OpenMS
OPXLSpectrumProcessingAlgorithms.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Eugen Netz $
6 // $Authors: Eugen Netz $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/CONCEPT/Types.h>
13 #include <OpenMS/KERNEL/Peak1D.h>
16 #include <numeric>
17 #include <vector>
18 
19 namespace OpenMS
20 {
22  {
23  public:
24 
31  static PeakSpectrum mergeAnnotatedSpectra(PeakSpectrum & first_spectrum, PeakSpectrum & second_spectrum);
32 
50  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);
51 
65  std::vector<std::pair<Size, Size> > & alignment, double fragment_mass_tolerance,
66  bool fragment_mass_tolerance_unit_ppm,
67  const PeakSpectrum& theo_spectrum,
68  const PeakSpectrum& exp_spectrum,
69  const DataArrays::IntegerDataArray& theo_charges,
70  const DataArrays::IntegerDataArray& exp_charges,
71  DataArrays::FloatDataArray& ppm_error_array,
72  double intensity_cutoff = 0.0);
73 
87  std::vector<std::pair<Size, Size> > & alignment,
88  double fragment_mass_tolerance,
89  bool fragment_mass_tolerance_unit_ppm,
90  const std::vector< SimpleTSGXLMS::SimplePeak >& theo_spectrum,
91  const PeakSpectrum& exp_spectrum,
92  const DataArrays::IntegerDataArray& exp_charges);
93  };
94 
95 }
Float data array class.
Definition: DataArrays.h:22
Integer data array class.
Definition: DataArrays.h:29
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:46
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
Definition: OPXLSpectrumProcessingAlgorithms.h:22
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)
Preprocesses spectra.
static PeakSpectrum mergeAnnotatedSpectra(PeakSpectrum &first_spectrum, PeakSpectrum &second_spectrum)
Merges two spectra into one while correctly considering metainfo in DataArrays.
static void getSpectrumAlignmentFastCharge(std::vector< std::pair< Size, Size > > &alignment, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &theo_spectrum, const PeakSpectrum &exp_spectrum, const DataArrays::IntegerDataArray &theo_charges, const DataArrays::IntegerDataArray &exp_charges, DataArrays::FloatDataArray &ppm_error_array, double intensity_cutoff=0.0)
Computes a spectrum alignment while considering fragment charges stored in a IntegerDataArray and a c...
static void getSpectrumAlignmentSimple(std::vector< std::pair< Size, Size > > &alignment, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const std::vector< SimpleTSGXLMS::SimplePeak > &theo_spectrum, const PeakSpectrum &exp_spectrum, const DataArrays::IntegerDataArray &exp_charges)
Computes a spectrum alignment while considering fragment charges. Uses TSGXLMS::SimplePeak for the th...
int Int
Signed integer type.
Definition: Types.h:76
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:101
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22