| OpenMS 2.5.0

MzXMLFile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/FORMAT/XMLFile.h>
39 #include <OpenMS/CONCEPT/ProgressLogger.h>
40 #include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
41 #include <OpenMS/INTERFACES/IMSDataConsumer.h>
42
43 namespace OpenMS
44 {
45 class String;
46
52 class OPENMS_DLLAPI MzXMLFile :
53 public Internal::XMLFile,
54 public ProgressLogger
55 {
56 typedef PeakMap MapType;
57
58 public:
60 MzXMLFile();
62 ~MzXMLFile() override;
63
65 PeakFileOptions & getOptions();
66
68 const PeakFileOptions & getOptions() const;
69
71 void setOptions(const PeakFileOptions &);
72
81 void load(const String & filename, MapType & map);
82
90 void store(const String & filename, const MapType & map) const;
91
110 void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count = false);
111
126 void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, MapType& map, bool skip_full_count = false);
127
128 protected:
129
131 void transformFirstPass_(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count);
132
133 private:
134
135 PeakFileOptions options_;
136 };
137 } // namespace OpenMS
138
OpenMS::String
A more convenient string class.
Definition: String.h:58
XMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MzXMLFile::options_
PeakFileOptions options_
Definition: MzXMLFile.h:135
StandardTypes.h
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
ProgressLogger.h
IMSDataConsumer.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
PeakFileOptions.h
OpenMS::MzXMLFile
File adapter for MzXML 3.1 files.
Definition: MzXMLFile.h:52
OpenMS::MzXMLFile::MapType
PeakMap MapType
Definition: MzXMLFile.h:56