| OpenMS 2.5.0

Namespaces
DIAHelper.h File Reference
`#include <OpenMS/CHEMISTRY/AASequence.h>`
`#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>`
`#include <vector>`

Go to the source code of this file.

## 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, UInt charge=1u)
| compute the b and y series masses for a given AASequence More...
void | getTheorMasses (const AASequence &a, std::vector< double > &masses, TheoreticalSpectrumGenerator const *g, UInt charge=1u)
| 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 > > &isotopesSpec, const double 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 > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeMasses, TheoreticalSpectrumGenerator const *g, double charge=1.)
| simulate spectrum from AASequence More...
void | modifyMassesByCharge (const std::vector< std::pair< double, double > > &masses, std::vector< std::pair< double, double > > &modmass, double charge=1.)
| modify masses by charge More...
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 More...
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. More...
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...