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_)
140 return meta_ms_experiment_->isSorted(
false);
146 return getNrSpectra();
152 return indexed_mzml_file_.getNrSpectra() == 0;
158 return indexed_mzml_file_.getNrSpectra();
164 return indexed_mzml_file_.getNrChromatograms();
175 return meta_ms_experiment_;
181 return getSpectrum(n);
191 MSSpectrum spectrum(meta_ms_experiment_->operator[](
id));
192 indexed_mzml_file_.getMSSpectrumById(static_cast<int>(
id), spectrum);
201 return indexed_mzml_file_.getSpectrumById(
id);
211 MSChromatogram chromatogram(meta_ms_experiment_->getChromatogram(
id));
212 indexed_mzml_file_.getMSChromatogramById(static_cast<int>(
id), chromatogram);
221 return indexed_mzml_file_.getChromatogramById(
id);
227 indexed_mzml_file_.setSkipXMLChecks(skip);
235 void loadMetaData_(
const String& filename);
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
Size getNrChromatograms() const
get the total number of chromatograms available
Definition: OnDiscMSExperiment.h:162
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
A more convenient string class.
Definition: String.h:57
bool openFile(const String &filename, bool skipMetaData=false)
Open a specific file on disk.
Definition: OnDiscMSExperiment.h:92
The representation of a chromatogram.
Definition: MSChromatogram.h:54
MSSpectrum operator[](Size n)
alias for getSpectrum
Definition: OnDiscMSExperiment.h:179
Peak1D PeakT
Definition: OnDiscMSExperiment.h:72
bool isSortedByRT() const
Checks if all spectra are sorted with respect to ascending RT.
Definition: OnDiscMSExperiment.h:138
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool operator==(const OnDiscMSExperiment &rhs) const
Equality operator.
Definition: OnDiscMSExperiment.h:118
Size size() const
alias for getNrSpectra
Definition: OnDiscMSExperiment.h:144
Internal::IndexedMzMLHandler indexed_mzml_file_
The index of the underlying data file.
Definition: OnDiscMSExperiment.h:242
boost::shared_ptr< PeakMap > getMetaData() const
Definition: OnDiscMSExperiment.h:173
String filename_
The filename of the underlying data file.
Definition: OnDiscMSExperiment.h:240
MSChromatogram getChromatogram(Size id)
returns a single chromatogram
Definition: OnDiscMSExperiment.h:209
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:68
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OnDiscMSExperiment()
Constructor.
Definition: OnDiscMSExperiment.h:81
boost::shared_ptr< const ExperimentalSettings > getExperimentalSettings() const
returns the meta information of this experiment (const access)
Definition: OnDiscMSExperiment.h:168
MSSpectrum getSpectrum(Size id)
returns a single spectrum
Definition: OnDiscMSExperiment.h:189
OpenMS::Interfaces::SpectrumPtr getSpectrumById(Size id)
returns a single spectrum
Definition: OnDiscMSExperiment.h:199
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::Interfaces::ChromatogramPtr getChromatogramById(Size id)
returns a single chromatogram
Definition: OnDiscMSExperiment.h:219
boost::shared_ptr< PeakMap > meta_ms_experiment_
The meta-data.
Definition: OnDiscMSExperiment.h:244
ChromatogramPeak ChromatogramPeakT
Definition: OnDiscMSExperiment.h:71
OnDiscMSExperiment(const OnDiscMSExperiment &source)
Copy constructor.
Definition: OnDiscMSExperiment.h:104
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::OnDiscMSExperiment OnDiscPeakMap
Definition: OnDiscMSExperiment.h:247
A 1-dimensional raw data point or peak for chromatograms.
Definition: ChromatogramPeak.h:54
bool empty() const
returns whether spectra are empty
Definition: OnDiscMSExperiment.h:150
Size getNrSpectra() const
get the total number of spectra available
Definition: OnDiscMSExperiment.h:156
bool operator!=(const OnDiscMSExperiment &rhs) const
Inequality operator.
Definition: OnDiscMSExperiment.h:127
Description of the experimental settings.
Definition: ExperimentalSettings.h:58
void setSkipXMLChecks(bool skip)
sets whether to skip some XML checks and be fast instead
Definition: OnDiscMSExperiment.h:225
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:78