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NCBI C++ ToolKit: include/objects/omssa/MSSearchSettings_.hpp Source File

e_precursorsearchtype,

e_searchctermproduct,

e_nocorrelationscore,

IsSetPrecursorsearchtype(

)

;

CanGetPrecursorsearchtype(

)

;

ResetPrecursorsearchtype(

);

IsSetProductsearchtype(

)

;

CanGetProductsearchtype(

)

;

ResetProductsearchtype(

);

IsSetIonstosearch(

)

;

CanGetIonstosearch(

)

;

ResetIonstosearch(

);

IsSetPeptol(

)

;

CanGetPeptol(

)

;

ResetPeptol(

);

GetPeptol(

)

;

IsSetMsmstol(

)

;

CanGetMsmstol(

)

;

ResetMsmstol(

);

IsSetZdep(

)

;

CanGetZdep(

)

;

ResetZdep(

);

GetZdep(

)

;

& SetZdep(

);

IsSetCutoff(

)

;

CanGetCutoff(

)

;

ResetCutoff(

);

GetCutoff(

)

;

IsSetCutlo(

)

;

CanGetCutlo(

)

;

ResetCutlo(

);

GetCutlo(

)

;

& SetCutlo(

);

IsSetCuthi(

)

;

CanGetCuthi(

)

;

ResetCuthi(

);

GetCuthi(

)

;

& SetCuthi(

);

IsSetCutinc(

)

;

CanGetCutinc(

)

;

ResetCutinc(

);

GetCutinc(

)

;

IsSetSinglewin(

)

;

CanGetSinglewin(

)

;

ResetSinglewin(

);

IsSetDoublewin(

)

;

CanGetDoublewin(

)

;

ResetDoublewin(

);

IsSetSinglenum(

)

;

CanGetSinglenum(

)

;

ResetSinglenum(

);

IsSetDoublenum(

)

;

CanGetDoublenum(

)

;

ResetDoublenum(

);

IsSetFixed(

)

;

CanGetFixed(

)

;

ResetFixed(

);

& GetFixed(

)

;

& SetFixed(

);

IsSetVariable(

)

;

CanGetVariable(

)

;

ResetVariable(

);

& GetVariable(

)

;

IsSetEnzyme(

)

;

CanGetEnzyme(

)

;

ResetEnzyme(

);

GetEnzyme(

)

;

IsSetMissedcleave(

)

;

CanGetMissedcleave(

)

;

ResetMissedcleave(

);

IsSetHitlistlen(

)

;

CanGetHitlistlen(

)

;

ResetHitlistlen(

);

SetDefaultHitlistlen(

);

IsSetDb(

)

;

CanGetDb(

)

;

ResetDb(

);

& GetDb(

)

;

IsSetTophitnum(

)

;

CanGetTophitnum(

)

;

ResetTophitnum(

);

IsSetMinhit(

)

;

CanGetMinhit(

)

;

ResetMinhit(

);

SetDefaultMinhit(

);

GetMinhit(

)

;

IsSetMinspectra(

)

;

CanGetMinspectra(

)

;

ResetMinspectra(

);

SetDefaultMinspectra(

);

IsSetScale(

)

;

CanGetScale(

)

;

ResetScale(

);

SetDefaultScale(

);

GetScale(

)

;

& SetScale(

);

IsSetMaxmods(

)

;

CanGetMaxmods(

)

;

ResetMaxmods(

);

SetDefaultMaxmods(

);

GetMaxmods(

)

;

IsSetTaxids(

)

;

CanGetTaxids(

)

;

ResetTaxids(

);

& GetTaxids(

)

;

IsSetChargehandling(

)

;

CanGetChargehandling(

)

;

ResetChargehandling(

);

IsSetUsermods(

)

;

CanGetUsermods(

)

;

ResetUsermods(

);

& GetUsermods(

)

;

IsSetPseudocount(

)

;

CanGetPseudocount(

)

;

ResetPseudocount(

);

SetDefaultPseudocount(

);

IsSetSearchb1(

)

;

CanGetSearchb1(

)

;

ResetSearchb1(

);

SetDefaultSearchb1(

);

IsSetSearchctermproduct(

)

;

CanGetSearchctermproduct(

)

;

ResetSearchctermproduct(

);

SetDefaultSearchctermproduct(

);

IsSetMaxproductions(

)

;

CanGetMaxproductions(

)

;

ResetMaxproductions(

);

SetDefaultMaxproductions(

);

IsSetMinnoenzyme(

)

;

CanGetMinnoenzyme(

)

;

ResetMinnoenzyme(

);

SetDefaultMinnoenzyme(

);

IsSetMaxnoenzyme(

)

;

CanGetMaxnoenzyme(

)

;

ResetMaxnoenzyme(

);

SetDefaultMaxnoenzyme(

);

IsSetExactmass(

)

;

CanGetExactmass(

)

;

ResetExactmass(

);

IsSetSettingid(

)

;

CanGetSettingid(

)

;

ResetSettingid(

);

IsSetIterativesettings(

)

;

CanGetIterativesettings(

)

;

ResetIterativesettings(

);

IsSetPrecursorcull(

)

;

CanGetPrecursorcull(

)

;

ResetPrecursorcull(

);

IsSetInfiles(

)

;

CanGetInfiles(

)

;

ResetInfiles(

);

& GetInfiles(

)

;

IsSetOutfiles(

)

;

CanGetOutfiles(

)

;

ResetOutfiles(

);

& GetOutfiles(

)

;

IsSetNocorrelationscore(

)

;

CanGetNocorrelationscore(

)

;

ResetNocorrelationscore(

);

IsSetProbfollowingion(

)

;

CanGetProbfollowingion(

)

;

ResetProbfollowingion(

);

IsSetNmethionine(

)

;

CanGetNmethionine(

)

;

ResetNmethionine(

);

IsSetAutomassadjust(

)

;

CanGetAutomassadjust(

)

;

ResetAutomassadjust(

);

IsSetLomasscutoff(

)

;

CanGetLomasscutoff(

)

;

ResetLomasscutoff(

);

IsSetLibsearchsettings(

)

;

CanGetLibsearchsettings(

)

;

ResetLibsearchsettings(

);

IsSetNoprolineions(

)

;

CanGetNoprolineions(

)

;

ResetNoprolineions(

);

IsSetReversesearch(

)

;

CanGetReversesearch(

)

;

ResetReversesearch(

);

IsSetOthersettings(

)

;

CanGetOthersettings(

)

;

ResetOthersettings(

);

IsSetNumisotopes(

)

;

CanGetNumisotopes(

)

;

ResetNumisotopes(

);

IsSetPepppm(

)

;

CanGetPepppm(

)

;

ResetPepppm(

);

GetPepppm(

)

;

IsSetMsmsppm(

)

;

CanGetMsmsppm(

)

;

ResetMsmsppm(

);

GetMsmsppm(

)

;

IsSetReportedhitcount(

)

;

CanGetReportedhitcount(

)

;

ResetReportedhitcount(

);

Reset(

);

= std::forward<CMSSearchSettings_Base::TDb>(

);

User-defined methods of the data storage class.

CMSIterativeSettings –.

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

Base class for all serializable objects.

static char UnassignedByte(void)

void ThrowUnassigned(TMemberIndex index) const

static string UnassignedString(void)

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_OMSSA_EXPORT

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.

DECLARE_INTERNAL_TYPE_INFO()

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.

int m_Precursorsearchtype

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.

list< int > TNoprolineions

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.

list< int > m_Noprolineions

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.

double m_Probfollowingion

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.

list< int > m_Ionstosearch

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.

list< int > TIonstosearch

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.

const GenericPointer< typename T::ValueType > T2 value

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