OpenMS  2.4.0
DIAHelper.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Witold Wolski, Hannes Roest $
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34 
35 #pragma once
36 
37 #include <vector>
39 
40 namespace OpenMS
41 {
42  class TheoreticalSpectrumGenerator;
43  namespace DIAHelpers
44  {
48  OPENMS_DLLAPI void getBYSeries(const AASequence& a,
51  std::vector<double>& bseries,
52  std::vector<double>& yseries,
54  UInt charge = 1u);
55 
57  OPENMS_DLLAPI void getTheorMasses(const AASequence& a,
58  std::vector<double>& masses,
60  UInt charge = 1u);
61 
63  OPENMS_DLLAPI void getAveragineIsotopeDistribution(const double product_mz,
64  std::vector<std::pair<double, double> >& isotopesSpec,
65  const double charge = 1.,
66  const int nr_isotopes = 4,
67  const double mannmass = 1.00048);
68 
70  OPENMS_DLLAPI void simulateSpectrumFromAASequence(const AASequence& aa,
71  std::vector<double>& firstIsotopeMasses, //[out]
72  std::vector<std::pair<double, double> >& isotopeMasses, //[out]
74  double charge = 1.);
75 
77  OPENMS_DLLAPI void modifyMassesByCharge(const std::vector<std::pair<double, double> >& masses,
78  std::vector<std::pair<double, double> >& modmass,
79  double charge = 1.);
80 
82  OPENMS_DLLAPI void addPreisotopeWeights(const std::vector<double>& firstIsotopeMasses,
83  std::vector<std::pair<double, double> >& isotopeSpec, // output
84  UInt nrpeaks = 2, //nr of pre-isotope peaks
85  double preIsotopePeaksWeight = -0.5, // weight of pre-isotope peaks
86  double mannmass = 1.000482, //
87  double charge = 1.);
88 
90  OPENMS_DLLAPI void addIsotopes2Spec(const std::vector<std::pair<double, double> >& spec,
91  std::vector<std::pair<double, double> >& isotopeMasses, //[out]
92  double charge = 1.);
93 
95  OPENMS_DLLAPI void sortByFirst(std::vector<std::pair<double, double> >& tmp);
97  OPENMS_DLLAPI void extractFirst(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
99  OPENMS_DLLAPI void extractSecond(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
100 
102  }
103 }
104 
void getBYSeries(const AASequence &a, std::vector< double > &bseries, std::vector< double > &yseries, TheoreticalSpectrumGenerator const *g, UInt charge=1u)
Helper functions for the DIA scoring of OpenSWATH.
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
void extractFirst(const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
extract first from vector of pairs
Generates theoretical spectra with various options.
Definition: TheoreticalSpectrumGenerator.h:63
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
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
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 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
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 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