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| 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...
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| |
| 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...
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| 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...
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| |
| 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...
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| |
| 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...
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| 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...
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| |
| 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...
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| |
| 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...
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| |
| 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...
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| |
| 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...
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| 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...
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| |
| 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...
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| |
| void | extractFirst (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass) |
| | extract first from vector of pairs More...
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| |
| void | extractSecond (const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass) |
| | extract second from vector of pairs More...
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| |
1.9.1