23#ifndef _SPECTRUMLIST_CHARGEFROMISOTOPE_HPP_
24#define _SPECTRUMLIST_CHARGEFROMISOTOPE_HPP_
65using namespace msdata;
74 int parentsBefore = 2,
76 double isolationWindow = 1.25,
77 int defaultChargeMax = 0,
78 int defaultChargeMin = 0);
87 void getParentPeaks(
const SpectrumPtr,
const std::vector <int> &,
const double,
const double,
const double,std::vector< std::vector <double> > &,std::vector< std::vector <double> > &)
const;
double getKLscore(const isotopeChain, const std::vector< double > &, const std::vector< double > &)
SpectrumList implementation that assigns (probable) charge states to tandem mass spectra.
void getParentIndices(const SpectrumPtr, std::vector< int > &) const
SpectrumListPtr instantiatePeakPicker(const std::vector< int > &, const double, const double, const double) const
double defaultIsolationWidth_
void simulateSSE(const int, const int)
SpectrumList_ChargeFromIsotope(const msdata::MSData &msd, int maxCharge=3, int minCharge=1, int parentsBefore=2, int parentsAfter=0, double isolationWindow=1.25, int defaultChargeMax=0, int defaultChargeMin=0)
void simulateTotIntensity(const int)
void getMS1RetentionTimes()
std::vector< int > simulatedIntensityRankSum
void getParentPeaks(const SpectrumPtr, const std::vector< int > &, const double, const double, const double, std::vector< std::vector< double > > &, std::vector< std::vector< double > > &) const
std::vector< double > simulatedSSEs
virtual msdata::SpectrumPtr spectrum(size_t index, bool getBinaryData=true) const
retrieve a spectrum by index
SpectrumListPtr instantiatePeakPicker(const std::vector< int > &) const
std::vector< rtimeMap > MS1retentionTimes
std::vector< double > simulatedKLs
void simulateKL(const double, const int, const int)
Inheritable pass-through implementation for wrapping a SpectrumList.
boost::shared_ptr< SpectrumList > SpectrumListPtr
boost::shared_ptr< Spectrum > SpectrumPtr
std::vector< int > indexList
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
double intensitySumPvalue