OpenMS  2.8.0
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:
65  ~MzMLFile() override;
66 
69 
71  const PeakFileOptions& getOptions() const;
72 
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
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
Base class for XML handlers.
Definition: XMLHandler.h:325
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
File adapter for MzML files.
Definition: MzMLFile.h:60
void setOptions(const PeakFileOptions &)
set options for loading/storing
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, PeakMap &map, bool skip_full_count=false, bool skip_first_pass=false)
Transforms a map while loading using the supplied MSDataConsumer.
bool isValid(const String &filename, std::ostream &os=std::cerr)
Checks if a file validates against the XML schema.
const PeakFileOptions & getOptions() const
Non-mutable access to the options for loading/storing.
PeakFileOptions options_
Options for loading / storing.
Definition: MzMLFile.h:218
MzMLFile()
Default constructor.
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 safeParse_(const String &filename, Internal::XMLHandler *handler)
Safe parse that catches exceptions and handles them accordingly.
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void storeBuffer(std::string &output, const PeakMap &map) const
Stores a map in an output string.
String indexed_schema_location_
Location of indexed mzML schema.
Definition: MzMLFile.h:221
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false)
Transforms a map while loading using the supplied MSDataConsumer.
void loadBuffer(const std::string &buffer, PeakMap &map)
Loads a map from a MzML file stored in a buffer (in memory).
~MzMLFile() override
Destructor.
std::map< UInt, SpecInfo > getCentroidInfo(const String &filename, const Size first_n_spectra_only=10)
Check type of spectra based on their metadata (if available) or by inspecting the peaks itself.
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
void loadSize(const String &filename, Size &scount, Size &ccount)
Only count the number of spectra and chromatograms from a file.
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
bool isSemanticallyValid(const String &filename, StringList &errors, StringList &warnings)
Checks if a file is valid with respect to the mapping file and the controlled vocabulary.
Definition: MzMLFile.h:182
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
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47