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SimpleSearchEngine Class Reference
Inheritance diagram for SimpleSearchEngine:
TOPPBase

Classes

class  HasInvalidPeptideLengthPredicate
 

Public Member Functions

 SimpleSearchEngine ()
 

Protected Member Functions

void registerOptionsAndFlags_ ()
 
vector< ResidueModification > getModifications_ (StringList modNames)
 
double logfactorial (UInt x)
 
double computeHyperScore (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const MSSpectrum< Peak1D > &exp_spectrum, const MSSpectrum< RichPeak1D > &theo_spectrum)
 
void preprocessSpectra_ (PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm)
 
void postProcessHits_ (const PeakMap &exp, const vector< vector< PeptideHit > > &peptide_hits, vector< ProteinIdentification > &protein_ids, vector< PeptideIdentification > &peptide_ids, Size top_hits)
 
ExitCodes main_ (int, const char **)
 

Static Protected Member Functions

template<typename SpectrumType >
static void deisotopeAndSingleChargeMSSpectrum (SpectrumType &in, Int min_charge, Int max_charge, double fragment_tolerance, bool fragment_unit_ppm, bool keep_only_deisotoped=false, Size min_isopeaks=3, Size max_isopeaks=10, bool make_single_charged=true)
 

Constructor & Destructor Documentation

SimpleSearchEngine ( )
inline

Member Function Documentation

double computeHyperScore ( double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_unit_ppm,
const MSSpectrum< Peak1D > &  exp_spectrum,
const MSSpectrum< RichPeak1D > &  theo_spectrum 
)
inlineprotected
static void deisotopeAndSingleChargeMSSpectrum ( SpectrumType &  in,
Int  min_charge,
Int  max_charge,
double  fragment_tolerance,
bool  fragment_unit_ppm,
bool  keep_only_deisotoped = false,
Size  min_isopeaks = 3,
Size  max_isopeaks = 10,
bool  make_single_charged = true 
)
inlinestaticprotected
vector<ResidueModification> getModifications_ ( StringList  modNames)
inlineprotected
double logfactorial ( UInt  x)
inlineprotected
ExitCodes main_ ( int  ,
const char **   
)
inlineprotected

References NUMBER_OF_THREADS.

void postProcessHits_ ( const PeakMap &  exp,
const vector< vector< PeptideHit > > &  peptide_hits,
vector< ProteinIdentification > &  protein_ids,
vector< PeptideIdentification > &  peptide_ids,
Size  top_hits 
)
inlineprotected
void preprocessSpectra_ ( PeakMap &  exp,
double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_unit_ppm 
)
inlineprotected
void registerOptionsAndFlags_ ( )
inlineprotected

OpenMS / TOPP release 2.0.0 Documentation generated on Sun Jul 31 2016 20:57:14 using doxygen 1.8.11