OpenMS  3.0.0
IndexedMzMLHandler.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
37 #include <OpenMS/config.h>
38 #include <OpenMS/CONCEPT/Types.h>
44 
45 #include <string>
46 #include <fstream>
47 #include <unordered_map>
48 
49 namespace OpenMS
50 {
51 
52 namespace Internal
53 {
54 
79  class OPENMS_DLLAPI IndexedMzMLHandler
80  {
84  std::vector< std::streampos > spectra_offsets_;
86  std::unordered_map< std::string, Size > spectra_native_ids_;
88  std::vector< std::streampos > chromatograms_offsets_;
90  std::unordered_map< std::string, Size > chromatograms_native_ids_;
92  std::streampos index_offset_;
96  std::ifstream filestream_;
101 
110  void parseFooter_();
111 
112  std::string getChromatogramById_helper_(int id);
113 
114  std::string getSpectrumById_helper_(int id);
115 
116  public:
117 
122 
128  explicit IndexedMzMLHandler(const String& filename);
129 
131  IndexedMzMLHandler(const IndexedMzMLHandler& source);
132 
135 
141  void openFile(const String& filename);
142 
152  bool getParsingSuccess() const;
153 
155  size_t getNrSpectra() const;
156 
158  size_t getNrChromatograms() const;
159 
168  OpenMS::Interfaces::SpectrumPtr getSpectrumById(int id);
169 
178  const OpenMS::MSSpectrum getMSSpectrumById(int id);
179 
189  void getMSSpectrumByNativeId(std::string id, OpenMS::MSSpectrum& s);
190 
200  void getMSSpectrumById(int id, OpenMS::MSSpectrum& s);
201 
210  OpenMS::Interfaces::ChromatogramPtr getChromatogramById(int id);
211 
220  const OpenMS::MSChromatogram getMSChromatogramById(int id);
221 
231  void getMSChromatogramByNativeId(const std::string& id, OpenMS::MSChromatogram& c);
232 
242  void getMSChromatogramById(int id, OpenMS::MSChromatogram& c);
243 
245  void setSkipXMLChecks(bool skip)
246  {
247  skip_xml_checks_ = skip;
248  }
249 
250  };
251 }
252 }
253 
OpenMS::Interfaces::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
DataStructures.h
Types.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Constants::c
const double c
Definition: Constants.h:209
OpenMS::Interfaces::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Internal::IndexedMzMLHandler::chromatograms_native_ids_
std::unordered_map< std::string, Size > chromatograms_native_ids_
Mapping of chromatogram native ids to offsets.
Definition: IndexedMzMLHandler.h:90
OpenMS::Internal::IndexedMzMLHandler::filestream_
std::ifstream filestream_
The current filestream (opened by openFile)
Definition: IndexedMzMLHandler.h:96
OpenMS::Internal::IndexedMzMLHandler::index_offset_
std::streampos index_offset_
offset to the <indexList> element
Definition: IndexedMzMLHandler.h:92
OpenMS::Internal::IndexedMzMLHandler::skip_xml_checks_
bool skip_xml_checks_
Whether to skip XML checks.
Definition: IndexedMzMLHandler.h:100
ISpectrumAccess.h
OpenMS::Internal::IndexedMzMLHandler::parsing_success_
bool parsing_success_
Whether parsing the indexedmzML file was successful.
Definition: IndexedMzMLHandler.h:98
MSChromatogram.h
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
String.h
OpenMS::Internal::IndexedMzMLHandler::spectra_native_ids_
std::unordered_map< std::string, Size > spectra_native_ids_
Mapping of spectra native ids to offsets.
Definition: IndexedMzMLHandler.h:86
OpenMS::Internal::IndexedMzMLHandler::spectra_before_chroms_
bool spectra_before_chroms_
Whether spectra are written before chromatograms in this file.
Definition: IndexedMzMLHandler.h:94
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::Internal::IndexedMzMLHandler::chromatograms_offsets_
std::vector< std::streampos > chromatograms_offsets_
Binary offsets to all chromatograms.
Definition: IndexedMzMLHandler.h:88
OpenMS::Internal::IndexedMzMLHandler::filename_
String filename_
Name of the file.
Definition: IndexedMzMLHandler.h:82
MSSpectrum.h
OpenMS::Internal::IndexedMzMLHandler
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:79
OpenMS::Internal::IndexedMzMLHandler::spectra_offsets_
std::vector< std::streampos > spectra_offsets_
Binary offsets to all spectra.
Definition: IndexedMzMLHandler.h:84
OpenMS::Internal::IndexedMzMLHandler::setSkipXMLChecks
void setSkipXMLChecks(bool skip)
Whether to skip some XML checks (removing whitespace from base64 arrays) and be fast instead.
Definition: IndexedMzMLHandler.h:245