OpenMS  3.0.0
OnDiscMSExperiment.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
38 
44 
45 #include <vector>
46 #include <limits>
47 
48 #include <boost/shared_ptr.hpp>
49 
50 namespace OpenMS
51 {
66  class OPENMS_DLLAPI OnDiscMSExperiment
67  {
68 
70  typedef Peak1D PeakT;
71 
72 public:
73 
79  OnDiscMSExperiment() = default;
80 
90  bool openFile(const String& filename, bool skipMetaData = false);
91 
94  filename_(source.filename_),
95  indexed_mzml_file_(source.indexed_mzml_file_),
96  meta_ms_experiment_(source.meta_ms_experiment_)
97  {
98  }
99 
107  bool operator==(const OnDiscMSExperiment& rhs) const
108  {
109  if (meta_ms_experiment_ == nullptr || rhs.meta_ms_experiment_ == nullptr)
110  {
111  return filename_ == rhs.filename_ &&
112  meta_ms_experiment_ == rhs.meta_ms_experiment_;
113  }
114 
115  // check if file and meta information is the same
116  return filename_ == rhs.filename_ &&
117  (*meta_ms_experiment_) == (*rhs.meta_ms_experiment_);
118  // do not check if indexed_mzml_file_ is equal -> they have the same filename...
119  }
120 
122  bool operator!=(const OnDiscMSExperiment& rhs) const
123  {
124  return !(operator==(rhs));
125  }
126 
133  bool isSortedByRT() const
134  {
135  if (!meta_ms_experiment_) return false;
136 
137  return meta_ms_experiment_->isSorted(false);
138  }
139 
141  inline Size size() const
142  {
143  return getNrSpectra();
144  }
145 
147  inline bool empty() const
148  {
149  return getNrSpectra() == 0;
150  }
151 
153  inline Size getNrSpectra() const
154  {
155  return indexed_mzml_file_.getNrSpectra();
156  }
157 
159  inline Size getNrChromatograms() const
160  {
161  return indexed_mzml_file_.getNrChromatograms();
162  }
163 
165  boost::shared_ptr<const ExperimentalSettings> getExperimentalSettings() const
166  {
167  return boost::static_pointer_cast<const ExperimentalSettings>(meta_ms_experiment_);
168  }
169 
170  boost::shared_ptr<PeakMap> getMetaData() const
171  {
172  return meta_ms_experiment_;
173  }
174 
177  {
178  return getSpectrum(n);
179  }
180 
187  {
188  if (!meta_ms_experiment_) return indexed_mzml_file_.getMSSpectrumById(int(id));
189 
190  MSSpectrum spectrum(meta_ms_experiment_->operator[](id));
191  indexed_mzml_file_.getMSSpectrumById(int(id), spectrum);
192  return spectrum;
193  }
194 
199  {
200  return indexed_mzml_file_.getSpectrumById((int)id);
201  }
202 
209  {
210  if (!meta_ms_experiment_) return indexed_mzml_file_.getMSChromatogramById(int(id));
211 
212  MSChromatogram chromatogram(meta_ms_experiment_->getChromatogram(id));
213  indexed_mzml_file_.getMSChromatogramById(int(id), chromatogram);
214  return chromatogram;
215  }
216 
222  MSChromatogram getChromatogramByNativeId(const std::string& id);
223 
229  MSSpectrum getSpectrumByNativeId(const std::string& id);
230 
234  OpenMS::Interfaces::ChromatogramPtr getChromatogramById(Size id);
235 
237  void setSkipXMLChecks(bool skip);
238 
239 private:
240 
242  OnDiscMSExperiment& operator=(const OnDiscMSExperiment& /* source */);
243 
244  void loadMetaData_(const String& filename);
245 
246  MSChromatogram getMetaChromatogramById_(const std::string& id);
247 
248  MSSpectrum getMetaSpectrumById_(const std::string& id);
249 
250 protected:
251 
257  boost::shared_ptr<PeakMap> meta_ms_experiment_;
259  std::unordered_map< std::string, Size > chromatograms_native_ids_;
261  std::unordered_map< std::string, Size > spectra_native_ids_;
262  };
263 
265 
266 } // namespace OpenMS
267 
268 
OpenMS::OnDiscMSExperiment::getSpectrumById
OpenMS::Interfaces::SpectrumPtr getSpectrumById(Size id)
returns a single spectrum
Definition: OnDiscMSExperiment.h:198
OpenMS::OnDiscMSExperiment::ChromatogramPeakT
ChromatogramPeak ChromatogramPeakT
Definition: OnDiscMSExperiment.h:69
OpenMS::Interfaces::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
OpenMS::OnDiscMSExperiment::filename_
String filename_
The filename of the underlying data file.
Definition: OnDiscMSExperiment.h:253
DataStructures.h
OpenMS::OnDiscMSExperiment::meta_ms_experiment_
boost::shared_ptr< PeakMap > meta_ms_experiment_
The meta-data.
Definition: OnDiscMSExperiment.h:257
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::OnDiscMSExperiment::empty
bool empty() const
returns whether spectra are empty
Definition: OnDiscMSExperiment.h:147
OpenMS::OnDiscMSExperiment::operator!=
bool operator!=(const OnDiscMSExperiment &rhs) const
Inequality operator.
Definition: OnDiscMSExperiment.h:122
OpenMS::OnDiscPeakMap
OpenMS::OnDiscMSExperiment OnDiscPeakMap
Definition: IndexedMzMLFileLoader.h:42
OpenMS::OnDiscMSExperiment::OnDiscMSExperiment
OnDiscMSExperiment(const OnDiscMSExperiment &source)
Copy constructor.
Definition: OnDiscMSExperiment.h:93
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::OnDiscMSExperiment::getNrSpectra
Size getNrSpectra() const
get the total number of spectra available
Definition: OnDiscMSExperiment.h:153
OpenMS::ChromatogramPeak
A 1-dimensional raw data point or peak for chromatograms.
Definition: ChromatogramPeak.h:53
OpenMS::OnDiscMSExperiment
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:66
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:53
OpenMS::OnDiscMSExperiment::getNrChromatograms
Size getNrChromatograms() const
get the total number of chromatograms available
Definition: OnDiscMSExperiment.h:159
OpenMS::OnDiscMSExperiment::operator[]
MSSpectrum operator[](Size n)
alias for getSpectrum
Definition: OnDiscMSExperiment.h:176
ExperimentalSettings.h
OpenMS::OnDiscMSExperiment::PeakT
Peak1D PeakT
Definition: OnDiscMSExperiment.h:70
OpenMS::OnDiscMSExperiment::chromatograms_native_ids_
std::unordered_map< std::string, Size > chromatograms_native_ids_
Mapping of chromatogram native ids to offsets.
Definition: OnDiscMSExperiment.h:259
MSExperiment.h
OpenMS::OnDiscMSExperiment::isSortedByRT
bool isSortedByRT() const
Checks if all spectra are sorted with respect to ascending RT.
Definition: OnDiscMSExperiment.h:133
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
MSChromatogram.h
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
OpenMS::OnDiscMSExperiment::getChromatogram
MSChromatogram getChromatogram(Size id)
returns a single chromatogram
Definition: OnDiscMSExperiment.h:208
OpenMS::OnDiscMSExperiment::getExperimentalSettings
boost::shared_ptr< const ExperimentalSettings > getExperimentalSettings() const
returns the meta information of this experiment (const access)
Definition: OnDiscMSExperiment.h:165
OpenMS::OnDiscMSExperiment::size
Size size() const
alias for getNrSpectra
Definition: OnDiscMSExperiment.h:141
OpenMS::OnDiscMSExperiment::operator==
bool operator==(const OnDiscMSExperiment &rhs) const
Equality operator.
Definition: OnDiscMSExperiment.h:107
OpenMS::OnDiscMSExperiment::getMetaData
boost::shared_ptr< PeakMap > getMetaData() const
Definition: OnDiscMSExperiment.h:170
IndexedMzMLHandler.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::OnDiscMSExperiment::getSpectrum
MSSpectrum getSpectrum(Size id)
returns a single spectrum
Definition: OnDiscMSExperiment.h:186
OpenMS::OnDiscMSExperiment::spectra_native_ids_
std::unordered_map< std::string, Size > spectra_native_ids_
Mapping of spectra native ids to offsets.
Definition: OnDiscMSExperiment.h:261
OpenMS::OnDiscMSExperiment::indexed_mzml_file_
Internal::IndexedMzMLHandler indexed_mzml_file_
The index of the underlying data file.
Definition: OnDiscMSExperiment.h:255
MSSpectrum.h
OpenMS::Internal::IndexedMzMLHandler
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:79