OpenMS
MzMLFile.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Marc Sturm, Chris Bielow, Hannes Roest $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
12 #include <OpenMS/FORMAT/XMLFile.h>
16 
17 #include <OpenMS/DATASTRUCTURES/ListUtils.h> // StringList
19 
20 #include <map>
21 
22 namespace OpenMS
23 {
31  class OPENMS_DLLAPI MzMLFile :
32  public Internal::XMLFile,
33  public ProgressLogger
34  {
35 public:
39  ~MzMLFile() override;
40 
43 
45  const PeakFileOptions& getOptions() const;
46 
49 
59  void load(const String& filename, PeakMap& map);
60 
69  void loadBuffer(const std::string& buffer, PeakMap& map);
70 
81  void loadSize(const String & filename, Size& scount, Size& ccount);
82 
90  void store(const String& filename, const PeakMap& map) const;
91 
98  void storeBuffer(std::string & output, const PeakMap& map) const;
99 
119  void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count = false, bool skip_first_pass = false);
120 
136  void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, PeakMap& map, bool skip_full_count = false, bool skip_first_pass = false);
137 
143  bool isValid(const String& filename, std::ostream& os = std::cerr);
144 
154  bool isSemanticallyValid(const String& filename, StringList& errors, StringList& warnings);
155 
163  bool hasIndex(const String& filename);
164 
165  struct SpecInfo
166  {
167  Size count_centroided = 0;
168  Size count_profile = 0;
169  Size count_unknown = 0;
170  };
171 
189  std::map<UInt, SpecInfo> getCentroidInfo(const String& filename, const Size first_n_spectra_only = 10);
190 
191 protected:
192 
194  void transformFirstPass_(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count);
195 
197  void safeParse_(const String & filename, Internal::XMLHandler * handler);
198 
199 private:
200 
203 
206  };
207 
208 } // namespace OpenMS
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:46
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:23
Base class for XML handlers.
Definition: XMLHandler.h:302
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:45
File adapter for MzML files.
Definition: MzMLFile.h:34
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:202
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:205
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.
bool hasIndex(const String &filename)
Checks if a file is an indexed MzML file or not.
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:166
Options for loading files containing peak data.
Definition: PeakFileOptions.h:22
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
A more convenient string class.
Definition: String.h:34
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:97
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19