NCBI C++ ToolKit
Public Member Functions | Private Types | Private Member Functions | List of all members
CMSSearchSettings Class Reference

Represents ASN.1 type MSSearchSettings defined in file omssa.asn

Search Toolkit Book for CMSSearchSettings

@MSSearchSettings.hpp User-defined methods of the data storage class. More...

#include <objects/omssa/MSSearchSettings.hpp>

+ Inheritance diagram for CMSSearchSettings:
+ Collaboration diagram for CMSSearchSettings:

Public Member Functions

 CMSSearchSettings (void)
 
 ~CMSSearchSettings (void)
 
int Validate (std::list< std::string > &Error) const
 Validate Search Settings returns 0 if OK, 1 if not Error contains explanations. More...
 
- Public Member Functions inherited from CMSSearchSettings_Base
 CMSSearchSettings_Base (void)
 
virtual ~CMSSearchSettings_Base (void)
 
 DECLARE_INTERNAL_TYPE_INFO ()
 
bool IsSetPrecursorsearchtype (void) const
 average or monoisotopic? Check if a value has been assigned to Precursorsearchtype data member. More...
 
bool CanGetPrecursorsearchtype (void) const
 Check if it is safe to call GetPrecursorsearchtype method. More...
 
void ResetPrecursorsearchtype (void)
 Reset Precursorsearchtype data member. More...
 
TPrecursorsearchtype GetPrecursorsearchtype (void) const
 Get the Precursorsearchtype member data. More...
 
void SetPrecursorsearchtype (TPrecursorsearchtype value)
 Assign a value to Precursorsearchtype data member. More...
 
TPrecursorsearchtypeSetPrecursorsearchtype (void)
 Assign a value to Precursorsearchtype data member. More...
 
bool IsSetProductsearchtype (void) const
 average or monoisotopic? Check if a value has been assigned to Productsearchtype data member. More...
 
bool CanGetProductsearchtype (void) const
 Check if it is safe to call GetProductsearchtype method. More...
 
void ResetProductsearchtype (void)
 Reset Productsearchtype data member. More...
 
TProductsearchtype GetProductsearchtype (void) const
 Get the Productsearchtype member data. More...
 
void SetProductsearchtype (TProductsearchtype value)
 Assign a value to Productsearchtype data member. More...
 
TProductsearchtypeSetProductsearchtype (void)
 Assign a value to Productsearchtype data member. More...
 
bool IsSetIonstosearch (void) const
 which ions to search? Check if a value has been assigned to Ionstosearch data member. More...
 
bool CanGetIonstosearch (void) const
 Check if it is safe to call GetIonstosearch method. More...
 
void ResetIonstosearch (void)
 Reset Ionstosearch data member. More...
 
const TIonstosearchGetIonstosearch (void) const
 Get the Ionstosearch member data. More...
 
TIonstosearchSetIonstosearch (void)
 Assign a value to Ionstosearch data member. More...
 
bool IsSetPeptol (void) const
 peptide mass tolerance Check if a value has been assigned to Peptol data member. More...
 
bool CanGetPeptol (void) const
 Check if it is safe to call GetPeptol method. More...
 
void ResetPeptol (void)
 Reset Peptol data member. More...
 
TPeptol GetPeptol (void) const
 Get the Peptol member data. More...
 
void SetPeptol (TPeptol value)
 Assign a value to Peptol data member. More...
 
TPeptolSetPeptol (void)
 Assign a value to Peptol data member. More...
 
bool IsSetMsmstol (void) const
 msms mass tolerance Check if a value has been assigned to Msmstol data member. More...
 
bool CanGetMsmstol (void) const
 Check if it is safe to call GetMsmstol method. More...
 
void ResetMsmstol (void)
 Reset Msmstol data member. More...
 
TMsmstol GetMsmstol (void) const
 Get the Msmstol member data. More...
 
void SetMsmstol (TMsmstol value)
 Assign a value to Msmstol data member. More...
 
TMsmstolSetMsmstol (void)
 Assign a value to Msmstol data member. More...
 
bool IsSetZdep (void) const
 what is the charge dependence of the mass tolerance? Check if a value has been assigned to Zdep data member. More...
 
bool CanGetZdep (void) const
 Check if it is safe to call GetZdep method. More...
 
void ResetZdep (void)
 Reset Zdep data member. More...
 
TZdep GetZdep (void) const
 Get the Zdep member data. More...
 
void SetZdep (TZdep value)
 Assign a value to Zdep data member. More...
 
TZdepSetZdep (void)
 Assign a value to Zdep data member. More...
 
bool IsSetCutoff (void) const
 evalue cutoff next 3 fields define intensity fraction below which peaks will be discard Check if a value has been assigned to Cutoff data member. More...
 
bool CanGetCutoff (void) const
 Check if it is safe to call GetCutoff method. More...
 
void ResetCutoff (void)
 Reset Cutoff data member. More...
 
TCutoff GetCutoff (void) const
 Get the Cutoff member data. More...
 
void SetCutoff (TCutoff value)
 Assign a value to Cutoff data member. More...
 
TCutoffSetCutoff (void)
 Assign a value to Cutoff data member. More...
 
bool IsSetCutlo (void) const
 the start of the cutoff, fraction of most intense peak Check if a value has been assigned to Cutlo data member. More...
 
bool CanGetCutlo (void) const
 Check if it is safe to call GetCutlo method. More...
 
void ResetCutlo (void)
 Reset Cutlo data member. More...
 
TCutlo GetCutlo (void) const
 Get the Cutlo member data. More...
 
void SetCutlo (TCutlo value)
 Assign a value to Cutlo data member. More...
 
TCutloSetCutlo (void)
 Assign a value to Cutlo data member. More...
 
bool IsSetCuthi (void) const
 the end of the cutoff Check if a value has been assigned to Cuthi data member. More...
 
bool CanGetCuthi (void) const
 Check if it is safe to call GetCuthi method. More...
 
void ResetCuthi (void)
 Reset Cuthi data member. More...
 
TCuthi GetCuthi (void) const
 Get the Cuthi member data. More...
 
void SetCuthi (TCuthi value)
 Assign a value to Cuthi data member. More...
 
TCuthiSetCuthi (void)
 Assign a value to Cuthi data member. More...
 
bool IsSetCutinc (void) const
 the increment of the cutoff Check if a value has been assigned to Cutinc data member. More...
 
bool CanGetCutinc (void) const
 Check if it is safe to call GetCutinc method. More...
 
void ResetCutinc (void)
 Reset Cutinc data member. More...
 
TCutinc GetCutinc (void) const
 Get the Cutinc member data. More...
 
void SetCutinc (TCutinc value)
 Assign a value to Cutinc data member. More...
 
TCutincSetCutinc (void)
 Assign a value to Cutinc data member. More...
 
bool IsSetSinglewin (void) const
 the size of the single charge filtering window Check if a value has been assigned to Singlewin data member. More...
 
bool CanGetSinglewin (void) const
 Check if it is safe to call GetSinglewin method. More...
 
void ResetSinglewin (void)
 Reset Singlewin data member. More...
 
TSinglewin GetSinglewin (void) const
 Get the Singlewin member data. More...
 
void SetSinglewin (TSinglewin value)
 Assign a value to Singlewin data member. More...
 
TSinglewinSetSinglewin (void)
 Assign a value to Singlewin data member. More...
 
bool IsSetDoublewin (void) const
 the size of the double charge filtering window Check if a value has been assigned to Doublewin data member. More...
 
bool CanGetDoublewin (void) const
 Check if it is safe to call GetDoublewin method. More...
 
void ResetDoublewin (void)
 Reset Doublewin data member. More...
 
TDoublewin GetDoublewin (void) const
 Get the Doublewin member data. More...
 
void SetDoublewin (TDoublewin value)
 Assign a value to Doublewin data member. More...
 
TDoublewinSetDoublewin (void)
 Assign a value to Doublewin data member. More...
 
bool IsSetSinglenum (void) const
 the number of peaks allowed in the single window Check if a value has been assigned to Singlenum data member. More...
 
bool CanGetSinglenum (void) const
 Check if it is safe to call GetSinglenum method. More...
 
void ResetSinglenum (void)
 Reset Singlenum data member. More...
 
TSinglenum GetSinglenum (void) const
 Get the Singlenum member data. More...
 
void SetSinglenum (TSinglenum value)
 Assign a value to Singlenum data member. More...
 
TSinglenumSetSinglenum (void)
 Assign a value to Singlenum data member. More...
 
bool IsSetDoublenum (void) const
 the number of peaks allowed in the double window Check if a value has been assigned to Doublenum data member. More...
 
bool CanGetDoublenum (void) const
 Check if it is safe to call GetDoublenum method. More...
 
void ResetDoublenum (void)
 Reset Doublenum data member. More...
 
TDoublenum GetDoublenum (void) const
 Get the Doublenum member data. More...
 
void SetDoublenum (TDoublenum value)
 Assign a value to Doublenum data member. More...
 
TDoublenumSetDoublenum (void)
 Assign a value to Doublenum data member. More...
 
bool IsSetFixed (void) const
 fixed PTM's Check if a value has been assigned to Fixed data member. More...
 
bool CanGetFixed (void) const
 Check if it is safe to call GetFixed method. More...
 
void ResetFixed (void)
 Reset Fixed data member. More...
 
const TFixedGetFixed (void) const
 Get the Fixed member data. More...
 
TFixedSetFixed (void)
 Assign a value to Fixed data member. More...
 
bool IsSetVariable (void) const
 variable PTM's Check if a value has been assigned to Variable data member. More...
 
bool CanGetVariable (void) const
 Check if it is safe to call GetVariable method. More...
 
void ResetVariable (void)
 Reset Variable data member. More...
 
const TVariableGetVariable (void) const
 Get the Variable member data. More...
 
TVariableSetVariable (void)
 Assign a value to Variable data member. More...
 
bool IsSetEnzyme (void) const
 digestion enzyme Check if a value has been assigned to Enzyme data member. More...
 
bool CanGetEnzyme (void) const
 Check if it is safe to call GetEnzyme method. More...
 
void ResetEnzyme (void)
 Reset Enzyme data member. More...
 
TEnzyme GetEnzyme (void) const
 Get the Enzyme member data. More...
 
void SetEnzyme (TEnzyme value)
 Assign a value to Enzyme data member. More...
 
TEnzymeSetEnzyme (void)
 Assign a value to Enzyme data member. More...
 
bool IsSetMissedcleave (void) const
 number of missed cleaves allowed Check if a value has been assigned to Missedcleave data member. More...
 
bool CanGetMissedcleave (void) const
 Check if it is safe to call GetMissedcleave method. More...
 
void ResetMissedcleave (void)
 Reset Missedcleave data member. More...
 
TMissedcleave GetMissedcleave (void) const
 Get the Missedcleave member data. More...
 
void SetMissedcleave (TMissedcleave value)
 Assign a value to Missedcleave data member. More...
 
TMissedcleaveSetMissedcleave (void)
 Assign a value to Missedcleave data member. More...
 
bool IsSetHitlistlen (void) const
 the number of hits kept in memory for a spectrum Check if a value has been assigned to Hitlistlen data member. More...
 
bool CanGetHitlistlen (void) const
 Check if it is safe to call GetHitlistlen method. More...
 
void ResetHitlistlen (void)
 Reset Hitlistlen data member. More...
 
void SetDefaultHitlistlen (void)
 Assign default value to Hitlistlen data member. More...
 
THitlistlen GetHitlistlen (void) const
 Get the Hitlistlen member data. More...
 
void SetHitlistlen (THitlistlen value)
 Assign a value to Hitlistlen data member. More...
 
THitlistlenSetHitlistlen (void)
 Assign a value to Hitlistlen data member. More...
 
bool IsSetDb (void) const
 sequence set to search, e.g. More...
 
bool CanGetDb (void) const
 Check if it is safe to call GetDb method. More...
 
void ResetDb (void)
 Reset Db data member. More...
 
const TDbGetDb (void) const
 Get the Db member data. More...
 
void SetDb (const TDb &value)
 Assign a value to Db data member. More...
 
void SetDb (TDb &&value)
 
TDbSetDb (void)
 Assign a value to Db data member. More...
 
bool IsSetTophitnum (void) const
 number of m/z to consider in first pass Check if a value has been assigned to Tophitnum data member. More...
 
bool CanGetTophitnum (void) const
 Check if it is safe to call GetTophitnum method. More...
 
void ResetTophitnum (void)
 Reset Tophitnum data member. More...
 
TTophitnum GetTophitnum (void) const
 Get the Tophitnum member data. More...
 
void SetTophitnum (TTophitnum value)
 Assign a value to Tophitnum data member. More...
 
TTophitnumSetTophitnum (void)
 Assign a value to Tophitnum data member. More...
 
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. More...
 
bool CanGetMinhit (void) const
 Check if it is safe to call GetMinhit method. More...
 
void ResetMinhit (void)
 Reset Minhit data member. More...
 
void SetDefaultMinhit (void)
 Assign default value to Minhit data member. More...
 
TMinhit GetMinhit (void) const
 Get the Minhit member data. More...
 
void SetMinhit (TMinhit value)
 Assign a value to Minhit data member. More...
 
TMinhitSetMinhit (void)
 Assign a value to Minhit data member. More...
 
bool IsSetMinspectra (void) const
 minimum number of m/z for a valid spectra Check if a value has been assigned to Minspectra data member. More...
 
bool CanGetMinspectra (void) const
 Check if it is safe to call GetMinspectra method. More...
 
void ResetMinspectra (void)
 Reset Minspectra data member. More...
 
void SetDefaultMinspectra (void)
 Assign default value to Minspectra data member. More...
 
TMinspectra GetMinspectra (void) const
 Get the Minspectra member data. More...
 
void SetMinspectra (TMinspectra value)
 Assign a value to Minspectra data member. More...
 
TMinspectraSetMinspectra (void)
 Assign a value to Minspectra data member. More...
 
bool IsSetScale (void) const
 scale for m/z float to integer Check if a value has been assigned to Scale data member. More...
 
bool CanGetScale (void) const
 Check if it is safe to call GetScale method. More...
 
void ResetScale (void)
 Reset Scale data member. More...
 
void SetDefaultScale (void)
 Assign default value to Scale data member. More...
 
TScale GetScale (void) const
 Get the Scale member data. More...
 
void SetScale (TScale value)
 Assign a value to Scale data member. More...
 
TScaleSetScale (void)
 Assign a value to Scale data member. More...
 
bool IsSetMaxmods (void) const
 maximum number of mass ladders per database peptide Check if a value has been assigned to Maxmods data member. More...
 
bool CanGetMaxmods (void) const
 Check if it is safe to call GetMaxmods method. More...
 
void ResetMaxmods (void)
 Reset Maxmods data member. More...
 
void SetDefaultMaxmods (void)
 Assign default value to Maxmods data member. More...
 
TMaxmods GetMaxmods (void) const
 Get the Maxmods member data. More...
 
void SetMaxmods (TMaxmods value)
 Assign a value to Maxmods data member. More...
 
TMaxmodsSetMaxmods (void)
 Assign a value to Maxmods data member. More...
 
bool IsSetTaxids (void) const
 taxa to limit search Check if a value has been assigned to Taxids data member. More...
 
bool CanGetTaxids (void) const
 Check if it is safe to call GetTaxids method. More...
 
void ResetTaxids (void)
 Reset Taxids data member. More...
 
const TTaxidsGetTaxids (void) const
 Get the Taxids member data. More...
 
TTaxidsSetTaxids (void)
 Assign a value to Taxids data member. More...
 
bool IsSetChargehandling (void) const
 how to deal with charges Check if a value has been assigned to Chargehandling data member. More...
 
bool CanGetChargehandling (void) const
 Check if it is safe to call GetChargehandling method. More...
 
void ResetChargehandling (void)
 Reset Chargehandling data member. More...
 
const TChargehandlingGetChargehandling (void) const
 Get the Chargehandling member data. More...
 
void SetChargehandling (TChargehandling &value)
 Assign a value to Chargehandling data member. More...
 
TChargehandlingSetChargehandling (void)
 Assign a value to Chargehandling data member. More...
 
bool IsSetUsermods (void) const
 user defined modifications Check if a value has been assigned to Usermods data member. More...
 
bool CanGetUsermods (void) const
 Check if it is safe to call GetUsermods method. More...
 
void ResetUsermods (void)
 Reset Usermods data member. More...
 
const TUsermodsGetUsermods (void) const
 Get the Usermods member data. More...
 
void SetUsermods (TUsermods &value)
 Assign a value to Usermods data member. More...
 
TUsermodsSetUsermods (void)
 Assign a value to Usermods data member. More...
 
bool IsSetPseudocount (void) const
 min number of counts per precursor bin Check if a value has been assigned to Pseudocount data member. More...
 
bool CanGetPseudocount (void) const
 Check if it is safe to call GetPseudocount method. More...
 
void ResetPseudocount (void)
 Reset Pseudocount data member. More...
 
void SetDefaultPseudocount (void)
 Assign default value to Pseudocount data member. More...
 
TPseudocount GetPseudocount (void) const
 Get the Pseudocount member data. More...
 
void SetPseudocount (TPseudocount value)
 Assign a value to Pseudocount data member. More...
 
TPseudocountSetPseudocount (void)
 Assign a value to Pseudocount data member. More...
 
bool IsSetSearchb1 (void) const
 should b1 product be in search (1=no, 0=yes) Check if a value has been assigned to Searchb1 data member. More...
 
bool CanGetSearchb1 (void) const
 Check if it is safe to call GetSearchb1 method. More...
 
void ResetSearchb1 (void)
 Reset Searchb1 data member. More...
 
void SetDefaultSearchb1 (void)
 Assign default value to Searchb1 data member. More...
 
TSearchb1 GetSearchb1 (void) const
 Get the Searchb1 member data. More...
 
void SetSearchb1 (TSearchb1 value)
 Assign a value to Searchb1 data member. More...
 
TSearchb1SetSearchb1 (void)
 Assign a value to Searchb1 data member. More...
 
bool IsSetSearchctermproduct (void) const
 should c terminus ion be searched (1=no, 0=yes) Check if a value has been assigned to Searchctermproduct data member. More...
 
bool CanGetSearchctermproduct (void) const
 Check if it is safe to call GetSearchctermproduct method. More...
 
void ResetSearchctermproduct (void)
 Reset Searchctermproduct data member. More...
 
void SetDefaultSearchctermproduct (void)
 Assign default value to Searchctermproduct data member. More...
 
TSearchctermproduct GetSearchctermproduct (void) const
 Get the Searchctermproduct member data. More...
 
void SetSearchctermproduct (TSearchctermproduct value)
 Assign a value to Searchctermproduct data member. More...
 
TSearchctermproductSetSearchctermproduct (void)
 Assign a value to Searchctermproduct data member. More...
 
bool IsSetMaxproductions (void) const
 max number of ions in each series (0=all) Check if a value has been assigned to Maxproductions data member. More...
 
bool CanGetMaxproductions (void) const
 Check if it is safe to call GetMaxproductions method. More...
 
void ResetMaxproductions (void)
 Reset Maxproductions data member. More...
 
void SetDefaultMaxproductions (void)
 Assign default value to Maxproductions data member. More...
 
TMaxproductions GetMaxproductions (void) const
 Get the Maxproductions member data. More...
 
void SetMaxproductions (TMaxproductions value)
 Assign a value to Maxproductions data member. More...
 
TMaxproductionsSetMaxproductions (void)
 Assign a value to Maxproductions data member. More...
 
bool IsSetMinnoenzyme (void) const
 min number of AA in peptide for noenzyme search Check if a value has been assigned to Minnoenzyme data member. More...
 
bool CanGetMinnoenzyme (void) const
 Check if it is safe to call GetMinnoenzyme method. More...
 
void ResetMinnoenzyme (void)
 Reset Minnoenzyme data member. More...
 
void SetDefaultMinnoenzyme (void)
 Assign default value to Minnoenzyme data member. More...
 
TMinnoenzyme GetMinnoenzyme (void) const
 Get the Minnoenzyme member data. More...
 
void SetMinnoenzyme (TMinnoenzyme value)
 Assign a value to Minnoenzyme data member. More...
 
TMinnoenzymeSetMinnoenzyme (void)
 Assign a value to Minnoenzyme data member. More...
 
bool IsSetMaxnoenzyme (void) const
 max number of AA in peptide for noenzyme search (0=none) Check if a value has been assigned to Maxnoenzyme data member. More...
 
bool CanGetMaxnoenzyme (void) const
 Check if it is safe to call GetMaxnoenzyme method. More...
 
void ResetMaxnoenzyme (void)
 Reset Maxnoenzyme data member. More...
 
void SetDefaultMaxnoenzyme (void)
 Assign default value to Maxnoenzyme data member. More...
 
TMaxnoenzyme GetMaxnoenzyme (void) const
 Get the Maxnoenzyme member data. More...
 
void SetMaxnoenzyme (TMaxnoenzyme value)
 Assign a value to Maxnoenzyme data member. More...
 
TMaxnoenzymeSetMaxnoenzyme (void)
 Assign a value to Maxnoenzyme data member. More...
 
bool IsSetExactmass (void) const
 the threshold in Da for adding neutron Check if a value has been assigned to Exactmass data member. More...
 
bool CanGetExactmass (void) const
 Check if it is safe to call GetExactmass method. More...
 
void ResetExactmass (void)
 Reset Exactmass data member. More...
 
TExactmass GetExactmass (void) const
 Get the Exactmass member data. More...
 
void SetExactmass (TExactmass value)
 Assign a value to Exactmass data member. More...
 
TExactmassSetExactmass (void)
 Assign a value to Exactmass data member. More...
 
bool IsSetSettingid (void) const
 id of the search settings Check if a value has been assigned to Settingid data member. More...
 
bool CanGetSettingid (void) const
 Check if it is safe to call GetSettingid method. More...
 
void ResetSettingid (void)
 Reset Settingid data member. More...
 
TSettingid GetSettingid (void) const
 Get the Settingid member data. More...
 
void SetSettingid (TSettingid value)
 Assign a value to Settingid data member. More...
 
TSettingidSetSettingid (void)
 Assign a value to Settingid data member. More...
 
bool IsSetIterativesettings (void) const
 iterative search settings Check if a value has been assigned to Iterativesettings data member. More...
 
bool CanGetIterativesettings (void) const
 Check if it is safe to call GetIterativesettings method. More...
 
void ResetIterativesettings (void)
 Reset Iterativesettings data member. More...
 
const TIterativesettingsGetIterativesettings (void) const
 Get the Iterativesettings member data. More...
 
void SetIterativesettings (TIterativesettings &value)
 Assign a value to Iterativesettings data member. More...
 
TIterativesettingsSetIterativesettings (void)
 Assign a value to Iterativesettings data member. More...
 
bool IsSetPrecursorcull (void) const
 turn on aggressive precursor culling for ETD (0=none) Check if a value has been assigned to Precursorcull data member. More...
 
bool CanGetPrecursorcull (void) const
 Check if it is safe to call GetPrecursorcull method. More...
 
void ResetPrecursorcull (void)
 Reset Precursorcull data member. More...
 
TPrecursorcull GetPrecursorcull (void) const
 Get the Precursorcull member data. More...
 
void SetPrecursorcull (TPrecursorcull value)
 Assign a value to Precursorcull data member. More...
 
TPrecursorcullSetPrecursorcull (void)
 Assign a value to Precursorcull data member. More...
 
bool IsSetInfiles (void) const
 input files Check if a value has been assigned to Infiles data member. More...
 
bool CanGetInfiles (void) const
 Check if it is safe to call GetInfiles method. More...
 
void ResetInfiles (void)
 Reset Infiles data member. More...
 
const TInfilesGetInfiles (void) const
 Get the Infiles member data. More...
 
TInfilesSetInfiles (void)
 Assign a value to Infiles data member. More...
 
bool IsSetOutfiles (void) const
 output files Check if a value has been assigned to Outfiles data member. More...
 
bool CanGetOutfiles (void) const
 Check if it is safe to call GetOutfiles method. More...
 
void ResetOutfiles (void)
 Reset Outfiles data member. More...
 
const TOutfilesGetOutfiles (void) const
 Get the Outfiles member data. More...
 
TOutfilesSetOutfiles (void)
 Assign a value to Outfiles data member. More...
 
bool IsSetNocorrelationscore (void) const
 turn on correlation score (1=nocorr) Check if a value has been assigned to Nocorrelationscore data member. More...
 
bool CanGetNocorrelationscore (void) const
 Check if it is safe to call GetNocorrelationscore method. More...
 
void ResetNocorrelationscore (void)
 Reset Nocorrelationscore data member. More...
 
TNocorrelationscore GetNocorrelationscore (void) const
 Get the Nocorrelationscore member data. More...
 
void SetNocorrelationscore (TNocorrelationscore value)
 Assign a value to Nocorrelationscore data member. More...
 
TNocorrelationscoreSetNocorrelationscore (void)
 Assign a value to Nocorrelationscore data member. More...
 
bool IsSetProbfollowingion (void) const
 probability of a consecutive ion (used in correlation) Check if a value has been assigned to Probfollowingion data member. More...
 
bool CanGetProbfollowingion (void) const
 Check if it is safe to call GetProbfollowingion method. More...
 
void ResetProbfollowingion (void)
 Reset Probfollowingion data member. More...
 
TProbfollowingion GetProbfollowingion (void) const
 Get the Probfollowingion member data. More...
 
void SetProbfollowingion (TProbfollowingion value)
 Assign a value to Probfollowingion data member. More...
 
TProbfollowingionSetProbfollowingion (void)
 Assign a value to Probfollowingion data member. More...
 
bool IsSetNmethionine (void) const
 should nmethionine be cleaved? Check if a value has been assigned to Nmethionine data member. More...
 
bool CanGetNmethionine (void) const
 Check if it is safe to call GetNmethionine method. More...
 
void ResetNmethionine (void)
 Reset Nmethionine data member. More...
 
TNmethionine GetNmethionine (void) const
 Get the Nmethionine member data. More...
 
void SetNmethionine (TNmethionine value)
 Assign a value to Nmethionine data member. More...
 
TNmethionineSetNmethionine (void)
 Assign a value to Nmethionine data member. More...
 
bool IsSetAutomassadjust (void) const
 fraction allowable adjustment of product mass tolerance Check if a value has been assigned to Automassadjust data member. More...
 
bool CanGetAutomassadjust (void) const
 Check if it is safe to call GetAutomassadjust method. More...
 
void ResetAutomassadjust (void)
 Reset Automassadjust data member. More...
 
TAutomassadjust GetAutomassadjust (void) const
 Get the Automassadjust member data. More...
 
void SetAutomassadjust (TAutomassadjust value)
 Assign a value to Automassadjust data member. More...
 
TAutomassadjustSetAutomassadjust (void)
 Assign a value to Automassadjust data member. More...
 
bool IsSetLomasscutoff (void) const
 low mass filter in Daltons, unscaled Check if a value has been assigned to Lomasscutoff data member. More...
 
bool CanGetLomasscutoff (void) const
 Check if it is safe to call GetLomasscutoff method. More...
 
void ResetLomasscutoff (void)
 Reset Lomasscutoff data member. More...
 
TLomasscutoff GetLomasscutoff (void) const
 Get the Lomasscutoff member data. More...
 
void SetLomasscutoff (TLomasscutoff value)
 Assign a value to Lomasscutoff data member. More...
 
TLomasscutoffSetLomasscutoff (void)
 Assign a value to Lomasscutoff data member. More...
 
bool IsSetLibsearchsettings (void) const
 library search settings Check if a value has been assigned to Libsearchsettings data member. More...
 
bool CanGetLibsearchsettings (void) const
 Check if it is safe to call GetLibsearchsettings method. More...
 
void ResetLibsearchsettings (void)
 Reset Libsearchsettings data member. More...
 
const TLibsearchsettingsGetLibsearchsettings (void) const
 Get the Libsearchsettings member data. More...
 
void SetLibsearchsettings (TLibsearchsettings &value)
 Assign a value to Libsearchsettings data member. More...
 
TLibsearchsettingsSetLibsearchsettings (void)
 Assign a value to Libsearchsettings data member. More...
 
bool IsSetNoprolineions (void) const
 which ions to use no proline rule Check if a value has been assigned to Noprolineions data member. More...
 
bool CanGetNoprolineions (void) const
 Check if it is safe to call GetNoprolineions method. More...
 
void ResetNoprolineions (void)
 Reset Noprolineions data member. More...
 
const TNoprolineionsGetNoprolineions (void) const
 Get the Noprolineions member data. More...
 
TNoprolineionsSetNoprolineions (void)
 Assign a value to Noprolineions data member. More...
 
bool IsSetReversesearch (void) const
 do reverse search Check if a value has been assigned to Reversesearch data member. More...
 
bool CanGetReversesearch (void) const
 Check if it is safe to call GetReversesearch method. More...
 
void ResetReversesearch (void)
 Reset Reversesearch data member. More...
 
TReversesearch GetReversesearch (void) const
 Get the Reversesearch member data. More...
 
void SetReversesearch (TReversesearch value)
 Assign a value to Reversesearch data member. More...
 
TReversesearchSetReversesearch (void)
 Assign a value to Reversesearch data member. More...
 
bool IsSetOthersettings (void) const
 extra search settings Check if a value has been assigned to Othersettings data member. More...
 
bool CanGetOthersettings (void) const
 Check if it is safe to call GetOthersettings method. More...
 
void ResetOthersettings (void)
 Reset Othersettings data member. More...
 
const TOthersettingsGetOthersettings (void) const
 Get the Othersettings member data. More...
 
TOthersettingsSetOthersettings (void)
 Assign a value to Othersettings data member. More...
 
bool IsSetNumisotopes (void) const
 number of isotopic peaks to search when using MSSearchType multiisotope Check if a value has been assigned to Numisotopes data member. More...
 
bool CanGetNumisotopes (void) const
 Check if it is safe to call GetNumisotopes method. More...
 
void ResetNumisotopes (void)
 Reset Numisotopes data member. More...
 
TNumisotopes GetNumisotopes (void) const
 Get the Numisotopes member data. More...
 
void SetNumisotopes (TNumisotopes value)
 Assign a value to Numisotopes data member. More...
 
TNumisotopesSetNumisotopes (void)
 Assign a value to Numisotopes data member. More...
 
bool IsSetPepppm (void) const
 search precursor as ppm Check if a value has been assigned to Pepppm data member. More...
 
bool CanGetPepppm (void) const
 Check if it is safe to call GetPepppm method. More...
 
void ResetPepppm (void)
 Reset Pepppm data member. More...
 
TPepppm GetPepppm (void) const
 Get the Pepppm member data. More...
 
void SetPepppm (TPepppm value)
 Assign a value to Pepppm data member. More...
 
TPepppmSetPepppm (void)
 Assign a value to Pepppm data member. More...
 
bool IsSetMsmsppm (void) const
 search product as ppm Check if a value has been assigned to Msmsppm data member. More...
 
bool CanGetMsmsppm (void) const
 Check if it is safe to call GetMsmsppm method. More...
 
void ResetMsmsppm (void)
 Reset Msmsppm data member. More...
 
TMsmsppm GetMsmsppm (void) const
 Get the Msmsppm member data. More...
 
void SetMsmsppm (TMsmsppm value)
 Assign a value to Msmsppm data member. More...
 
TMsmsppmSetMsmsppm (void)
 Assign a value to Msmsppm data member. More...
 
bool IsSetReportedhitcount (void) const
 the maximum number of hits to report per spectrum, 0=all Check if a value has been assigned to Reportedhitcount data member. More...
 
bool CanGetReportedhitcount (void) const
 Check if it is safe to call GetReportedhitcount method. More...
 
void ResetReportedhitcount (void)
 Reset Reportedhitcount data member. More...
 
TReportedhitcount GetReportedhitcount (void) const
 Get the Reportedhitcount member data. More...
 
void SetReportedhitcount (TReportedhitcount value)
 Assign a value to Reportedhitcount data member. More...
 
TReportedhitcountSetReportedhitcount (void)
 Assign a value to Reportedhitcount data member. More...
 
virtual void Reset (void)
 Reset the whole object. More...
 
- Public Member Functions inherited from CSerialObject
 CSerialObject (void)
 
virtual ~CSerialObject (void)
 
virtual const CTypeInfoGetThisTypeInfo (void) const =0
 
virtual void Assign (const CSerialObject &source, ESerialRecursionMode how=eRecursive)
 Set object to copy of another one. More...
 
virtual bool Equals (const CSerialObject &object, ESerialRecursionMode how=eRecursive) const
 Check if both objects contain the same values. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
void ThrowUnassigned (TMemberIndex index) const
 
void ThrowUnassigned (TMemberIndex index, const char *file_name, int file_line) const
 
bool HasNamespaceName (void) const
 Check if object data type has namespace name. More...
 
const stringGetNamespaceName (void) const
 Get namespace name. More...
 
bool HasNamespacePrefix (void) const
 Check if data type has namespace prefix. More...
 
const stringGetNamespacePrefix (void) const
 Get namespace prefix. More...
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Private Types

typedef CMSSearchSettings_Base Tparent
 

Private Member Functions

 CMSSearchSettings (const CMSSearchSettings &value)
 
CMSSearchSettingsoperator= (const CMSSearchSettings &value)
 

Additional Inherited Members

- Public Types inherited from CMSSearchSettings_Base
enum class  E_memberIndex {
  e__allMandatory = 0 , e_precursorsearchtype , e_productsearchtype , e_ionstosearch ,
  e_peptol , e_msmstol , e_zdep , e_cutoff ,
  e_cutlo , e_cuthi , e_cutinc , e_singlewin ,
  e_doublewin , e_singlenum , e_doublenum , e_fixed ,
  e_variable , e_enzyme , e_missedcleave , e_hitlistlen ,
  e_db , e_tophitnum , e_minhit , e_minspectra ,
  e_scale , e_maxmods , e_taxids , e_chargehandling ,
  e_usermods , e_pseudocount , e_searchb1 , e_searchctermproduct ,
  e_maxproductions , e_minnoenzyme , e_maxnoenzyme , e_exactmass ,
  e_settingid , e_iterativesettings , e_precursorcull , e_infiles ,
  e_outfiles , e_nocorrelationscore , e_probfollowingion , e_nmethionine ,
  e_automassadjust , e_lomasscutoff , e_libsearchsettings , e_noprolineions ,
  e_reversesearch , e_othersettings , e_numisotopes , e_pepppm ,
  e_msmsppm , e_reportedhitcount
}
 
typedef int TPrecursorsearchtype
 
typedef int TProductsearchtype
 
typedef list< intTIonstosearch
 
typedef double TPeptol
 
typedef double TMsmstol
 
typedef int TZdep
 
typedef double TCutoff
 
typedef double TCutlo
 
typedef double TCuthi
 
typedef double TCutinc
 
typedef int TSinglewin
 
typedef int TDoublewin
 
typedef int TSinglenum
 
typedef int TDoublenum
 
typedef list< intTFixed
 
typedef list< intTVariable
 
typedef int TEnzyme
 
typedef int TMissedcleave
 
typedef int THitlistlen
 
typedef string TDb
 
typedef int TTophitnum
 
typedef int TMinhit
 
typedef int TMinspectra
 
typedef int TScale
 
typedef int TMaxmods
 
typedef list< intTTaxids
 
typedef CMSChargeHandle TChargehandling
 
typedef CMSModSpecSet TUsermods
 
typedef int TPseudocount
 
typedef int TSearchb1
 
typedef int TSearchctermproduct
 
typedef int TMaxproductions
 
typedef int TMinnoenzyme
 
typedef int TMaxnoenzyme
 
typedef double TExactmass
 
typedef int TSettingid
 
typedef CMSIterativeSettings TIterativesettings
 
typedef int TPrecursorcull
 
typedef list< CRef< CMSInFile > > TInfiles
 
typedef list< CRef< CMSOutFile > > TOutfiles
 
typedef int TNocorrelationscore
 
typedef double TProbfollowingion
 
typedef bool TNmethionine
 
typedef double TAutomassadjust
 
typedef double TLomasscutoff
 
typedef CMSLibrarySettings TLibsearchsettings
 
typedef list< intTNoprolineions
 
typedef bool TReversesearch
 
typedef list< CRef< CNameValue > > TOthersettings
 
typedef int TNumisotopes
 
typedef bool TPepppm
 
typedef bool TMsmsppm
 
typedef int TReportedhitcount
 
typedef Tparent::CMemberIndex< E_memberIndex, 54 > TmemberIndex
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CSerialObject
static void SetVerifyDataThread (ESerialVerifyData verify)
 
static void SetVerifyDataGlobal (ESerialVerifyData verify)
 
static string UnassignedString (void)
 
static CStringUTF8 UnassignedStringUTF8 (void)
 
static char UnassignedByte (void)
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CSerialObject
static const char * ms_UnassignedStr = "<*unassigned*>"
 
static const char ms_UnassignedByte = char(0xcd)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

@MSSearchSettings.hpp User-defined methods of the data storage class.

This file was originally generated by application DATATOOL using the following specifications: 'omssa.asn'.

New methods or data members can be added to it if needed. See also: MSSearchSettings_.hpp

Definition at line 53 of file MSSearchSettings.hpp.

Member Typedef Documentation

◆ Tparent

Definition at line 55 of file MSSearchSettings.hpp.

Constructor & Destructor Documentation

◆ CMSSearchSettings() [1/2]

CMSSearchSettings::CMSSearchSettings ( void  )
inline

Definition at line 81 of file MSSearchSettings.hpp.

◆ ~CMSSearchSettings()

CMSSearchSettings::~CMSSearchSettings ( void  )

Definition at line 50 of file MSSearchSettings.cpp.

◆ CMSSearchSettings() [2/2]

CMSSearchSettings::CMSSearchSettings ( const CMSSearchSettings value)
private

Member Function Documentation

◆ operator=()

CMSSearchSettings& CMSSearchSettings::operator= ( const CMSSearchSettings value)
private

◆ Validate()

int CMSSearchSettings::Validate ( std::list< std::string > &  Error) const

Validate Search Settings returns 0 if OK, 1 if not Error contains explanations.

Validate Search Settings returns 0 if OK, 1 if not Error contains explanation.

Definition at line 60 of file MSSearchSettings.cpp.

References CMSSearchSettings_Base::CanGetAutomassadjust(), CMSChargeHandle_Base::CanGetCalccharge(), CMSChargeHandle_Base::CanGetCalcplusone(), CMSChargeHandle_Base::CanGetConsidermult(), CMSSearchSettings_Base::CanGetCuthi(), CMSSearchSettings_Base::CanGetCutinc(), CMSSearchSettings_Base::CanGetCutlo(), CMSSearchSettings_Base::CanGetDb(), CMSSearchSettings_Base::CanGetDoublenum(), CMSSearchSettings_Base::CanGetDoublewin(), CMSSearchSettings_Base::CanGetEnzyme(), CMSSearchSettings_Base::CanGetExactmass(), CMSSearchSettings_Base::CanGetFixed(), CMSSearchSettings_Base::CanGetHitlistlen(), CMSSearchSettings_Base::CanGetIonstosearch(), CMSChargeHandle_Base::CanGetMaxcharge(), CMSSearchSettings_Base::CanGetMaxmods(), CMSSearchSettings_Base::CanGetMaxnoenzyme(), CMSChargeHandle_Base::CanGetMaxproductcharge(), CMSSearchSettings_Base::CanGetMaxproductions(), CMSChargeHandle_Base::CanGetMincharge(), CMSSearchSettings_Base::CanGetMinhit(), CMSSearchSettings_Base::CanGetMinnoenzyme(), CMSSearchSettings_Base::CanGetMinspectra(), CMSSearchSettings_Base::CanGetMissedcleave(), CMSSearchSettings_Base::CanGetMsmstol(), CMSSearchSettings_Base::CanGetNocorrelationscore(), CMSSearchSettings_Base::CanGetNoprolineions(), CMSSearchSettings_Base::CanGetNumisotopes(), CMSSearchSettings_Base::CanGetPeptol(), CMSChargeHandle_Base::CanGetPlusone(), CMSSearchSettings_Base::CanGetPrecursorcull(), CMSSearchSettings_Base::CanGetPrecursorsearchtype(), CMSSearchSettings_Base::CanGetProbfollowingion(), CMSSearchSettings_Base::CanGetProductsearchtype(), CMSSearchSettings_Base::CanGetPseudocount(), CMSIterativeSettings_Base::CanGetReplacethresh(), CMSSearchSettings_Base::CanGetReportedhitcount(), CMSIterativeSettings_Base::CanGetResearchthresh(), CMSSearchSettings_Base::CanGetScale(), CMSSearchSettings_Base::CanGetSearchb1(), CMSSearchSettings_Base::CanGetSearchctermproduct(), CMSSearchSettings_Base::CanGetSinglenum(), CMSSearchSettings_Base::CanGetSinglewin(), CMSIterativeSettings_Base::CanGetSubsetthresh(), CMSSearchSettings_Base::CanGetTophitnum(), CMSSearchSettings_Base::CanGetVariable(), CMSSearchSettings_Base::CanGetZdep(), eMSIonType_max, eMSIonType_parent, eMSSearchType_max, eMSZdependence_independent, eMSZdependence_max, Error(), CMSSearchSettings_Base::GetAutomassadjust(), CMSChargeHandle_Base::GetCalccharge(), CMSChargeHandle_Base::GetCalcplusone(), CMSSearchSettings_Base::GetChargehandling(), CMSChargeHandle_Base::GetConsidermult(), CMSSearchSettings_Base::GetCuthi(), CMSSearchSettings_Base::GetCutinc(), CMSSearchSettings_Base::GetCutlo(), CMSSearchSettings_Base::GetDb(), CMSSearchSettings_Base::GetDoublenum(), CMSSearchSettings_Base::GetDoublewin(), CMSSearchSettings_Base::GetEnzyme(), CMSSearchSettings_Base::GetExactmass(), CMSSearchSettings_Base::GetFixed(), CMSSearchSettings_Base::GetHitlistlen(), CMSSearchSettings_Base::GetIonstosearch(), CMSSearchSettings_Base::GetIterativesettings(), CMSChargeHandle_Base::GetMaxcharge(), CMSSearchSettings_Base::GetMaxmods(), CMSSearchSettings_Base::GetMaxnoenzyme(), CMSChargeHandle_Base::GetMaxproductcharge(), CMSSearchSettings_Base::GetMaxproductions(), CMSChargeHandle_Base::GetMincharge(), CMSSearchSettings_Base::GetMinhit(), CMSSearchSettings_Base::GetMinnoenzyme(), CMSSearchSettings_Base::GetMinspectra(), CMSSearchSettings_Base::GetMissedcleave(), CMSSearchSettings_Base::GetMsmstol(), CMSChargeHandle_Base::GetNegative(), CMSSearchSettings_Base::GetNocorrelationscore(), CMSSearchSettings_Base::GetNoprolineions(), CMSSearchSettings_Base::GetNumisotopes(), CMSSearchSettings_Base::GetPeptol(), CMSChargeHandle_Base::GetPlusone(), CMSSearchSettings_Base::GetPrecursorcull(), CMSSearchSettings_Base::GetPrecursorsearchtype(), CMSSearchSettings_Base::GetProbfollowingion(), CMSSearchSettings_Base::GetProductsearchtype(), CMSSearchSettings_Base::GetPseudocount(), CMSIterativeSettings_Base::GetReplacethresh(), CMSSearchSettings_Base::GetReportedhitcount(), CMSIterativeSettings_Base::GetResearchthresh(), CMSSearchSettings_Base::GetScale(), CMSSearchSettings_Base::GetSearchb1(), CMSSearchSettings_Base::GetSearchctermproduct(), CMSSearchSettings_Base::GetSinglenum(), CMSSearchSettings_Base::GetSinglewin(), CMSIterativeSettings_Base::GetSubsetthresh(), CMSSearchSettings_Base::GetTaxids(), CMSSearchSettings_Base::GetTophitnum(), CMSSearchSettings_Base::GetVariable(), CMSSearchSettings_Base::GetZdep(), i, CMSSearchSettings_Base::IsSetChargehandling(), CMSSearchSettings_Base::IsSetIterativesettings(), and CMSSearchSettings_Base::IsSetTaxids().

Referenced by CSearchHelper::ValidateSearchSettings().


The documentation for this class was generated from the following files:
Modified on Sun Apr 14 05:27:42 2024 by modify_doxy.py rev. 669887