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);
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
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:108
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
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 pre-isotope 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