| OpenMS 2.5.0

MascotXMLFile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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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: Timo Sachsenberg $
32 // $Authors: Nico Pfeifer $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CHEMISTRY/AASequence.h>
38 #include <OpenMS/FORMAT/XMLFile.h>
39 #include <OpenMS/FORMAT/HANDLERS/MascotXMLHandler.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41 #include <OpenMS/KERNEL/StandardTypes.h>
42 #include <OpenMS/METADATA/PeptideIdentification.h>
43
44
45 namespace OpenMS
46 {
47 class ProteinIdentification;
48
57 class OPENMS_DLLAPI MascotXMLFile :
58 public Internal::XMLFile
59 {
60 public:
61
63 MascotXMLFile();
64
76 void load(const String& filename,
77 ProteinIdentification& protein_identification,
78 std::vector<PeptideIdentification>& id_data,
79 const SpectrumMetaDataLookup& lookup);
80
93 void load(const String& filename,
94 ProteinIdentification& protein_identification,
95 std::vector<PeptideIdentification>& id_data,
96 std::map<String, std::vector<AASequence> >& peptides,
97 const SpectrumMetaDataLookup& lookup);
98
106 static void initializeLookup(SpectrumMetaDataLookup& lookup, const PeakMap& experiment, const String& scan_regex = "");
107
108 };
109
110 } // namespace OpenMS
111
OpenMS::String
A more convenient string class.
Definition: String.h:58
XMLFile.h
AASequence.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
StandardTypes.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::MascotXMLFile
Used to load Mascot XML files.
Definition: MascotXMLFile.h:57
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SpectrumMetaDataLookup
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:142
MSExperiment.h
MascotXMLHandler.h