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OpenMS
2.6.0
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Go to the documentation of this file.
44 class TheoreticalSpectrumGenerator;
65 double mz_end,
double& mz,
double& intensity,
bool centroided =
false);
71 const std::vector<double>& windows_center,
73 std::vector<double>& integrated_windows_intensity,
74 std::vector<double>& integrated_windows_mz,
75 bool remove_zero =
false);
97 OPENMS_DLLAPI
void adjustExtractionWindow(
double& right,
double& left,
const double& mz_extract_window,
const bool& mz_extraction_ppm);
101 std::vector<double>& bseries,
102 std::vector<double>& yseries,
108 std::vector<double>& masses,
114 std::vector<std::pair<double, double> >& isotopesSpec,
115 const double charge = 1.,
116 const int nr_isotopes = 4,
117 const double mannmass = 1.00048);
121 std::vector<double>& firstIsotopeMasses,
122 std::vector<std::pair<double, double> >& isotopeMasses,
128 std::vector<std::pair<double, double> >& modmass,
133 std::vector<std::pair<double, double> >& isotopeSpec,
135 double preIsotopePeaksWeight = -0.5,
136 double mannmass = 1.000482,
140 OPENMS_DLLAPI
void addIsotopes2Spec(
const std::vector<std::pair<double, double> >& spec,
141 std::vector<std::pair<double, double> >& isotopeMasses,
145 OPENMS_DLLAPI
void sortByFirst(std::vector<std::pair<double, double> >& tmp);
147 OPENMS_DLLAPI
void extractFirst(
const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
149 OPENMS_DLLAPI
void extractSecond(
const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass);
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
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.
void extractSecond(const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
extract second from vector of pairs
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 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.
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 extractFirst(const std::vector< std::pair< double, double > > &peaks, std::vector< double > &mass)
extract first from vector of pairs
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.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
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.
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
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Generates theoretical spectra for peptides with various options.
Definition: TheoreticalSpectrumGenerator.h:68
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 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
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:292
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
void sortByFirst(std::vector< std::pair< double, double > > &tmp)
sorts vector of pairs by first
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