OpenMS
IndexedMzMLHandler.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: Hannes Roest $
6 // $Authors: Hannes Roest $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/config.h>
12 #include <OpenMS/CONCEPT/Types.h>
18 
19 #include <string>
20 #include <fstream>
21 #include <unordered_map>
22 
23 namespace OpenMS
24 {
25 
26 namespace Internal
27 {
28 
53  class OPENMS_DLLAPI IndexedMzMLHandler
54  {
58  std::vector< std::streampos > spectra_offsets_;
60  std::unordered_map< std::string, Size > spectra_native_ids_;
62  std::vector< std::streampos > chromatograms_offsets_;
64  std::unordered_map< std::string, Size > chromatograms_native_ids_;
66  std::streampos index_offset_;
70  std::ifstream filestream_;
75 
84  void parseFooter_();
85 
86  std::string getChromatogramById_helper_(int id);
87 
88  std::string getSpectrumById_helper_(int id);
89 
90  public:
91 
96 
102  explicit IndexedMzMLHandler(const String& filename);
103 
106 
109 
115  void openFile(const String& filename);
116 
126  bool getParsingSuccess() const;
127 
129  size_t getNrSpectra() const;
130 
132  size_t getNrChromatograms() const;
133 
143 
153 
163  void getMSSpectrumByNativeId(const std::string& id, OpenMS::MSSpectrum& s);
164 
175 
185 
195 
205  void getMSChromatogramByNativeId(const std::string& id, OpenMS::MSChromatogram& c);
206 
217 
219  void setSkipXMLChecks(bool skip)
220  {
221  skip_xml_checks_ = skip;
222  }
223 
224  };
225 }
226 }
227 
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:54
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:219
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:68
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:56
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:62
std::vector< std::streampos > spectra_offsets_
Binary offsets to all spectra.
Definition: IndexedMzMLHandler.h:58
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:60
bool parsing_success_
Whether parsing the indexedmzML file was successful.
Definition: IndexedMzMLHandler.h:72
std::streampos index_offset_
offset to the <indexList> element
Definition: IndexedMzMLHandler.h:66
std::ifstream filestream_
The current filestream (opened by openFile)
Definition: IndexedMzMLHandler.h:70
std::unordered_map< std::string, Size > chromatograms_native_ids_
Mapping of chromatogram native ids to offsets.
Definition: IndexedMzMLHandler.h:64
IndexedMzMLHandler()
Default constructor.
bool skip_xml_checks_
Whether to skip XML checks.
Definition: IndexedMzMLHandler.h:74
The representation of a chromatogram.
Definition: MSChromatogram.h:30
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
A more convenient string class.
Definition: String.h:34
const double c
Definition: Constants.h:188
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:130
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:210
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19