NCBI C++ ToolKit
MSHits_.hpp
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27 
28 /// @file MSHits_.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/omssa/omssa.asn">omssa.asn</a>
34 /// and additional tune-up parameters:
35 /// <a href="/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/omssa/omssa.def">omssa.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_OMSSA_MSHITS_BASE_HPP
42 #define OBJECTS_OMSSA_MSHITS_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 CMSMZHit;
62 class CMSModHit;
63 class CMSPepHit;
64 class CMSScoreSet;
65 
66 
67 // generated classes
68 
69 
70 /** @addtogroup dataspec_OMSSA
71  *
72  * @{
73  */
74 
75 /////////////////////////////////////////////////////////////////////////////
76 /// hits to a given spectrum
77 ///
78 /// CMSHits_Base --
79 ///
80 
82 {
84 public:
85  // constructor
86  CMSHits_Base(void);
87  // destructor
88  virtual ~CMSHits_Base(void);
89 
90  // type info
92 
93  // types
94  typedef double TEvalue;
95  typedef double TPvalue;
96  typedef int TCharge;
97  typedef list< CRef< CMSPepHit > > TPephits;
98  typedef list< CRef< CMSMZHit > > TMzhits;
99  typedef string TPepstring;
100  typedef int TMass;
101  typedef list< CRef< CMSModHit > > TMods;
102  typedef string TPepstart;
103  typedef string TPepstop;
104  typedef int TProtlength;
105  typedef int TTheomass;
106  typedef int TOid;
107  typedef list< CRef< CMSScoreSet > > TScores;
108  typedef string TLibaccession;
109 
110  // member index
111  enum class E_memberIndex {
112  e__allMandatory = 0,
113  e_evalue,
114  e_pvalue,
115  e_charge,
116  e_pephits,
117  e_mzhits,
118  e_pepstring,
119  e_mass,
120  e_mods,
121  e_pepstart,
122  e_pepstop,
123  e_protlength,
124  e_theomass,
125  e_oid,
126  e_scores,
127  e_libaccession
128  };
130 
131  // getters
132  // setters
133 
134  /// E-value (expect value)
135  /// Check if a value has been assigned to Evalue data member.
136  ///
137  /// Data member Evalue is mandatory;
138  /// its type is defined as 'typedef double TEvalue'
139  /// @return
140  /// - true, if a value has been assigned.
141  /// - false, otherwise.
142  bool IsSetEvalue(void) const;
143 
144  /// Check if it is safe to call GetEvalue method.
145  ///
146  /// @return
147  /// - true, if the data member is getatable.
148  /// - false, otherwise.
149  bool CanGetEvalue(void) const;
150 
151  /// Reset Evalue data member.
152  void ResetEvalue(void);
153 
154  /// Get the Evalue member data.
155  ///
156  /// @return
157  /// Copy of the member data.
158  TEvalue GetEvalue(void) const;
159 
160  /// Assign a value to Evalue data member.
161  ///
162  /// @param value
163  /// Value to assign
164  void SetEvalue(TEvalue value);
165 
166  /// Assign a value to Evalue data member.
167  ///
168  /// @return
169  /// Reference to the data value.
170  TEvalue& SetEvalue(void);
171 
172  /// P-value (probability value)
173  /// Check if a value has been assigned to Pvalue data member.
174  ///
175  /// Data member Pvalue is mandatory;
176  /// its type is defined as 'typedef double TPvalue'
177  /// @return
178  /// - true, if a value has been assigned.
179  /// - false, otherwise.
180  bool IsSetPvalue(void) const;
181 
182  /// Check if it is safe to call GetPvalue method.
183  ///
184  /// @return
185  /// - true, if the data member is getatable.
186  /// - false, otherwise.
187  bool CanGetPvalue(void) const;
188 
189  /// Reset Pvalue data member.
190  void ResetPvalue(void);
191 
192  /// Get the Pvalue member data.
193  ///
194  /// @return
195  /// Copy of the member data.
196  TPvalue GetPvalue(void) const;
197 
198  /// Assign a value to Pvalue data member.
199  ///
200  /// @param value
201  /// Value to assign
202  void SetPvalue(TPvalue value);
203 
204  /// Assign a value to Pvalue data member.
205  ///
206  /// @return
207  /// Reference to the data value.
208  TPvalue& SetPvalue(void);
209 
210  /// the charge state used in search. -1 == not +1
211  /// Check if a value has been assigned to Charge data member.
212  ///
213  /// Data member Charge is mandatory;
214  /// its type is defined as 'typedef int TCharge'
215  /// @return
216  /// - true, if a value has been assigned.
217  /// - false, otherwise.
218  bool IsSetCharge(void) const;
219 
220  /// Check if it is safe to call GetCharge method.
221  ///
222  /// @return
223  /// - true, if the data member is getatable.
224  /// - false, otherwise.
225  bool CanGetCharge(void) const;
226 
227  /// Reset Charge data member.
228  void ResetCharge(void);
229 
230  /// Get the Charge member data.
231  ///
232  /// @return
233  /// Copy of the member data.
234  TCharge GetCharge(void) const;
235 
236  /// Assign a value to Charge data member.
237  ///
238  /// @param value
239  /// Value to assign
240  void SetCharge(TCharge value);
241 
242  /// Assign a value to Charge data member.
243  ///
244  /// @return
245  /// Reference to the data value.
246  TCharge& SetCharge(void);
247 
248  /// peptides that match this hit
249  /// Check if a value has been assigned to Pephits data member.
250  ///
251  /// Data member Pephits is mandatory;
252  /// its type is defined as 'typedef list< CRef< CMSPepHit > > TPephits'
253  /// @return
254  /// - true, if a value has been assigned.
255  /// - false, otherwise.
256  bool IsSetPephits(void) const;
257 
258  /// Check if it is safe to call GetPephits method.
259  ///
260  /// @return
261  /// - true, if the data member is getatable.
262  /// - false, otherwise.
263  bool CanGetPephits(void) const;
264 
265  /// Reset Pephits data member.
266  void ResetPephits(void);
267 
268  /// Get the Pephits member data.
269  ///
270  /// @return
271  /// Reference to the member data.
272  const TPephits& GetPephits(void) const;
273 
274  /// Assign a value to Pephits data member.
275  ///
276  /// @return
277  /// Reference to the data value.
278  TPephits& SetPephits(void);
279 
280  /// ions hit
281  /// Check if a value has been assigned to Mzhits data member.
282  ///
283  /// Data member Mzhits is optional;
284  /// its type is defined as 'typedef list< CRef< CMSMZHit > > TMzhits'
285  /// @return
286  /// - true, if a value has been assigned.
287  /// - false, otherwise.
288  bool IsSetMzhits(void) const;
289 
290  /// Check if it is safe to call GetMzhits method.
291  ///
292  /// @return
293  /// - true, if the data member is getatable.
294  /// - false, otherwise.
295  bool CanGetMzhits(void) const;
296 
297  /// Reset Mzhits data member.
298  void ResetMzhits(void);
299 
300  /// Get the Mzhits member data.
301  ///
302  /// @return
303  /// Reference to the member data.
304  const TMzhits& GetMzhits(void) const;
305 
306  /// Assign a value to Mzhits data member.
307  ///
308  /// @return
309  /// Reference to the data value.
310  TMzhits& SetMzhits(void);
311 
312  /// the peptide sequence
313  /// Check if a value has been assigned to Pepstring data member.
314  ///
315  /// Data member Pepstring is optional;
316  /// its type is defined as 'typedef string TPepstring'
317  /// @return
318  /// - true, if a value has been assigned.
319  /// - false, otherwise.
320  bool IsSetPepstring(void) const;
321 
322  /// Check if it is safe to call GetPepstring method.
323  ///
324  /// @return
325  /// - true, if the data member is getatable.
326  /// - false, otherwise.
327  bool CanGetPepstring(void) const;
328 
329  /// Reset Pepstring data member.
330  void ResetPepstring(void);
331 
332  /// Get the Pepstring member data.
333  ///
334  /// @return
335  /// Reference to the member data.
336  const TPepstring& GetPepstring(void) const;
337 
338  /// Assign a value to Pepstring data member.
339  ///
340  /// @param value
341  /// Value to assign
342  void SetPepstring(const TPepstring& value);
343  void SetPepstring(TPepstring&& value);
344 
345  /// Assign a value to Pepstring data member.
346  ///
347  /// @return
348  /// Reference to the data value.
349  TPepstring& SetPepstring(void);
350 
351  /// scaled experimental mass of peptide in Da
352  /// Check if a value has been assigned to Mass data member.
353  ///
354  /// Data member Mass is optional;
355  /// its type is defined as 'typedef int TMass'
356  /// @return
357  /// - true, if a value has been assigned.
358  /// - false, otherwise.
359  bool IsSetMass(void) const;
360 
361  /// Check if it is safe to call GetMass method.
362  ///
363  /// @return
364  /// - true, if the data member is getatable.
365  /// - false, otherwise.
366  bool CanGetMass(void) const;
367 
368  /// Reset Mass data member.
369  void ResetMass(void);
370 
371  /// Get the Mass member data.
372  ///
373  /// @return
374  /// Copy of the member data.
375  TMass GetMass(void) const;
376 
377  /// Assign a value to Mass data member.
378  ///
379  /// @param value
380  /// Value to assign
381  void SetMass(TMass value);
382 
383  /// Assign a value to Mass data member.
384  ///
385  /// @return
386  /// Reference to the data value.
387  TMass& SetMass(void);
388 
389  /// modifications to sequence
390  /// Check if a value has been assigned to Mods data member.
391  ///
392  /// Data member Mods is optional;
393  /// its type is defined as 'typedef list< CRef< CMSModHit > > TMods'
394  /// @return
395  /// - true, if a value has been assigned.
396  /// - false, otherwise.
397  bool IsSetMods(void) const;
398 
399  /// Check if it is safe to call GetMods method.
400  ///
401  /// @return
402  /// - true, if the data member is getatable.
403  /// - false, otherwise.
404  bool CanGetMods(void) const;
405 
406  /// Reset Mods data member.
407  void ResetMods(void);
408 
409  /// Get the Mods member data.
410  ///
411  /// @return
412  /// Reference to the member data.
413  const TMods& GetMods(void) const;
414 
415  /// Assign a value to Mods data member.
416  ///
417  /// @return
418  /// Reference to the data value.
419  TMods& SetMods(void);
420 
421  /// AA before the peptide (depricated)
422  /// Check if a value has been assigned to Pepstart data member.
423  ///
424  /// Data member Pepstart is optional;
425  /// its type is defined as 'typedef string TPepstart'
426  /// @return
427  /// - true, if a value has been assigned.
428  /// - false, otherwise.
429  bool IsSetPepstart(void) const;
430 
431  /// Check if it is safe to call GetPepstart method.
432  ///
433  /// @return
434  /// - true, if the data member is getatable.
435  /// - false, otherwise.
436  bool CanGetPepstart(void) const;
437 
438  /// Reset Pepstart data member.
439  void ResetPepstart(void);
440 
441  /// Get the Pepstart member data.
442  ///
443  /// @return
444  /// Reference to the member data.
445  const TPepstart& GetPepstart(void) const;
446 
447  /// Assign a value to Pepstart data member.
448  ///
449  /// @param value
450  /// Value to assign
451  void SetPepstart(const TPepstart& value);
452  void SetPepstart(TPepstart&& value);
453 
454  /// Assign a value to Pepstart data member.
455  ///
456  /// @return
457  /// Reference to the data value.
458  TPepstart& SetPepstart(void);
459 
460  /// AA after the peptide (depricated)
461  /// Check if a value has been assigned to Pepstop data member.
462  ///
463  /// Data member Pepstop is optional;
464  /// its type is defined as 'typedef string TPepstop'
465  /// @return
466  /// - true, if a value has been assigned.
467  /// - false, otherwise.
468  bool IsSetPepstop(void) const;
469 
470  /// Check if it is safe to call GetPepstop method.
471  ///
472  /// @return
473  /// - true, if the data member is getatable.
474  /// - false, otherwise.
475  bool CanGetPepstop(void) const;
476 
477  /// Reset Pepstop data member.
478  void ResetPepstop(void);
479 
480  /// Get the Pepstop member data.
481  ///
482  /// @return
483  /// Reference to the member data.
484  const TPepstop& GetPepstop(void) const;
485 
486  /// Assign a value to Pepstop data member.
487  ///
488  /// @param value
489  /// Value to assign
490  void SetPepstop(const TPepstop& value);
491  void SetPepstop(TPepstop&& value);
492 
493  /// Assign a value to Pepstop data member.
494  ///
495  /// @return
496  /// Reference to the data value.
497  TPepstop& SetPepstop(void);
498 
499  /// length of protein hit (depricated)
500  /// Check if a value has been assigned to Protlength data member.
501  ///
502  /// Data member Protlength is optional;
503  /// its type is defined as 'typedef int TProtlength'
504  /// @return
505  /// - true, if a value has been assigned.
506  /// - false, otherwise.
507  bool IsSetProtlength(void) const;
508 
509  /// Check if it is safe to call GetProtlength method.
510  ///
511  /// @return
512  /// - true, if the data member is getatable.
513  /// - false, otherwise.
514  bool CanGetProtlength(void) const;
515 
516  /// Reset Protlength data member.
517  void ResetProtlength(void);
518 
519  /// Get the Protlength member data.
520  ///
521  /// @return
522  /// Copy of the member data.
523  TProtlength GetProtlength(void) const;
524 
525  /// Assign a value to Protlength data member.
526  ///
527  /// @param value
528  /// Value to assign
529  void SetProtlength(TProtlength value);
530 
531  /// Assign a value to Protlength data member.
532  ///
533  /// @return
534  /// Reference to the data value.
535  TProtlength& SetProtlength(void);
536 
537  /// scaled theoretical mass of peptide hit
538  /// Check if a value has been assigned to Theomass data member.
539  ///
540  /// Data member Theomass is optional;
541  /// its type is defined as 'typedef int TTheomass'
542  /// @return
543  /// - true, if a value has been assigned.
544  /// - false, otherwise.
545  bool IsSetTheomass(void) const;
546 
547  /// Check if it is safe to call GetTheomass method.
548  ///
549  /// @return
550  /// - true, if the data member is getatable.
551  /// - false, otherwise.
552  bool CanGetTheomass(void) const;
553 
554  /// Reset Theomass data member.
555  void ResetTheomass(void);
556 
557  /// Get the Theomass member data.
558  ///
559  /// @return
560  /// Copy of the member data.
561  TTheomass GetTheomass(void) const;
562 
563  /// Assign a value to Theomass data member.
564  ///
565  /// @param value
566  /// Value to assign
567  void SetTheomass(TTheomass value);
568 
569  /// Assign a value to Theomass data member.
570  ///
571  /// @return
572  /// Reference to the data value.
573  TTheomass& SetTheomass(void);
574 
575  /// blast library oid (depricated)
576  /// Check if a value has been assigned to Oid data member.
577  ///
578  /// Data member Oid is optional;
579  /// its type is defined as 'typedef int TOid'
580  /// @return
581  /// - true, if a value has been assigned.
582  /// - false, otherwise.
583  bool IsSetOid(void) const;
584 
585  /// Check if it is safe to call GetOid method.
586  ///
587  /// @return
588  /// - true, if the data member is getatable.
589  /// - false, otherwise.
590  bool CanGetOid(void) const;
591 
592  /// Reset Oid data member.
593  void ResetOid(void);
594 
595  /// Get the Oid member data.
596  ///
597  /// @return
598  /// Copy of the member data.
599  TOid GetOid(void) const;
600 
601  /// Assign a value to Oid data member.
602  ///
603  /// @param value
604  /// Value to assign
605  void SetOid(TOid value);
606 
607  /// Assign a value to Oid data member.
608  ///
609  /// @return
610  /// Reference to the data value.
611  TOid& SetOid(void);
612 
613  /// optional scores (for library search)
614  /// Check if a value has been assigned to Scores data member.
615  ///
616  /// Data member Scores is optional;
617  /// its type is defined as 'typedef list< CRef< CMSScoreSet > > TScores'
618  /// @return
619  /// - true, if a value has been assigned.
620  /// - false, otherwise.
621  bool IsSetScores(void) const;
622 
623  /// Check if it is safe to call GetScores method.
624  ///
625  /// @return
626  /// - true, if the data member is getatable.
627  /// - false, otherwise.
628  bool CanGetScores(void) const;
629 
630  /// Reset Scores data member.
631  void ResetScores(void);
632 
633  /// Get the Scores member data.
634  ///
635  /// @return
636  /// Reference to the member data.
637  const TScores& GetScores(void) const;
638 
639  /// Assign a value to Scores data member.
640  ///
641  /// @return
642  /// Reference to the data value.
643  TScores& SetScores(void);
644 
645  /// library search accesssion
646  /// Check if a value has been assigned to Libaccession data member.
647  ///
648  /// Data member Libaccession is optional;
649  /// its type is defined as 'typedef string TLibaccession'
650  /// @return
651  /// - true, if a value has been assigned.
652  /// - false, otherwise.
653  bool IsSetLibaccession(void) const;
654 
655  /// Check if it is safe to call GetLibaccession method.
656  ///
657  /// @return
658  /// - true, if the data member is getatable.
659  /// - false, otherwise.
660  bool CanGetLibaccession(void) const;
661 
662  /// Reset Libaccession data member.
663  void ResetLibaccession(void);
664 
665  /// Get the Libaccession member data.
666  ///
667  /// @return
668  /// Reference to the member data.
669  const TLibaccession& GetLibaccession(void) const;
670 
671  /// Assign a value to Libaccession data member.
672  ///
673  /// @param value
674  /// Value to assign
675  void SetLibaccession(const TLibaccession& value);
676  void SetLibaccession(TLibaccession&& value);
677 
678  /// Assign a value to Libaccession data member.
679  ///
680  /// @return
681  /// Reference to the data value.
682  TLibaccession& SetLibaccession(void);
683 
684  /// Reset the whole object
685  virtual void Reset(void);
686 
687 
688 private:
689  // Prohibit copy constructor and assignment operator
692 
693  // data
694  Uint4 m_set_State[1];
695  double m_Evalue;
696  double m_Pvalue;
697  int m_Charge;
698  list< CRef< CMSPepHit > > m_Pephits;
699  list< CRef< CMSMZHit > > m_Mzhits;
700  string m_Pepstring;
701  int m_Mass;
702  list< CRef< CMSModHit > > m_Mods;
703  string m_Pepstart;
704  string m_Pepstop;
707  int m_Oid;
708  list< CRef< CMSScoreSet > > m_Scores;
710 };
711 
712 /* @} */
713 
714 
715 
716 
717 
718 ///////////////////////////////////////////////////////////
719 ///////////////////// inline methods //////////////////////
720 ///////////////////////////////////////////////////////////
721 inline
723 {
724  return ((m_set_State[0] & 0x3) != 0);
725 }
726 
727 inline
729 {
730  return IsSetEvalue();
731 }
732 
733 inline
735 {
736  m_Evalue = 0;
737  m_set_State[0] &= ~0x3;
738 }
739 
740 inline
742 {
743  if (!CanGetEvalue()) {
744  ThrowUnassigned(0);
745  }
746  return m_Evalue;
747 }
748 
749 inline
751 {
752  m_Evalue = value;
753  m_set_State[0] |= 0x3;
754 }
755 
756 inline
758 {
759 #ifdef _DEBUG
760  if (!IsSetEvalue()) {
761  memset(&m_Evalue,UnassignedByte(),sizeof(m_Evalue));
762  }
763 #endif
764  m_set_State[0] |= 0x1;
765  return m_Evalue;
766 }
767 
768 inline
770 {
771  return ((m_set_State[0] & 0xc) != 0);
772 }
773 
774 inline
776 {
777  return IsSetPvalue();
778 }
779 
780 inline
782 {
783  m_Pvalue = 0;
784  m_set_State[0] &= ~0xc;
785 }
786 
787 inline
789 {
790  if (!CanGetPvalue()) {
791  ThrowUnassigned(1);
792  }
793  return m_Pvalue;
794 }
795 
796 inline
798 {
799  m_Pvalue = value;
800  m_set_State[0] |= 0xc;
801 }
802 
803 inline
805 {
806 #ifdef _DEBUG
807  if (!IsSetPvalue()) {
808  memset(&m_Pvalue,UnassignedByte(),sizeof(m_Pvalue));
809  }
810 #endif
811  m_set_State[0] |= 0x4;
812  return m_Pvalue;
813 }
814 
815 inline
817 {
818  return ((m_set_State[0] & 0x30) != 0);
819 }
820 
821 inline
823 {
824  return IsSetCharge();
825 }
826 
827 inline
829 {
830  m_Charge = 0;
831  m_set_State[0] &= ~0x30;
832 }
833 
834 inline
836 {
837  if (!CanGetCharge()) {
838  ThrowUnassigned(2);
839  }
840  return m_Charge;
841 }
842 
843 inline
845 {
846  m_Charge = value;
847  m_set_State[0] |= 0x30;
848 }
849 
850 inline
852 {
853 #ifdef _DEBUG
854  if (!IsSetCharge()) {
855  memset(&m_Charge,UnassignedByte(),sizeof(m_Charge));
856  }
857 #endif
858  m_set_State[0] |= 0x10;
859  return m_Charge;
860 }
861 
862 inline
864 {
865  return ((m_set_State[0] & 0xc0) != 0);
866 }
867 
868 inline
870 {
871  return true;
872 }
873 
874 inline
876 {
877  return m_Pephits;
878 }
879 
880 inline
882 {
883  m_set_State[0] |= 0x40;
884  return m_Pephits;
885 }
886 
887 inline
889 {
890  return ((m_set_State[0] & 0x300) != 0);
891 }
892 
893 inline
895 {
896  return true;
897 }
898 
899 inline
901 {
902  return m_Mzhits;
903 }
904 
905 inline
907 {
908  m_set_State[0] |= 0x100;
909  return m_Mzhits;
910 }
911 
912 inline
914 {
915  return ((m_set_State[0] & 0xc00) != 0);
916 }
917 
918 inline
920 {
921  return IsSetPepstring();
922 }
923 
924 inline
926 {
927  if (!CanGetPepstring()) {
928  ThrowUnassigned(5);
929  }
930  return m_Pepstring;
931 }
932 
933 inline
935 {
936  m_Pepstring = value;
937  m_set_State[0] |= 0xc00;
938 }
939 
940 inline
942 {
943  m_Pepstring = std::forward<CMSHits_Base::TPepstring>(value);
944  m_set_State[0] |= 0xc00;
945 }
946 
947 inline
949 {
950 #ifdef _DEBUG
951  if (!IsSetPepstring()) {
953  }
954 #endif
955  m_set_State[0] |= 0x400;
956  return m_Pepstring;
957 }
958 
959 inline
960 bool CMSHits_Base::IsSetMass(void) const
961 {
962  return ((m_set_State[0] & 0x3000) != 0);
963 }
964 
965 inline
966 bool CMSHits_Base::CanGetMass(void) const
967 {
968  return IsSetMass();
969 }
970 
971 inline
973 {
974  m_Mass = 0;
975  m_set_State[0] &= ~0x3000;
976 }
977 
978 inline
980 {
981  if (!CanGetMass()) {
982  ThrowUnassigned(6);
983  }
984  return m_Mass;
985 }
986 
987 inline
989 {
990  m_Mass = value;
991  m_set_State[0] |= 0x3000;
992 }
993 
994 inline
996 {
997 #ifdef _DEBUG
998  if (!IsSetMass()) {
999  memset(&m_Mass,UnassignedByte(),sizeof(m_Mass));
1000  }
1001 #endif
1002  m_set_State[0] |= 0x1000;
1003  return m_Mass;
1004 }
1005 
1006 inline
1007 bool CMSHits_Base::IsSetMods(void) const
1008 {
1009  return ((m_set_State[0] & 0xc000) != 0);
1010 }
1011 
1012 inline
1014 {
1015  return true;
1016 }
1017 
1018 inline
1020 {
1021  return m_Mods;
1022 }
1023 
1024 inline
1026 {
1027  m_set_State[0] |= 0x4000;
1028  return m_Mods;
1029 }
1030 
1031 inline
1033 {
1034  return ((m_set_State[0] & 0x30000) != 0);
1035 }
1036 
1037 inline
1039 {
1040  return IsSetPepstart();
1041 }
1042 
1043 inline
1045 {
1046  if (!CanGetPepstart()) {
1047  ThrowUnassigned(8);
1048  }
1049  return m_Pepstart;
1050 }
1051 
1052 inline
1054 {
1055  m_Pepstart = value;
1056  m_set_State[0] |= 0x30000;
1057 }
1058 
1059 inline
1061 {
1062  m_Pepstart = std::forward<CMSHits_Base::TPepstart>(value);
1063  m_set_State[0] |= 0x30000;
1064 }
1065 
1066 inline
1068 {
1069 #ifdef _DEBUG
1070  if (!IsSetPepstart()) {
1072  }
1073 #endif
1074  m_set_State[0] |= 0x10000;
1075  return m_Pepstart;
1076 }
1077 
1078 inline
1080 {
1081  return ((m_set_State[0] & 0xc0000) != 0);
1082 }
1083 
1084 inline
1086 {
1087  return IsSetPepstop();
1088 }
1089 
1090 inline
1092 {
1093  if (!CanGetPepstop()) {
1094  ThrowUnassigned(9);
1095  }
1096  return m_Pepstop;
1097 }
1098 
1099 inline
1101 {
1102  m_Pepstop = value;
1103  m_set_State[0] |= 0xc0000;
1104 }
1105 
1106 inline
1108 {
1109  m_Pepstop = std::forward<CMSHits_Base::TPepstop>(value);
1110  m_set_State[0] |= 0xc0000;
1111 }
1112 
1113 inline
1115 {
1116 #ifdef _DEBUG
1117  if (!IsSetPepstop()) {
1119  }
1120 #endif
1121  m_set_State[0] |= 0x40000;
1122  return m_Pepstop;
1123 }
1124 
1125 inline
1127 {
1128  return ((m_set_State[0] & 0x300000) != 0);
1129 }
1130 
1131 inline
1133 {
1134  return IsSetProtlength();
1135 }
1136 
1137 inline
1139 {
1140  m_Protlength = 0;
1141  m_set_State[0] &= ~0x300000;
1142 }
1143 
1144 inline
1146 {
1147  if (!CanGetProtlength()) {
1148  ThrowUnassigned(10);
1149  }
1150  return m_Protlength;
1151 }
1152 
1153 inline
1155 {
1156  m_Protlength = value;
1157  m_set_State[0] |= 0x300000;
1158 }
1159 
1160 inline
1162 {
1163 #ifdef _DEBUG
1164  if (!IsSetProtlength()) {
1165  memset(&m_Protlength,UnassignedByte(),sizeof(m_Protlength));
1166  }
1167 #endif
1168  m_set_State[0] |= 0x100000;
1169  return m_Protlength;
1170 }
1171 
1172 inline
1174 {
1175  return ((m_set_State[0] & 0xc00000) != 0);
1176 }
1177 
1178 inline
1180 {
1181  return IsSetTheomass();
1182 }
1183 
1184 inline
1186 {
1187  m_Theomass = 0;
1188  m_set_State[0] &= ~0xc00000;
1189 }
1190 
1191 inline
1193 {
1194  if (!CanGetTheomass()) {
1195  ThrowUnassigned(11);
1196  }
1197  return m_Theomass;
1198 }
1199 
1200 inline
1202 {
1203  m_Theomass = value;
1204  m_set_State[0] |= 0xc00000;
1205 }
1206 
1207 inline
1209 {
1210 #ifdef _DEBUG
1211  if (!IsSetTheomass()) {
1212  memset(&m_Theomass,UnassignedByte(),sizeof(m_Theomass));
1213  }
1214 #endif
1215  m_set_State[0] |= 0x400000;
1216  return m_Theomass;
1217 }
1218 
1219 inline
1220 bool CMSHits_Base::IsSetOid(void) const
1221 {
1222  return ((m_set_State[0] & 0x3000000) != 0);
1223 }
1224 
1225 inline
1226 bool CMSHits_Base::CanGetOid(void) const
1227 {
1228  return IsSetOid();
1229 }
1230 
1231 inline
1233 {
1234  m_Oid = 0;
1235  m_set_State[0] &= ~0x3000000;
1236 }
1237 
1238 inline
1240 {
1241  if (!CanGetOid()) {
1242  ThrowUnassigned(12);
1243  }
1244  return m_Oid;
1245 }
1246 
1247 inline
1249 {
1250  m_Oid = value;
1251  m_set_State[0] |= 0x3000000;
1252 }
1253 
1254 inline
1256 {
1257 #ifdef _DEBUG
1258  if (!IsSetOid()) {
1259  memset(&m_Oid,UnassignedByte(),sizeof(m_Oid));
1260  }
1261 #endif
1262  m_set_State[0] |= 0x1000000;
1263  return m_Oid;
1264 }
1265 
1266 inline
1268 {
1269  return ((m_set_State[0] & 0xc000000) != 0);
1270 }
1271 
1272 inline
1274 {
1275  return true;
1276 }
1277 
1278 inline
1280 {
1281  return m_Scores;
1282 }
1283 
1284 inline
1286 {
1287  m_set_State[0] |= 0x4000000;
1288  return m_Scores;
1289 }
1290 
1291 inline
1293 {
1294  return ((m_set_State[0] & 0x30000000) != 0);
1295 }
1296 
1297 inline
1299 {
1300  return IsSetLibaccession();
1301 }
1302 
1303 inline
1305 {
1306  if (!CanGetLibaccession()) {
1307  ThrowUnassigned(14);
1308  }
1309  return m_Libaccession;
1310 }
1311 
1312 inline
1314 {
1316  m_set_State[0] |= 0x30000000;
1317 }
1318 
1319 inline
1321 {
1322  m_Libaccession = std::forward<CMSHits_Base::TLibaccession>(value);
1323  m_set_State[0] |= 0x30000000;
1324 }
1325 
1326 inline
1328 {
1329 #ifdef _DEBUG
1330  if (!IsSetLibaccession()) {
1332  }
1333 #endif
1334  m_set_State[0] |= 0x10000000;
1335  return m_Libaccession;
1336 }
1337 
1338 ///////////////////////////////////////////////////////////
1339 ////////////////// end of inline methods //////////////////
1340 ///////////////////////////////////////////////////////////
1341 
1342 
1343 
1344 
1345 
1346 END_objects_SCOPE // namespace ncbi::objects::
1347 
1349 
1350 
1351 #endif // OBJECTS_OMSSA_MSHITS_BASE_HPP
void SetScores(objects::CSeq_align &seq_align, objects::CScope &scope, const string &matrix_name="BLOSUM62")
hits to a given spectrum
Definition: MSHits_.hpp:82
CMSMZHit –.
Definition: MSMZHit.hpp:66
CMSModHit –.
Definition: MSModHit.hpp:66
CMSPepHit –.
Definition: MSPepHit.hpp:66
CMSScoreSet –.
Definition: MSScoreSet.hpp:66
Base class for all serializable objects.
Definition: serialbase.hpp:150
static char UnassignedByte(void)
Definition: serialbase.hpp:181
void ThrowUnassigned(TMemberIndex index) const
static string UnassignedString(void)
Definition: serialbase.hpp:175
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_OMSSA_EXPORT
Definition: ncbi_export.h:672
double m_Pvalue
Definition: MSHits_.hpp:696
list< CRef< CMSScoreSet > > TScores
Definition: MSHits_.hpp:107
list< CRef< CMSMZHit > > TMzhits
Definition: MSHits_.hpp:98
bool CanGetTheomass(void) const
Check if it is safe to call GetTheomass method.
Definition: MSHits_.hpp:1179
bool IsSetPephits(void) const
peptides that match this hit Check if a value has been assigned to Pephits data member.
Definition: MSHits_.hpp:863
bool IsSetTheomass(void) const
scaled theoretical mass of peptide hit Check if a value has been assigned to Theomass data member.
Definition: MSHits_.hpp:1173
TPvalue GetPvalue(void) const
Get the Pvalue member data.
Definition: MSHits_.hpp:788
double m_Evalue
Definition: MSHits_.hpp:695
bool IsSetCharge(void) const
the charge state used in search.
Definition: MSHits_.hpp:816
TProtlength & SetProtlength(void)
Assign a value to Protlength data member.
Definition: MSHits_.hpp:1161
TMods & SetMods(void)
Assign a value to Mods data member.
Definition: MSHits_.hpp:1025
string TPepstart
Definition: MSHits_.hpp:102
void ResetTheomass(void)
Reset Theomass data member.
Definition: MSHits_.hpp:1185
int TProtlength
Definition: MSHits_.hpp:104
TScores & SetScores(void)
Assign a value to Scores data member.
Definition: MSHits_.hpp:1285
TLibaccession & SetLibaccession(void)
Assign a value to Libaccession data member.
Definition: MSHits_.hpp:1327
bool IsSetProtlength(void) const
length of protein hit (depricated) Check if a value has been assigned to Protlength data member.
Definition: MSHits_.hpp:1126
TPepstring & SetPepstring(void)
Assign a value to Pepstring data member.
Definition: MSHits_.hpp:948
list< CRef< CMSModHit > > m_Mods
Definition: MSHits_.hpp:702
const TScores & GetScores(void) const
Get the Scores member data.
Definition: MSHits_.hpp:1279
const TPephits & GetPephits(void) const
Get the Pephits member data.
Definition: MSHits_.hpp:875
void ResetEvalue(void)
Reset Evalue data member.
Definition: MSHits_.hpp:734
double TPvalue
Definition: MSHits_.hpp:95
bool CanGetMods(void) const
Check if it is safe to call GetMods method.
Definition: MSHits_.hpp:1013
int m_Theomass
Definition: MSHits_.hpp:706
Tparent::CMemberIndex< E_memberIndex, 16 > TmemberIndex
Definition: MSHits_.hpp:129
TCharge GetCharge(void) const
Get the Charge member data.
Definition: MSHits_.hpp:835
CMSHits_Base(const CMSHits_Base &)
TMass & SetMass(void)
Assign a value to Mass data member.
Definition: MSHits_.hpp:995
list< CRef< CMSPepHit > > m_Pephits
Definition: MSHits_.hpp:698
bool IsSetLibaccession(void) const
library search accesssion Check if a value has been assigned to Libaccession data member.
Definition: MSHits_.hpp:1292
list< CRef< CMSModHit > > TMods
Definition: MSHits_.hpp:101
CMSHits_Base & operator=(const CMSHits_Base &)
bool CanGetPepstring(void) const
Check if it is safe to call GetPepstring method.
Definition: MSHits_.hpp:919
string m_Pepstop
Definition: MSHits_.hpp:704
bool IsSetMods(void) const
modifications to sequence Check if a value has been assigned to Mods data member.
Definition: MSHits_.hpp:1007
bool CanGetCharge(void) const
Check if it is safe to call GetCharge method.
Definition: MSHits_.hpp:822
list< CRef< CMSMZHit > > m_Mzhits
Definition: MSHits_.hpp:699
TOid GetOid(void) const
Get the Oid member data.
Definition: MSHits_.hpp:1239
TPvalue & SetPvalue(void)
Assign a value to Pvalue data member.
Definition: MSHits_.hpp:804
bool CanGetPepstart(void) const
Check if it is safe to call GetPepstart method.
Definition: MSHits_.hpp:1038
TProtlength GetProtlength(void) const
Get the Protlength member data.
Definition: MSHits_.hpp:1145
string m_Libaccession
Definition: MSHits_.hpp:709
const TPepstart & GetPepstart(void) const
Get the Pepstart member data.
Definition: MSHits_.hpp:1044
DECLARE_INTERNAL_TYPE_INFO()
TMass GetMass(void) const
Get the Mass member data.
Definition: MSHits_.hpp:979
bool CanGetPepstop(void) const
Check if it is safe to call GetPepstop method.
Definition: MSHits_.hpp:1085
bool IsSetMass(void) const
scaled experimental mass of peptide in Da Check if a value has been assigned to Mass data member.
Definition: MSHits_.hpp:960
bool IsSetScores(void) const
optional scores (for library search) Check if a value has been assigned to Scores data member.
Definition: MSHits_.hpp:1267
const TMzhits & GetMzhits(void) const
Get the Mzhits member data.
Definition: MSHits_.hpp:900
const TPepstring & GetPepstring(void) const
Get the Pepstring member data.
Definition: MSHits_.hpp:925
TPepstop & SetPepstop(void)
Assign a value to Pepstop data member.
Definition: MSHits_.hpp:1114
list< CRef< CMSScoreSet > > m_Scores
Definition: MSHits_.hpp:708
TMzhits & SetMzhits(void)
Assign a value to Mzhits data member.
Definition: MSHits_.hpp:906
const TLibaccession & GetLibaccession(void) const
Get the Libaccession member data.
Definition: MSHits_.hpp:1304
const TMods & GetMods(void) const
Get the Mods member data.
Definition: MSHits_.hpp:1019
TCharge & SetCharge(void)
Assign a value to Charge data member.
Definition: MSHits_.hpp:851
TEvalue GetEvalue(void) const
Get the Evalue member data.
Definition: MSHits_.hpp:741
void ResetCharge(void)
Reset Charge data member.
Definition: MSHits_.hpp:828
bool CanGetProtlength(void) const
Check if it is safe to call GetProtlength method.
Definition: MSHits_.hpp:1132
string m_Pepstring
Definition: MSHits_.hpp:700
int m_Protlength
Definition: MSHits_.hpp:705
void ResetOid(void)
Reset Oid data member.
Definition: MSHits_.hpp:1232
string TPepstop
Definition: MSHits_.hpp:103
bool CanGetEvalue(void) const
Check if it is safe to call GetEvalue method.
Definition: MSHits_.hpp:728
bool CanGetPephits(void) const
Check if it is safe to call GetPephits method.
Definition: MSHits_.hpp:869
string TPepstring
Definition: MSHits_.hpp:99
bool CanGetPvalue(void) const
Check if it is safe to call GetPvalue method.
Definition: MSHits_.hpp:775
bool IsSetMzhits(void) const
ions hit Check if a value has been assigned to Mzhits data member.
Definition: MSHits_.hpp:888
bool CanGetMzhits(void) const
Check if it is safe to call GetMzhits method.
Definition: MSHits_.hpp:894
bool CanGetMass(void) const
Check if it is safe to call GetMass method.
Definition: MSHits_.hpp:966
void ResetProtlength(void)
Reset Protlength data member.
Definition: MSHits_.hpp:1138
void ResetMass(void)
Reset Mass data member.
Definition: MSHits_.hpp:972
bool IsSetEvalue(void) const
E-value (expect value) Check if a value has been assigned to Evalue data member.
Definition: MSHits_.hpp:722
bool CanGetScores(void) const
Check if it is safe to call GetScores method.
Definition: MSHits_.hpp:1273
bool IsSetOid(void) const
blast library oid (depricated) Check if a value has been assigned to Oid data member.
Definition: MSHits_.hpp:1220
bool CanGetOid(void) const
Check if it is safe to call GetOid method.
Definition: MSHits_.hpp:1226
bool IsSetPvalue(void) const
P-value (probability value) Check if a value has been assigned to Pvalue data member.
Definition: MSHits_.hpp:769
TTheomass GetTheomass(void) const
Get the Theomass member data.
Definition: MSHits_.hpp:1192
Uint4 m_set_State[1]
Definition: MSHits_.hpp:694
void ResetPvalue(void)
Reset Pvalue data member.
Definition: MSHits_.hpp:781
const TPepstop & GetPepstop(void) const
Get the Pepstop member data.
Definition: MSHits_.hpp:1091
bool CanGetLibaccession(void) const
Check if it is safe to call GetLibaccession method.
Definition: MSHits_.hpp:1298
TEvalue & SetEvalue(void)
Assign a value to Evalue data member.
Definition: MSHits_.hpp:757
CSerialObject Tparent
Definition: MSHits_.hpp:83
double TEvalue
Definition: MSHits_.hpp:94
TOid & SetOid(void)
Assign a value to Oid data member.
Definition: MSHits_.hpp:1255
bool IsSetPepstart(void) const
AA before the peptide (depricated) Check if a value has been assigned to Pepstart data member.
Definition: MSHits_.hpp:1032
list< CRef< CMSPepHit > > TPephits
Definition: MSHits_.hpp:97
string m_Pepstart
Definition: MSHits_.hpp:703
TTheomass & SetTheomass(void)
Assign a value to Theomass data member.
Definition: MSHits_.hpp:1208
bool IsSetPepstop(void) const
AA after the peptide (depricated) Check if a value has been assigned to Pepstop data member.
Definition: MSHits_.hpp:1079
TPepstart & SetPepstart(void)
Assign a value to Pepstart data member.
Definition: MSHits_.hpp:1067
bool IsSetPepstring(void) const
the peptide sequence Check if a value has been assigned to Pepstring data member.
Definition: MSHits_.hpp:913
string TLibaccession
Definition: MSHits_.hpp:108
TPephits & SetPephits(void)
Assign a value to Pephits data member.
Definition: MSHits_.hpp:881
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
int GetCharge(char code)
Modified on Fri May 24 14:56:12 2024 by modify_doxy.py rev. 669887