OpenMS
OPXLSpectrumProcessingAlgorithms.h
Go to the documentation of this file.
1 // Copyright (c) 2002-present, 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 
51  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);
52 
66  std::vector<std::pair<Size, Size> > & alignment, double fragment_mass_tolerance,
67  bool fragment_mass_tolerance_unit_ppm,
68  const PeakSpectrum& theo_spectrum,
69  const PeakSpectrum& exp_spectrum,
70  const DataArrays::IntegerDataArray& theo_charges,
71  const DataArrays::IntegerDataArray& exp_charges,
72  DataArrays::FloatDataArray& ppm_error_array,
73  double intensity_cutoff = 0.0);
74 
85  std::vector<std::pair<Size, Size> > & alignment,
86  double fragment_mass_tolerance,
87  bool fragment_mass_tolerance_unit_ppm,
88  const std::vector< SimpleTSGXLMS::SimplePeak >& theo_spectrum,
89  const PeakSpectrum& exp_spectrum,
90  const DataArrays::IntegerDataArray& exp_charges);
91  };
92 
93 }
Float data array class.
Definition: DataArrays.h:22
Integer data array class.
Definition: DataArrays.h:30
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:45
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:72
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19