OpenMS  3.0.0
DIAHelper.h
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34 
35 #pragma once
36 
39 
40 #include <vector>
41 
42 namespace OpenMS
43 {
44  class TheoreticalSpectrumGenerator;
45  namespace DIAHelpers
46  {
47 
51 
64  OPENMS_DLLAPI bool integrateWindow(const OpenSwath::SpectrumPtr spectrum, double mz_start,
65  double mz_end, double& mz, double& intensity, bool centroided = false);
66 
70  OPENMS_DLLAPI void integrateWindows(const OpenSwath::SpectrumPtr spectrum,
71  const std::vector<double>& windows_center,
72  double width,
73  std::vector<double>& integrated_windows_intensity,
74  std::vector<double>& integrated_windows_mz,
75  bool remove_zero = false);
76 
86  OPENMS_DLLAPI void integrateDriftSpectrum(OpenSwath::SpectrumPtr spectrum,
87  double mz_start,
88  double mz_end,
89  double & im,
90  double & intensity,
91  double drift_start,
92  double drift_end);
93 
97  OPENMS_DLLAPI void adjustExtractionWindow(double& right, double& left, const double& mz_extract_window, const bool& mz_extraction_ppm);
98 
100  OPENMS_DLLAPI void getBYSeries(const AASequence& a,
101  std::vector<double>& bseries,
102  std::vector<double>& yseries,
104  int charge = 1);
105 
107  OPENMS_DLLAPI void getTheorMasses(const AASequence& a,
108  std::vector<double>& masses,
110  int charge = 1);
111 
113  OPENMS_DLLAPI void getAveragineIsotopeDistribution(const double product_mz,
114  std::vector<std::pair<double, double> >& isotopes_spec,
115  const int charge = 1,
116  const int nr_isotopes = 4,
117  const double mannmass = 1.00048);
118 
120  OPENMS_DLLAPI void simulateSpectrumFromAASequence(const AASequence& aa,
121  std::vector<double>& first_isotope_masses, //[out]
122  std::vector<std::pair<double, double> >& isotope_masses, //[out]
124  int charge = 1);
125 
127  OPENMS_DLLAPI void modifyMassesByCharge(const std::vector<std::pair<double, double> >& masses,
128  std::vector<std::pair<double, double> >& modmass,
129  int charge = 1);
130 
132  OPENMS_DLLAPI void addPreisotopeWeights(const std::vector<double>& first_isotope_masses,
133  std::vector<std::pair<double, double> >& isotope_spec, // output
134  UInt nr_peaks = 2, //nr of pre-isotope peaks
135  double pre_isotope_peaks_weight = -0.5, // weight of pre-isotope peaks
136  double mannmass = 1.000482, //
137  int charge = 1);
138 
140  OPENMS_DLLAPI void addPreisotopeWeights(double mz,
141  std::vector<std::pair<double, double> >& isotope_spec, // output
142  UInt nr_peaks = 2, //nr of pre-isotope peaks
143  double pre_isotope_peaks_weight = -0.5, // weight of pre-isotope peaks
144  double mannmass = 1.000482, //
145  int charge = 1);
146 
149  OPENMS_DLLAPI void addIsotopes2Spec(const std::vector<std::pair<double, double> >& spec,
150  std::vector<std::pair<double, double> >& isotope_masses, //[out]
151  Size nr_isotopes, int charge = 1);
152 
155  OPENMS_DLLAPI void addSinglePeakIsotopes2Spec(double mz, double ity,
156  std::vector<std::pair<double, double> >& isotope_masses, //[out]
157  Size nr_isotopes, int charge);
158 
160  OPENMS_DLLAPI void sortByFirst(std::vector<std::pair<double, double> >& tmp);
162  OPENMS_DLLAPI void extractFirst(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
164  OPENMS_DLLAPI void extractSecond(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
165 
167  }
168 }
169 
OpenMS::DIAHelpers::getAveragineIsotopeDistribution
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
OpenMS::DIAHelpers::integrateWindow
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.
OpenMS::DIAHelpers::getTheorMasses
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
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
DataStructures.h
OpenMS::DIAHelpers::extractSecond
void extractSecond(const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
extract second from vector of pairs
OpenMS::DIAHelpers::addIsotopes2Spec
void addIsotopes2Spec(const std::vector< std::pair< double, double > > &spec, std::vector< std::pair< double, double > > &isotope_masses, Size nr_isotopes, int charge=1)
OpenMS::DIAHelpers::modifyMassesByCharge
void modifyMassesByCharge(const std::vector< std::pair< double, double > > &masses, std::vector< std::pair< double, double > > &modmass, int charge=1)
modify masses by charge
OpenMS::DIAHelpers::integrateDriftSpectrum
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.
OpenMS::DIAHelpers::extractFirst
void extractFirst(const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
extract first from vector of pairs
OpenMS::DIAHelpers::integrateWindows
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.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::DIAHelpers::getBYSeries
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
OpenMS::DIAHelpers::adjustExtractionWindow
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.
OpenMS::DIAHelpers::addSinglePeakIsotopes2Spec
void addSinglePeakIsotopes2Spec(double mz, double ity, std::vector< std::pair< double, double > > &isotope_masses, Size nr_isotopes, int charge)
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::TheoreticalSpectrumGenerator
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:68
AASequence.h
OpenMS::DIAHelpers::simulateSpectrumFromAASequence
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
OpenSwath::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:296
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::DIAHelpers::addPreisotopeWeights
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
OpenMS::DIAHelpers::sortByFirst
void sortByFirst(std::vector< std::pair< double, double > > &tmp)
sorts vector of pairs by first