CMSSearchSettings Class Reference

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...
TPrecursorsearchtype &	SetPrecursorsearchtype (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...
TProductsearchtype &	SetProductsearchtype (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 TIonstosearch &	GetIonstosearch (void) const
	Get the Ionstosearch member data. More...
TIonstosearch &	SetIonstosearch (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...
TPeptol &	SetPeptol (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...
TMsmstol &	SetMsmstol (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...
TZdep &	SetZdep (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...
TCutoff &	SetCutoff (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...
TCutlo &	SetCutlo (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...
TCuthi &	SetCuthi (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...
TCutinc &	SetCutinc (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...
TSinglewin &	SetSinglewin (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...
TDoublewin &	SetDoublewin (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...
TSinglenum &	SetSinglenum (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...
TDoublenum &	SetDoublenum (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 TFixed &	GetFixed (void) const
	Get the Fixed member data. More...
TFixed &	SetFixed (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 TVariable &	GetVariable (void) const
	Get the Variable member data. More...
TVariable &	SetVariable (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...
TEnzyme &	SetEnzyme (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...
TMissedcleave &	SetMissedcleave (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...
THitlistlen &	SetHitlistlen (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 TDb &	GetDb (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)
TDb &	SetDb (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...
TTophitnum &	SetTophitnum (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...
TMinhit &	SetMinhit (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...
TMinspectra &	SetMinspectra (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...
TScale &	SetScale (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...
TMaxmods &	SetMaxmods (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 TTaxids &	GetTaxids (void) const
	Get the Taxids member data. More...
TTaxids &	SetTaxids (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 TChargehandling &	GetChargehandling (void) const
	Get the Chargehandling member data. More...
void	SetChargehandling (TChargehandling &value)
	Assign a value to Chargehandling data member. More...
TChargehandling &	SetChargehandling (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 TUsermods &	GetUsermods (void) const
	Get the Usermods member data. More...
void	SetUsermods (TUsermods &value)
	Assign a value to Usermods data member. More...
TUsermods &	SetUsermods (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...
TPseudocount &	SetPseudocount (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...
TSearchb1 &	SetSearchb1 (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...
TSearchctermproduct &	SetSearchctermproduct (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...
TMaxproductions &	SetMaxproductions (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...
TMinnoenzyme &	SetMinnoenzyme (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...
TMaxnoenzyme &	SetMaxnoenzyme (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...
TExactmass &	SetExactmass (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...
TSettingid &	SetSettingid (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 TIterativesettings &	GetIterativesettings (void) const
	Get the Iterativesettings member data. More...
void	SetIterativesettings (TIterativesettings &value)
	Assign a value to Iterativesettings data member. More...
TIterativesettings &	SetIterativesettings (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...
TPrecursorcull &	SetPrecursorcull (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 TInfiles &	GetInfiles (void) const
	Get the Infiles member data. More...
TInfiles &	SetInfiles (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 TOutfiles &	GetOutfiles (void) const
	Get the Outfiles member data. More...
TOutfiles &	SetOutfiles (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...
TNocorrelationscore &	SetNocorrelationscore (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...
TProbfollowingion &	SetProbfollowingion (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...
TNmethionine &	SetNmethionine (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...
TAutomassadjust &	SetAutomassadjust (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...
TLomasscutoff &	SetLomasscutoff (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 TLibsearchsettings &	GetLibsearchsettings (void) const
	Get the Libsearchsettings member data. More...
void	SetLibsearchsettings (TLibsearchsettings &value)
	Assign a value to Libsearchsettings data member. More...
TLibsearchsettings &	SetLibsearchsettings (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 TNoprolineions &	GetNoprolineions (void) const
	Get the Noprolineions member data. More...
TNoprolineions &	SetNoprolineions (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...
TReversesearch &	SetReversesearch (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 TOthersettings &	GetOthersettings (void) const
	Get the Othersettings member data. More...
TOthersettings &	SetOthersettings (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...
TNumisotopes &	SetNumisotopes (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...
TPepppm &	SetPepppm (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...
TMsmsppm &	SetMsmsppm (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...
TReportedhitcount &	SetReportedhitcount (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 CTypeInfo *	GetThisTypeInfo (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 string &	GetNamespaceName (void) const
	Get namespace name. More...
bool	HasNamespacePrefix (void) const
	Check if data type has namespace prefix. More...
const string &	GetNamespacePrefix (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...
CObject &	operator= (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)
CMSSearchSettings &	operator= (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< int >	TIonstosearch
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< int >	TFixed
typedef list< int >	TVariable
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< int >	TTaxids
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< int >	TNoprolineions
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< Uint8 >	TCounter
	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

typedef CMSSearchSettings_Base CMSSearchSettings::Tparent

private

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:

• include/objects/omssa/MSSearchSettings.hpp
• src/objects/omssa/MSSearchSettings.cpp