OpenMS  3.0.0
DIAHelper.h File Reference
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Namespaces

 OpenMS
 Main OpenMS namespace.
 
 OpenMS::DIAHelpers
 

Functions

bool integrateWindow (const OpenSwath::SpectrumPtr spectrum, double mz_start, double mz_end, double &mz, double &intensity, bool centroided=false)
 Helper functions for the DIA scoring of OpenSWATH. More...
 
void integrateWindows (const OpenSwath::SpectrumPtr spectrum, const std::vector< double > &windows_center, double width, std::vector< double > &integrated_windows_intensity, std::vector< double > &integrated_windows_mz, bool remove_zero=false)
 Integrate intensities in a spectrum from start to end. More...
 
void integrateDriftSpectrum (OpenSwath::SpectrumPtr spectrum, double mz_start, double mz_end, double &im, double &intensity, double drift_start, double drift_end)
 Integrate intensity in an ion mobility spectrum from start to end. More...
 
void adjustExtractionWindow (double &right, double &left, const double &mz_extract_window, const bool &mz_extraction_ppm)
 Adjust left/right window based on window and whether its ppm or not. More...
 
void getBYSeries (const AASequence &a, std::vector< double > &bseries, std::vector< double > &yseries, TheoreticalSpectrumGenerator const *g, int charge=1)
 compute the b and y series masses for a given AASequence More...
 
void getTheorMasses (const AASequence &a, std::vector< double > &masses, TheoreticalSpectrumGenerator const *g, int charge=1)
 for SWATH – get the theoretical b and y series masses for a sequence More...
 
void getAveragineIsotopeDistribution (const double product_mz, std::vector< std::pair< double, double > > &isotopes_spec, const int charge=1, const int nr_isotopes=4, const double mannmass=1.00048)
 get averagine distribution given mass More...
 
void simulateSpectrumFromAASequence (const AASequence &aa, std::vector< double > &first_isotope_masses, std::vector< std::pair< double, double > > &isotope_masses, TheoreticalSpectrumGenerator const *g, int charge=1)
 simulate spectrum from AASequence More...
 
void modifyMassesByCharge (const std::vector< std::pair< double, double > > &masses, std::vector< std::pair< double, double > > &modmass, int charge=1)
 modify masses by charge More...
 
void addPreisotopeWeights (const std::vector< double > &first_isotope_masses, std::vector< std::pair< double, double > > &isotope_spec, UInt nr_peaks=2, double pre_isotope_peaks_weight=-0.5, double mannmass=1.000482, int charge=1)
 add (potentially negative) pre-isotope weights to spectrum More...
 
void addPreisotopeWeights (double mz, std::vector< std::pair< double, double > > &isotope_spec, UInt nr_peaks=2, double pre_isotope_peaks_weight=-0.5, double mannmass=1.000482, int charge=1)
 add negative pre-isotope weights to spectrum More...
 
void addIsotopes2Spec (const std::vector< std::pair< double, double > > &spec, std::vector< std::pair< double, double > > &isotope_masses, Size nr_isotopes, int charge=1)
 
void addSinglePeakIsotopes2Spec (double mz, double ity, std::vector< std::pair< double, double > > &isotope_masses, Size nr_isotopes, int charge)
 
void sortByFirst (std::vector< std::pair< double, double > > &tmp)
 sorts vector of pairs by first More...
 
void extractFirst (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
 extract first from vector of pairs More...
 
void extractSecond (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
 extract second from vector of pairs More...