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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/MSSearchSettings_8cpp_source.html below:

NCBI C++ ToolKit: src/objects/omssa/MSSearchSettings.cpp Source File

67 Error

.push_back(

"Invalid precursor search type"

);

72 Error

.push_back(

"Precursor search type missing"

);

78 Error

.push_back(

"Invalid Product search type"

);

83 Error

.push_back(

"Product search type missing"

);

89

TNoprolineions::const_iterator

;

92 Error

.push_back(

"Unknown proline rule ion series"

);

99

TIonstosearch::const_iterator

;

102 Error

.push_back(

"Unknown search ion"

);

107 Error

.push_back(

"Ion search type missing"

);

114 Error

.push_back(

"Precursor mass tolerance less than 0"

);

119 Error

.push_back(

"Precursor mass tolerance missing"

);

126 Error

.push_back(

"Product mass tolerance less than 0"

);

131 Error

.push_back(

"Product mass tolerance missing"

);

137 Error

.push_back(

"Exact Mass threshold less than 0"

);

142 Error

.push_back(

"Exact Mass threshold missing"

);

150 Error

.push_back(

"Precursor mass tolerance charge dependence setting invalid"

);

155 Error

.push_back(

"Precursor mass tolerance charge dependence missing"

);

162 Error

.push_back(

"Low cut value out of range"

);

167 Error

.push_back(

"Low cut value missing"

);

174 Error

.push_back(

"Hi cut value out of range"

);

179 Error

.push_back(

"Hi cut value missing"

);

186 Error

.push_back(

"Lo cut exceeds Hi cut value"

);

190 Error

.push_back(

"Cut increment too small"

);

197 Error

.push_back(

"Cut increment less than 0"

);

202 Error

.push_back(

"Cut increment missing"

);

209 Error

.push_back(

"Single win size less than 0"

);

214 Error

.push_back(

"Single win size missing"

);

221 Error

.push_back(

"Double win size less than 0"

);

226 Error

.push_back(

"Double win size missing"

);

233 Error

.push_back(

"Single num less than 0"

);

238 Error

.push_back(

"Single num missing"

);

245 Error

.push_back(

"Double num less than 0"

);

250 Error

.push_back(

"Double num missing"

);

256

TFixed::const_iterator

;

259 Error

.push_back(

"Unknown fixed mod"

);

266

TVariable::const_iterator

;

269 Error

.push_back(

"Unknown variable mod"

);

277 Error

.push_back(

"Unknown enzyme"

);

282 Error

.push_back(

"Enzyme missing"

);

289 Error

.push_back(

"Invalid missed cleavage value"

);

294 Error

.push_back(

"Missed cleavage value missing"

);

301 Error

.push_back(

"Invalid hit list length"

);

306 Error

.push_back(

"Hit list length missing"

);

312 if

(

GetDb

().empty()) {

313 Error

.push_back(

"Empty BLAST library name"

);

318 Error

.push_back(

"BLAST library name missing"

);

325 Error

.push_back(

"Less than one top hit needed"

);

330 Error

.push_back(

"Missing top hit value"

);

337 Error

.push_back(

"Less than one match need for hit"

);

342 Error

.push_back(

"Missing minimum number of matches"

);

349 Error

.push_back(

"Less than two peaks required in input spectra"

);

354 Error

.push_back(

"Missing minimum peaks value for valid spectra"

);

361 Error

.push_back(

"m/z scaling value less than one"

);

366 Error

.push_back(

"missing m/z scaling value"

);

373

TTaxids::const_iterator

;

376 Error

.push_back(

"taxid < 0"

);

386 Error

.push_back(

"unknown iterative search setting"

);

391 Error

.push_back(

"threshold to iteratively search a spectrum again < 0"

);

395 Error

.push_back(

"threshold to include a sequence in the iterative search < 0"

);

399 Error

.push_back(

"threshold to replace a hit < 0"

);

414 Error

.push_back(

"charge handling option is missing"

);

420 Error

.push_back(

"invalid min/max charge value"

);

424 Error

.push_back(

"consider multiply charge product ions value out of range"

);

429 Error

.push_back(

"invalid calc charge setting"

);

434 Error

.push_back(

"invalid 1+ charge calc setting"

);

439 Error

.push_back(

"invalid 1+ charge determination threshold"

);

444 Error

.push_back(

"invalid maximum product ion charge"

);

449 Error

.push_back(

"invalid charge sign"

);

457 Error

.push_back(

"maximum number of modifications is negative"

);

462 Error

.push_back(

"unable to get maximum number of modifications"

);

468 Error

.push_back(

"pseudocount value less than zero"

);

473 Error

.push_back(

"unable to get pseudocount"

);

479 Error

.push_back(

"invalid setting for first forward ion search"

);

484 Error

.push_back(

"unable to get setting for first forward ion search"

);

490 Error

.push_back(

"invalid setting for c-term ion search"

);

495 Error

.push_back(

"unable to get setting for c-term ion search"

);

501 Error

.push_back(

"maximum number of product ions < 0"

);

506 Error

.push_back(

"unable to get maximum number of product ions"

);

512 Error

.push_back(

"minimum size of peptide in noenzyme search < 1"

);

517 Error

.push_back(

"maximum size of peptide in noenzyme search exceeds minimum peptide size"

);

522 Error

.push_back(

"unable to get maximum size of peptide in noenzyme search"

);

527 Error

.push_back(

"unable to get minimum size of peptide in noenzyme search"

);

534 Error

.push_back(

"exact mass threshold set to < 0"

);

539 Error

.push_back(

"unable to get exact mass threshold"

);

545 Error

.push_back(

"precursor cull setting < 0 or > 1"

);

550 Error

.push_back(

"unable to precursor cull setting"

);

556 Error

.push_back(

"unknown correlation score setting"

);

561 Error

.push_back(

"unable to get correlation score setting"

);

567 Error

.push_back(

"probability of consecutive ions is < 0 or > 1"

);

572 Error

.push_back(

"unable to get probability of consecutive ions"

);

578 Error

.push_back(

"automatic mass tolerance adjustment fraction is < 0 or > 1"

);

583 Error

.push_back(

"unable to get automatic mass tolerance adjustment fraction "

);

589 Error

.push_back(

"number of isotopes < 0 or > 10"

);

596 Error

.push_back(

"number of hits to report < 0"

);

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

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

void Error(CExceptionArgs_Base &args)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TNegative GetNegative(void) const

Get the Negative member data.

TSearchb1 GetSearchb1(void) const

Get the Searchb1 member data.

const TVariable & GetVariable(void) const

Get the Variable member data.

bool CanGetNumisotopes(void) const

Check if it is safe to call GetNumisotopes method.

TTophitnum GetTophitnum(void) const

Get the Tophitnum member data.

TReportedhitcount GetReportedhitcount(void) const

Get the Reportedhitcount member data.

bool IsSetTaxids(void) const

taxa to limit search Check if a value has been assigned to Taxids data member.

bool CanGetPeptol(void) const

Check if it is safe to call GetPeptol method.

TPseudocount GetPseudocount(void) const

Get the Pseudocount member data.

TPeptol GetPeptol(void) const

Get the Peptol member data.

TReplacethresh GetReplacethresh(void) const

Get the Replacethresh member data.

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.

bool CanGetNoprolineions(void) const

Check if it is safe to call GetNoprolineions method.

const TFixed & GetFixed(void) const

Get the Fixed member data.

TScale GetScale(void) const

Get the Scale member data.

const TNoprolineions & GetNoprolineions(void) const

Get the Noprolineions member data.

bool CanGetSinglewin(void) const

Check if it is safe to call GetSinglewin method.

TMincharge GetMincharge(void) const

Get the Mincharge member 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.

bool CanGetFixed(void) const

Check if it is safe to call GetFixed method.

TMinspectra GetMinspectra(void) const

Get the Minspectra member data.

const TIonstosearch & GetIonstosearch(void) const

Get the Ionstosearch member data.

bool CanGetCalcplusone(void) const

Check if it is safe to call GetCalcplusone method.

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 CanGetMissedcleave(void) const

Check if it is safe to call GetMissedcleave method.

TMaxcharge GetMaxcharge(void) const

Get the Maxcharge member data.

bool CanGetSearchb1(void) const

Check if it is safe to call GetSearchb1 method.

TProductsearchtype GetProductsearchtype(void) const

Get the Productsearchtype member data.

TDoublewin GetDoublewin(void) const

Get the Doublewin member data.

const TChargehandling & GetChargehandling(void) const

Get the Chargehandling member data.

const TDb & GetDb(void) const

Get the Db member data.

bool CanGetHitlistlen(void) const

Check if it is safe to call GetHitlistlen method.

bool CanGetPlusone(void) const

Check if it is safe to call GetPlusone method.

bool CanGetVariable(void) const

Check if it is safe to call GetVariable method.

bool CanGetMincharge(void) const

Check if it is safe to call GetMincharge method.

bool CanGetSubsetthresh(void) const

Check if it is safe to call GetSubsetthresh method.

TPlusone GetPlusone(void) const

Get the Plusone member data.

TMissedcleave GetMissedcleave(void) const

Get the Missedcleave member data.

bool CanGetIonstosearch(void) const

Check if it is safe to call GetIonstosearch method.

TConsidermult GetConsidermult(void) const

Get the Considermult member data.

bool CanGetResearchthresh(void) const

Check if it is safe to call GetResearchthresh method.

bool CanGetDoublenum(void) const

Check if it is safe to call GetDoublenum method.

TDoublenum GetDoublenum(void) const

Get the Doublenum member data.

bool CanGetReplacethresh(void) const

Check if it is safe to call GetReplacethresh method.

bool CanGetConsidermult(void) const

Check if it is safe to call GetConsidermult method.

bool CanGetProductsearchtype(void) const

Check if it is safe to call GetProductsearchtype method.

TNocorrelationscore GetNocorrelationscore(void) const

Get the Nocorrelationscore member data.

bool CanGetCutlo(void) const

Check if it is safe to call GetCutlo method.

TSubsetthresh GetSubsetthresh(void) const

Get the Subsetthresh 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.

THitlistlen GetHitlistlen(void) const

Get the Hitlistlen member data.

TCuthi GetCuthi(void) const

Get the Cuthi member data.

bool CanGetSearchctermproduct(void) const

Check if it is safe to call GetSearchctermproduct method.

TMaxproductions GetMaxproductions(void) const

Get the Maxproductions member data.

bool CanGetCalccharge(void) const

Check if it is safe to call GetCalccharge method.

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.

bool CanGetMaxproductions(void) const

Check if it is safe to call GetMaxproductions method.

TCalccharge GetCalccharge(void) const

Get the Calccharge member data.

TProbfollowingion GetProbfollowingion(void) const

Get the Probfollowingion member data.

bool CanGetMinspectra(void) const

Check if it is safe to call GetMinspectra method.

bool CanGetPseudocount(void) const

Check if it is safe to call GetPseudocount method.

TMsmstol GetMsmstol(void) const

Get the Msmstol member data.

bool CanGetNocorrelationscore(void) const

Check if it is safe to call GetNocorrelationscore method.

TResearchthresh GetResearchthresh(void) const

Get the Researchthresh member data.

TExactmass GetExactmass(void) const

Get the Exactmass member data.

TCalcplusone GetCalcplusone(void) const

Get the Calcplusone member data.

bool CanGetDb(void) const

Check if it is safe to call GetDb method.

TCutlo GetCutlo(void) const

Get the Cutlo member data.

TSearchctermproduct GetSearchctermproduct(void) const

Get the Searchctermproduct member data.

TMinhit GetMinhit(void) const

Get the Minhit member data.

bool CanGetPrecursorsearchtype(void) const

Check if it is safe to call GetPrecursorsearchtype method.

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.

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.

bool CanGetExactmass(void) const

Check if it is safe to call GetExactmass method.

const TIterativesettings & GetIterativesettings(void) const

Get the Iterativesettings member data.

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.

TEnzyme GetEnzyme(void) const

Get the Enzyme member data.

const TTaxids & GetTaxids(void) const

Get the Taxids member data.

bool CanGetCutinc(void) const

Check if it is safe to call GetCutinc method.

TNumisotopes GetNumisotopes(void) const

Get the Numisotopes member data.

TSinglenum GetSinglenum(void) const

Get the Singlenum member data.

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 CanGetMaxproductcharge(void) const

Check if it is safe to call GetMaxproductcharge method.

bool IsSetIterativesettings(void) const

iterative search settings Check if a value has been assigned to Iterativesettings data member.

TMaxproductcharge GetMaxproductcharge(void) const

Get the Maxproductcharge member data.

TMaxmods GetMaxmods(void) const

Get the Maxmods member data.

TSinglewin GetSinglewin(void) const

Get the Singlewin member data.

bool CanGetMaxcharge(void) const

Check if it is safe to call GetMaxcharge method.

TCutinc GetCutinc(void) const

Get the Cutinc member data.

@ eMSZdependence_independent

mass tol. invariant with charge

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