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| SpectrumAccessSqMass (const OpenMS::Internal::MzMLSqliteHandler &handler) |
| Constructor. More...
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| SpectrumAccessSqMass (const OpenMS::Internal::MzMLSqliteHandler &handler, const std::vector< int > &indices) |
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| SpectrumAccessSqMass (const SpectrumAccessSqMass &sp, const std::vector< int > &indices) |
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| ~SpectrumAccessSqMass () override |
| Destructor. More...
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| SpectrumAccessSqMass (const SpectrumAccessSqMass &rhs) |
| Copy constructor. More...
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boost::shared_ptr< OpenSwath::ISpectrumAccess > | lightClone () const override |
| Light clone operator (actual data will not get copied) More...
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OpenSwath::SpectrumPtr | getSpectrumById (int) override |
| Return a pointer to a spectrum at the given id. More...
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OpenSwath::SpectrumMeta | getSpectrumMetaById (int) const override |
| Returns the meta information for a spectrum. More...
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void | getAllSpectra (std::vector< OpenSwath::SpectrumPtr > &spectra, std::vector< OpenSwath::SpectrumMeta > &spectra_meta) const |
| Load all spectra from the underlying sqMass file into memory. More...
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std::vector< std::size_t > | getSpectraByRT (double, double) const override |
| Return a vector of ids of spectra that are within RT +/- deltaRT. More...
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size_t | getNrSpectra () const override |
| Returns the number of spectra available. More...
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OpenSwath::ChromatogramPtr | getChromatogramById (int) override |
| Return a pointer to a chromatogram at the given id. More...
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size_t | getNrChromatograms () const override |
| Returns the number of chromatograms available. More...
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std::string | getChromatogramNativeID (int) const override |
| Returns the native id of the chromatogram at the given id. More...
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virtual | ~ISpectrumAccess () |
| Destructor. More...
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SpectrumPtr | getSpectrumById (int id, double drift_start, double drift_end) |
| Return pointer to a spectrum at the given id, the spectrum will be filtered by drift time. More...
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SpectrumSequence | getMultipleSpectra (double RT, int nr_spectra_to_fetch) |
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SpectrumSequence | getMultipleSpectra (double RT, int nr_spectra_to_fetch, double drift_start, double drift_end) |
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An implementation of the Spectrum Access interface using SQL files.
The interface takes an MzMLSqliteHandler object to access spectra and chromatograms from a sqlite file (sqMass). Currently access to individual spectra and chromatograms are not supported due to large overhead of opening a DB connection and performing a single query.
Instead, the users should use getAllSpectra which returns all available spectra together.
The interface allows to be constructed in a way as to only provide access to a subset of spectra / chromatograms by supplying a set of indices which are then used to provide a transparent interface to any consumer who will get access to the described subset of spectra / chromatograms. This can be useful to provide a specific interface to MS1 or MS2 spectra only or to different DIA / SWATH-MS windows.
Parallel access is supported through this interface as it is read-only and sqlite3 supports multiple parallel read threads as long as they use a different db connection.
Sample usage:
std::vector<int> indices = sql_mass_reader.readSpectraForWindow(swath_map);
swath_maps[
k].sptr = sptr;
Sqlite handler for storing spectra and chromatograms in sqMass format.
Definition: MzMLSqliteHandler.h:52
An implementation of the Spectrum Access interface using SQL files.
Definition: SpectrumAccessSqMass.h:61
const double k
Definition: Constants.h:132
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:131