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OpenMS
2.5.0
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Go to the documentation of this file.
50 #include <boost/shared_ptr.hpp>
95 indexed_mzml_file_.openFile(filename);
96 if (filename !=
"" && !skipMetaData)
98 loadMetaData_(filename);
100 return indexed_mzml_file_.getParsingSuccess();
105 filename_(source.filename_),
106 indexed_mzml_file_(source.indexed_mzml_file_),
107 meta_ms_experiment_(source.meta_ms_experiment_)
146 if (!meta_ms_experiment_)
return false;
148 return meta_ms_experiment_->isSorted(
false);
154 return getNrSpectra();
160 return indexed_mzml_file_.getNrSpectra() == 0;
166 return indexed_mzml_file_.getNrSpectra();
172 return indexed_mzml_file_.getNrChromatograms();
178 return boost::static_pointer_cast<const ExperimentalSettings>(meta_ms_experiment_);
183 return meta_ms_experiment_;
189 return getSpectrum(n);
199 if (!meta_ms_experiment_)
return indexed_mzml_file_.getMSSpectrumById(
int(
id));
201 MSSpectrum spectrum(meta_ms_experiment_->operator[](
id));
202 indexed_mzml_file_.getMSSpectrumById(
int(
id), spectrum);
211 return indexed_mzml_file_.getSpectrumById(
id);
221 if (!meta_ms_experiment_)
return indexed_mzml_file_.getMSChromatogramById(
int(
id));
223 MSChromatogram chromatogram(meta_ms_experiment_->getChromatogram(
id));
224 indexed_mzml_file_.getMSChromatogramById(
int(
id), chromatogram);
240 MSSpectrum getSpectrumByNativeId(
const std::string&
id);
247 return indexed_mzml_file_.getChromatogramById(
id);
253 indexed_mzml_file_.setSkipXMLChecks(skip);
261 void loadMetaData_(
const String& filename);
265 MSSpectrum getMetaSpectrumById_(
const std::string&
id);
OpenMS::Interfaces::SpectrumPtr getSpectrumById(Size id)
returns a single spectrum
Definition: OnDiscMSExperiment.h:209
ChromatogramPeak ChromatogramPeakT
Definition: OnDiscMSExperiment.h:71
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
String filename_
The filename of the underlying data file.
Definition: OnDiscMSExperiment.h:270
OpenMS::Interfaces::ChromatogramPtr getChromatogramById(Size id)
returns a single chromatogram
Definition: OnDiscMSExperiment.h:245
OnDiscMSExperiment()
Constructor.
Definition: OnDiscMSExperiment.h:81
boost::shared_ptr< PeakMap > meta_ms_experiment_
The meta-data.
Definition: OnDiscMSExperiment.h:274
A more convenient string class.
Definition: String.h:58
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
bool empty() const
returns whether spectra are empty
Definition: OnDiscMSExperiment.h:158
bool operator!=(const OnDiscMSExperiment &rhs) const
Inequality operator.
Definition: OnDiscMSExperiment.h:133
OpenMS::OnDiscMSExperiment OnDiscPeakMap
Definition: OnDiscMSExperiment.h:281
OnDiscMSExperiment(const OnDiscMSExperiment &source)
Copy constructor.
Definition: OnDiscMSExperiment.h:104
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Size getNrSpectra() const
get the total number of spectra available
Definition: OnDiscMSExperiment.h:164
A 1-dimensional raw data point or peak for chromatograms.
Definition: ChromatogramPeak.h:54
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:68
void setSkipXMLChecks(bool skip)
sets whether to skip some XML checks and be fast instead
Definition: OnDiscMSExperiment.h:251
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
Size getNrChromatograms() const
get the total number of chromatograms available
Definition: OnDiscMSExperiment.h:170
MSSpectrum operator[](Size n)
alias for getSpectrum
Definition: OnDiscMSExperiment.h:187
bool openFile(const String &filename, bool skipMetaData=false)
Open a specific file on disk.
Definition: OnDiscMSExperiment.h:92
Peak1D PeakT
Definition: OnDiscMSExperiment.h:72
std::unordered_map< std::string, Size > chromatograms_native_ids_
Mapping of chromatogram native ids to offsets.
Definition: OnDiscMSExperiment.h:276
bool isSortedByRT() const
Checks if all spectra are sorted with respect to ascending RT.
Definition: OnDiscMSExperiment.h:144
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
The representation of a chromatogram.
Definition: MSChromatogram.h:54
MSChromatogram getChromatogram(Size id)
returns a single chromatogram
Definition: OnDiscMSExperiment.h:219
boost::shared_ptr< const ExperimentalSettings > getExperimentalSettings() const
returns the meta information of this experiment (const access)
Definition: OnDiscMSExperiment.h:176
Size size() const
alias for getNrSpectra
Definition: OnDiscMSExperiment.h:152
bool operator==(const OnDiscMSExperiment &rhs) const
Equality operator.
Definition: OnDiscMSExperiment.h:118
boost::shared_ptr< PeakMap > getMetaData() const
Definition: OnDiscMSExperiment.h:181
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
MSSpectrum getSpectrum(Size id)
returns a single spectrum
Definition: OnDiscMSExperiment.h:197
std::unordered_map< std::string, Size > spectra_native_ids_
Mapping of spectra native ids to offsets.
Definition: OnDiscMSExperiment.h:278
Internal::IndexedMzMLHandler indexed_mzml_file_
The index of the underlying data file.
Definition: OnDiscMSExperiment.h:272
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:79