OpenMS  3.0.0
MzMLFile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm, Chris Bielow, Hannes Roest $
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34 
35 #pragma once
36 
38 #include <OpenMS/FORMAT/XMLFile.h>
42 
43 #include <OpenMS/DATASTRUCTURES/ListUtils.h> // StringList
45 
46 #include <map>
47 
48 namespace OpenMS
49 {
57  class OPENMS_DLLAPI MzMLFile :
58  public Internal::XMLFile,
59  public ProgressLogger
60  {
61 public:
63  MzMLFile();
65  ~MzMLFile() override;
66 
68  PeakFileOptions& getOptions();
69 
71  const PeakFileOptions& getOptions() const;
72 
74  void setOptions(const PeakFileOptions&);
75 
85  void load(const String& filename, PeakMap& map);
86 
95  void loadBuffer(const std::string& buffer, PeakMap& map);
96 
107  void loadSize(const String & filename, Size& scount, Size& ccount);
108 
116  void store(const String& filename, const PeakMap& map) const;
117 
124  void storeBuffer(std::string & output, const PeakMap& map) const;
125 
144  void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count = false, bool skip_first_pass = false);
145 
160  void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, PeakMap& map, bool skip_full_count = false, bool skip_first_pass = false);
161 
167  bool isValid(const String& filename, std::ostream& os = std::cerr);
168 
178  bool isSemanticallyValid(const String& filename, StringList& errors, StringList& warnings);
179 
180 
181  struct SpecInfo
182  {
183  Size count_centroided = 0;
184  Size count_profile = 0;
185  Size count_unknown = 0;
186  };
187 
205  std::map<UInt, SpecInfo> getCentroidInfo(const String& filename, const Size first_n_spectra_only = 10);
206 
207 protected:
208 
210  void transformFirstPass_(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count);
211 
213  void safeParse_(const String & filename, Internal::XMLHandler * handler);
214 
215 private:
216 
219 
222  };
223 
224 } // namespace OpenMS
XMLFile.h
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
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
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IMSDataConsumer.h
OpenMS::MzMLFile::indexed_schema_location_
String indexed_schema_location_
Location of indexed mzML schema.
Definition: MzMLFile.h:221
ListUtils.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Exception.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::MzMLFile::options_
PeakFileOptions options_
Options for loading / storing.
Definition: MzMLFile.h:218
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
PeakFileOptions.h
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::MzMLFile::SpecInfo
Definition: MzMLFile.h:181
StandardTypes.h