35 #ifndef OPENMS_ANALYSIS_OPENSWATH_DIAHELPER_H 
   36 #define OPENMS_ANALYSIS_OPENSWATH_DIAHELPER_H 
   51                      std::vector<double>& bseries, std::vector<double>& yseries, 
UInt charge = 1u);
 
   58                                          std::vector<std::pair<double, double> >& isotopesSpec, 
 
   61                                          double mannmass = 1.00048);
 
   65                                         std::vector<double>& firstIsotopeMasses, 
 
   66                                         std::vector<std::pair<double, double> >& isotopeMasses, 
 
   71                               std::vector<std::pair<double, double> >& modmass, 
 
   76                               std::vector<std::pair<double, double> >& isotopeSpec, 
 
   78                               double preIsotopePeaksWeight = -0.5, 
 
   79                               double mannmass = 1.000482, 
 
   83     OPENMS_DLLAPI 
void addIsotopes2Spec(
const std::vector<std::pair<double, double> >& spec,
 
   84                           std::vector<std::pair<double, double> >& isotopeMasses, 
 
   88     OPENMS_DLLAPI 
void sortByFirst(std::vector<std::pair<double, double> >& tmp);
 
   90     OPENMS_DLLAPI 
void extractFirst(
const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
 
   92     OPENMS_DLLAPI 
void extractSecond(
const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
 
void extractFirst(const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
extract first from vector of pairs 
Representation of a peptide/protein sequence. 
Definition: AASequence.h:84
void getTheorMasses(AASequence &a, std::vector< double > &masses, UInt charge=1u)
for SWATH – get the theoretical b and y series masses for a sequence 
void modifyMassesByCharge(const std::vector< std::pair< double, double > > &masses, std::vector< std::pair< double, double > > &modmass, double charge=1.)
modify masses by charge 
void getAveragineIsotopeDistribution(double product_mz, std::vector< std::pair< double, double > > &isotopesSpec, double charge=1., int nr_isotopes=4, double mannmass=1.00048)
get averagine distribution given mass 
void sortByFirst(std::vector< std::pair< double, double > > &tmp)
sorts vector of pairs by first 
void addIsotopes2Spec(const std::vector< std::pair< double, double > > &spec, std::vector< std::pair< double, double > > &isotopeMasses, double charge=1.)
given an experimental spectrum add isotope pattern. 
void extractSecond(const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
extract second from vector of pairs 
void addPreisotopeWeights(const std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeSpec, UInt nrpeaks=2, double preIsotopePeaksWeight=-0.5, double mannmass=1.000482, double charge=1.)
add negative preisotope weights to spectrum 
void getBYSeries(AASequence &a, std::vector< double > &bseries, std::vector< double > &yseries, UInt charge=1u)
Helper functions for the DIA scoring of OpenSWATH. 
void simulateSpectrumFromAASequence(AASequence &aa, std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeMasses, double charge=1.)
simulate spectrum from AASequence