OpenMS  3.0.0
OPXLSpectrumProcessingAlgorithms.h
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31 // $Maintainer: Eugen Netz $
32 // $Authors: Eugen Netz $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
39 #include <OpenMS/KERNEL/Peak1D.h>
42 #include <numeric>
43 #include <vector>
44 
45 namespace OpenMS
46 {
48  {
49  public:
50 
57  static PeakSpectrum mergeAnnotatedSpectra(PeakSpectrum & first_spectrum, PeakSpectrum & second_spectrum);
58 
76  static PeakMap preprocessSpectra(PeakMap& exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, Size peptide_min_size, Int min_precursor_charge, Int max_precursor_charge, bool deisotope, bool labeled);
77 
90  static void getSpectrumAlignmentFastCharge(
91  std::vector<std::pair<Size, Size> > & alignment, double fragment_mass_tolerance,
92  bool fragment_mass_tolerance_unit_ppm,
93  const PeakSpectrum& theo_spectrum,
94  const PeakSpectrum& exp_spectrum,
95  const DataArrays::IntegerDataArray& theo_charges,
96  const DataArrays::IntegerDataArray& exp_charges,
97  DataArrays::FloatDataArray& ppm_error_array,
98  double intensity_cutoff = 0.0);
99 
112  static void getSpectrumAlignmentSimple(
113  std::vector<std::pair<Size, Size> > & alignment,
114  double fragment_mass_tolerance,
115  bool fragment_mass_tolerance_unit_ppm,
116  const std::vector< SimpleTSGXLMS::SimplePeak >& theo_spectrum,
117  const PeakSpectrum& exp_spectrum,
118  const DataArrays::IntegerDataArray& exp_charges);
119  };
120 
121 }
OpenMS::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:52
DataArrays.h
Types.h
Peak1D.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
SimpleTSGXLMS.h
OpenMS::OPXLSpectrumProcessingAlgorithms
Definition: OPXLSpectrumProcessingAlgorithms.h:47
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::DataArrays::FloatDataArray
Float data array class.
Definition: DataArrays.h:45
StandardTypes.h