| OpenMS 2.5.0

OPXLSpectrumProcessingAlgorithms.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Eugen Netz $
32 // $Authors: Eugen Netz $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/Types.h>
38 #include <OpenMS/KERNEL/StandardTypes.h>
39 #include <OpenMS/KERNEL/Peak1D.h>
40 #include <OpenMS/METADATA/DataArrays.h>
41 #include <OpenMS/CHEMISTRY/SimpleTSGXLMS.h>
42 #include <numeric>
43 #include <vector>
44
45 namespace OpenMS
46 {
47 class OPENMS_DLLAPI OPXLSpectrumProcessingAlgorithms
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 }
SimpleTSGXLMS.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
StandardTypes.h
OpenMS::DataArrays::FloatDataArray
Float data array class.
Definition: DataArrays.h:45
DataArrays.h
Peak1D.h
Types.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::OPXLSpectrumProcessingAlgorithms
Definition: OPXLSpectrumProcessingAlgorithms.h:47
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:52
int
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127