OpenMS
2.5.0
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An implementation of the Spectrum Access interface using SQL files. More...
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessSqMass.h>
Public Types | |
typedef OpenMS::MSSpectrum | MSSpectrumType |
typedef OpenMS::MSChromatogram | MSChromatogramType |
Public Member Functions | |
SpectrumAccessSqMass (const OpenMS::Internal::MzMLSqliteHandler &handler) | |
Constructor. More... | |
SpectrumAccessSqMass (const OpenMS::Internal::MzMLSqliteHandler &handler, const std::vector< int > &indices) | |
SpectrumAccessSqMass (const SpectrumAccessSqMass &sp, const std::vector< int > &indices) | |
~SpectrumAccessSqMass () override | |
Destructor. More... | |
SpectrumAccessSqMass (const SpectrumAccessSqMass &rhs) | |
Copy constructor. More... | |
boost::shared_ptr< OpenSwath::ISpectrumAccess > | lightClone () const override |
Light clone operator (actual data will not get copied) More... | |
OpenSwath::SpectrumPtr | getSpectrumById (int) override |
Return a pointer to a spectrum at the given id. More... | |
OpenSwath::SpectrumMeta | getSpectrumMetaById (int) const override |
Returns the meta information for a spectrum. More... | |
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... | |
std::vector< std::size_t > | getSpectraByRT (double, double) const override |
Return a vector of ids of spectra that are within RT +/- deltaRT. More... | |
size_t | getNrSpectra () const override |
Returns the number of spectra available. More... | |
OpenSwath::ChromatogramPtr | getChromatogramById (int) override |
Return a pointer to a chromatogram at the given id. More... | |
size_t | getNrChromatograms () const override |
Returns the number of chromatograms available. More... | |
std::string | getChromatogramNativeID (int) const override |
Returns the native id of the chromatogram at the given id. More... | |
Public Member Functions inherited from ISpectrumAccess | |
virtual | ~ISpectrumAccess () |
Destructor. More... | |
Private Attributes | |
OpenMS::Internal::MzMLSqliteHandler | handler_ |
Access to underlying sqMass file. More... | |
std::vector< int > | sidx_ |
Optional subset of spectral indices. More... | |
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:
typedef OpenMS::MSSpectrum MSSpectrumType |
SpectrumAccessSqMass | ( | const OpenMS::Internal::MzMLSqliteHandler & | handler | ) |
Constructor.
SpectrumAccessSqMass | ( | const OpenMS::Internal::MzMLSqliteHandler & | handler, |
const std::vector< int > & | indices | ||
) |
SpectrumAccessSqMass | ( | const SpectrumAccessSqMass & | sp, |
const std::vector< int > & | indices | ||
) |
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override |
Destructor.
SpectrumAccessSqMass | ( | const SpectrumAccessSqMass & | rhs | ) |
Copy constructor.
void getAllSpectra | ( | std::vector< OpenSwath::SpectrumPtr > & | spectra, |
std::vector< OpenSwath::SpectrumMeta > & | spectra_meta | ||
) | const |
Load all spectra from the underlying sqMass file into memory.
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overridevirtual |
Return a pointer to a chromatogram at the given id.
Implements ISpectrumAccess.
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overridevirtual |
Returns the native id of the chromatogram at the given id.
Implements ISpectrumAccess.
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overridevirtual |
Returns the number of chromatograms available.
Implements ISpectrumAccess.
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overridevirtual |
Returns the number of spectra available.
Implements ISpectrumAccess.
Return a vector of ids of spectra that are within RT +/- deltaRT.
Implements ISpectrumAccess.
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overridevirtual |
Return a pointer to a spectrum at the given id.
Implements ISpectrumAccess.
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overridevirtual |
Returns the meta information for a spectrum.
Implements ISpectrumAccess.
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overridevirtual |
Light clone operator (actual data will not get copied)
Implements ISpectrumAccess.
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private |
Access to underlying sqMass file.
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private |
Optional subset of spectral indices.