// Contains Pseudo Autosomal regions on chromosomes and scaffolds in the
259  /// following format:
260  /// Id = <ID of PAR (ex:"PAR#1")>
261  /// Desc (set of Annot-descr)
262  /// Name: "pseudo autosomal region"
263  /// Region (seq-loc): int (seq-interval)
264  /// Id: <GI of chromosome>
265  /// From: <start-position of region>
266  /// To : <end-position of region>
267  /// Data: locs (set of seq-loc):
268  /// List of int (seq-interval):
269  /// Id: GI of scaffold
270  /// From/to: position on scaffold that belongs to this PAR region.
271  /// <and repeat this for additional scaffolds on same PAR region>
272  ///
273  /// in alt-loci units - contain alignment of this sequence to the primary
274  /// unit
275  /// Check if a value has been assigned to Annot data member.
276  ///
277  /// Data member Annot is optional;
278  /// its type is defined as 'typedef list< CRef< CSeq_annot > > TAnnot'
279  /// @return
280  /// - true, if a value has been assigned.
281  /// - false, otherwise.
282  bool IsSetAnnot(void) const;
283 
284  /// Check if it is safe to call GetAnnot method.
285  ///
286  /// @return
287  /// - true, if the data member is getatable.
288  /// - false, otherwise.
289  bool CanGetAnnot(void) const;
290 
291  /// Reset Annot data member.
292  void ResetAnnot(void);
293 
294  /// Get the Annot member data.
295  ///
296  /// @return
297  /// Reference to the member data.
298  const TAnnot& GetAnnot(void) const;
299 
300  /// Assign a value to Annot data member.
301  ///
302  /// @return
303  /// Reference to the data value.
304  TAnnot& SetAnnot(void);
305 
306  /// placed: populated both on chromosome and scaffold levels
307  /// unlocalized: populated on chromosome level
308  /// Check if a value has been assigned to Sequences data member.
309  ///
310  /// Data member Sequences is optional;
311  /// its type is defined as 'typedef list< CRef< CGC_TaggedSequences > > TSequences'
312  /// @return
313  /// - true, if a value has been assigned.
314  /// - false, otherwise.
315  bool IsSetSequences(void) const;
316 
317  /// Check if it is safe to call GetSequences method.
318  ///
319  /// @return
320  /// - true, if the data member is getatable.
321  /// - false, otherwise.
322  bool CanGetSequences(void) const;
323 
324  /// Reset Sequences data member.
325  void ResetSequences(void);
326 
327  /// Get the Sequences member data.
328  ///
329  /// @return
330  /// Reference to the member data.
331  const TSequences& GetSequences(void) const;
332 
333  /// Assign a value to Sequences data member.
334  ///
335  /// @return
336  /// Reference to the data value.
337  TSequences& SetSequences(void);
338 
339  /// locations of ordered scaffolds/components
340  /// Check if a value has been assigned to Structure data member.
341  ///
342  /// Data member Structure is optional;
343  /// its type is defined as 'typedef CDelta_ext TStructure'
344  /// @return
345  /// - true, if a value has been assigned.
346  /// - false, otherwise.
347  bool IsSetStructure(void) const;
348 
349  /// Check if it is safe to call GetStructure method.
350  ///
351  /// @return
352  /// - true, if the data member is getatable.
353  /// - false, otherwise.
354  bool CanGetStructure(void) const;
355 
356  /// Reset Structure data member.
357  void ResetStructure(void);
358 
359  /// Get the Structure member data.
360  ///
361  /// @return
362  /// Reference to the member data.
363  const TStructure& GetStructure(void) const;
364 
365  /// Assign a value to Structure data member.
366  ///
367  /// @param value
368  /// Reference to value.
369  void SetStructure(TStructure& value);
370 
371  /// Assign a value to Structure data member.
372  ///
373  /// @return
374  /// Reference to the data value.
375  TStructure& SetStructure(void);
376 
377  /// statistics
378  /// Check if a value has been assigned to Stats data member.
379  ///
380  /// Data member Stats is optional;
381  /// its type is defined as 'typedef CGC_SequenceStats TStats'
382  /// @return
383  /// - true, if a value has been assigned.
384  /// - false, otherwise.
385  bool IsSetStats(void) const;
386 
387  /// Check if it is safe to call GetStats method.
388  ///
389  /// @return
390  /// - true, if the data member is getatable.
391  /// - false, otherwise.
392  bool CanGetStats(void) const;
393 
394  /// Reset Stats data member.
395  void ResetStats(void);
396 
397  /// Get the Stats member data.
398  ///
399  /// @return
400  /// Reference to the member data.
401  const TStats& GetStats(void) const;
402 
403  /// Assign a value to Stats data member.
404  ///
405  /// @param value
406  /// Reference to value.
407  void SetStats(TStats& value);
408 
409  /// Assign a value to Stats data member.
410  ///
411  /// @return
412  /// Reference to the data value.
413  TStats& SetStats(void);
414 
415  /// Check if a value has been assigned to Patch_type data member.
416  ///
417  /// Data member Patch_type is optional;
418  /// its type is defined as 'typedef int TPatch_type'
419  /// @return
420  /// - true, if a value has been assigned.
421  /// - false, otherwise.
422  bool IsSetPatch_type(void) const;
423 
424  /// Check if it is safe to call GetPatch_type method.
425  ///
426  /// @return
427  /// - true, if the data member is getatable.
428  /// - false, otherwise.
429  bool CanGetPatch_type(void) const;
430 
431  /// Reset Patch_type data member.
432  void ResetPatch_type(void);
433 
434  /// Get the Patch_type member data.
435  ///
436  /// @return
437  /// Copy of the member data.
438  TPatch_type GetPatch_type(void) const;
439 
440  /// Assign a value to Patch_type data member.
441  ///
442  /// @param value
443  /// Value to assign
444  void SetPatch_type(TPatch_type value);
445 
446  /// Assign a value to Patch_type data member.
447  ///
448  /// @return
449  /// Reference to the data value.
450  TPatch_type& SetPatch_type(void);
451 
452  /// sequence-role: what role(s) does this sequence have in the assembly
453  /// Check if a value has been assigned to Roles data member.
454  ///
455  /// Data member Roles is optional;
456  /// its type is defined as 'typedef list< int > TRoles'
457  /// @return
458  /// - true, if a value has been assigned.
459  /// - false, otherwise.
460  bool IsSetRoles(void) const;
461 
462  /// Check if it is safe to call GetRoles method.
463  ///
464  /// @return
465  /// - true, if the data member is getatable.
466  /// - false, otherwise.
467  bool CanGetRoles(void) const;
468 
469  /// Reset Roles data member.
470  void ResetRoles(void);
471 
472  /// Get the Roles member data.
473  ///
474  /// @return
475  /// Reference to the member data.
476  const TRoles& GetRoles(void) const;
477 
478  /// Assign a value to Roles data member.
479  ///
480  /// @return
481  /// Reference to the data value.
482  TRoles& SetRoles(void);
483 
484  /// Reset the whole object
485  virtual void Reset(void);
486 
487 
488 private:
489  // Prohibit copy constructor and assignment operator
492 
493  // data
494  Uint4 m_set_State[1];
496  list< CRef< CGC_TypedSeqId > > m_Seq_id_synonyms;
498  list< CRef< CSeq_annot > > m_Annot;
499  list< CRef< CGC_TaggedSequences > > m_Sequences;
503  list< int > m_Roles;
504 };
505 
506 /* @} */
507 
508 
509 
510 
511 
512 ///////////////////////////////////////////////////////////
513 ///////////////////// inline methods //////////////////////
514 ///////////////////////////////////////////////////////////
515 inline
517 {
518  return m_Seq_id.NotEmpty();
519 }
520 
521 inline
523 {
524  return true;
525 }
526 
527 inline
529 {
530  if ( !m_Seq_id ) {
531  const_cast<CGC_Sequence_Base*>(this)->ResetSeq_id();
532  }
533  return (*m_Seq_id);
534 }
535 
536 inline
538 {
539  if ( !m_Seq_id ) {
540  ResetSeq_id();
541  }
542  return (*m_Seq_id);
543 }
544 
545 inline
547 {
548  return ((m_set_State[0] & 0xc) != 0);
549 }
550 
551 inline
553 {
554  return true;
555 }
556 
557 inline
559 {
560  return m_Seq_id_synonyms;
561 }
562 
563 inline
565 {
566  m_set_State[0] |= 0x4;
567  return m_Seq_id_synonyms;
568 }
569 
570 inline
572 {
573  return m_Descr.NotEmpty();
574 }
575 
576 inline
578 {
579  return IsSetDescr();
580 }
581 
582 inline
584 {
585  if (!CanGetDescr()) {
586  ThrowUnassigned(2);
587  }
588  return (*m_Descr);
589 }
590 
591 inline
593 {
594  return ((m_set_State[0] & 0xc0) != 0);
595 }
596 
597 inline
599 {
600  return true;
601 }
602 
603 inline
605 {
606  return m_Annot;
607 }
608 
609 inline
611 {
612  m_set_State[0] |= 0x40;
613  return m_Annot;
614 }
615 
616 inline
618 {
619  return ((m_set_State[0] & 0x300) != 0);
620 }
621 
622 inline
624 {
625  return true;
626 }
627 
628 inline
630 {
631  return m_Sequences;
632 }
633 
634 inline
636 {
637  m_set_State[0] |= 0x100;
638  return m_Sequences;
639 }
640 
641 inline
643 {
644  return m_Structure.NotEmpty();
645 }
646 
647 inline
649 {
650  return IsSetStructure();
651 }
652 
653 inline
655 {
656  if (!CanGetStructure()) {
657  ThrowUnassigned(5);
658  }
659  return (*m_Structure);
660 }
661 
662 inline
664 {
665  return m_Stats.NotEmpty();
666 }
667 
668 inline
670 {
671  return IsSetStats();
672 }
673 
674 inline
676 {
677  if (!CanGetStats()) {
678  ThrowUnassigned(6);
679  }
680  return (*m_Stats);
681 }
682 
683 inline
685 {
686  return ((m_set_State[0] & 0xc000) != 0);
687 }
688 
689 inline
691 {
692  return IsSetPatch_type();
693 }
694 
695 inline
697 {
698  m_Patch_type = (EPatch_type)(0);
699  m_set_State[0] &= ~0xc000;
700 }
701 
702 inline
704 {
705  if (!CanGetPatch_type()) {
706  ThrowUnassigned(7);
707  }
708  return m_Patch_type;
709 }
710 
711 inline
713 {
715  m_set_State[0] |= 0xc000;
716 }
717 
718 inline
720 {
721 #ifdef _DEBUG
722  if (!IsSetPatch_type()) {
723  memset(&m_Patch_type,UnassignedByte(),sizeof(m_Patch_type));
724  }
725 #endif
726  m_set_State[0] |= 0x4000;
727  return m_Patch_type;
728 }
729 
730 inline
732 {
733  return ((m_set_State[0] & 0x30000) != 0);
734 }
735 
736 inline
738 {
739  return true;
740 }
741 
742 inline
744 {
745  return m_Roles;
746 }
747 
748 inline
750 {
751  m_set_State[0] |= 0x10000;
752  return m_Roles;
753 }
754 
755 ///////////////////////////////////////////////////////////
756 ////////////////// end of inline methods //////////////////
757 ///////////////////////////////////////////////////////////
758 
759 
760 
761 
762 
763 END_objects_SCOPE // namespace ncbi::objects::
764 
766 
767 
768 #endif // OBJECTS_GENOMECOLL_GC_SEQUENCE_BASE_HPP
User-defined methods of the data storage class.
CGC_SequenceStats –.
GC-Sequence: Used for scaffolds, scaffold-sets and components in Gencoll terminology.
CGC_TaggedSequences –.
CGC_TypedSeqId –.
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
static char UnassignedByte(void)
Definition: serialbase.hpp:181
void ThrowUnassigned(TMemberIndex index) const
#define ENUM_METHOD_NAME(EnumName)
Definition: serialbase.hpp:994
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_GENOME_COLLECTION_EXPORT
Definition: ncbi_export.h:528
bool CanGetSequences(void) const
Check if it is safe to call GetSequences method.
bool CanGetSeq_id(void) const
Check if it is safe to call GetSeq_id method.
TPatch_type & SetPatch_type(void)
Assign a value to Patch_type data member.
const TStats & GetStats(void) const
Get the Stats member data.
const TDescr & GetDescr(void) const
Get the Descr member data.
Tparent::CMemberIndex< E_memberIndex, 10 > TmemberIndex
bool IsSetDescr(void) const
Various attributes assigned at this level: biosrc, comments, publications...
const TRoles & GetRoles(void) const
Get the Roles member data.
const TStructure & GetStructure(void) const
Get the Structure member data.
bool CanGetAnnot(void) const
Check if it is safe to call GetAnnot method.
list< CRef< CSeq_annot > > TAnnot
bool CanGetSeq_id_synonyms(void) const
Check if it is safe to call GetSeq_id_synonyms method.
CRef< TDescr > m_Descr
bool CanGetStats(void) const
Check if it is safe to call GetStats method.
list< CRef< CSeq_annot > > m_Annot
TSeq_id_synonyms & SetSeq_id_synonyms(void)
Assign a value to Seq_id_synonyms data member.
list< CRef< CGC_TypedSeqId > > TSeq_id_synonyms
CGC_SequenceStats TStats
TSeq_id & SetSeq_id(void)
Assign a value to Seq_id data member.
CRef< TSeq_id > m_Seq_id
list< int > m_Roles
TRoles & SetRoles(void)
Assign a value to Roles data member.
TAnnot & SetAnnot(void)
Assign a value to Annot data member.
bool IsSetPatch_type(void) const
Check if a value has been assigned to Patch_type data member.
CRef< TStructure > m_Structure
CGC_Sequence_Base & operator=(const CGC_Sequence_Base &)
TSequences & SetSequences(void)
Assign a value to Sequences data member.
bool IsSetAnnot(void) const
Feature annotation; Contains Pseudo Autosomal regions on chromosomes and scaffolds in the following f...
bool IsSetStructure(void) const
locations of ordered scaffolds/components Check if a value has been assigned to Structure data member...
const TSeq_id_synonyms & GetSeq_id_synonyms(void) const
Get the Seq_id_synonyms member data.
const TAnnot & GetAnnot(void) const
Get the Annot member data.
bool CanGetRoles(void) const
Check if it is safe to call GetRoles method.
CDelta_ext TStructure
list< CRef< CGC_TaggedSequences > > TSequences
bool IsSetSequences(void) const
placed: populated both on chromosome and scaffold levels unlocalized: populated on chromosome level C...
void ResetSeq_id(void)
Reset Seq_id data member.
list< CRef< CGC_TaggedSequences > > m_Sequences
CSerialObject Tparent
bool CanGetPatch_type(void) const
Check if it is safe to call GetPatch_type method.
const TSequences & GetSequences(void) const
Get the Sequences member data.
void ResetPatch_type(void)
Reset Patch_type data member.
bool CanGetStructure(void) const
Check if it is safe to call GetStructure method.
bool IsSetStats(void) const
statistics Check if a value has been assigned to Stats data member.
bool IsSetRoles(void) const
sequence-role: what role(s) does this sequence have in the assembly Check if a value has been assigne...
bool IsSetSeq_id(void) const
identifiers are: Local / gpipe-satellite / genbank / refseq local is merely local name (or maybe with...
CRef< TStats > m_Stats
CGC_Sequence_Base(const CGC_Sequence_Base &)
bool IsSetSeq_id_synonyms(void) const
Other known identifiers: Local / gpipe-satellite / genbank / refseq Check if a value has been assigne...
TPatch_type GetPatch_type(void) const
Get the Patch_type member data.
list< CRef< CGC_TypedSeqId > > m_Seq_id_synonyms
bool CanGetDescr(void) const
Check if it is safe to call GetDescr method.
list< int > TRoles
const TSeq_id & GetSeq_id(void) const
Get the Seq_id member data.
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
Modified on Wed Apr 24 14:13:17 2024 by modify_doxy.py rev. 669887