Representation of a mass spectrometry experiment on disk. More...
#include <OpenMS/KERNEL/OnDiscMSExperiment.h>
Public Member Functions | |
OnDiscMSExperiment () | |
OnDiscMSExperiment (const String &filename) | |
Constructor. More... | |
bool | openFile (const String &filename) |
OnDiscMSExperiment (const OnDiscMSExperiment &source) | |
Copy constructor. More... | |
bool | operator== (const OnDiscMSExperiment &rhs) const |
Equality operator. More... | |
bool | operator!= (const OnDiscMSExperiment &rhs) const |
Inequality operator. More... | |
bool | isSortedByRT () const |
Checks if all spectra are sorted with respect to ascending RT. More... | |
Size | size () const |
alias for getNrSpectra More... | |
bool | empty () const |
returns whether spectra are empty More... | |
Size | getNrSpectra () const |
get the total number of spectra available More... | |
Size | getNrChromatograms () const |
get the total number of chromatograms available More... | |
boost::shared_ptr< const ExperimentalSettings > | getExperimentalSettings () const |
returns the meta information of this experiment (const access) More... | |
MSSpectrum< PeakT > | operator[] (Size n) |
alias for getSpectrum More... | |
MSSpectrum< PeakT > | getSpectrum (Size id) |
returns a single spectrum More... | |
OpenMS::Interfaces::SpectrumPtr | getSpectrumById (Size id) |
returns a single spectrum More... | |
MSChromatogram< ChromatogramPeakT > | getChromatogram (Size id) |
returns a single chromatogram More... | |
OpenMS::Interfaces::ChromatogramPtr | getChromatogramById (Size id) |
returns a single chromatogram More... | |
Protected Attributes | |
String | filename_ |
The filename of the underlying data file. More... | |
IndexedMzMLFile | indexed_mzml_file_ |
The index of the underlying data file. More... | |
boost::shared_ptr< MSExperiment<> > | meta_ms_experiment_ |
The meta-data. More... | |
Private Member Functions | |
OnDiscMSExperiment & | operator= (const OnDiscMSExperiment &) |
Private Assignment operator -> we cannot copy file streams in IndexedMzMLFile. More... | |
Representation of a mass spectrometry experiment on disk.
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Constructor.
This initializes the object and attempts to read the indexed mzML by parsing the index and then reading the meta information into memory.
References OnDiscMSExperiment< PeakT, ChromatogramPeakT >::openFile().
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Copy constructor.
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returns whether spectra are empty
References IndexedMzMLFile::getNrSpectra(), and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::indexed_mzml_file_.
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returns a single chromatogram
TODO: make this more efficient by reducing the copying
References IndexedMzMLFile::getChromatogramById(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::indexed_mzml_file_, and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::meta_ms_experiment_.
Referenced by PeakPickerHiRes::pickExperiment(), and IndexedMzMLFileLoader::store().
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returns a single chromatogram
References IndexedMzMLFile::getChromatogramById(), and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::indexed_mzml_file_.
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returns the meta information of this experiment (const access)
References OnDiscMSExperiment< PeakT, ChromatogramPeakT >::meta_ms_experiment_.
Referenced by PeakPickerHiRes::pickExperiment(), and IndexedMzMLFileLoader::store().
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get the total number of chromatograms available
References IndexedMzMLFile::getNrChromatograms(), and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::indexed_mzml_file_.
Referenced by PeakPickerHiRes::pickExperiment(), and IndexedMzMLFileLoader::store().
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get the total number of spectra available
References IndexedMzMLFile::getNrSpectra(), and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::indexed_mzml_file_.
Referenced by PeakPickerHiRes::pickExperiment(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::size(), and IndexedMzMLFileLoader::store().
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returns a single spectrum
TODO: make this more efficient by reducing the copying
References IndexedMzMLFile::getSpectrumById(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::indexed_mzml_file_, and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::meta_ms_experiment_.
Referenced by OnDiscMSExperiment< PeakT, ChromatogramPeakT >::operator[](), and IndexedMzMLFileLoader::store().
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returns a single spectrum
References IndexedMzMLFile::getSpectrumById(), and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::indexed_mzml_file_.
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Checks if all spectra are sorted with respect to ascending RT.
Note that we cannot check whether all spectra are sorted (except if we were to load them all and check).
References OnDiscMSExperiment< PeakT, ChromatogramPeakT >::meta_ms_experiment_.
References OnDiscMSExperiment< PeakT, ChromatogramPeakT >::filename_, IndexedMzMLFile::getParsingSuccess(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::indexed_mzml_file_, OnDiscMSExperiment< PeakT, ChromatogramPeakT >::meta_ms_experiment_, IndexedMzMLFile::openFile(), and PeakFileOptions::setFillData().
Referenced by IndexedMzMLFileLoader::load(), and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::OnDiscMSExperiment().
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Inequality operator.
References OnDiscMSExperiment< PeakT, ChromatogramPeakT >::operator==().
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Private Assignment operator -> we cannot copy file streams in IndexedMzMLFile.
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Equality operator.
This only checks whether the underlying file is the same and the parsed meta-information is the same. Note that the file reader (e.g. the std::ifstream of the file) might be in a different state.
References OnDiscMSExperiment< PeakT, ChromatogramPeakT >::filename_, and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::meta_ms_experiment_.
Referenced by OnDiscMSExperiment< PeakT, ChromatogramPeakT >::operator!=().
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alias for getSpectrum
References OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getSpectrum().
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alias for getNrSpectra
References OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getNrSpectra().
Referenced by PeakPickerHiRes::pickExperiment().
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The filename of the underlying data file.
Referenced by OnDiscMSExperiment< PeakT, ChromatogramPeakT >::openFile(), and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::operator==().
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The index of the underlying data file.
Referenced by OnDiscMSExperiment< PeakT, ChromatogramPeakT >::empty(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getChromatogram(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getChromatogramById(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getNrChromatograms(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getNrSpectra(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getSpectrum(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getSpectrumById(), and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::openFile().
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The meta-data.
Referenced by OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getChromatogram(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getExperimentalSettings(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::getSpectrum(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::isSortedByRT(), OnDiscMSExperiment< PeakT, ChromatogramPeakT >::openFile(), and OnDiscMSExperiment< PeakT, ChromatogramPeakT >::operator==().
OpenMS / TOPP release 2.0.0 | Documentation generated on Sat May 16 2015 16:14:00 using doxygen 1.8.9.1 |