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| void | getBYSeries (AASequence &a, std::vector< double > &bseries, std::vector< double > &yseries, UInt charge=1u) | 
|  | Helper functions for the DIA scoring of OpenSWATH.  More... 
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| void | getTheorMasses (AASequence &a, std::vector< double > &masses, UInt charge=1u) | 
|  | for SWATH – get the theoretical b and y series masses for a sequence  More... 
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| 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  More... 
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| void | simulateSpectrumFromAASequence (AASequence &aa, std::vector< double > &firstIsotopeMasses, std::vector< std::pair< double, double > > &isotopeMasses, double 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, double charge=1.) | 
|  | modify masses by charge  More... 
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| 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  More... 
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| 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... 
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| 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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