OpenMS  2.8.0
MzXMLFile.h
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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:
62  ~MzXMLFile() override;
63 
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 
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:70
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:49
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
File adapter for MzXML 3.1 files.
Definition: MzXMLFile.h:55
~MzXMLFile() override
Destructor.
void setOptions(const PeakFileOptions &)
set options for loading/storing
const PeakFileOptions & getOptions() const
Non-mutable access to the options for loading/storing.
PeakFileOptions options_
Definition: MzXMLFile.h:135
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false)
Transforms a map while loading using the supplied MSDataConsumer.
void transformFirstPass_(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count)
Perform first pass through the file and retrieve the meta-data to initialize the consumer.
void load(const String &filename, MapType &map)
Loads a map from a MzXML file.
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
MzXMLFile()
Default constructor.
PeakMap MapType
Definition: MzXMLFile.h:56
void store(const String &filename, const MapType &map) const
Stores a map in a MzXML file.
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, MapType &map, bool skip_full_count=false)
Transforms a map while loading using the supplied MSDataConsumer.
Options for loading files containing peak data.
Definition: PeakFileOptions.h:48
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47