| OpenMS 2.5.0

DataAccessHelper.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <fstream>
38
39 #include <boost/numeric/conversion/cast.hpp>
40
41 #include <OpenMS/KERNEL/MSSpectrum.h>
42 #include <OpenMS/KERNEL/MSChromatogram.h>
43 #include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
44 #include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
45 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
46
47 namespace OpenMS
48 {
53 class OPENMS_DLLAPI OpenSwathDataAccessHelper
54 {
55 public:
57 static void convertToOpenMSSpectrum(const OpenSwath::SpectrumPtr sptr, OpenMS::MSSpectrum & spectrum);
58
60 static OpenSwath::SpectrumPtr convertToSpectrumPtr(const OpenMS::MSSpectrum & spectrum);
61
63 static void convertToOpenMSChromatogram(const OpenSwath::ChromatogramPtr cptr, OpenMS::MSChromatogram & chromatogram);
64
66 static OpenSwath::ChromatogramPtr convertToChromatogramPtr(const OpenMS::MSChromatogram & chromatogram);
67
68 static void convertToOpenMSChromatogramFilter(OpenMS::MSChromatogram & chromatogram,
69 const OpenSwath::ChromatogramPtr cptr,
70 double rt_min,
71 double rt_max);
72
74 static void convertTargetedExp(const OpenMS::TargetedExperiment & transition_exp_, OpenSwath::LightTargetedExperiment & transition_exp);
75
77 static void convertTargetedCompound(const TargetedExperiment::Peptide& pep, OpenSwath::LightCompound& comp);
78
80 static void convertTargetedCompound(const TargetedExperiment::Compound& compound, OpenSwath::LightCompound& comp);
81
83 static void convertPeptideToAASequence(const OpenSwath::LightCompound & peptide, AASequence & aa_sequence);
84
85 };
86
87 } //end namespace OpenMS
88
89
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:54
TargetedExperiment.h
OpenSwath::LightCompound
Definition: TransitionExperiment.h:149
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::TargetedExperimentHelper::Compound
Represents a compound (small molecule)
Definition: TargetedExperimentHelper.h:333
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSSpectrum.h
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:207
OpenMS::OpenSwathDataAccessHelper
Several helpers to convert OpenMS datastructures to structures that implement the OpenSWATH interface...
Definition: DataAccessHelper.h:53
OpenSwath::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:292
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
MSChromatogram.h
TransitionExperiment.h
ISpectrumAccess.h
OpenSwath::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172