OpenMS
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 
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 
169 
179 
189  void getMSSpectrumByNativeId(const std::string& id, OpenMS::MSSpectrum& s);
190 
201 
211 
221 
231  void getMSChromatogramByNativeId(const std::string& id, OpenMS::MSChromatogram& c);
232 
243 
245  void setSkipXMLChecks(bool skip)
246  {
247  skip_xml_checks_ = skip;
248  }
249 
250  };
251 }
252 }
253 
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:80
void getMSSpectrumById(int id, OpenMS::MSSpectrum &s)
Retrieve the raw data for the spectrum at position "id".
void openFile(const String &filename)
Open a file.
std::string getSpectrumById_helper_(int id)
void setSkipXMLChecks(bool skip)
Whether to skip some XML checks (removing whitespace from base64 arrays) and be fast instead.
Definition: IndexedMzMLHandler.h:245
void getMSChromatogramById(int id, OpenMS::MSChromatogram &c)
Retrieve the raw data for the chromatogram at position "id".
void getMSSpectrumByNativeId(const std::string &id, OpenMS::MSSpectrum &s)
Retrieve the raw data for the spectrum with native id "id".
bool spectra_before_chroms_
Whether spectra are written before chromatograms in this file.
Definition: IndexedMzMLHandler.h:94
size_t getNrSpectra() const
Returns the number of spectra available.
const OpenMS::MSSpectrum getMSSpectrumById(int id)
Retrieve the raw data for the spectrum at position "id".
String filename_
Name of the file.
Definition: IndexedMzMLHandler.h:82
IndexedMzMLHandler(const String &filename)
Constructor.
IndexedMzMLHandler(const IndexedMzMLHandler &source)
Copy constructor.
std::string getChromatogramById_helper_(int id)
void getMSChromatogramByNativeId(const std::string &id, OpenMS::MSChromatogram &c)
Retrieve the raw data for the chromatogram with native id "id".
void parseFooter_()
Try to parse the footer of the indexedmzML.
bool getParsingSuccess() const
Returns whether parsing was successful.
const OpenMS::MSChromatogram getMSChromatogramById(int id)
Retrieve the raw data for the chromatogram at position "id".
OpenMS::Interfaces::ChromatogramPtr getChromatogramById(int id)
Retrieve the raw data for the chromatogram at position "id".
std::vector< std::streampos > chromatograms_offsets_
Binary offsets to all chromatograms.
Definition: IndexedMzMLHandler.h:88
std::vector< std::streampos > spectra_offsets_
Binary offsets to all spectra.
Definition: IndexedMzMLHandler.h:84
size_t getNrChromatograms() const
Returns the number of chromatograms available.
OpenMS::Interfaces::SpectrumPtr getSpectrumById(int id)
Retrieve the raw data for the spectrum at position "id".
std::unordered_map< std::string, Size > spectra_native_ids_
Mapping of spectra native ids to offsets.
Definition: IndexedMzMLHandler.h:86
bool parsing_success_
Whether parsing the indexedmzML file was successful.
Definition: IndexedMzMLHandler.h:98
std::streampos index_offset_
offset to the <indexList> element
Definition: IndexedMzMLHandler.h:92
std::ifstream filestream_
The current filestream (opened by openFile)
Definition: IndexedMzMLHandler.h:96
std::unordered_map< std::string, Size > chromatograms_native_ids_
Mapping of chromatogram native ids to offsets.
Definition: IndexedMzMLHandler.h:90
IndexedMzMLHandler()
Default constructor.
bool skip_xml_checks_
Whether to skip XML checks.
Definition: IndexedMzMLHandler.h:100
The representation of a chromatogram.
Definition: MSChromatogram.h:57
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
A more convenient string class.
Definition: String.h:60
const double c
Definition: Constants.h:214
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48