OpenMS
DataAccessHelper.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: Hannes Roest $
6 // $Authors: Hannes Roest $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <fstream>
12 
13 #include <boost/numeric/conversion/cast.hpp>
14 
20 
21 namespace OpenMS
22 {
27  class OPENMS_DLLAPI OpenSwathDataAccessHelper
28  {
29 public:
32 
35 
38 
41 
43  const OpenSwath::ChromatogramPtr& cptr,
44  double rt_min,
45  double rt_max);
46 
48  static void convertTargetedExp(const OpenMS::TargetedExperiment & transition_exp_, OpenSwath::LightTargetedExperiment & transition_exp);
49 
52 
55 
57  static void convertPeptideToAASequence(const OpenSwath::LightCompound & peptide, AASequence & aa_sequence);
58 
59  };
60 
61 } //end namespace OpenMS
62 
63 
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
The representation of a chromatogram.
Definition: MSChromatogram.h:31
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interface...
Definition: DataAccessHelper.h:28
static void convertTargetedExp(const OpenMS::TargetedExperiment &transition_exp_, OpenSwath::LightTargetedExperiment &transition_exp)
convert from the OpenMS TargetedExperiment to the LightTargetedExperiment
static void convertToOpenMSChromatogram(const OpenSwath::ChromatogramPtr &cptr, OpenMS::MSChromatogram &chromatogram)
Convert a ChromatogramPtr to an OpenMS Chromatogram.
static void convertPeptideToAASequence(const OpenSwath::LightCompound &peptide, AASequence &aa_sequence)
convert from the LightCompound to an OpenMS AASequence (with correct modifications)
static OpenSwath::SpectrumPtr convertToSpectrumPtr(const OpenMS::MSSpectrum &spectrum)
Convert an OpenMS Spectrum to an SpectrumPtr.
static void convertToOpenMSChromatogramFilter(OpenMS::MSChromatogram &chromatogram, const OpenSwath::ChromatogramPtr &cptr, double rt_min, double rt_max)
static void convertTargetedCompound(const TargetedExperiment::Compound &compound, OpenSwath::LightCompound &comp)
convert from the OpenMS TargetedExperiment Compound to the LightTargetedExperiment Compound
static void convertTargetedCompound(const TargetedExperiment::Peptide &pep, OpenSwath::LightCompound &comp)
convert from the OpenMS TargetedExperiment Peptide to the LightTargetedExperiment Peptide
static OpenSwath::ChromatogramPtr convertToChromatogramPtr(const OpenMS::MSChromatogram &chromatogram)
Convert an OpenMS Chromatogram to an ChromatogramPtr.
static void convertToOpenMSSpectrum(const OpenSwath::SpectrumPtr &sptr, OpenMS::MSSpectrum &spectrum)
Convert a SpectrumPtr to an OpenMS Spectrum.
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:297
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:334
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:39
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:146
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:270
Definition: TransitionExperiment.h:127
Definition: TransitionExperiment.h:185