OpenMS  3.0.0
MzXMLFile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
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34 
35 #pragma once
36 
38 #include <OpenMS/FORMAT/XMLFile.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 
136  };
137 } // namespace OpenMS
138 
XMLFile.h
OpenMS::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
IMSDataConsumer.h
OpenMS::MzXMLFile
File adapter for MzXML 3.1 files.
Definition: MzXMLFile.h:52
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
PeakFileOptions.h
OpenMS::MzXMLFile::options_
PeakFileOptions options_
Definition: MzXMLFile.h:135
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::MzXMLFile::MapType
PeakMap MapType
Definition: MzXMLFile.h:56
StandardTypes.h