NCBI C++ ToolKit
MSSearchSettings_.hpp
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27 
28 /// @file MSSearchSettings_.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_MSSEARCHSETTINGS_BASE_HPP
42 #define OBJECTS_OMSSA_MSSEARCHSETTINGS_BASE_HPP
43 
44 // standard includes
45 #include <serial/serialbase.hpp>
46 
47 // generated includes
48 #include <list>
49 #include <string>
52 #include <objects/omssa/MSMod.hpp>
55 
57 
58 #ifndef BEGIN_objects_SCOPE
59 # define BEGIN_objects_SCOPE BEGIN_SCOPE(objects)
60 # define END_objects_SCOPE END_SCOPE(objects)
61 #endif
62 BEGIN_objects_SCOPE // namespace ncbi::objects::
63 
64 
65 // forward declarations
66 class CMSChargeHandle;
67 class CMSInFile;
69 class CMSLibrarySettings;
70 class CMSModSpecSet;
71 class CMSOutFile;
72 class CNameValue;
73 
74 
75 // generated classes
76 
77 
78 /** @addtogroup dataspec_OMSSA
79  *
80  * @{
81  */
82 
83 /////////////////////////////////////////////////////////////////////////////
84 /// Generic search settings
85 ///
86 /// CMSSearchSettings_Base --
87 ///
88 
90 {
92 public:
93  // constructor
95  // destructor
96  virtual ~CMSSearchSettings_Base(void);
97 
98  // type info
100 
101  // types
102  typedef int TPrecursorsearchtype;
103  typedef int TProductsearchtype;
104  typedef list< int > TIonstosearch;
105  typedef double TPeptol;
106  typedef double TMsmstol;
107  typedef int TZdep;
108  typedef double TCutoff;
109  typedef double TCutlo;
110  typedef double TCuthi;
111  typedef double TCutinc;
112  typedef int TSinglewin;
113  typedef int TDoublewin;
114  typedef int TSinglenum;
115  typedef int TDoublenum;
116  typedef list< int > TFixed;
117  typedef list< int > TVariable;
118  typedef int TEnzyme;
119  typedef int TMissedcleave;
120  typedef int THitlistlen;
121  typedef string TDb;
122  typedef int TTophitnum;
123  typedef int TMinhit;
124  typedef int TMinspectra;
125  typedef int TScale;
126  typedef int TMaxmods;
127  typedef list< int > TTaxids;
130  typedef int TPseudocount;
131  typedef int TSearchb1;
132  typedef int TSearchctermproduct;
133  typedef int TMaxproductions;
134  typedef int TMinnoenzyme;
135  typedef int TMaxnoenzyme;
136  typedef double TExactmass;
137  typedef int TSettingid;
139  typedef int TPrecursorcull;
140  typedef list< CRef< CMSInFile > > TInfiles;
141  typedef list< CRef< CMSOutFile > > TOutfiles;
142  typedef int TNocorrelationscore;
143  typedef double TProbfollowingion;
144  typedef bool TNmethionine;
145  typedef double TAutomassadjust;
146  typedef double TLomasscutoff;
148  typedef list< int > TNoprolineions;
149  typedef bool TReversesearch;
150  typedef list< CRef< CNameValue > > TOthersettings;
151  typedef int TNumisotopes;
152  typedef bool TPepppm;
153  typedef bool TMsmsppm;
154  typedef int TReportedhitcount;
155 
156  // member index
157  enum class E_memberIndex {
158  e__allMandatory = 0,
159  e_precursorsearchtype,
160  e_productsearchtype,
161  e_ionstosearch,
162  e_peptol,
163  e_msmstol,
164  e_zdep,
165  e_cutoff,
166  e_cutlo,
167  e_cuthi,
168  e_cutinc,
169  e_singlewin,
170  e_doublewin,
171  e_singlenum,
172  e_doublenum,
173  e_fixed,
174  e_variable,
175  e_enzyme,
176  e_missedcleave,
177  e_hitlistlen,
178  e_db,
179  e_tophitnum,
180  e_minhit,
181  e_minspectra,
182  e_scale,
183  e_maxmods,
184  e_taxids,
185  e_chargehandling,
186  e_usermods,
187  e_pseudocount,
188  e_searchb1,
189  e_searchctermproduct,
190  e_maxproductions,
191  e_minnoenzyme,
192  e_maxnoenzyme,
193  e_exactmass,
194  e_settingid,
195  e_iterativesettings,
196  e_precursorcull,
197  e_infiles,
198  e_outfiles,
199  e_nocorrelationscore,
200  e_probfollowingion,
201  e_nmethionine,
202  e_automassadjust,
203  e_lomasscutoff,
204  e_libsearchsettings,
205  e_noprolineions,
206  e_reversesearch,
207  e_othersettings,
208  e_numisotopes,
209  e_pepppm,
210  e_msmsppm,
211  e_reportedhitcount
212  };
214 
215  // getters
216  // setters
217 
218  /// average or monoisotopic?
219  /// Check if a value has been assigned to Precursorsearchtype data member.
220  ///
221  /// Data member Precursorsearchtype is mandatory;
222  /// its type is defined as 'typedef int TPrecursorsearchtype'
223  /// @return
224  /// - true, if a value has been assigned.
225  /// - false, otherwise.
226  bool IsSetPrecursorsearchtype(void) const;
227 
228  /// Check if it is safe to call GetPrecursorsearchtype method.
229  ///
230  /// @return
231  /// - true, if the data member is getatable.
232  /// - false, otherwise.
233  bool CanGetPrecursorsearchtype(void) const;
234 
235  /// Reset Precursorsearchtype data member.
236  void ResetPrecursorsearchtype(void);
237 
238  /// Get the Precursorsearchtype member data.
239  ///
240  /// @return
241  /// Copy of the member data.
242  TPrecursorsearchtype GetPrecursorsearchtype(void) const;
243 
244  /// Assign a value to Precursorsearchtype data member.
245  ///
246  /// @param value
247  /// Value to assign
248  void SetPrecursorsearchtype(TPrecursorsearchtype value);
249 
250  /// Assign a value to Precursorsearchtype data member.
251  ///
252  /// @return
253  /// Reference to the data value.
254  TPrecursorsearchtype& SetPrecursorsearchtype(void);
255 
256  /// average or monoisotopic?
257  /// Check if a value has been assigned to Productsearchtype data member.
258  ///
259  /// Data member Productsearchtype is mandatory;
260  /// its type is defined as 'typedef int TProductsearchtype'
261  /// @return
262  /// - true, if a value has been assigned.
263  /// - false, otherwise.
264  bool IsSetProductsearchtype(void) const;
265 
266  /// Check if it is safe to call GetProductsearchtype method.
267  ///
268  /// @return
269  /// - true, if the data member is getatable.
270  /// - false, otherwise.
271  bool CanGetProductsearchtype(void) const;
272 
273  /// Reset Productsearchtype data member.
274  void ResetProductsearchtype(void);
275 
276  /// Get the Productsearchtype member data.
277  ///
278  /// @return
279  /// Copy of the member data.
280  TProductsearchtype GetProductsearchtype(void) const;
281 
282  /// Assign a value to Productsearchtype data member.
283  ///
284  /// @param value
285  /// Value to assign
286  void SetProductsearchtype(TProductsearchtype value);
287 
288  /// Assign a value to Productsearchtype data member.
289  ///
290  /// @return
291  /// Reference to the data value.
292  TProductsearchtype& SetProductsearchtype(void);
293 
294  /// which ions to search?
295  /// Check if a value has been assigned to Ionstosearch data member.
296  ///
297  /// Data member Ionstosearch is mandatory;
298  /// its type is defined as 'typedef list< int > TIonstosearch'
299  /// @return
300  /// - true, if a value has been assigned.
301  /// - false, otherwise.
302  bool IsSetIonstosearch(void) const;
303 
304  /// Check if it is safe to call GetIonstosearch method.
305  ///
306  /// @return
307  /// - true, if the data member is getatable.
308  /// - false, otherwise.
309  bool CanGetIonstosearch(void) const;
310 
311  /// Reset Ionstosearch data member.
312  void ResetIonstosearch(void);
313 
314  /// Get the Ionstosearch member data.
315  ///
316  /// @return
317  /// Reference to the member data.
318  const TIonstosearch& GetIonstosearch(void) const;
319 
320  /// Assign a value to Ionstosearch data member.
321  ///
322  /// @return
323  /// Reference to the data value.
324  TIonstosearch& SetIonstosearch(void);
325 
326  /// peptide mass tolerance
327  /// Check if a value has been assigned to Peptol data member.
328  ///
329  /// Data member Peptol is mandatory;
330  /// its type is defined as 'typedef double TPeptol'
331  /// @return
332  /// - true, if a value has been assigned.
333  /// - false, otherwise.
334  bool IsSetPeptol(void) const;
335 
336  /// Check if it is safe to call GetPeptol method.
337  ///
338  /// @return
339  /// - true, if the data member is getatable.
340  /// - false, otherwise.
341  bool CanGetPeptol(void) const;
342 
343  /// Reset Peptol data member.
344  void ResetPeptol(void);
345 
346  /// Get the Peptol member data.
347  ///
348  /// @return
349  /// Copy of the member data.
350  TPeptol GetPeptol(void) const;
351 
352  /// Assign a value to Peptol data member.
353  ///
354  /// @param value
355  /// Value to assign
356  void SetPeptol(TPeptol value);
357 
358  /// Assign a value to Peptol data member.
359  ///
360  /// @return
361  /// Reference to the data value.
362  TPeptol& SetPeptol(void);
363 
364  /// msms mass tolerance
365  /// Check if a value has been assigned to Msmstol data member.
366  ///
367  /// Data member Msmstol is mandatory;
368  /// its type is defined as 'typedef double TMsmstol'
369  /// @return
370  /// - true, if a value has been assigned.
371  /// - false, otherwise.
372  bool IsSetMsmstol(void) const;
373 
374  /// Check if it is safe to call GetMsmstol method.
375  ///
376  /// @return
377  /// - true, if the data member is getatable.
378  /// - false, otherwise.
379  bool CanGetMsmstol(void) const;
380 
381  /// Reset Msmstol data member.
382  void ResetMsmstol(void);
383 
384  /// Get the Msmstol member data.
385  ///
386  /// @return
387  /// Copy of the member data.
388  TMsmstol GetMsmstol(void) const;
389 
390  /// Assign a value to Msmstol data member.
391  ///
392  /// @param value
393  /// Value to assign
394  void SetMsmstol(TMsmstol value);
395 
396  /// Assign a value to Msmstol data member.
397  ///
398  /// @return
399  /// Reference to the data value.
400  TMsmstol& SetMsmstol(void);
401 
402  /// what is the charge dependence of the mass tolerance?
403  /// Check if a value has been assigned to Zdep data member.
404  ///
405  /// Data member Zdep is mandatory;
406  /// its type is defined as 'typedef int TZdep'
407  /// @return
408  /// - true, if a value has been assigned.
409  /// - false, otherwise.
410  bool IsSetZdep(void) const;
411 
412  /// Check if it is safe to call GetZdep method.
413  ///
414  /// @return
415  /// - true, if the data member is getatable.
416  /// - false, otherwise.
417  bool CanGetZdep(void) const;
418 
419  /// Reset Zdep data member.
420  void ResetZdep(void);
421 
422  /// Get the Zdep member data.
423  ///
424  /// @return
425  /// Copy of the member data.
426  TZdep GetZdep(void) const;
427 
428  /// Assign a value to Zdep data member.
429  ///
430  /// @param value
431  /// Value to assign
432  void SetZdep(TZdep value);
433 
434  /// Assign a value to Zdep data member.
435  ///
436  /// @return
437  /// Reference to the data value.
438  TZdep& SetZdep(void);
439 
440  /// evalue cutoff
441  /// next 3 fields define intensity fraction below
442  /// which peaks will be discard
443  /// Check if a value has been assigned to Cutoff data member.
444  ///
445  /// Data member Cutoff is mandatory;
446  /// its type is defined as 'typedef double TCutoff'
447  /// @return
448  /// - true, if a value has been assigned.
449  /// - false, otherwise.
450  bool IsSetCutoff(void) const;
451 
452  /// Check if it is safe to call GetCutoff method.
453  ///
454  /// @return
455  /// - true, if the data member is getatable.
456  /// - false, otherwise.
457  bool CanGetCutoff(void) const;
458 
459  /// Reset Cutoff data member.
460  void ResetCutoff(void);
461 
462  /// Get the Cutoff member data.
463  ///
464  /// @return
465  /// Copy of the member data.
466  TCutoff GetCutoff(void) const;
467 
468  /// Assign a value to Cutoff data member.
469  ///
470  /// @param value
471  /// Value to assign
472  void SetCutoff(TCutoff value);
473 
474  /// Assign a value to Cutoff data member.
475  ///
476  /// @return
477  /// Reference to the data value.
478  TCutoff& SetCutoff(void);
479 
480  /// the start of the cutoff, fraction of most intense peak
481  /// Check if a value has been assigned to Cutlo data member.
482  ///
483  /// Data member Cutlo is mandatory;
484  /// its type is defined as 'typedef double TCutlo'
485  /// @return
486  /// - true, if a value has been assigned.
487  /// - false, otherwise.
488  bool IsSetCutlo(void) const;
489 
490  /// Check if it is safe to call GetCutlo method.
491  ///
492  /// @return
493  /// - true, if the data member is getatable.
494  /// - false, otherwise.
495  bool CanGetCutlo(void) const;
496 
497  /// Reset Cutlo data member.
498  void ResetCutlo(void);
499 
500  /// Get the Cutlo member data.
501  ///
502  /// @return
503  /// Copy of the member data.
504  TCutlo GetCutlo(void) const;
505 
506  /// Assign a value to Cutlo data member.
507  ///
508  /// @param value
509  /// Value to assign
510  void SetCutlo(TCutlo value);
511 
512  /// Assign a value to Cutlo data member.
513  ///
514  /// @return
515  /// Reference to the data value.
516  TCutlo& SetCutlo(void);
517 
518  /// the end of the cutoff
519  /// Check if a value has been assigned to Cuthi data member.
520  ///
521  /// Data member Cuthi is mandatory;
522  /// its type is defined as 'typedef double TCuthi'
523  /// @return
524  /// - true, if a value has been assigned.
525  /// - false, otherwise.
526  bool IsSetCuthi(void) const;
527 
528  /// Check if it is safe to call GetCuthi method.
529  ///
530  /// @return
531  /// - true, if the data member is getatable.
532  /// - false, otherwise.
533  bool CanGetCuthi(void) const;
534 
535  /// Reset Cuthi data member.
536  void ResetCuthi(void);
537 
538  /// Get the Cuthi member data.
539  ///
540  /// @return
541  /// Copy of the member data.
542  TCuthi GetCuthi(void) const;
543 
544  /// Assign a value to Cuthi data member.
545  ///
546  /// @param value
547  /// Value to assign
548  void SetCuthi(TCuthi value);
549 
550  /// Assign a value to Cuthi data member.
551  ///
552  /// @return
553  /// Reference to the data value.
554  TCuthi& SetCuthi(void);
555 
556  /// the increment of the cutoff
557  /// Check if a value has been assigned to Cutinc data member.
558  ///
559  /// Data member Cutinc is mandatory;
560  /// its type is defined as 'typedef double TCutinc'
561  /// @return
562  /// - true, if a value has been assigned.
563  /// - false, otherwise.
564  bool IsSetCutinc(void) const;
565 
566  /// Check if it is safe to call GetCutinc method.
567  ///
568  /// @return
569  /// - true, if the data member is getatable.
570  /// - false, otherwise.
571  bool CanGetCutinc(void) const;
572 
573  /// Reset Cutinc data member.
574  void ResetCutinc(void);
575 
576  /// Get the Cutinc member data.
577  ///
578  /// @return
579  /// Copy of the member data.
580  TCutinc GetCutinc(void) const;
581 
582  /// Assign a value to Cutinc data member.
583  ///
584  /// @param value
585  /// Value to assign
586  void SetCutinc(TCutinc value);
587 
588  /// Assign a value to Cutinc data member.
589  ///
590  /// @return
591  /// Reference to the data value.
592  TCutinc& SetCutinc(void);
593 
594  /// the size of the single charge filtering window
595  /// Check if a value has been assigned to Singlewin data member.
596  ///
597  /// Data member Singlewin is mandatory;
598  /// its type is defined as 'typedef int TSinglewin'
599  /// @return
600  /// - true, if a value has been assigned.
601  /// - false, otherwise.
602  bool IsSetSinglewin(void) const;
603 
604  /// Check if it is safe to call GetSinglewin method.
605  ///
606  /// @return
607  /// - true, if the data member is getatable.
608  /// - false, otherwise.
609  bool CanGetSinglewin(void) const;
610 
611  /// Reset Singlewin data member.
612  void ResetSinglewin(void);
613 
614  /// Get the Singlewin member data.
615  ///
616  /// @return
617  /// Copy of the member data.
618  TSinglewin GetSinglewin(void) const;
619 
620  /// Assign a value to Singlewin data member.
621  ///
622  /// @param value
623  /// Value to assign
624  void SetSinglewin(TSinglewin value);
625 
626  /// Assign a value to Singlewin data member.
627  ///
628  /// @return
629  /// Reference to the data value.
630  TSinglewin& SetSinglewin(void);
631 
632  /// the size of the double charge filtering window
633  /// Check if a value has been assigned to Doublewin data member.
634  ///
635  /// Data member Doublewin is mandatory;
636  /// its type is defined as 'typedef int TDoublewin'
637  /// @return
638  /// - true, if a value has been assigned.
639  /// - false, otherwise.
640  bool IsSetDoublewin(void) const;
641 
642  /// Check if it is safe to call GetDoublewin method.
643  ///
644  /// @return
645  /// - true, if the data member is getatable.
646  /// - false, otherwise.
647  bool CanGetDoublewin(void) const;
648 
649  /// Reset Doublewin data member.
650  void ResetDoublewin(void);
651 
652  /// Get the Doublewin member data.
653  ///
654  /// @return
655  /// Copy of the member data.
656  TDoublewin GetDoublewin(void) const;
657 
658  /// Assign a value to Doublewin data member.
659  ///
660  /// @param value
661  /// Value to assign
662  void SetDoublewin(TDoublewin value);
663 
664  /// Assign a value to Doublewin data member.
665  ///
666  /// @return
667  /// Reference to the data value.
668  TDoublewin& SetDoublewin(void);
669 
670  /// the number of peaks allowed in the single window
671  /// Check if a value has been assigned to Singlenum data member.
672  ///
673  /// Data member Singlenum is mandatory;
674  /// its type is defined as 'typedef int TSinglenum'
675  /// @return
676  /// - true, if a value has been assigned.
677  /// - false, otherwise.
678  bool IsSetSinglenum(void) const;
679 
680  /// Check if it is safe to call GetSinglenum method.
681  ///
682  /// @return
683  /// - true, if the data member is getatable.
684  /// - false, otherwise.
685  bool CanGetSinglenum(void) const;
686 
687  /// Reset Singlenum data member.
688  void ResetSinglenum(void);
689 
690  /// Get the Singlenum member data.
691  ///
692  /// @return
693  /// Copy of the member data.
694  TSinglenum GetSinglenum(void) const;
695 
696  /// Assign a value to Singlenum data member.
697  ///
698  /// @param value
699  /// Value to assign
700  void SetSinglenum(TSinglenum value);
701 
702  /// Assign a value to Singlenum data member.
703  ///
704  /// @return
705  /// Reference to the data value.
706  TSinglenum& SetSinglenum(void);
707 
708  /// the number of peaks allowed in the double window
709  /// Check if a value has been assigned to Doublenum data member.
710  ///
711  /// Data member Doublenum is mandatory;
712  /// its type is defined as 'typedef int TDoublenum'
713  /// @return
714  /// - true, if a value has been assigned.
715  /// - false, otherwise.
716  bool IsSetDoublenum(void) const;
717 
718  /// Check if it is safe to call GetDoublenum method.
719  ///
720  /// @return
721  /// - true, if the data member is getatable.
722  /// - false, otherwise.
723  bool CanGetDoublenum(void) const;
724 
725  /// Reset Doublenum data member.
726  void ResetDoublenum(void);
727 
728  /// Get the Doublenum member data.
729  ///
730  /// @return
731  /// Copy of the member data.
732  TDoublenum GetDoublenum(void) const;
733 
734  /// Assign a value to Doublenum data member.
735  ///
736  /// @param value
737  /// Value to assign
738  void SetDoublenum(TDoublenum value);
739 
740  /// Assign a value to Doublenum data member.
741  ///
742  /// @return
743  /// Reference to the data value.
744  TDoublenum& SetDoublenum(void);
745 
746  /// fixed PTM's
747  /// Check if a value has been assigned to Fixed data member.
748  ///
749  /// Data member Fixed is mandatory;
750  /// its type is defined as 'typedef list< int > TFixed'
751  /// @return
752  /// - true, if a value has been assigned.
753  /// - false, otherwise.
754  bool IsSetFixed(void) const;
755 
756  /// Check if it is safe to call GetFixed method.
757  ///
758  /// @return
759  /// - true, if the data member is getatable.
760  /// - false, otherwise.
761  bool CanGetFixed(void) const;
762 
763  /// Reset Fixed data member.
764  void ResetFixed(void);
765 
766  /// Get the Fixed member data.
767  ///
768  /// @return
769  /// Reference to the member data.
770  const TFixed& GetFixed(void) const;
771 
772  /// Assign a value to Fixed data member.
773  ///
774  /// @return
775  /// Reference to the data value.
776  TFixed& SetFixed(void);
777 
778  /// variable PTM's
779  /// Check if a value has been assigned to Variable data member.
780  ///
781  /// Data member Variable is mandatory;
782  /// its type is defined as 'typedef list< int > TVariable'
783  /// @return
784  /// - true, if a value has been assigned.
785  /// - false, otherwise.
786  bool IsSetVariable(void) const;
787 
788  /// Check if it is safe to call GetVariable method.
789  ///
790  /// @return
791  /// - true, if the data member is getatable.
792  /// - false, otherwise.
793  bool CanGetVariable(void) const;
794 
795  /// Reset Variable data member.
796  void ResetVariable(void);
797 
798  /// Get the Variable member data.
799  ///
800  /// @return
801  /// Reference to the member data.
802  const TVariable& GetVariable(void) const;
803 
804  /// Assign a value to Variable data member.
805  ///
806  /// @return
807  /// Reference to the data value.
808  TVariable& SetVariable(void);
809 
810  /// digestion enzyme
811  /// Check if a value has been assigned to Enzyme data member.
812  ///
813  /// Data member Enzyme is mandatory;
814  /// its type is defined as 'typedef int TEnzyme'
815  /// @return
816  /// - true, if a value has been assigned.
817  /// - false, otherwise.
818  bool IsSetEnzyme(void) const;
819 
820  /// Check if it is safe to call GetEnzyme method.
821  ///
822  /// @return
823  /// - true, if the data member is getatable.
824  /// - false, otherwise.
825  bool CanGetEnzyme(void) const;
826 
827  /// Reset Enzyme data member.
828  void ResetEnzyme(void);
829 
830  /// Get the Enzyme member data.
831  ///
832  /// @return
833  /// Copy of the member data.
834  TEnzyme GetEnzyme(void) const;
835 
836  /// Assign a value to Enzyme data member.
837  ///
838  /// @param value
839  /// Value to assign
840  void SetEnzyme(TEnzyme value);
841 
842  /// Assign a value to Enzyme data member.
843  ///
844  /// @return
845  /// Reference to the data value.
846  TEnzyme& SetEnzyme(void);
847 
848  /// number of missed cleaves allowed
849  /// Check if a value has been assigned to Missedcleave data member.
850  ///
851  /// Data member Missedcleave is mandatory;
852  /// its type is defined as 'typedef int TMissedcleave'
853  /// @return
854  /// - true, if a value has been assigned.
855  /// - false, otherwise.
856  bool IsSetMissedcleave(void) const;
857 
858  /// Check if it is safe to call GetMissedcleave method.
859  ///
860  /// @return
861  /// - true, if the data member is getatable.
862  /// - false, otherwise.
863  bool CanGetMissedcleave(void) const;
864 
865  /// Reset Missedcleave data member.
866  void ResetMissedcleave(void);
867 
868  /// Get the Missedcleave member data.
869  ///
870  /// @return
871  /// Copy of the member data.
872  TMissedcleave GetMissedcleave(void) const;
873 
874  /// Assign a value to Missedcleave data member.
875  ///
876  /// @param value
877  /// Value to assign
878  void SetMissedcleave(TMissedcleave value);
879 
880  /// Assign a value to Missedcleave data member.
881  ///
882  /// @return
883  /// Reference to the data value.
884  TMissedcleave& SetMissedcleave(void);
885 
886  /// the number of hits kept in memory
887  /// for a spectrum
888  /// Check if a value has been assigned to Hitlistlen data member.
889  ///
890  /// Data member Hitlistlen is optional with default 25;
891  /// its type is defined as 'typedef int THitlistlen'
892  /// @return
893  /// - true, if a value has been assigned.
894  /// - false, otherwise.
895  bool IsSetHitlistlen(void) const;
896 
897  /// Check if it is safe to call GetHitlistlen method.
898  ///
899  /// @return
900  /// - true, if the data member is getatable.
901  /// - false, otherwise.
902  bool CanGetHitlistlen(void) const;
903 
904  /// Reset Hitlistlen data member.
905  void ResetHitlistlen(void);
906 
907  /// Assign default value to Hitlistlen data member.
908  void SetDefaultHitlistlen(void);
909 
910  /// Get the Hitlistlen member data.
911  ///
912  /// @return
913  /// Copy of the member data.
914  THitlistlen GetHitlistlen(void) const;
915 
916  /// Assign a value to Hitlistlen data member.
917  ///
918  /// @param value
919  /// Value to assign
920  void SetHitlistlen(THitlistlen value);
921 
922  /// Assign a value to Hitlistlen data member.
923  ///
924  /// @return
925  /// Reference to the data value.
926  THitlistlen& SetHitlistlen(void);
927 
928  /// sequence set to search, e.g. "nr"
929  /// Check if a value has been assigned to Db data member.
930  ///
931  /// Data member Db is mandatory;
932  /// its type is defined as 'typedef string TDb'
933  /// @return
934  /// - true, if a value has been assigned.
935  /// - false, otherwise.
936  bool IsSetDb(void) const;
937 
938  /// Check if it is safe to call GetDb method.
939  ///
940  /// @return
941  /// - true, if the data member is getatable.
942  /// - false, otherwise.
943  bool CanGetDb(void) const;
944 
945  /// Reset Db data member.
946  void ResetDb(void);
947 
948  /// Get the Db member data.
949  ///
950  /// @return
951  /// Reference to the member data.
952  const TDb& GetDb(void) const;
953 
954  /// Assign a value to Db data member.
955  ///
956  /// @param value
957  /// Value to assign
958  void SetDb(const TDb& value);
959  void SetDb(TDb&& value);
960 
961  /// Assign a value to Db data member.
962  ///
963  /// @return
964  /// Reference to the data value.
965  TDb& SetDb(void);
966 
967  /// number of m/z to consider in first pass
968  /// Check if a value has been assigned to Tophitnum data member.
969  ///
970  /// Data member Tophitnum is mandatory;
971  /// its type is defined as 'typedef int TTophitnum'
972  /// @return
973  /// - true, if a value has been assigned.
974  /// - false, otherwise.
975  bool IsSetTophitnum(void) const;
976 
977  /// Check if it is safe to call GetTophitnum method.
978  ///
979  /// @return
980  /// - true, if the data member is getatable.
981  /// - false, otherwise.
982  bool CanGetTophitnum(void) const;
983 
984  /// Reset Tophitnum data member.
985  void ResetTophitnum(void);
986 
987  /// Get the Tophitnum member data.
988  ///
989  /// @return
990  /// Copy of the member data.
991  TTophitnum GetTophitnum(void) const;
992 
993  /// Assign a value to Tophitnum data member.
994  ///
995  /// @param value
996  /// Value to assign
997  void SetTophitnum(TTophitnum value);
998 
999  /// Assign a value to Tophitnum data member.
1000  ///
1001  /// @return
1002  /// Reference to the data value.
1003  TTophitnum& SetTophitnum(void);
1004 
1005  /// minimum number of m/z values for a valid hit
1006  /// Check if a value has been assigned to Minhit data member.
1007  ///
1008  /// Data member Minhit is optional with default 2;
1009  /// its type is defined as 'typedef int TMinhit'
1010  /// @return
1011  /// - true, if a value has been assigned.
1012  /// - false, otherwise.
1013  bool IsSetMinhit(void) const;
1014 
1015  /// Check if it is safe to call GetMinhit method.
1016  ///
1017  /// @return
1018  /// - true, if the data member is getatable.
1019  /// - false, otherwise.
1020  bool CanGetMinhit(void) const;
1021 
1022  /// Reset Minhit data member.
1023  void ResetMinhit(void);
1024 
1025  /// Assign default value to Minhit data member.
1026  void SetDefaultMinhit(void);
1027 
1028  /// Get the Minhit member data.
1029  ///
1030  /// @return
1031  /// Copy of the member data.
1032  TMinhit GetMinhit(void) const;
1033 
1034  /// Assign a value to Minhit data member.
1035  ///
1036  /// @param value
1037  /// Value to assign
1038  void SetMinhit(TMinhit value);
1039 
1040  /// Assign a value to Minhit data member.
1041  ///
1042  /// @return
1043  /// Reference to the data value.
1044  TMinhit& SetMinhit(void);
1045 
1046  /// minimum number of m/z for a valid spectra
1047  /// Check if a value has been assigned to Minspectra data member.
1048  ///
1049  /// Data member Minspectra is optional with default 4;
1050  /// its type is defined as 'typedef int TMinspectra'
1051  /// @return
1052  /// - true, if a value has been assigned.
1053  /// - false, otherwise.
1054  bool IsSetMinspectra(void) const;
1055 
1056  /// Check if it is safe to call GetMinspectra method.
1057  ///
1058  /// @return
1059  /// - true, if the data member is getatable.
1060  /// - false, otherwise.
1061  bool CanGetMinspectra(void) const;
1062 
1063  /// Reset Minspectra data member.
1064  void ResetMinspectra(void);
1065 
1066  /// Assign default value to Minspectra data member.
1067  void SetDefaultMinspectra(void);
1068 
1069  /// Get the Minspectra member data.
1070  ///
1071  /// @return
1072  /// Copy of the member data.
1073  TMinspectra GetMinspectra(void) const;
1074 
1075  /// Assign a value to Minspectra data member.
1076  ///
1077  /// @param value
1078  /// Value to assign
1079  void SetMinspectra(TMinspectra value);
1080 
1081  /// Assign a value to Minspectra data member.
1082  ///
1083  /// @return
1084  /// Reference to the data value.
1085  TMinspectra& SetMinspectra(void);
1086 
1087  /// scale for m/z float to integer
1088  /// Check if a value has been assigned to Scale data member.
1089  ///
1090  /// Data member Scale is optional with default 100;
1091  /// its type is defined as 'typedef int TScale'
1092  /// @return
1093  /// - true, if a value has been assigned.
1094  /// - false, otherwise.
1095  bool IsSetScale(void) const;
1096 
1097  /// Check if it is safe to call GetScale method.
1098  ///
1099  /// @return
1100  /// - true, if the data member is getatable.
1101  /// - false, otherwise.
1102  bool CanGetScale(void) const;
1103 
1104  /// Reset Scale data member.
1105  void ResetScale(void);
1106 
1107  /// Assign default value to Scale data member.
1108  void SetDefaultScale(void);
1109 
1110  /// Get the Scale member data.
1111  ///
1112  /// @return
1113  /// Copy of the member data.
1114  TScale GetScale(void) const;
1115 
1116  /// Assign a value to Scale data member.
1117  ///
1118  /// @param value
1119  /// Value to assign
1120  void SetScale(TScale value);
1121 
1122  /// Assign a value to Scale data member.
1123  ///
1124  /// @return
1125  /// Reference to the data value.
1126  TScale& SetScale(void);
1127 
1128  /// maximum number of mass ladders per
1129  /// database peptide
1130  /// Check if a value has been assigned to Maxmods data member.
1131  ///
1132  /// Data member Maxmods is optional with default 64;
1133  /// its type is defined as 'typedef int TMaxmods'
1134  /// @return
1135  /// - true, if a value has been assigned.
1136  /// - false, otherwise.
1137  bool IsSetMaxmods(void) const;
1138 
1139  /// Check if it is safe to call GetMaxmods method.
1140  ///
1141  /// @return
1142  /// - true, if the data member is getatable.
1143  /// - false, otherwise.
1144  bool CanGetMaxmods(void) const;
1145 
1146  /// Reset Maxmods data member.
1147  void ResetMaxmods(void);
1148 
1149  /// Assign default value to Maxmods data member.
1150  void SetDefaultMaxmods(void);
1151 
1152  /// Get the Maxmods member data.
1153  ///
1154  /// @return
1155  /// Copy of the member data.
1156  TMaxmods GetMaxmods(void) const;
1157 
1158  /// Assign a value to Maxmods data member.
1159  ///
1160  /// @param value
1161  /// Value to assign
1162  void SetMaxmods(TMaxmods value);
1163 
1164  /// Assign a value to Maxmods data member.
1165  ///
1166  /// @return
1167  /// Reference to the data value.
1168  TMaxmods& SetMaxmods(void);
1169 
1170  /// taxa to limit search
1171  /// Check if a value has been assigned to Taxids data member.
1172  ///
1173  /// Data member Taxids is optional;
1174  /// its type is defined as 'typedef list< int > TTaxids'
1175  /// @return
1176  /// - true, if a value has been assigned.
1177  /// - false, otherwise.
1178  bool IsSetTaxids(void) const;
1179 
1180  /// Check if it is safe to call GetTaxids method.
1181  ///
1182  /// @return
1183  /// - true, if the data member is getatable.
1184  /// - false, otherwise.
1185  bool CanGetTaxids(void) const;
1186 
1187  /// Reset Taxids data member.
1188  void ResetTaxids(void);
1189 
1190  /// Get the Taxids member data.
1191  ///
1192  /// @return
1193  /// Reference to the member data.
1194  const TTaxids& GetTaxids(void) const;
1195 
1196  /// Assign a value to Taxids data member.
1197  ///
1198  /// @return
1199  /// Reference to the data value.
1200  TTaxids& SetTaxids(void);
1201 
1202  /// how to deal with charges
1203  /// Check if a value has been assigned to Chargehandling data member.
1204  ///
1205  /// Data member Chargehandling is optional;
1206  /// its type is defined as 'typedef CMSChargeHandle TChargehandling'
1207  /// @return
1208  /// - true, if a value has been assigned.
1209  /// - false, otherwise.
1210  bool IsSetChargehandling(void) const;
1211 
1212  /// Check if it is safe to call GetChargehandling method.
1213  ///
1214  /// @return
1215  /// - true, if the data member is getatable.
1216  /// - false, otherwise.
1217  bool CanGetChargehandling(void) const;
1218 
1219  /// Reset Chargehandling data member.
1220  void ResetChargehandling(void);
1221 
1222  /// Get the Chargehandling member data.
1223  ///
1224  /// @return
1225  /// Reference to the member data.
1226  const TChargehandling& GetChargehandling(void) const;
1227 
1228  /// Assign a value to Chargehandling data member.
1229  ///
1230  /// @param value
1231  /// Reference to value.
1232  void SetChargehandling(TChargehandling& value);
1233 
1234  /// Assign a value to Chargehandling data member.
1235  ///
1236  /// @return
1237  /// Reference to the data value.
1238  TChargehandling& SetChargehandling(void);
1239 
1240  /// user defined modifications
1241  /// Check if a value has been assigned to Usermods data member.
1242  ///
1243  /// Data member Usermods is optional;
1244  /// its type is defined as 'typedef CMSModSpecSet TUsermods'
1245  /// @return
1246  /// - true, if a value has been assigned.
1247  /// - false, otherwise.
1248  bool IsSetUsermods(void) const;
1249 
1250  /// Check if it is safe to call GetUsermods method.
1251  ///
1252  /// @return
1253  /// - true, if the data member is getatable.
1254  /// - false, otherwise.
1255  bool CanGetUsermods(void) const;
1256 
1257  /// Reset Usermods data member.
1258  void ResetUsermods(void);
1259 
1260  /// Get the Usermods member data.
1261  ///
1262  /// @return
1263  /// Reference to the member data.
1264  const TUsermods& GetUsermods(void) const;
1265 
1266  /// Assign a value to Usermods data member.
1267  ///
1268  /// @param value
1269  /// Reference to value.
1270  void SetUsermods(TUsermods& value);
1271 
1272  /// Assign a value to Usermods data member.
1273  ///
1274  /// @return
1275  /// Reference to the data value.
1276  TUsermods& SetUsermods(void);
1277 
1278  /// min number of counts per precursor bin
1279  /// Check if a value has been assigned to Pseudocount data member.
1280  ///
1281  /// Data member Pseudocount is optional with default 1;
1282  /// its type is defined as 'typedef int TPseudocount'
1283  /// @return
1284  /// - true, if a value has been assigned.
1285  /// - false, otherwise.
1286  bool IsSetPseudocount(void) const;
1287 
1288  /// Check if it is safe to call GetPseudocount method.
1289  ///
1290  /// @return
1291  /// - true, if the data member is getatable.
1292  /// - false, otherwise.
1293  bool CanGetPseudocount(void) const;
1294 
1295  /// Reset Pseudocount data member.
1296  void ResetPseudocount(void);
1297 
1298  /// Assign default value to Pseudocount data member.
1299  void SetDefaultPseudocount(void);
1300 
1301  /// Get the Pseudocount member data.
1302  ///
1303  /// @return
1304  /// Copy of the member data.
1305  TPseudocount GetPseudocount(void) const;
1306 
1307  /// Assign a value to Pseudocount data member.
1308  ///
1309  /// @param value
1310  /// Value to assign
1311  void SetPseudocount(TPseudocount value);
1312 
1313  /// Assign a value to Pseudocount data member.
1314  ///
1315  /// @return
1316  /// Reference to the data value.
1317  TPseudocount& SetPseudocount(void);
1318 
1319  /// should b1 product be in search (1=no, 0=yes)
1320  /// Check if a value has been assigned to Searchb1 data member.
1321  ///
1322  /// Data member Searchb1 is optional with default 0;
1323  /// its type is defined as 'typedef int TSearchb1'
1324  /// @return
1325  /// - true, if a value has been assigned.
1326  /// - false, otherwise.
1327  bool IsSetSearchb1(void) const;
1328 
1329  /// Check if it is safe to call GetSearchb1 method.
1330  ///
1331  /// @return
1332  /// - true, if the data member is getatable.
1333  /// - false, otherwise.
1334  bool CanGetSearchb1(void) const;
1335 
1336  /// Reset Searchb1 data member.
1337  void ResetSearchb1(void);
1338 
1339  /// Assign default value to Searchb1 data member.
1340  void SetDefaultSearchb1(void);
1341 
1342  /// Get the Searchb1 member data.
1343  ///
1344  /// @return
1345  /// Copy of the member data.
1346  TSearchb1 GetSearchb1(void) const;
1347 
1348  /// Assign a value to Searchb1 data member.
1349  ///
1350  /// @param value
1351  /// Value to assign
1352  void SetSearchb1(TSearchb1 value);
1353 
1354  /// Assign a value to Searchb1 data member.
1355  ///
1356  /// @return
1357  /// Reference to the data value.
1358  TSearchb1& SetSearchb1(void);
1359 
1360  /// should c terminus ion be searched (1=no, 0=yes)
1361  /// Check if a value has been assigned to Searchctermproduct data member.
1362  ///
1363  /// Data member Searchctermproduct is optional with default 0;
1364  /// its type is defined as 'typedef int TSearchctermproduct'
1365  /// @return
1366  /// - true, if a value has been assigned.
1367  /// - false, otherwise.
1368  bool IsSetSearchctermproduct(void) const;
1369 
1370  /// Check if it is safe to call GetSearchctermproduct method.
1371  ///
1372  /// @return
1373  /// - true, if the data member is getatable.
1374  /// - false, otherwise.
1375  bool CanGetSearchctermproduct(void) const;
1376 
1377  /// Reset Searchctermproduct data member.
1378  void ResetSearchctermproduct(void);
1379 
1380  /// Assign default value to Searchctermproduct data member.
1381  void SetDefaultSearchctermproduct(void);
1382 
1383  /// Get the Searchctermproduct member data.
1384  ///
1385  /// @return
1386  /// Copy of the member data.
1387  TSearchctermproduct GetSearchctermproduct(void) const;
1388 
1389  /// Assign a value to Searchctermproduct data member.
1390  ///
1391  /// @param value
1392  /// Value to assign
1393  void SetSearchctermproduct(TSearchctermproduct value);
1394 
1395  /// Assign a value to Searchctermproduct data member.
1396  ///
1397  /// @return
1398  /// Reference to the data value.
1399  TSearchctermproduct& SetSearchctermproduct(void);
1400 
1401  /// max number of ions in each series (0=all)
1402  /// Check if a value has been assigned to Maxproductions data member.
1403  ///
1404  /// Data member Maxproductions is optional with default 0;
1405  /// its type is defined as 'typedef int TMaxproductions'
1406  /// @return
1407  /// - true, if a value has been assigned.
1408  /// - false, otherwise.
1409  bool IsSetMaxproductions(void) const;
1410 
1411  /// Check if it is safe to call GetMaxproductions method.
1412  ///
1413  /// @return
1414  /// - true, if the data member is getatable.
1415  /// - false, otherwise.
1416  bool CanGetMaxproductions(void) const;
1417 
1418  /// Reset Maxproductions data member.
1419  void ResetMaxproductions(void);
1420 
1421  /// Assign default value to Maxproductions data member.
1422  void SetDefaultMaxproductions(void);
1423 
1424  /// Get the Maxproductions member data.
1425  ///
1426  /// @return
1427  /// Copy of the member data.
1428  TMaxproductions GetMaxproductions(void) const;
1429 
1430  /// Assign a value to Maxproductions data member.
1431  ///
1432  /// @param value
1433  /// Value to assign
1434  void SetMaxproductions(TMaxproductions value);
1435 
1436  /// Assign a value to Maxproductions data member.
1437  ///
1438  /// @return
1439  /// Reference to the data value.
1440  TMaxproductions& SetMaxproductions(void);
1441 
1442  /// min number of AA in peptide for noenzyme search
1443  /// Check if a value has been assigned to Minnoenzyme data member.
1444  ///
1445  /// Data member Minnoenzyme is optional with default 4;
1446  /// its type is defined as 'typedef int TMinnoenzyme'
1447  /// @return
1448  /// - true, if a value has been assigned.
1449  /// - false, otherwise.
1450  bool IsSetMinnoenzyme(void) const;
1451 
1452  /// Check if it is safe to call GetMinnoenzyme method.
1453  ///
1454  /// @return
1455  /// - true, if the data member is getatable.
1456  /// - false, otherwise.
1457  bool CanGetMinnoenzyme(void) const;
1458 
1459  /// Reset Minnoenzyme data member.
1460  void ResetMinnoenzyme(void);
1461 
1462  /// Assign default value to Minnoenzyme data member.
1463  void SetDefaultMinnoenzyme(void);
1464 
1465  /// Get the Minnoenzyme member data.
1466  ///
1467  /// @return
1468  /// Copy of the member data.
1469  TMinnoenzyme GetMinnoenzyme(void) const;
1470 
1471  /// Assign a value to Minnoenzyme data member.
1472  ///
1473  /// @param value
1474  /// Value to assign
1475  void SetMinnoenzyme(TMinnoenzyme value);
1476 
1477  /// Assign a value to Minnoenzyme data member.
1478  ///
1479  /// @return
1480  /// Reference to the data value.
1481  TMinnoenzyme& SetMinnoenzyme(void);
1482 
1483  /// max number of AA in peptide for noenzyme search (0=none)
1484  /// Check if a value has been assigned to Maxnoenzyme data member.
1485  ///
1486  /// Data member Maxnoenzyme is optional with default 0;
1487  /// its type is defined as 'typedef int TMaxnoenzyme'
1488  /// @return
1489  /// - true, if a value has been assigned.
1490  /// - false, otherwise.
1491  bool IsSetMaxnoenzyme(void) const;
1492 
1493  /// Check if it is safe to call GetMaxnoenzyme method.
1494  ///
1495  /// @return
1496  /// - true, if the data member is getatable.
1497  /// - false, otherwise.
1498  bool CanGetMaxnoenzyme(void) const;
1499 
1500  /// Reset Maxnoenzyme data member.
1501  void ResetMaxnoenzyme(void);
1502 
1503  /// Assign default value to Maxnoenzyme data member.
1504  void SetDefaultMaxnoenzyme(void);
1505 
1506  /// Get the Maxnoenzyme member data.
1507  ///
1508  /// @return
1509  /// Copy of the member data.
1510  TMaxnoenzyme GetMaxnoenzyme(void) const;
1511 
1512  /// Assign a value to Maxnoenzyme data member.
1513  ///
1514  /// @param value
1515  /// Value to assign
1516  void SetMaxnoenzyme(TMaxnoenzyme value);
1517 
1518  /// Assign a value to Maxnoenzyme data member.
1519  ///
1520  /// @return
1521  /// Reference to the data value.
1522  TMaxnoenzyme& SetMaxnoenzyme(void);
1523 
1524  /// the threshold in Da for adding neutron
1525  /// Check if a value has been assigned to Exactmass data member.
1526  ///
1527  /// Data member Exactmass is optional;
1528  /// its type is defined as 'typedef double TExactmass'
1529  /// @return
1530  /// - true, if a value has been assigned.
1531  /// - false, otherwise.
1532  bool IsSetExactmass(void) const;
1533 
1534  /// Check if it is safe to call GetExactmass method.
1535  ///
1536  /// @return
1537  /// - true, if the data member is getatable.
1538  /// - false, otherwise.
1539  bool CanGetExactmass(void) const;
1540 
1541  /// Reset Exactmass data member.
1542  void ResetExactmass(void);
1543 
1544  /// Get the Exactmass member data.
1545  ///
1546  /// @return
1547  /// Copy of the member data.
1548  TExactmass GetExactmass(void) const;
1549 
1550  /// Assign a value to Exactmass data member.
1551  ///
1552  /// @param value
1553  /// Value to assign
1554  void SetExactmass(TExactmass value);
1555 
1556  /// Assign a value to Exactmass data member.
1557  ///
1558  /// @return
1559  /// Reference to the data value.
1560  TExactmass& SetExactmass(void);
1561 
1562  /// id of the search settings
1563  /// Check if a value has been assigned to Settingid data member.
1564  ///
1565  /// Data member Settingid is optional;
1566  /// its type is defined as 'typedef int TSettingid'
1567  /// @return
1568  /// - true, if a value has been assigned.
1569  /// - false, otherwise.
1570  bool IsSetSettingid(void) const;
1571 
1572  /// Check if it is safe to call GetSettingid method.
1573  ///
1574  /// @return
1575  /// - true, if the data member is getatable.
1576  /// - false, otherwise.
1577  bool CanGetSettingid(void) const;
1578 
1579  /// Reset Settingid data member.
1580  void ResetSettingid(void);
1581 
1582  /// Get the Settingid member data.
1583  ///
1584  /// @return
1585  /// Copy of the member data.
1586  TSettingid GetSettingid(void) const;
1587 
1588  /// Assign a value to Settingid data member.
1589  ///
1590  /// @param value
1591  /// Value to assign
1592  void SetSettingid(TSettingid value);
1593 
1594  /// Assign a value to Settingid data member.
1595  ///
1596  /// @return
1597  /// Reference to the data value.
1598  TSettingid& SetSettingid(void);
1599 
1600  /// iterative search settings
1601  /// Check if a value has been assigned to Iterativesettings data member.
1602  ///
1603  /// Data member Iterativesettings is optional;
1604  /// its type is defined as 'typedef CMSIterativeSettings TIterativesettings'
1605  /// @return
1606  /// - true, if a value has been assigned.
1607  /// - false, otherwise.
1608  bool IsSetIterativesettings(void) const;
1609 
1610  /// Check if it is safe to call GetIterativesettings method.
1611  ///
1612  /// @return
1613  /// - true, if the data member is getatable.
1614  /// - false, otherwise.
1615  bool CanGetIterativesettings(void) const;
1616 
1617  /// Reset Iterativesettings data member.
1618  void ResetIterativesettings(void);
1619 
1620  /// Get the Iterativesettings member data.
1621  ///
1622  /// @return
1623  /// Reference to the member data.
1624  const TIterativesettings& GetIterativesettings(void) const;
1625 
1626  /// Assign a value to Iterativesettings data member.
1627  ///
1628  /// @param value
1629  /// Reference to value.
1630  void SetIterativesettings(TIterativesettings& value);
1631 
1632  /// Assign a value to Iterativesettings data member.
1633  ///
1634  /// @return
1635  /// Reference to the data value.
1636  TIterativesettings& SetIterativesettings(void);
1637 
1638  /// turn on aggressive precursor culling for ETD (0=none)
1639  /// Check if a value has been assigned to Precursorcull data member.
1640  ///
1641  /// Data member Precursorcull is optional;
1642  /// its type is defined as 'typedef int TPrecursorcull'
1643  /// @return
1644  /// - true, if a value has been assigned.
1645  /// - false, otherwise.
1646  bool IsSetPrecursorcull(void) const;
1647 
1648  /// Check if it is safe to call GetPrecursorcull method.
1649  ///
1650  /// @return
1651  /// - true, if the data member is getatable.
1652  /// - false, otherwise.
1653  bool CanGetPrecursorcull(void) const;
1654 
1655  /// Reset Precursorcull data member.
1656  void ResetPrecursorcull(void);
1657 
1658  /// Get the Precursorcull member data.
1659  ///
1660  /// @return
1661  /// Copy of the member data.
1662  TPrecursorcull GetPrecursorcull(void) const;
1663 
1664  /// Assign a value to Precursorcull data member.
1665  ///
1666  /// @param value
1667  /// Value to assign
1668  void SetPrecursorcull(TPrecursorcull value);
1669 
1670  /// Assign a value to Precursorcull data member.
1671  ///
1672  /// @return
1673  /// Reference to the data value.
1674  TPrecursorcull& SetPrecursorcull(void);
1675 
1676  /// input files
1677  /// Check if a value has been assigned to Infiles data member.
1678  ///
1679  /// Data member Infiles is optional;
1680  /// its type is defined as 'typedef list< CRef< CMSInFile > > TInfiles'
1681  /// @return
1682  /// - true, if a value has been assigned.
1683  /// - false, otherwise.
1684  bool IsSetInfiles(void) const;
1685 
1686  /// Check if it is safe to call GetInfiles method.
1687  ///
1688  /// @return
1689  /// - true, if the data member is getatable.
1690  /// - false, otherwise.
1691  bool CanGetInfiles(void) const;
1692 
1693  /// Reset Infiles data member.
1694  void ResetInfiles(void);
1695 
1696  /// Get the Infiles member data.
1697  ///
1698  /// @return
1699  /// Reference to the member data.
1700  const TInfiles& GetInfiles(void) const;
1701 
1702  /// Assign a value to Infiles data member.
1703  ///
1704  /// @return
1705  /// Reference to the data value.
1706  TInfiles& SetInfiles(void);
1707 
1708  /// output files
1709  /// Check if a value has been assigned to Outfiles data member.
1710  ///
1711  /// Data member Outfiles is optional;
1712  /// its type is defined as 'typedef list< CRef< CMSOutFile > > TOutfiles'
1713  /// @return
1714  /// - true, if a value has been assigned.
1715  /// - false, otherwise.
1716  bool IsSetOutfiles(void) const;
1717 
1718  /// Check if it is safe to call GetOutfiles method.
1719  ///
1720  /// @return
1721  /// - true, if the data member is getatable.
1722  /// - false, otherwise.
1723  bool CanGetOutfiles(void) const;
1724 
1725  /// Reset Outfiles data member.
1726  void ResetOutfiles(void);
1727 
1728  /// Get the Outfiles member data.
1729  ///
1730  /// @return
1731  /// Reference to the member data.
1732  const TOutfiles& GetOutfiles(void) const;
1733 
1734  /// Assign a value to Outfiles data member.
1735  ///
1736  /// @return
1737  /// Reference to the data value.
1738  TOutfiles& SetOutfiles(void);
1739 
1740  /// turn on correlation score (1=nocorr)
1741  /// Check if a value has been assigned to Nocorrelationscore data member.
1742  ///
1743  /// Data member Nocorrelationscore is optional;
1744  /// its type is defined as 'typedef int TNocorrelationscore'
1745  /// @return
1746  /// - true, if a value has been assigned.
1747  /// - false, otherwise.
1748  bool IsSetNocorrelationscore(void) const;
1749 
1750  /// Check if it is safe to call GetNocorrelationscore method.
1751  ///
1752  /// @return
1753  /// - true, if the data member is getatable.
1754  /// - false, otherwise.
1755  bool CanGetNocorrelationscore(void) const;
1756 
1757  /// Reset Nocorrelationscore data member.
1758  void ResetNocorrelationscore(void);
1759 
1760  /// Get the Nocorrelationscore member data.
1761  ///
1762  /// @return
1763  /// Copy of the member data.
1764  TNocorrelationscore GetNocorrelationscore(void) const;
1765 
1766  /// Assign a value to Nocorrelationscore data member.
1767  ///
1768  /// @param value
1769  /// Value to assign
1770  void SetNocorrelationscore(TNocorrelationscore value);
1771 
1772  /// Assign a value to Nocorrelationscore data member.
1773  ///
1774  /// @return
1775  /// Reference to the data value.
1776  TNocorrelationscore& SetNocorrelationscore(void);
1777 
1778  /// probability of a consecutive ion (used in correlation)
1779  /// Check if a value has been assigned to Probfollowingion data member.
1780  ///
1781  /// Data member Probfollowingion is optional;
1782  /// its type is defined as 'typedef double TProbfollowingion'
1783  /// @return
1784  /// - true, if a value has been assigned.
1785  /// - false, otherwise.
1786  bool IsSetProbfollowingion(void) const;
1787 
1788  /// Check if it is safe to call GetProbfollowingion method.
1789  ///
1790  /// @return
1791  /// - true, if the data member is getatable.
1792  /// - false, otherwise.
1793  bool CanGetProbfollowingion(void) const;
1794 
1795  /// Reset Probfollowingion data member.
1796  void ResetProbfollowingion(void);
1797 
1798  /// Get the Probfollowingion member data.
1799  ///
1800  /// @return
1801  /// Copy of the member data.
1802  TProbfollowingion GetProbfollowingion(void) const;
1803 
1804  /// Assign a value to Probfollowingion data member.
1805  ///
1806  /// @param value
1807  /// Value to assign
1808  void SetProbfollowingion(TProbfollowingion value);
1809 
1810  /// Assign a value to Probfollowingion data member.
1811  ///
1812  /// @return
1813  /// Reference to the data value.
1814  TProbfollowingion& SetProbfollowingion(void);
1815 
1816  /// should nmethionine be cleaved?
1817  /// Check if a value has been assigned to Nmethionine data member.
1818  ///
1819  /// Data member Nmethionine is optional;
1820  /// its type is defined as 'typedef bool TNmethionine'
1821  /// @return
1822  /// - true, if a value has been assigned.
1823  /// - false, otherwise.
1824  bool IsSetNmethionine(void) const;
1825 
1826  /// Check if it is safe to call GetNmethionine method.
1827  ///
1828  /// @return
1829  /// - true, if the data member is getatable.
1830  /// - false, otherwise.
1831  bool CanGetNmethionine(void) const;
1832 
1833  /// Reset Nmethionine data member.
1834  void ResetNmethionine(void);
1835 
1836  /// Get the Nmethionine member data.
1837  ///
1838  /// @return
1839  /// Copy of the member data.
1840  TNmethionine GetNmethionine(void) const;
1841 
1842  /// Assign a value to Nmethionine data member.
1843  ///
1844  /// @param value
1845  /// Value to assign
1846  void SetNmethionine(TNmethionine value);
1847 
1848  /// Assign a value to Nmethionine data member.
1849  ///
1850  /// @return
1851  /// Reference to the data value.
1852  TNmethionine& SetNmethionine(void);
1853 
1854  /// fraction allowable adjustment of product mass tolerance
1855  /// Check if a value has been assigned to Automassadjust data member.
1856  ///
1857  /// Data member Automassadjust is optional;
1858  /// its type is defined as 'typedef double TAutomassadjust'
1859  /// @return
1860  /// - true, if a value has been assigned.
1861  /// - false, otherwise.
1862  bool IsSetAutomassadjust(void) const;
1863 
1864  /// Check if it is safe to call GetAutomassadjust method.
1865  ///
1866  /// @return
1867  /// - true, if the data member is getatable.
1868  /// - false, otherwise.
1869  bool CanGetAutomassadjust(void) const;
1870 
1871  /// Reset Automassadjust data member.
1872  void ResetAutomassadjust(void);
1873 
1874  /// Get the Automassadjust member data.
1875  ///
1876  /// @return
1877  /// Copy of the member data.
1878  TAutomassadjust GetAutomassadjust(void) const;
1879 
1880  /// Assign a value to Automassadjust data member.
1881  ///
1882  /// @param value
1883  /// Value to assign
1884  void SetAutomassadjust(TAutomassadjust value);
1885 
1886  /// Assign a value to Automassadjust data member.
1887  ///
1888  /// @return
1889  /// Reference to the data value.
1890  TAutomassadjust& SetAutomassadjust(void);
1891 
1892  /// low mass filter in Daltons, unscaled
1893  /// Check if a value has been assigned to Lomasscutoff data member.
1894  ///
1895  /// Data member Lomasscutoff is optional;
1896  /// its type is defined as 'typedef double TLomasscutoff'
1897  /// @return
1898  /// - true, if a value has been assigned.
1899  /// - false, otherwise.
1900  bool IsSetLomasscutoff(void) const;
1901 
1902  /// Check if it is safe to call GetLomasscutoff method.
1903  ///
1904  /// @return
1905  /// - true, if the data member is getatable.
1906  /// - false, otherwise.
1907  bool CanGetLomasscutoff(void) const;
1908 
1909  /// Reset Lomasscutoff data member.
1910  void ResetLomasscutoff(void);
1911 
1912  /// Get the Lomasscutoff member data.
1913  ///
1914  /// @return
1915  /// Copy of the member data.
1916  TLomasscutoff GetLomasscutoff(void) const;
1917 
1918  /// Assign a value to Lomasscutoff data member.
1919  ///
1920  /// @param value
1921  /// Value to assign
1922  void SetLomasscutoff(TLomasscutoff value);
1923 
1924  /// Assign a value to Lomasscutoff data member.
1925  ///
1926  /// @return
1927  /// Reference to the data value.
1928  TLomasscutoff& SetLomasscutoff(void);
1929 
1930  /// library search settings
1931  /// Check if a value has been assigned to Libsearchsettings data member.
1932  ///
1933  /// Data member Libsearchsettings is optional;
1934  /// its type is defined as 'typedef CMSLibrarySettings TLibsearchsettings'
1935  /// @return
1936  /// - true, if a value has been assigned.
1937  /// - false, otherwise.
1938  bool IsSetLibsearchsettings(void) const;
1939 
1940  /// Check if it is safe to call GetLibsearchsettings method.
1941  ///
1942  /// @return
1943  /// - true, if the data member is getatable.
1944  /// - false, otherwise.
1945  bool CanGetLibsearchsettings(void) const;
1946 
1947  /// Reset Libsearchsettings data member.
1948  void ResetLibsearchsettings(void);
1949 
1950  /// Get the Libsearchsettings member data.
1951  ///
1952  /// @return
1953  /// Reference to the member data.
1954  const TLibsearchsettings& GetLibsearchsettings(void) const;
1955 
1956  /// Assign a value to Libsearchsettings data member.
1957  ///
1958  /// @param value
1959  /// Reference to value.
1960  void SetLibsearchsettings(TLibsearchsettings& value);
1961 
1962  /// Assign a value to Libsearchsettings data member.
1963  ///
1964  /// @return
1965  /// Reference to the data value.
1966  TLibsearchsettings& SetLibsearchsettings(void);
1967 
1968  /// which ions to use no proline rule
1969  /// Check if a value has been assigned to Noprolineions data member.
1970  ///
1971  /// Data member Noprolineions is optional;
1972  /// its type is defined as 'typedef list< int > TNoprolineions'
1973  /// @return
1974  /// - true, if a value has been assigned.
1975  /// - false, otherwise.
1976  bool IsSetNoprolineions(void) const;
1977 
1978  /// Check if it is safe to call GetNoprolineions method.
1979  ///
1980  /// @return
1981  /// - true, if the data member is getatable.
1982  /// - false, otherwise.
1983  bool CanGetNoprolineions(void) const;
1984 
1985  /// Reset Noprolineions data member.
1986  void ResetNoprolineions(void);
1987 
1988  /// Get the Noprolineions member data.
1989  ///
1990  /// @return
1991  /// Reference to the member data.
1992  const TNoprolineions& GetNoprolineions(void) const;
1993 
1994  /// Assign a value to Noprolineions data member.
1995  ///
1996  /// @return
1997  /// Reference to the data value.
1998  TNoprolineions& SetNoprolineions(void);
1999 
2000  /// do reverse search
2001  /// Check if a value has been assigned to Reversesearch data member.
2002  ///
2003  /// Data member Reversesearch is optional;
2004  /// its type is defined as 'typedef bool TReversesearch'
2005  /// @return
2006  /// - true, if a value has been assigned.
2007  /// - false, otherwise.
2008  bool IsSetReversesearch(void) const;
2009 
2010  /// Check if it is safe to call GetReversesearch method.
2011  ///
2012  /// @return
2013  /// - true, if the data member is getatable.
2014  /// - false, otherwise.
2015  bool CanGetReversesearch(void) const;
2016 
2017  /// Reset Reversesearch data member.
2018  void ResetReversesearch(void);
2019 
2020  /// Get the Reversesearch member data.
2021  ///
2022  /// @return
2023  /// Copy of the member data.
2024  TReversesearch GetReversesearch(void) const;
2025 
2026  /// Assign a value to Reversesearch data member.
2027  ///
2028  /// @param value
2029  /// Value to assign
2030  void SetReversesearch(TReversesearch value);
2031 
2032  /// Assign a value to Reversesearch data member.
2033  ///
2034  /// @return
2035  /// Reference to the data value.
2036  TReversesearch& SetReversesearch(void);
2037 
2038  /// extra search settings
2039  /// Check if a value has been assigned to Othersettings data member.
2040  ///
2041  /// Data member Othersettings is optional;
2042  /// its type is defined as 'typedef list< CRef< CNameValue > > TOthersettings'
2043  /// @return
2044  /// - true, if a value has been assigned.
2045  /// - false, otherwise.
2046  bool IsSetOthersettings(void) const;
2047 
2048  /// Check if it is safe to call GetOthersettings method.
2049  ///
2050  /// @return
2051  /// - true, if the data member is getatable.
2052  /// - false, otherwise.
2053  bool CanGetOthersettings(void) const;
2054 
2055  /// Reset Othersettings data member.
2056  void ResetOthersettings(void);
2057 
2058  /// Get the Othersettings member data.
2059  ///
2060  /// @return
2061  /// Reference to the member data.
2062  const TOthersettings& GetOthersettings(void) const;
2063 
2064  /// Assign a value to Othersettings data member.
2065  ///
2066  /// @return
2067  /// Reference to the data value.
2068  TOthersettings& SetOthersettings(void);
2069 
2070  /// number of isotopic peaks to search when using MSSearchType multiisotope
2071  /// Check if a value has been assigned to Numisotopes data member.
2072  ///
2073  /// Data member Numisotopes is optional;
2074  /// its type is defined as 'typedef int TNumisotopes'
2075  /// @return
2076  /// - true, if a value has been assigned.
2077  /// - false, otherwise.
2078  bool IsSetNumisotopes(void) const;
2079 
2080  /// Check if it is safe to call GetNumisotopes method.
2081  ///
2082  /// @return
2083  /// - true, if the data member is getatable.
2084  /// - false, otherwise.
2085  bool CanGetNumisotopes(void) const;
2086 
2087  /// Reset Numisotopes data member.
2088  void ResetNumisotopes(void);
2089 
2090  /// Get the Numisotopes member data.
2091  ///
2092  /// @return
2093  /// Copy of the member data.
2094  TNumisotopes GetNumisotopes(void) const;
2095 
2096  /// Assign a value to Numisotopes data member.
2097  ///
2098  /// @param value
2099  /// Value to assign
2100  void SetNumisotopes(TNumisotopes value);
2101 
2102  /// Assign a value to Numisotopes data member.
2103  ///
2104  /// @return
2105  /// Reference to the data value.
2106  TNumisotopes& SetNumisotopes(void);
2107 
2108  /// search precursor as ppm
2109  /// Check if a value has been assigned to Pepppm data member.
2110  ///
2111  /// Data member Pepppm is optional;
2112  /// its type is defined as 'typedef bool TPepppm'
2113  /// @return
2114  /// - true, if a value has been assigned.
2115  /// - false, otherwise.
2116  bool IsSetPepppm(void) const;
2117 
2118  /// Check if it is safe to call GetPepppm method.
2119  ///
2120  /// @return
2121  /// - true, if the data member is getatable.
2122  /// - false, otherwise.
2123  bool CanGetPepppm(void) const;
2124 
2125  /// Reset Pepppm data member.
2126  void ResetPepppm(void);
2127 
2128  /// Get the Pepppm member data.
2129  ///
2130  /// @return
2131  /// Copy of the member data.
2132  TPepppm GetPepppm(void) const;
2133 
2134  /// Assign a value to Pepppm data member.
2135  ///
2136  /// @param value
2137  /// Value to assign
2138  void SetPepppm(TPepppm value);
2139 
2140  /// Assign a value to Pepppm data member.
2141  ///
2142  /// @return
2143  /// Reference to the data value.
2144  TPepppm& SetPepppm(void);
2145 
2146  /// search product as ppm
2147  /// Check if a value has been assigned to Msmsppm data member.
2148  ///
2149  /// Data member Msmsppm is optional;
2150  /// its type is defined as 'typedef bool TMsmsppm'
2151  /// @return
2152  /// - true, if a value has been assigned.
2153  /// - false, otherwise.
2154  bool IsSetMsmsppm(void) const;
2155 
2156  /// Check if it is safe to call GetMsmsppm method.
2157  ///
2158  /// @return
2159  /// - true, if the data member is getatable.
2160  /// - false, otherwise.
2161  bool CanGetMsmsppm(void) const;
2162 
2163  /// Reset Msmsppm data member.
2164  void ResetMsmsppm(void);
2165 
2166  /// Get the Msmsppm member data.
2167  ///
2168  /// @return
2169  /// Copy of the member data.
2170  TMsmsppm GetMsmsppm(void) const;
2171 
2172  /// Assign a value to Msmsppm data member.
2173  ///
2174  /// @param value
2175  /// Value to assign
2176  void SetMsmsppm(TMsmsppm value);
2177 
2178  /// Assign a value to Msmsppm data member.
2179  ///
2180  /// @return
2181  /// Reference to the data value.
2182  TMsmsppm& SetMsmsppm(void);
2183 
2184  /// the maximum number of hits to report per spectrum, 0=all
2185  /// Check if a value has been assigned to Reportedhitcount data member.
2186  ///
2187  /// Data member Reportedhitcount is optional;
2188  /// its type is defined as 'typedef int TReportedhitcount'
2189  /// @return
2190  /// - true, if a value has been assigned.
2191  /// - false, otherwise.
2192  bool IsSetReportedhitcount(void) const;
2193 
2194  /// Check if it is safe to call GetReportedhitcount method.
2195  ///
2196  /// @return
2197  /// - true, if the data member is getatable.
2198  /// - false, otherwise.
2199  bool CanGetReportedhitcount(void) const;
2200 
2201  /// Reset Reportedhitcount data member.
2202  void ResetReportedhitcount(void);
2203 
2204  /// Get the Reportedhitcount member data.
2205  ///
2206  /// @return
2207  /// Copy of the member data.
2208  TReportedhitcount GetReportedhitcount(void) const;
2209 
2210  /// Assign a value to Reportedhitcount data member.
2211  ///
2212  /// @param value
2213  /// Value to assign
2214  void SetReportedhitcount(TReportedhitcount value);
2215 
2216  /// Assign a value to Reportedhitcount data member.
2217  ///
2218  /// @return
2219  /// Reference to the data value.
2220  TReportedhitcount& SetReportedhitcount(void);
2221 
2222  /// Reset the whole object
2223  virtual void Reset(void);
2224 
2225 
2226 private:
2227  // Prohibit copy constructor and assignment operator
2230 
2231  // data
2232  Uint4 m_set_State[4];
2235  list< int > m_Ionstosearch;
2236  double m_Peptol;
2237  double m_Msmstol;
2238  int m_Zdep;
2239  double m_Cutoff;
2240  double m_Cutlo;
2241  double m_Cuthi;
2242  double m_Cutinc;
2247  list< int > m_Fixed;
2248  list< int > m_Variable;
2252  string m_Db;
2256  int m_Scale;
2258  list< int > m_Taxids;
2267  double m_Exactmass;
2271  list< CRef< CMSInFile > > m_Infiles;
2272  list< CRef< CMSOutFile > > m_Outfiles;
2279  list< int > m_Noprolineions;
2281  list< CRef< CNameValue > > m_Othersettings;
2283  bool m_Pepppm;
2286 };
2287 
2288 /* @} */
2289 
2290 
2291 
2292 
2293 
2294 ///////////////////////////////////////////////////////////
2295 ///////////////////// inline methods //////////////////////
2296 ///////////////////////////////////////////////////////////
2297 inline
2299 {
2300  return ((m_set_State[0] & 0x3) != 0);
2301 }
2302 
2303 inline
2305 {
2306  return IsSetPrecursorsearchtype();
2307 }
2308 
2309 inline
2311 {
2312  m_Precursorsearchtype = (int)(0);
2313  m_set_State[0] &= ~0x3;
2314 }
2315 
2316 inline
2318 {
2319  if (!CanGetPrecursorsearchtype()) {
2320  ThrowUnassigned(0);
2321  }
2322  return m_Precursorsearchtype;
2323 }
2324 
2325 inline
2327 {
2329  m_set_State[0] |= 0x3;
2330 }
2331 
2332 inline
2334 {
2335 #ifdef _DEBUG
2336  if (!IsSetPrecursorsearchtype()) {
2338  }
2339 #endif
2340  m_set_State[0] |= 0x1;
2341  return m_Precursorsearchtype;
2342 }
2343 
2344 inline
2346 {
2347  return ((m_set_State[0] & 0xc) != 0);
2348 }
2349 
2350 inline
2352 {
2353  return IsSetProductsearchtype();
2354 }
2355 
2356 inline
2358 {
2359  m_Productsearchtype = (int)(0);
2360  m_set_State[0] &= ~0xc;
2361 }
2362 
2363 inline
2365 {
2366  if (!CanGetProductsearchtype()) {
2367  ThrowUnassigned(1);
2368  }
2369  return m_Productsearchtype;
2370 }
2371 
2372 inline
2374 {
2376  m_set_State[0] |= 0xc;
2377 }
2378 
2379 inline
2381 {
2382 #ifdef _DEBUG
2383  if (!IsSetProductsearchtype()) {
2385  }
2386 #endif
2387  m_set_State[0] |= 0x4;
2388  return m_Productsearchtype;
2389 }
2390 
2391 inline
2393 {
2394  return ((m_set_State[0] & 0x30) != 0);
2395 }
2396 
2397 inline
2399 {
2400  return true;
2401 }
2402 
2403 inline
2405 {
2406  return m_Ionstosearch;
2407 }
2408 
2409 inline
2411 {
2412  m_set_State[0] |= 0x10;
2413  return m_Ionstosearch;
2414 }
2415 
2416 inline
2418 {
2419  return ((m_set_State[0] & 0xc0) != 0);
2420 }
2421 
2422 inline
2424 {
2425  return IsSetPeptol();
2426 }
2427 
2428 inline
2430 {
2431  m_Peptol = 0;
2432  m_set_State[0] &= ~0xc0;
2433 }
2434 
2435 inline
2437 {
2438  if (!CanGetPeptol()) {
2439  ThrowUnassigned(3);
2440  }
2441  return m_Peptol;
2442 }
2443 
2444 inline
2446 {
2447  m_Peptol = value;
2448  m_set_State[0] |= 0xc0;
2449 }
2450 
2451 inline
2453 {
2454 #ifdef _DEBUG
2455  if (!IsSetPeptol()) {
2456  memset(&m_Peptol,UnassignedByte(),sizeof(m_Peptol));
2457  }
2458 #endif
2459  m_set_State[0] |= 0x40;
2460  return m_Peptol;
2461 }
2462 
2463 inline
2465 {
2466  return ((m_set_State[0] & 0x300) != 0);
2467 }
2468 
2469 inline
2471 {
2472  return IsSetMsmstol();
2473 }
2474 
2475 inline
2477 {
2478  m_Msmstol = 0;
2479  m_set_State[0] &= ~0x300;
2480 }
2481 
2482 inline
2484 {
2485  if (!CanGetMsmstol()) {
2486  ThrowUnassigned(4);
2487  }
2488  return m_Msmstol;
2489 }
2490 
2491 inline
2493 {
2494  m_Msmstol = value;
2495  m_set_State[0] |= 0x300;
2496 }
2497 
2498 inline
2500 {
2501 #ifdef _DEBUG
2502  if (!IsSetMsmstol()) {
2503  memset(&m_Msmstol,UnassignedByte(),sizeof(m_Msmstol));
2504  }
2505 #endif
2506  m_set_State[0] |= 0x100;
2507  return m_Msmstol;
2508 }
2509 
2510 inline
2512 {
2513  return ((m_set_State[0] & 0xc00) != 0);
2514 }
2515 
2516 inline
2518 {
2519  return IsSetZdep();
2520 }
2521 
2522 inline
2524 {
2525  m_Zdep = (int)(0);
2526  m_set_State[0] &= ~0xc00;
2527 }
2528 
2529 inline
2531 {
2532  if (!CanGetZdep()) {
2533  ThrowUnassigned(5);
2534  }
2535  return m_Zdep;
2536 }
2537 
2538 inline
2540 {
2541  m_Zdep = value;
2542  m_set_State[0] |= 0xc00;
2543 }
2544 
2545 inline
2547 {
2548 #ifdef _DEBUG
2549  if (!IsSetZdep()) {
2550  memset(&m_Zdep,UnassignedByte(),sizeof(m_Zdep));
2551  }
2552 #endif
2553  m_set_State[0] |= 0x400;
2554  return m_Zdep;
2555 }
2556 
2557 inline
2559 {
2560  return ((m_set_State[0] & 0x3000) != 0);
2561 }
2562 
2563 inline
2565 {
2566  return IsSetCutoff();
2567 }
2568 
2569 inline
2571 {
2572  m_Cutoff = 0;
2573  m_set_State[0] &= ~0x3000;
2574 }
2575 
2576 inline
2578 {
2579  if (!CanGetCutoff()) {
2580  ThrowUnassigned(6);
2581  }
2582  return m_Cutoff;
2583 }
2584 
2585 inline
2587 {
2588  m_Cutoff = value;
2589  m_set_State[0] |= 0x3000;
2590 }
2591 
2592 inline
2594 {
2595 #ifdef _DEBUG
2596  if (!IsSetCutoff()) {
2597  memset(&m_Cutoff,UnassignedByte(),sizeof(m_Cutoff));
2598  }
2599 #endif
2600  m_set_State[0] |= 0x1000;
2601  return m_Cutoff;
2602 }
2603 
2604 inline
2606 {
2607  return ((m_set_State[0] & 0xc000) != 0);
2608 }
2609 
2610 inline
2612 {
2613  return IsSetCutlo();
2614 }
2615 
2616 inline
2618 {
2619  m_Cutlo = 0;
2620  m_set_State[0] &= ~0xc000;
2621 }
2622 
2623 inline
2625 {
2626  if (!CanGetCutlo()) {
2627  ThrowUnassigned(7);
2628  }
2629  return m_Cutlo;
2630 }
2631 
2632 inline
2634 {
2635  m_Cutlo = value;
2636  m_set_State[0] |= 0xc000;
2637 }
2638 
2639 inline
2641 {
2642 #ifdef _DEBUG
2643  if (!IsSetCutlo()) {
2644  memset(&m_Cutlo,UnassignedByte(),sizeof(m_Cutlo));
2645  }
2646 #endif
2647  m_set_State[0] |= 0x4000;
2648  return m_Cutlo;
2649 }
2650 
2651 inline
2653 {
2654  return ((m_set_State[0] & 0x30000) != 0);
2655 }
2656 
2657 inline
2659 {
2660  return IsSetCuthi();
2661 }
2662 
2663 inline
2665 {
2666  m_Cuthi = 0;
2667  m_set_State[0] &= ~0x30000;
2668 }
2669 
2670 inline
2672 {
2673  if (!CanGetCuthi()) {
2674  ThrowUnassigned(8);
2675  }
2676  return m_Cuthi;
2677 }
2678 
2679 inline
2681 {
2682  m_Cuthi = value;
2683  m_set_State[0] |= 0x30000;
2684 }
2685 
2686 inline
2688 {
2689 #ifdef _DEBUG
2690  if (!IsSetCuthi()) {
2691  memset(&m_Cuthi,UnassignedByte(),sizeof(m_Cuthi));
2692  }
2693 #endif
2694  m_set_State[0] |= 0x10000;
2695  return m_Cuthi;
2696 }
2697 
2698 inline
2700 {
2701  return ((m_set_State[0] & 0xc0000) != 0);
2702 }
2703 
2704 inline
2706 {
2707  return IsSetCutinc();
2708 }
2709 
2710 inline
2712 {
2713  m_Cutinc = 0;
2714  m_set_State[0] &= ~0xc0000;
2715 }
2716 
2717 inline
2719 {
2720  if (!CanGetCutinc()) {
2721  ThrowUnassigned(9);
2722  }
2723  return m_Cutinc;
2724 }
2725 
2726 inline
2728 {
2729  m_Cutinc = value;
2730  m_set_State[0] |= 0xc0000;
2731 }
2732 
2733 inline
2735 {
2736 #ifdef _DEBUG
2737  if (!IsSetCutinc()) {
2738  memset(&m_Cutinc,UnassignedByte(),sizeof(m_Cutinc));
2739  }
2740 #endif
2741  m_set_State[0] |= 0x40000;
2742  return m_Cutinc;
2743 }
2744 
2745 inline
2747 {
2748  return ((m_set_State[0] & 0x300000) != 0);
2749 }
2750 
2751 inline
2753 {
2754  return IsSetSinglewin();
2755 }
2756 
2757 inline
2759 {
2760  m_Singlewin = 0;
2761  m_set_State[0] &= ~0x300000;
2762 }
2763 
2764 inline
2766 {
2767  if (!CanGetSinglewin()) {
2768  ThrowUnassigned(10);
2769  }
2770  return m_Singlewin;
2771 }
2772 
2773 inline
2775 {
2776  m_Singlewin = value;
2777  m_set_State[0] |= 0x300000;
2778 }
2779 
2780 inline
2782 {
2783 #ifdef _DEBUG
2784  if (!IsSetSinglewin()) {
2785  memset(&m_Singlewin,UnassignedByte(),sizeof(m_Singlewin));
2786  }
2787 #endif
2788  m_set_State[0] |= 0x100000;
2789  return m_Singlewin;
2790 }
2791 
2792 inline
2794 {
2795  return ((m_set_State[0] & 0xc00000) != 0);
2796 }
2797 
2798 inline
2800 {
2801  return IsSetDoublewin();
2802 }
2803 
2804 inline
2806 {
2807  m_Doublewin = 0;
2808  m_set_State[0] &= ~0xc00000;
2809 }
2810 
2811 inline
2813 {
2814  if (!CanGetDoublewin()) {
2815  ThrowUnassigned(11);
2816  }
2817  return m_Doublewin;
2818 }
2819 
2820 inline
2822 {
2823  m_Doublewin = value;
2824  m_set_State[0] |= 0xc00000;
2825 }
2826 
2827 inline
2829 {
2830 #ifdef _DEBUG
2831  if (!IsSetDoublewin()) {
2832  memset(&m_Doublewin,UnassignedByte(),sizeof(m_Doublewin));
2833  }
2834 #endif
2835  m_set_State[0] |= 0x400000;
2836  return m_Doublewin;
2837 }
2838 
2839 inline
2841 {
2842  return ((m_set_State[0] & 0x3000000) != 0);
2843 }
2844 
2845 inline
2847 {
2848  return IsSetSinglenum();
2849 }
2850 
2851 inline
2853 {
2854  m_Singlenum = 0;
2855  m_set_State[0] &= ~0x3000000;
2856 }
2857 
2858 inline
2860 {
2861  if (!CanGetSinglenum()) {
2862  ThrowUnassigned(12);
2863  }
2864  return m_Singlenum;
2865 }
2866 
2867 inline
2869 {
2870  m_Singlenum = value;
2871  m_set_State[0] |= 0x3000000;
2872 }
2873 
2874 inline
2876 {
2877 #ifdef _DEBUG
2878  if (!IsSetSinglenum()) {
2879  memset(&m_Singlenum,UnassignedByte(),sizeof(m_Singlenum));
2880  }
2881 #endif
2882  m_set_State[0] |= 0x1000000;
2883  return m_Singlenum;
2884 }
2885 
2886 inline
2888 {
2889  return ((m_set_State[0] & 0xc000000) != 0);
2890 }
2891 
2892 inline
2894 {
2895  return IsSetDoublenum();
2896 }
2897 
2898 inline
2900 {
2901  m_Doublenum = 0;
2902  m_set_State[0] &= ~0xc000000;
2903 }
2904 
2905 inline
2907 {
2908  if (!CanGetDoublenum()) {
2909  ThrowUnassigned(13);
2910  }
2911  return m_Doublenum;
2912 }
2913 
2914 inline
2916 {
2917  m_Doublenum = value;
2918  m_set_State[0] |= 0xc000000;
2919 }
2920 
2921 inline
2923 {
2924 #ifdef _DEBUG
2925  if (!IsSetDoublenum()) {
2926  memset(&m_Doublenum,UnassignedByte(),sizeof(m_Doublenum));
2927  }
2928 #endif
2929  m_set_State[0] |= 0x4000000;
2930  return m_Doublenum;
2931 }
2932 
2933 inline
2935 {
2936  return ((m_set_State[0] & 0x30000000) != 0);
2937 }
2938 
2939 inline
2941 {
2942  return true;
2943 }
2944 
2945 inline
2947 {
2948  return m_Fixed;
2949 }
2950 
2951 inline
2953 {
2954  m_set_State[0] |= 0x10000000;
2955  return m_Fixed;
2956 }
2957 
2958 inline
2960 {
2961  return ((m_set_State[0] & 0xc0000000) != 0);
2962 }
2963 
2964 inline
2966 {
2967  return true;
2968 }
2969 
2970 inline
2972 {
2973  return m_Variable;
2974 }
2975 
2976 inline
2978 {
2979  m_set_State[0] |= 0x40000000;
2980  return m_Variable;
2981 }
2982 
2983 inline
2985 {
2986  return ((m_set_State[1] & 0x3) != 0);
2987 }
2988 
2989 inline
2991 {
2992  return IsSetEnzyme();
2993 }
2994 
2995 inline
2997 {
2998  m_Enzyme = (int)(0);
2999  m_set_State[1] &= ~0x3;
3000 }
3001 
3002 inline
3004 {
3005  if (!CanGetEnzyme()) {
3006  ThrowUnassigned(16);
3007  }
3008  return m_Enzyme;
3009 }
3010 
3011 inline
3013 {
3014  m_Enzyme = value;
3015  m_set_State[1] |= 0x3;
3016 }
3017 
3018 inline
3020 {
3021 #ifdef _DEBUG
3022  if (!IsSetEnzyme()) {
3023  memset(&m_Enzyme,UnassignedByte(),sizeof(m_Enzyme));
3024  }
3025 #endif
3026  m_set_State[1] |= 0x1;
3027  return m_Enzyme;
3028 }
3029 
3030 inline
3032 {
3033  return ((m_set_State[1] & 0xc) != 0);
3034 }
3035 
3036 inline
3038 {
3039  return IsSetMissedcleave();
3040 }
3041 
3042 inline
3044 {
3045  m_Missedcleave = 0;
3046  m_set_State[1] &= ~0xc;
3047 }
3048 
3049 inline
3051 {
3052  if (!CanGetMissedcleave()) {
3053  ThrowUnassigned(17);
3054  }
3055  return m_Missedcleave;
3056 }
3057 
3058 inline
3060 {
3062  m_set_State[1] |= 0xc;
3063 }
3064 
3065 inline
3067 {
3068 #ifdef _DEBUG
3069  if (!IsSetMissedcleave()) {
3070  memset(&m_Missedcleave,UnassignedByte(),sizeof(m_Missedcleave));
3071  }
3072 #endif
3073  m_set_State[1] |= 0x4;
3074  return m_Missedcleave;
3075 }
3076 
3077 inline
3079 {
3080  return ((m_set_State[1] & 0x30) != 0);
3081 }
3082 
3083 inline
3085 {
3086  return true;
3087 }
3088 
3089 inline
3091 {
3092  m_Hitlistlen = 25;
3093  m_set_State[1] &= ~0x30;
3094 }
3095 
3096 inline
3098 {
3099  ResetHitlistlen();
3100 }
3101 
3102 inline
3104 {
3105  return m_Hitlistlen;
3106 }
3107 
3108 inline
3110 {
3111  m_Hitlistlen = value;
3112  m_set_State[1] |= 0x30;
3113 }
3114 
3115 inline
3117 {
3118 #ifdef _DEBUG
3119  if (!IsSetHitlistlen()) {
3120  memset(&m_Hitlistlen,UnassignedByte(),sizeof(m_Hitlistlen));
3121  }
3122 #endif
3123  m_set_State[1] |= 0x10;
3124  return m_Hitlistlen;
3125 }
3126 
3127 inline
3129 {
3130  return ((m_set_State[1] & 0xc0) != 0);
3131 }
3132 
3133 inline
3135 {
3136  return IsSetDb();
3137 }
3138 
3139 inline
3141 {
3142  if (!CanGetDb()) {
3143  ThrowUnassigned(19);
3144  }
3145  return m_Db;
3146 }
3147 
3148 inline
3150 {
3151  m_Db = value;
3152  m_set_State[1] |= 0xc0;
3153 }
3154 
3155 inline
3157 {
3158  m_Db = std::forward<CMSSearchSettings_Base::TDb>(value);
3159  m_set_State[1] |= 0xc0;
3160 }
3161 
3162 inline
3164 {
3165 #ifdef _DEBUG
3166  if (!IsSetDb()) {
3167  m_Db = UnassignedString();
3168  }
3169 #endif
3170  m_set_State[1] |= 0x40;
3171  return m_Db;
3172 }
3173 
3174 inline
3176 {
3177  return ((m_set_State[1] & 0x300) != 0);
3178 }
3179 
3180 inline
3182 {
3183  return IsSetTophitnum();
3184 }
3185 
3186 inline
3188 {
3189  m_Tophitnum = 0;
3190  m_set_State[1] &= ~0x300;
3191 }
3192 
3193 inline
3195 {
3196  if (!CanGetTophitnum()) {
3197  ThrowUnassigned(20);
3198  }
3199  return m_Tophitnum;
3200 }
3201 
3202 inline
3204 {
3205  m_Tophitnum = value;
3206  m_set_State[1] |= 0x300;
3207 }
3208 
3209 inline
3211 {
3212 #ifdef _DEBUG
3213  if (!IsSetTophitnum()) {
3214  memset(&m_Tophitnum,UnassignedByte(),sizeof(m_Tophitnum));
3215  }
3216 #endif
3217  m_set_State[1] |= 0x100;
3218  return m_Tophitnum;
3219 }
3220 
3221 inline
3223 {
3224  return ((m_set_State[1] & 0xc00) != 0);
3225 }
3226 
3227 inline
3229 {
3230  return true;
3231 }
3232 
3233 inline
3235 {
3236  m_Minhit = 2;
3237  m_set_State[1] &= ~0xc00;
3238 }
3239 
3240 inline
3242 {
3243  ResetMinhit();
3244 }
3245 
3246 inline
3248 {
3249  return m_Minhit;
3250 }
3251 
3252 inline
3254 {
3255  m_Minhit = value;
3256  m_set_State[1] |= 0xc00;
3257 }
3258 
3259 inline
3261 {
3262 #ifdef _DEBUG
3263  if (!IsSetMinhit()) {
3264  memset(&m_Minhit,UnassignedByte(),sizeof(m_Minhit));
3265  }
3266 #endif
3267  m_set_State[1] |= 0x400;
3268  return m_Minhit;
3269 }
3270 
3271 inline
3273 {
3274  return ((m_set_State[1] & 0x3000) != 0);
3275 }
3276 
3277 inline
3279 {
3280  return true;
3281 }
3282 
3283 inline
3285 {
3286  m_Minspectra = 4;
3287  m_set_State[1] &= ~0x3000;
3288 }
3289 
3290 inline
3292 {
3293  ResetMinspectra();
3294 }
3295 
3296 inline
3298 {
3299  return m_Minspectra;
3300 }
3301 
3302 inline
3304 {
3305  m_Minspectra = value;
3306  m_set_State[1] |= 0x3000;
3307 }
3308 
3309 inline
3311 {
3312 #ifdef _DEBUG
3313  if (!IsSetMinspectra()) {
3314  memset(&m_Minspectra,UnassignedByte(),sizeof(m_Minspectra));
3315  }
3316 #endif
3317  m_set_State[1] |= 0x1000;
3318  return m_Minspectra;
3319 }
3320 
3321 inline
3323 {
3324  return ((m_set_State[1] & 0xc000) != 0);
3325 }
3326 
3327 inline
3329 {
3330  return true;
3331 }
3332 
3333 inline
3335 {
3336  m_Scale = 100;
3337  m_set_State[1] &= ~0xc000;
3338 }
3339 
3340 inline
3342 {
3343  ResetScale();
3344 }
3345 
3346 inline
3348 {
3349  return m_Scale;
3350 }
3351 
3352 inline
3354 {
3355  m_Scale = value;
3356  m_set_State[1] |= 0xc000;
3357 }
3358 
3359 inline
3361 {
3362 #ifdef _DEBUG
3363  if (!IsSetScale()) {
3364  memset(&m_Scale,UnassignedByte(),sizeof(m_Scale));
3365  }
3366 #endif
3367  m_set_State[1] |= 0x4000;
3368  return m_Scale;
3369 }
3370 
3371 inline
3373 {
3374  return ((m_set_State[1] & 0x30000) != 0);
3375 }
3376 
3377 inline
3379 {
3380  return true;
3381 }
3382 
3383 inline
3385 {
3386  m_Maxmods = 64;
3387  m_set_State[1] &= ~0x30000;
3388 }
3389 
3390 inline
3392 {
3393  ResetMaxmods();
3394 }
3395 
3396 inline
3398 {
3399  return m_Maxmods;
3400 }
3401 
3402 inline
3404 {
3405  m_Maxmods = value;
3406  m_set_State[1] |= 0x30000;
3407 }
3408 
3409 inline
3411 {
3412 #ifdef _DEBUG
3413  if (!IsSetMaxmods()) {
3414  memset(&m_Maxmods,UnassignedByte(),sizeof(m_Maxmods));
3415  }
3416 #endif
3417  m_set_State[1] |= 0x10000;
3418  return m_Maxmods;
3419 }
3420 
3421 inline
3423 {
3424  return ((m_set_State[1] & 0xc0000) != 0);
3425 }
3426 
3427 inline
3429 {
3430  return true;
3431 }
3432 
3433 inline
3435 {
3436  return m_Taxids;
3437 }
3438 
3439 inline
3441 {
3442  m_set_State[1] |= 0x40000;
3443  return m_Taxids;
3444 }
3445 
3446 inline
3448 {
3449  return m_Chargehandling.NotEmpty();
3450 }
3451 
3452 inline
3454 {
3455  return IsSetChargehandling();
3456 }
3457 
3458 inline
3460 {
3461  if (!CanGetChargehandling()) {
3462  ThrowUnassigned(26);
3463  }
3464  return (*m_Chargehandling);
3465 }
3466 
3467 inline
3469 {
3470  return m_Usermods.NotEmpty();
3471 }
3472 
3473 inline
3475 {
3476  return IsSetUsermods();
3477 }
3478 
3479 inline
3481 {
3482  if (!CanGetUsermods()) {
3483  ThrowUnassigned(27);
3484  }
3485  return (*m_Usermods);
3486 }
3487 
3488 inline
3490 {
3491  return ((m_set_State[1] & 0x3000000) != 0);
3492 }
3493 
3494 inline
3496 {
3497  return true;
3498 }
3499 
3500 inline
3502 {
3503  m_Pseudocount = 1;
3504  m_set_State[1] &= ~0x3000000;
3505 }
3506 
3507 inline
3509 {
3510  ResetPseudocount();
3511 }
3512 
3513 inline
3515 {
3516  return m_Pseudocount;
3517 }
3518 
3519 inline
3521 {
3522  m_Pseudocount = value;
3523  m_set_State[1] |= 0x3000000;
3524 }
3525 
3526 inline
3528 {
3529 #ifdef _DEBUG
3530  if (!IsSetPseudocount()) {
3531  memset(&m_Pseudocount,UnassignedByte(),sizeof(m_Pseudocount));
3532  }
3533 #endif
3534  m_set_State[1] |= 0x1000000;
3535  return m_Pseudocount;
3536 }
3537 
3538 inline
3540 {
3541  return ((m_set_State[1] & 0xc000000) != 0);
3542 }
3543 
3544 inline
3546 {
3547  return true;
3548 }
3549 
3550 inline
3552 {
3553  m_Searchb1 = 0;
3554  m_set_State[1] &= ~0xc000000;
3555 }
3556 
3557 inline
3559 {
3560  ResetSearchb1();
3561 }
3562 
3563 inline
3565 {
3566  return m_Searchb1;
3567 }
3568 
3569 inline
3571 {
3572  m_Searchb1 = value;
3573  m_set_State[1] |= 0xc000000;
3574 }
3575 
3576 inline
3578 {
3579 #ifdef _DEBUG
3580  if (!IsSetSearchb1()) {
3581  memset(&m_Searchb1,UnassignedByte(),sizeof(m_Searchb1));
3582  }
3583 #endif
3584  m_set_State[1] |= 0x4000000;
3585  return m_Searchb1;
3586 }
3587 
3588 inline
3590 {
3591  return ((m_set_State[1] & 0x30000000) != 0);
3592 }
3593 
3594 inline
3596 {
3597  return true;
3598 }
3599 
3600 inline
3602 {
3604  m_set_State[1] &= ~0x30000000;
3605 }
3606 
3607 inline
3609 {
3611 }
3612 
3613 inline
3615 {
3616  return m_Searchctermproduct;
3617 }
3618 
3619 inline
3621 {
3623  m_set_State[1] |= 0x30000000;
3624 }
3625 
3626 inline
3628 {
3629 #ifdef _DEBUG
3630  if (!IsSetSearchctermproduct()) {
3632  }
3633 #endif
3634  m_set_State[1] |= 0x10000000;
3635  return m_Searchctermproduct;
3636 }
3637 
3638 inline
3640 {
3641  return ((m_set_State[1] & 0xc0000000) != 0);
3642 }
3643 
3644 inline
3646 {
3647  return true;
3648 }
3649 
3650 inline
3652 {
3653  m_Maxproductions = 0;
3654  m_set_State[1] &= ~0xc0000000;
3655 }
3656 
3657 inline
3659 {
3661 }
3662 
3663 inline
3665 {
3666  return m_Maxproductions;
3667 }
3668 
3669 inline
3671 {
3673  m_set_State[1] |= 0xc0000000;
3674 }
3675 
3676 inline
3678 {
3679 #ifdef _DEBUG
3680  if (!IsSetMaxproductions()) {
3682  }
3683 #endif
3684  m_set_State[1] |= 0x40000000;
3685  return m_Maxproductions;
3686 }
3687 
3688 inline
3690 {
3691  return ((m_set_State[2] & 0x3) != 0);
3692 }
3693 
3694 inline
3696 {
3697  return true;
3698 }
3699 
3700 inline
3702 {
3703  m_Minnoenzyme = 4;
3704  m_set_State[2] &= ~0x3;
3705 }
3706 
3707 inline
3709 {
3710  ResetMinnoenzyme();
3711 }
3712 
3713 inline
3715 {
3716  return m_Minnoenzyme;
3717 }
3718 
3719 inline
3721 {
3722  m_Minnoenzyme = value;
3723  m_set_State[2] |= 0x3;
3724 }
3725 
3726 inline
3728 {
3729 #ifdef _DEBUG
3730  if (!IsSetMinnoenzyme()) {
3731  memset(&m_Minnoenzyme,UnassignedByte(),sizeof(m_Minnoenzyme));
3732  }
3733 #endif
3734  m_set_State[2] |= 0x1;
3735  return m_Minnoenzyme;
3736 }
3737 
3738 inline
3740 {
3741  return ((m_set_State[2] & 0xc) != 0);
3742 }
3743 
3744 inline
3746 {
3747  return true;
3748 }
3749 
3750 inline
3752 {
3753  m_Maxnoenzyme = 0;
3754  m_set_State[2] &= ~0xc;
3755 }
3756 
3757 inline
3759 {
3760  ResetMaxnoenzyme();
3761 }
3762 
3763 inline
3765 {
3766  return m_Maxnoenzyme;
3767 }
3768 
3769 inline
3771 {
3772  m_Maxnoenzyme = value;
3773  m_set_State[2] |= 0xc;
3774 }
3775 
3776 inline
3778 {
3779 #ifdef _DEBUG
3780  if (!IsSetMaxnoenzyme()) {
3781  memset(&m_Maxnoenzyme,UnassignedByte(),sizeof(m_Maxnoenzyme));
3782  }
3783 #endif
3784  m_set_State[2] |= 0x4;
3785  return m_Maxnoenzyme;
3786 }
3787 
3788 inline
3790 {
3791  return ((m_set_State[2] & 0x30) != 0);
3792 }
3793 
3794 inline
3796 {
3797  return IsSetExactmass();
3798 }
3799 
3800 inline
3802 {
3803  m_Exactmass = 0;
3804  m_set_State[2] &= ~0x30;
3805 }
3806 
3807 inline
3809 {
3810  if (!CanGetExactmass()) {
3811  ThrowUnassigned(34);
3812  }
3813  return m_Exactmass;
3814 }
3815 
3816 inline
3818 {
3819  m_Exactmass = value;
3820  m_set_State[2] |= 0x30;
3821 }
3822 
3823 inline
3825 {
3826 #ifdef _DEBUG
3827  if (!IsSetExactmass()) {
3828  memset(&m_Exactmass,UnassignedByte(),sizeof(m_Exactmass));
3829  }
3830 #endif
3831  m_set_State[2] |= 0x10;
3832  return m_Exactmass;
3833 }
3834 
3835 inline
3837 {
3838  return ((m_set_State[2] & 0xc0) != 0);
3839 }
3840 
3841 inline
3843 {
3844  return IsSetSettingid();
3845 }
3846 
3847 inline
3849 {
3850  m_Settingid = 0;
3851  m_set_State[2] &= ~0xc0;
3852 }
3853 
3854 inline
3856 {
3857  if (!CanGetSettingid()) {
3858  ThrowUnassigned(35);
3859  }
3860  return m_Settingid;
3861 }
3862 
3863 inline
3865 {
3866  m_Settingid = value;
3867  m_set_State[2] |= 0xc0;
3868 }
3869 
3870 inline
3872 {
3873 #ifdef _DEBUG
3874  if (!IsSetSettingid()) {
3875  memset(&m_Settingid,UnassignedByte(),sizeof(m_Settingid));
3876  }
3877 #endif
3878  m_set_State[2] |= 0x40;
3879  return m_Settingid;
3880 }
3881 
3882 inline
3884 {
3885  return m_Iterativesettings.NotEmpty();
3886 }
3887 
3888 inline
3890 {
3891  return IsSetIterativesettings();
3892 }
3893 
3894 inline
3896 {
3897  if (!CanGetIterativesettings()) {
3898  ThrowUnassigned(36);
3899  }
3900  return (*m_Iterativesettings);
3901 }
3902 
3903 inline
3905 {
3906  return ((m_set_State[2] & 0xc00) != 0);
3907 }
3908 
3909 inline
3911 {
3912  return IsSetPrecursorcull();
3913 }
3914 
3915 inline
3917 {
3918  m_Precursorcull = 0;
3919  m_set_State[2] &= ~0xc00;
3920 }
3921 
3922 inline
3924 {
3925  if (!CanGetPrecursorcull()) {
3926  ThrowUnassigned(37);
3927  }
3928  return m_Precursorcull;
3929 }
3930 
3931 inline
3933 {
3935  m_set_State[2] |= 0xc00;
3936 }
3937 
3938 inline
3940 {
3941 #ifdef _DEBUG
3942  if (!IsSetPrecursorcull()) {
3943  memset(&m_Precursorcull,UnassignedByte(),sizeof(m_Precursorcull));
3944  }
3945 #endif
3946  m_set_State[2] |= 0x400;
3947  return m_Precursorcull;
3948 }
3949 
3950 inline
3952 {
3953  return ((m_set_State[2] & 0x3000) != 0);
3954 }
3955 
3956 inline
3958 {
3959  return true;
3960 }
3961 
3962 inline
3964 {
3965  return m_Infiles;
3966 }
3967 
3968 inline
3970 {
3971  m_set_State[2] |= 0x1000;
3972  return m_Infiles;
3973 }
3974 
3975 inline
3977 {
3978  return ((m_set_State[2] & 0xc000) != 0);
3979 }
3980 
3981 inline
3983 {
3984  return true;
3985 }
3986 
3987 inline
3989 {
3990  return m_Outfiles;
3991 }
3992 
3993 inline
3995 {
3996  m_set_State[2] |= 0x4000;
3997  return m_Outfiles;
3998 }
3999 
4000 inline
4002 {
4003  return ((m_set_State[2] & 0x30000) != 0);
4004 }
4005 
4006 inline
4008 {
4009  return IsSetNocorrelationscore();
4010 }
4011 
4012 inline
4014 {
4016  m_set_State[2] &= ~0x30000;
4017 }
4018 
4019 inline
4021 {
4022  if (!CanGetNocorrelationscore()) {
4023  ThrowUnassigned(40);
4024  }
4025  return m_Nocorrelationscore;
4026 }
4027 
4028 inline
4030 {
4032  m_set_State[2] |= 0x30000;
4033 }
4034 
4035 inline
4037 {
4038 #ifdef _DEBUG
4039  if (!IsSetNocorrelationscore()) {
4041  }
4042 #endif
4043  m_set_State[2] |= 0x10000;
4044  return m_Nocorrelationscore;
4045 }
4046 
4047 inline
4049 {
4050  return ((m_set_State[2] & 0xc0000) != 0);
4051 }
4052 
4053 inline
4055 {
4056  return IsSetProbfollowingion();
4057 }
4058 
4059 inline
4061 {
4062  m_Probfollowingion = 0;
4063  m_set_State[2] &= ~0xc0000;
4064 }
4065 
4066 inline
4068 {
4069  if (!CanGetProbfollowingion()) {
4070  ThrowUnassigned(41);
4071  }
4072  return m_Probfollowingion;
4073 }
4074 
4075 inline
4077 {
4079  m_set_State[2] |= 0xc0000;
4080 }
4081 
4082 inline
4084 {
4085 #ifdef _DEBUG
4086  if (!IsSetProbfollowingion()) {
4088  }
4089 #endif
4090  m_set_State[2] |= 0x40000;
4091  return m_Probfollowingion;
4092 }
4093 
4094 inline
4096 {
4097  return ((m_set_State[2] & 0x300000) != 0);
4098 }
4099 
4100 inline
4102 {
4103  return IsSetNmethionine();
4104 }
4105 
4106 inline
4108 {
4109  m_Nmethionine = 0;
4110  m_set_State[2] &= ~0x300000;
4111 }
4112 
4113 inline
4115 {
4116  if (!CanGetNmethionine()) {
4117  ThrowUnassigned(42);
4118  }
4119  return m_Nmethionine;
4120 }
4121 
4122 inline
4124 {
4125  m_Nmethionine = value;
4126  m_set_State[2] |= 0x300000;
4127 }
4128 
4129 inline
4131 {
4132 #ifdef _DEBUG
4133  if (!IsSetNmethionine()) {
4134  memset(&m_Nmethionine,UnassignedByte(),sizeof(m_Nmethionine));
4135  }
4136 #endif
4137  m_set_State[2] |= 0x100000;
4138  return m_Nmethionine;
4139 }
4140 
4141 inline
4143 {
4144  return ((m_set_State[2] & 0xc00000) != 0);
4145 }
4146 
4147 inline
4149 {
4150  return IsSetAutomassadjust();
4151 }
4152 
4153 inline
4155 {
4156  m_Automassadjust = 0;
4157  m_set_State[2] &= ~0xc00000;
4158 }
4159 
4160 inline
4162 {
4163  if (!CanGetAutomassadjust()) {
4164  ThrowUnassigned(43);
4165  }
4166  return m_Automassadjust;
4167 }
4168 
4169 inline
4171 {
4173  m_set_State[2] |= 0xc00000;
4174 }
4175 
4176 inline
4178 {
4179 #ifdef _DEBUG
4180  if (!IsSetAutomassadjust()) {
4182  }
4183 #endif
4184  m_set_State[2] |= 0x400000;
4185  return m_Automassadjust;
4186 }
4187 
4188 inline
4190 {
4191  return ((m_set_State[2] & 0x3000000) != 0);
4192 }
4193 
4194 inline
4196 {
4197  return IsSetLomasscutoff();
4198 }
4199 
4200 inline
4202 {
4203  m_Lomasscutoff = 0;
4204  m_set_State[2] &= ~0x3000000;
4205 }
4206 
4207 inline
4209 {
4210  if (!CanGetLomasscutoff()) {
4211  ThrowUnassigned(44);
4212  }
4213  return m_Lomasscutoff;
4214 }
4215 
4216 inline
4218 {
4220  m_set_State[2] |= 0x3000000;
4221 }
4222 
4223 inline
4225 {
4226 #ifdef _DEBUG
4227  if (!IsSetLomasscutoff()) {
4228  memset(&m_Lomasscutoff,UnassignedByte(),sizeof(m_Lomasscutoff));
4229  }
4230 #endif
4231  m_set_State[2] |= 0x1000000;
4232  return m_Lomasscutoff;
4233 }
4234 
4235 inline
4237 {
4238  return m_Libsearchsettings.NotEmpty();
4239 }
4240 
4241 inline
4243 {
4244  return IsSetLibsearchsettings();
4245 }
4246 
4247 inline
4249 {
4250  if (!CanGetLibsearchsettings()) {
4251  ThrowUnassigned(45);
4252  }
4253  return (*m_Libsearchsettings);
4254 }
4255 
4256 inline
4258 {
4259  return ((m_set_State[2] & 0x30000000) != 0);
4260 }
4261 
4262 inline
4264 {
4265  return true;
4266 }
4267 
4268 inline
4270 {
4271  return m_Noprolineions;
4272 }
4273 
4274 inline
4276 {
4277  m_set_State[2] |= 0x10000000;
4278  return m_Noprolineions;
4279 }
4280 
4281 inline
4283 {
4284  return ((m_set_State[2] & 0xc0000000) != 0);
4285 }
4286 
4287 inline
4289 {
4290  return IsSetReversesearch();
4291 }
4292 
4293 inline
4295 {
4296  m_Reversesearch = 0;
4297  m_set_State[2] &= ~0xc0000000;
4298 }
4299 
4300 inline
4302 {
4303  if (!CanGetReversesearch()) {
4304  ThrowUnassigned(47);
4305  }
4306  return m_Reversesearch;
4307 }
4308 
4309 inline
4311 {
4313  m_set_State[2] |= 0xc0000000;
4314 }
4315 
4316 inline
4318 {
4319 #ifdef _DEBUG
4320  if (!IsSetReversesearch()) {
4321  memset(&m_Reversesearch,UnassignedByte(),sizeof(m_Reversesearch));
4322  }
4323 #endif
4324  m_set_State[2] |= 0x40000000;
4325  return m_Reversesearch;
4326 }
4327 
4328 inline
4330 {
4331  return ((m_set_State[3] & 0x3) != 0);
4332 }
4333 
4334 inline
4336 {
4337  return true;
4338 }
4339 
4340 inline
4342 {
4343  return m_Othersettings;
4344 }
4345 
4346 inline
4348 {
4349  m_set_State[3] |= 0x1;
4350  return m_Othersettings;
4351 }
4352 
4353 inline
4355 {
4356  return ((m_set_State[3] & 0xc) != 0);
4357 }
4358 
4359 inline
4361 {
4362  return IsSetNumisotopes();
4363 }
4364 
4365 inline
4367 {
4368  m_Numisotopes = 0;
4369  m_set_State[3] &= ~0xc;
4370 }
4371 
4372 inline
4374 {
4375  if (!CanGetNumisotopes()) {
4376  ThrowUnassigned(49);
4377  }
4378  return m_Numisotopes;
4379 }
4380 
4381 inline
4383 {
4384  m_Numisotopes = value;
4385  m_set_State[3] |= 0xc;
4386 }
4387 
4388 inline
4390 {
4391 #ifdef _DEBUG
4392  if (!IsSetNumisotopes()) {
4393  memset(&m_Numisotopes,UnassignedByte(),sizeof(m_Numisotopes));
4394  }
4395 #endif
4396  m_set_State[3] |= 0x4;
4397  return m_Numisotopes;
4398 }
4399 
4400 inline
4402 {
4403  return ((m_set_State[3] & 0x30) != 0);
4404 }
4405 
4406 inline
4408 {
4409  return IsSetPepppm();
4410 }
4411 
4412 inline
4414 {
4415  m_Pepppm = 0;
4416  m_set_State[3] &= ~0x30;
4417 }
4418 
4419 inline
4421 {
4422  if (!CanGetPepppm()) {
4423  ThrowUnassigned(50);
4424  }
4425  return m_Pepppm;
4426 }
4427 
4428 inline
4430 {
4431  m_Pepppm = value;
4432  m_set_State[3] |= 0x30;
4433 }
4434 
4435 inline
4437 {
4438 #ifdef _DEBUG
4439  if (!IsSetPepppm()) {
4440  memset(&m_Pepppm,UnassignedByte(),sizeof(m_Pepppm));
4441  }
4442 #endif
4443  m_set_State[3] |= 0x10;
4444  return m_Pepppm;
4445 }
4446 
4447 inline
4449 {
4450  return ((m_set_State[3] & 0xc0) != 0);
4451 }
4452 
4453 inline
4455 {
4456  return IsSetMsmsppm();
4457 }
4458 
4459 inline
4461 {
4462  m_Msmsppm = 0;
4463  m_set_State[3] &= ~0xc0;
4464 }
4465 
4466 inline
4468 {
4469  if (!CanGetMsmsppm()) {
4470  ThrowUnassigned(51);
4471  }
4472  return m_Msmsppm;
4473 }
4474 
4475 inline
4477 {
4478  m_Msmsppm = value;
4479  m_set_State[3] |= 0xc0;
4480 }
4481 
4482 inline
4484 {
4485 #ifdef _DEBUG
4486  if (!IsSetMsmsppm()) {
4487  memset(&m_Msmsppm,UnassignedByte(),sizeof(m_Msmsppm));
4488  }
4489 #endif
4490  m_set_State[3] |= 0x40;
4491  return m_Msmsppm;
4492 }
4493 
4494 inline
4496 {
4497  return ((m_set_State[3] & 0x300) != 0);
4498 }
4499 
4500 inline
4502 {
4503  return IsSetReportedhitcount();
4504 }
4505 
4506 inline
4508 {
4509  m_Reportedhitcount = 0;
4510  m_set_State[3] &= ~0x300;
4511 }
4512 
4513 inline
4515 {
4516  if (!CanGetReportedhitcount()) {
4517  ThrowUnassigned(52);
4518  }
4519  return m_Reportedhitcount;
4520 }
4521 
4522 inline
4524 {
4526  m_set_State[3] |= 0x300;
4527 }
4528 
4529 inline
4531 {
4532 #ifdef _DEBUG
4533  if (!IsSetReportedhitcount()) {
4535  }
4536 #endif
4537  m_set_State[3] |= 0x100;
4538  return m_Reportedhitcount;
4539 }
4540 
4541 ///////////////////////////////////////////////////////////
4542 ////////////////// end of inline methods //////////////////
4543 ///////////////////////////////////////////////////////////
4544 
4545 
4546 
4547 
4548 
4549 END_objects_SCOPE // namespace ncbi::objects::
4550 
4552 
4553 
4554 #endif // OBJECTS_OMSSA_MSSEARCHSETTINGS_BASE_HPP
User-defined methods of the data storage class.
CMSChargeHandle –.
CMSInFile –.
Definition: MSInFile.hpp:66
CMSIterativeSettings –.
CMSLibrarySettings –.
@MSModSpecSet.hpp User-defined methods of the data storage class.
CMSOutFile –.
Definition: MSOutFile.hpp:66
Generic search settings.
CNameValue –.
Definition: NameValue.hpp:66
CRef –.
Definition: ncbiobj.hpp:618
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
const TOthersettings & GetOthersettings(void) const
Get the Othersettings member data.
bool IsSetPepppm(void) const
search precursor as ppm Check if a value has been assigned to Pepppm data member.
TSearchctermproduct & SetSearchctermproduct(void)
Assign a value to Searchctermproduct data member.
bool CanGetUsermods(void) const
Check if it is safe to call GetUsermods method.
TSearchb1 GetSearchb1(void) const
Get the Searchb1 member data.
bool CanGetReversesearch(void) const
Check if it is safe to call GetReversesearch method.
bool IsSetInfiles(void) const
input files Check if a value has been assigned to Infiles data member.
bool CanGetLibsearchsettings(void) const
Check if it is safe to call GetLibsearchsettings method.
TSearchb1 & SetSearchb1(void)
Assign a value to Searchb1 data member.
bool IsSetSinglenum(void) const
the number of peaks allowed in the single window Check if a value has been assigned to Singlenum data...
CMSChargeHandle TChargehandling
const TVariable & GetVariable(void) const
Get the Variable member data.
list< CRef< CMSInFile > > m_Infiles
void ResetCuthi(void)
Reset Cuthi data member.
bool IsSetNocorrelationscore(void) const
turn on correlation score (1=nocorr) Check if a value has been assigned to Nocorrelationscore data me...
bool CanGetNumisotopes(void) const
Check if it is safe to call GetNumisotopes method.
TSettingid GetSettingid(void) const
Get the Settingid member data.
void ResetSearchctermproduct(void)
Reset Searchctermproduct data member.
TTophitnum GetTophitnum(void) const
Get the Tophitnum member data.
bool IsSetReversesearch(void) const
do reverse search Check if a value has been assigned to Reversesearch data member.
CRef< TLibsearchsettings > m_Libsearchsettings
bool IsSetPrecursorcull(void) const
turn on aggressive precursor culling for ETD (0=none) Check if a value has been assigned to Precursor...
TReportedhitcount GetReportedhitcount(void) const
Get the Reportedhitcount member data.
void ResetAutomassadjust(void)
Reset Automassadjust data member.
bool CanGetCutoff(void) const
Check if it is safe to call GetCutoff method.
bool IsSetTaxids(void) const
taxa to limit search Check if a value has been assigned to Taxids data member.
TSinglenum & SetSinglenum(void)
Assign a value to Singlenum data member.
bool CanGetPeptol(void) const
Check if it is safe to call GetPeptol method.
TProductsearchtype & SetProductsearchtype(void)
Assign a value to Productsearchtype data member.
bool IsSetHitlistlen(void) const
the number of hits kept in memory for a spectrum Check if a value has been assigned to Hitlistlen dat...
TCutinc & SetCutinc(void)
Assign a value to Cutinc data member.
TPseudocount GetPseudocount(void) const
Get the Pseudocount member data.
TLomasscutoff & SetLomasscutoff(void)
Assign a value to Lomasscutoff data member.
TPeptol GetPeptol(void) const
Get the Peptol member data.
void ResetTophitnum(void)
Reset Tophitnum data member.
void SetDefaultMinnoenzyme(void)
Assign default value to Minnoenzyme data member.
bool IsSetProbfollowingion(void) const
probability of a consecutive ion (used in correlation) Check if a value has been assigned to Probfoll...
void ResetDoublenum(void)
Reset Doublenum data member.
TPrecursorsearchtype GetPrecursorsearchtype(void) const
Get the Precursorsearchtype member data.
TMinnoenzyme GetMinnoenzyme(void) const
Get the Minnoenzyme member data.
bool CanGetMinnoenzyme(void) const
Check if it is safe to call GetMinnoenzyme method.
TFixed & SetFixed(void)
Assign a value to Fixed data member.
CMSSearchSettings_Base(const CMSSearchSettings_Base &)
bool CanGetNoprolineions(void) const
Check if it is safe to call GetNoprolineions method.
bool IsSetEnzyme(void) const
digestion enzyme Check if a value has been assigned to Enzyme data member.
void ResetCutinc(void)
Reset Cutinc data member.
const TFixed & GetFixed(void) const
Get the Fixed member data.
TVariable & SetVariable(void)
Assign a value to Variable data member.
void ResetMaxmods(void)
Reset Maxmods data member.
bool IsSetMaxproductions(void) const
max number of ions in each series (0=all) Check if a value has been assigned to Maxproductions data m...
void ResetCutoff(void)
Reset Cutoff data member.
void ResetPepppm(void)
Reset Pepppm data member.
TScale GetScale(void) const
Get the Scale member data.
bool IsSetTophitnum(void) const
number of m/z to consider in first pass Check if a value has been assigned to Tophitnum data member.
const TUsermods & GetUsermods(void) const
Get the Usermods member data.
TInfiles & SetInfiles(void)
Assign a value to Infiles data member.
const TNoprolineions & GetNoprolineions(void) const
Get the Noprolineions member data.
bool CanGetSinglewin(void) const
Check if it is safe to call GetSinglewin method.
void ResetMissedcleave(void)
Reset Missedcleave data member.
void ResetMsmsppm(void)
Reset Msmsppm data member.
bool IsSetZdep(void) const
what is the charge dependence of the mass tolerance? Check if a value has been assigned to Zdep data ...
bool CanGetSinglenum(void) const
Check if it is safe to call GetSinglenum method.
TZdep GetZdep(void) const
Get the Zdep member data.
TMaxnoenzyme GetMaxnoenzyme(void) const
Get the Maxnoenzyme member data.
void SetDefaultMaxnoenzyme(void)
Assign default value to Maxnoenzyme data member.
bool IsSetOthersettings(void) const
extra search settings Check if a value has been assigned to Othersettings data member.
bool CanGetFixed(void) const
Check if it is safe to call GetFixed method.
TMinspectra GetMinspectra(void) const
Get the Minspectra member data.
bool IsSetMaxnoenzyme(void) const
max number of AA in peptide for noenzyme search (0=none) Check if a value has been assigned to Maxnoe...
void ResetCutlo(void)
Reset Cutlo data member.
const TIonstosearch & GetIonstosearch(void) const
Get the Ionstosearch member data.
void ResetProbfollowingion(void)
Reset Probfollowingion data member.
void ResetExactmass(void)
Reset Exactmass data member.
CMSIterativeSettings TIterativesettings
TAutomassadjust GetAutomassadjust(void) const
Get the Automassadjust member data.
bool CanGetProbfollowingion(void) const
Check if it is safe to call GetProbfollowingion method.
bool CanGetMaxmods(void) const
Check if it is safe to call GetMaxmods method.
bool IsSetSettingid(void) const
id of the search settings Check if a value has been assigned to Settingid data member.
bool IsSetNumisotopes(void) const
number of isotopic peaks to search when using MSSearchType multiisotope Check if a value has been ass...
TEnzyme & SetEnzyme(void)
Assign a value to Enzyme data member.
bool CanGetIterativesettings(void) const
Check if it is safe to call GetIterativesettings method.
bool CanGetMissedcleave(void) const
Check if it is safe to call GetMissedcleave method.
bool IsSetMinnoenzyme(void) const
min number of AA in peptide for noenzyme search Check if a value has been assigned to Minnoenzyme dat...
TDoublenum & SetDoublenum(void)
Assign a value to Doublenum data member.
bool IsSetSinglewin(void) const
the size of the single charge filtering window Check if a value has been assigned to Singlewin data m...
TMaxnoenzyme & SetMaxnoenzyme(void)
Assign a value to Maxnoenzyme data member.
TExactmass & SetExactmass(void)
Assign a value to Exactmass data member.
list< CRef< CNameValue > > TOthersettings
bool IsSetPseudocount(void) const
min number of counts per precursor bin Check if a value has been assigned to Pseudocount data member.
bool CanGetSearchb1(void) const
Check if it is safe to call GetSearchb1 method.
TNoprolineions & SetNoprolineions(void)
Assign a value to Noprolineions data member.
TProductsearchtype GetProductsearchtype(void) const
Get the Productsearchtype member data.
void ResetLomasscutoff(void)
Reset Lomasscutoff data member.
void ResetProductsearchtype(void)
Reset Productsearchtype data member.
TLomasscutoff GetLomasscutoff(void) const
Get the Lomasscutoff member data.
TOutfiles & SetOutfiles(void)
Assign a value to Outfiles data member.
TDoublewin GetDoublewin(void) const
Get the Doublewin member data.
TIonstosearch & SetIonstosearch(void)
Assign a value to Ionstosearch data member.
bool IsSetDoublenum(void) const
the number of peaks allowed in the double window Check if a value has been assigned to Doublenum data...
const TChargehandling & GetChargehandling(void) const
Get the Chargehandling member data.
const TDb & GetDb(void) const
Get the Db member data.
TPrecursorsearchtype & SetPrecursorsearchtype(void)
Assign a value to Precursorsearchtype data member.
bool IsSetPrecursorsearchtype(void) const
average or monoisotopic? Check if a value has been assigned to Precursorsearchtype data member.
bool IsSetDb(void) const
sequence set to search, e.g.
TMaxmods & SetMaxmods(void)
Assign a value to Maxmods data member.
bool CanGetHitlistlen(void) const
Check if it is safe to call GetHitlistlen method.
bool IsSetNoprolineions(void) const
which ions to use no proline rule Check if a value has been assigned to Noprolineions data member.
bool CanGetChargehandling(void) const
Check if it is safe to call GetChargehandling method.
void ResetPeptol(void)
Reset Peptol data member.
void ResetZdep(void)
Reset Zdep data member.
bool IsSetLibsearchsettings(void) const
library search settings Check if a value has been assigned to Libsearchsettings data member.
bool CanGetVariable(void) const
Check if it is safe to call GetVariable method.
Tparent::CMemberIndex< E_memberIndex, 54 > TmemberIndex
TCuthi & SetCuthi(void)
Assign a value to Cuthi data member.
TMsmsppm & SetMsmsppm(void)
Assign a value to Msmsppm data member.
TSinglewin & SetSinglewin(void)
Assign a value to Singlewin data member.
TMissedcleave GetMissedcleave(void) const
Get the Missedcleave member data.
TPseudocount & SetPseudocount(void)
Assign a value to Pseudocount data member.
bool CanGetIonstosearch(void) const
Check if it is safe to call GetIonstosearch method.
void SetDefaultScale(void)
Assign default value to Scale data member.
TPepppm GetPepppm(void) const
Get the Pepppm member data.
const TInfiles & GetInfiles(void) const
Get the Infiles member data.
void ResetScale(void)
Reset Scale data member.
TMsmsppm GetMsmsppm(void) const
Get the Msmsppm member data.
CRef< TChargehandling > m_Chargehandling
void ResetNocorrelationscore(void)
Reset Nocorrelationscore data member.
TCutoff & SetCutoff(void)
Assign a value to Cutoff data member.
CRef< TUsermods > m_Usermods
bool IsSetMissedcleave(void) const
number of missed cleaves allowed Check if a value has been assigned to Missedcleave data member.
list< CRef< CMSOutFile > > TOutfiles
void ResetHitlistlen(void)
Reset Hitlistlen data member.
TCutoff GetCutoff(void) const
Get the Cutoff member data.
bool IsSetSearchb1(void) const
should b1 product be in search (1=no, 0=yes) Check if a value has been assigned to Searchb1 data memb...
bool CanGetDoublenum(void) const
Check if it is safe to call GetDoublenum method.
TSettingid & SetSettingid(void)
Assign a value to Settingid data member.
void ResetMinhit(void)
Reset Minhit data member.
TDoublenum GetDoublenum(void) const
Get the Doublenum member data.
void ResetDoublewin(void)
Reset Doublewin data member.
bool CanGetPepppm(void) const
Check if it is safe to call GetPepppm method.
TNocorrelationscore & SetNocorrelationscore(void)
Assign a value to Nocorrelationscore data member.
void ResetMinnoenzyme(void)
Reset Minnoenzyme data member.
bool CanGetProductsearchtype(void) const
Check if it is safe to call GetProductsearchtype method.
TReversesearch & SetReversesearch(void)
Assign a value to Reversesearch data member.
bool IsSetMinspectra(void) const
minimum number of m/z for a valid spectra Check if a value has been assigned to Minspectra data membe...
bool CanGetNmethionine(void) const
Check if it is safe to call GetNmethionine method.
TNocorrelationscore GetNocorrelationscore(void) const
Get the Nocorrelationscore member data.
bool CanGetCutlo(void) const
Check if it is safe to call GetCutlo method.
bool IsSetScale(void) const
scale for m/z float to integer Check if a value has been assigned to Scale data member.
TMaxproductions & SetMaxproductions(void)
Assign a value to Maxproductions data member.
TNmethionine GetNmethionine(void) const
Get the Nmethionine member data.
bool CanGetAutomassadjust(void) const
Check if it is safe to call GetAutomassadjust method.
bool CanGetScale(void) const
Check if it is safe to call GetScale method.
bool CanGetReportedhitcount(void) const
Check if it is safe to call GetReportedhitcount method.
void SetDefaultPseudocount(void)
Assign default value to Pseudocount data member.
bool IsSetSearchctermproduct(void) const
should c terminus ion be searched (1=no, 0=yes) Check if a value has been assigned to Searchctermprod...
THitlistlen GetHitlistlen(void) const
Get the Hitlistlen member data.
bool IsSetMsmsppm(void) const
search product as ppm Check if a value has been assigned to Msmsppm data member.
bool IsSetExactmass(void) const
the threshold in Da for adding neutron Check if a value has been assigned to Exactmass data member.
TMsmstol & SetMsmstol(void)
Assign a value to Msmstol data member.
TMinspectra & SetMinspectra(void)
Assign a value to Minspectra data member.
bool IsSetIonstosearch(void) const
which ions to search? Check if a value has been assigned to Ionstosearch data member.
void SetDefaultMaxmods(void)
Assign default value to Maxmods data member.
CRef< TIterativesettings > m_Iterativesettings
TCuthi GetCuthi(void) const
Get the Cuthi member data.
bool CanGetSearchctermproduct(void) const
Check if it is safe to call GetSearchctermproduct method.
TMinnoenzyme & SetMinnoenzyme(void)
Assign a value to Minnoenzyme data member.
TMaxproductions GetMaxproductions(void) const
Get the Maxproductions member data.
TTophitnum & SetTophitnum(void)
Assign a value to Tophitnum data member.
void ResetMaxnoenzyme(void)
Reset Maxnoenzyme data member.
void ResetPrecursorcull(void)
Reset Precursorcull data member.
TTaxids & SetTaxids(void)
Assign a value to Taxids data member.
bool CanGetPrecursorcull(void) const
Check if it is safe to call GetPrecursorcull method.
bool CanGetMsmstol(void) const
Check if it is safe to call GetMsmstol method.
void ResetPrecursorsearchtype(void)
Reset Precursorsearchtype data member.
TReversesearch GetReversesearch(void) const
Get the Reversesearch member data.
TNmethionine & SetNmethionine(void)
Assign a value to Nmethionine data member.
bool CanGetMaxproductions(void) const
Check if it is safe to call GetMaxproductions method.
void ResetSinglenum(void)
Reset Singlenum data member.
bool IsSetCutlo(void) const
the start of the cutoff, fraction of most intense peak Check if a value has been assigned to Cutlo da...
TNumisotopes & SetNumisotopes(void)
Assign a value to Numisotopes data member.
TMinhit & SetMinhit(void)
Assign a value to Minhit data member.
bool IsSetUsermods(void) const
user defined modifications Check if a value has been assigned to Usermods data member.
TMissedcleave & SetMissedcleave(void)
Assign a value to Missedcleave data member.
void ResetMsmstol(void)
Reset Msmstol data member.
bool CanGetMsmsppm(void) const
Check if it is safe to call GetMsmsppm method.
bool IsSetPeptol(void) const
peptide mass tolerance Check if a value has been assigned to Peptol data member.
TProbfollowingion GetProbfollowingion(void) const
Get the Probfollowingion member data.
bool CanGetMinspectra(void) const
Check if it is safe to call GetMinspectra method.
TPepppm & SetPepppm(void)
Assign a value to Pepppm data member.
bool CanGetPseudocount(void) const
Check if it is safe to call GetPseudocount method.
void ResetMaxproductions(void)
Reset Maxproductions data member.
TZdep & SetZdep(void)
Assign a value to Zdep data member.
TMsmstol GetMsmstol(void) const
Get the Msmstol member data.
bool CanGetTaxids(void) const
Check if it is safe to call GetTaxids method.
bool CanGetNocorrelationscore(void) const
Check if it is safe to call GetNocorrelationscore method.
TProbfollowingion & SetProbfollowingion(void)
Assign a value to Probfollowingion data member.
void ResetReportedhitcount(void)
Reset Reportedhitcount data member.
TExactmass GetExactmass(void) const
Get the Exactmass member data.
bool CanGetOutfiles(void) const
Check if it is safe to call GetOutfiles method.
TDoublewin & SetDoublewin(void)
Assign a value to Doublewin data member.
TDb & SetDb(void)
Assign a value to Db data member.
void ResetPseudocount(void)
Reset Pseudocount data member.
void SetDefaultSearchctermproduct(void)
Assign default value to Searchctermproduct data member.
void SetDefaultMinhit(void)
Assign default value to Minhit data member.
bool IsSetMaxmods(void) const
maximum number of mass ladders per database peptide Check if a value has been assigned to Maxmods dat...
void ResetSinglewin(void)
Reset Singlewin data member.
void SetDefaultHitlistlen(void)
Assign default value to Hitlistlen data member.
bool CanGetDb(void) const
Check if it is safe to call GetDb method.
void ResetSearchb1(void)
Reset Searchb1 data member.
bool IsSetCutinc(void) const
the increment of the cutoff Check if a value has been assigned to Cutinc data member.
TCutlo GetCutlo(void) const
Get the Cutlo member data.
TSearchctermproduct GetSearchctermproduct(void) const
Get the Searchctermproduct member data.
TOthersettings & SetOthersettings(void)
Assign a value to Othersettings data member.
TPrecursorcull & SetPrecursorcull(void)
Assign a value to Precursorcull data member.
TMinhit GetMinhit(void) const
Get the Minhit member data.
bool CanGetInfiles(void) const
Check if it is safe to call GetInfiles method.
bool CanGetPrecursorsearchtype(void) const
Check if it is safe to call GetPrecursorsearchtype method.
void SetDefaultMaxproductions(void)
Assign default value to Maxproductions data member.
bool IsSetReportedhitcount(void) const
the maximum number of hits to report per spectrum, 0=all Check if a value has been assigned to Report...
TPrecursorcull GetPrecursorcull(void) const
Get the Precursorcull member data.
bool CanGetMinhit(void) const
Check if it is safe to call GetMinhit method.
bool CanGetEnzyme(void) const
Check if it is safe to call GetEnzyme method.
THitlistlen & SetHitlistlen(void)
Assign a value to Hitlistlen data member.
bool CanGetZdep(void) const
Check if it is safe to call GetZdep method.
bool CanGetTophitnum(void) const
Check if it is safe to call GetTophitnum method.
list< CRef< CMSInFile > > TInfiles
bool CanGetSettingid(void) const
Check if it is safe to call GetSettingid method.
bool CanGetExactmass(void) const
Check if it is safe to call GetExactmass method.
const TIterativesettings & GetIterativesettings(void) const
Get the Iterativesettings member data.
void ResetReversesearch(void)
Reset Reversesearch data member.
TScale & SetScale(void)
Assign a value to Scale data member.
TReportedhitcount & SetReportedhitcount(void)
Assign a value to Reportedhitcount data member.
list< CRef< CNameValue > > m_Othersettings
bool IsSetAutomassadjust(void) const
fraction allowable adjustment of product mass tolerance Check if a value has been assigned to Automas...
bool CanGetDoublewin(void) const
Check if it is safe to call GetDoublewin method.
bool CanGetMaxnoenzyme(void) const
Check if it is safe to call GetMaxnoenzyme method.
bool IsSetMsmstol(void) const
msms mass tolerance Check if a value has been assigned to Msmstol data member.
TCutlo & SetCutlo(void)
Assign a value to Cutlo data member.
bool IsSetOutfiles(void) const
output files Check if a value has been assigned to Outfiles data member.
TEnzyme GetEnzyme(void) const
Get the Enzyme member data.
list< CRef< CMSOutFile > > m_Outfiles
const TTaxids & GetTaxids(void) const
Get the Taxids member data.
bool CanGetCutinc(void) const
Check if it is safe to call GetCutinc method.
void ResetNmethionine(void)
Reset Nmethionine data member.
bool IsSetVariable(void) const
variable PTM's Check if a value has been assigned to Variable data member.
bool IsSetMinhit(void) const
minimum number of m/z values for a valid hit Check if a value has been assigned to Minhit data member...
bool IsSetDoublewin(void) const
the size of the double charge filtering window Check if a value has been assigned to Doublewin data m...
void ResetSettingid(void)
Reset Settingid data member.
void ResetMinspectra(void)
Reset Minspectra data member.
TNumisotopes GetNumisotopes(void) const
Get the Numisotopes member data.
void ResetEnzyme(void)
Reset Enzyme data member.
bool IsSetProductsearchtype(void) const
average or monoisotopic? Check if a value has been assigned to Productsearchtype data member.
TSinglenum GetSinglenum(void) const
Get the Singlenum member data.
bool IsSetNmethionine(void) const
should nmethionine be cleaved? Check if a value has been assigned to Nmethionine data member.
void SetDefaultMinspectra(void)
Assign default value to Minspectra data member.
bool IsSetChargehandling(void) const
how to deal with charges Check if a value has been assigned to Chargehandling data member.
bool CanGetCuthi(void) const
Check if it is safe to call GetCuthi method.
bool IsSetIterativesettings(void) const
iterative search settings Check if a value has been assigned to Iterativesettings data member.
bool IsSetFixed(void) const
fixed PTM's Check if a value has been assigned to Fixed data member.
bool CanGetLomasscutoff(void) const
Check if it is safe to call GetLomasscutoff method.
const TLibsearchsettings & GetLibsearchsettings(void) const
Get the Libsearchsettings member data.
CMSLibrarySettings TLibsearchsettings
bool IsSetLomasscutoff(void) const
low mass filter in Daltons, unscaled Check if a value has been assigned to Lomasscutoff data member.
bool IsSetCuthi(void) const
the end of the cutoff Check if a value has been assigned to Cuthi data member.
TMaxmods GetMaxmods(void) const
Get the Maxmods member data.
TPeptol & SetPeptol(void)
Assign a value to Peptol data member.
TSinglewin GetSinglewin(void) const
Get the Singlewin member data.
void ResetNumisotopes(void)
Reset Numisotopes data member.
TAutomassadjust & SetAutomassadjust(void)
Assign a value to Automassadjust data member.
bool CanGetOthersettings(void) const
Check if it is safe to call GetOthersettings method.
void SetDefaultSearchb1(void)
Assign default value to Searchb1 data member.
bool IsSetCutoff(void) const
evalue cutoff next 3 fields define intensity fraction below which peaks will be discard Check if a va...
CMSSearchSettings_Base & operator=(const CMSSearchSettings_Base &)
TCutinc GetCutinc(void) const
Get the Cutinc member data.
const TOutfiles & GetOutfiles(void) const
Get the Outfiles member data.
unsigned int
A callback function used to compare two keys in a database.
Definition: types.hpp:1210
const GenericPointer< typename T::ValueType > T2 value
Definition: pointer.h:1227
Modified on Sun Apr 21 03:43:12 2024 by modify_doxy.py rev. 669887