MzMLSqliteHandler

class pyopenms.MzMLSqliteHandler

Bases: object

Cython implementation of _MzMLSqliteHandler

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS::Internal_1_1MzMLSqliteHandler.html

__init__()

  • Cython signature: void MzMLSqliteHandler(String filename, uint64_t run_id)

  • Cython signature: void MzMLSqliteHandler(MzMLSqliteHandler &)

Methods

__init__

  • Cython signature: void MzMLSqliteHandler(String filename, uint64_t run_id)

createTables

Cython signature: void createTables() Create data tables for a new file

getNrChromatograms

Cython signature: size_t getNrChromatograms() Returns the number of chromatograms in the file

getNrSpectra

Cython signature: size_t getNrSpectra() Returns number of spectra in the file, reutrns the number of spectra

getRunID

Cython signature: uint64_t getRunID() Extract the RUN ID from the sqMass file

getSpectraIndicesbyRT

Cython signature: libcpp_vector[size_t] getSpectraIndicesbyRT(double RT, double deltaRT, libcpp_vector[int] indices)

readChromatograms

Cython signature: void readChromatograms(libcpp_vector[MSChromatogram] & exp, libcpp_vector[int] indices, bool meta_only)

readExperiment

Cython signature: void readExperiment(MSExperiment & exp, bool meta_only)

readSpectra

Cython signature: void readSpectra(libcpp_vector[MSSpectrum] & exp, libcpp_vector[int] indices, bool meta_only)

setConfig

Cython signature: void setConfig(bool write_full_meta, bool use_lossy_compression, double linear_abs_mass_acc)

writeChromatograms

Cython signature: void writeChromatograms(libcpp_vector[MSChromatogram] chroms) Writes a set of chromatograms to disk

writeExperiment

Cython signature: void writeExperiment(MSExperiment exp) Write an MSExperiment to disk

writeRunLevelInformation

Cython signature: void writeRunLevelInformation(MSExperiment exp, bool write_full_meta)

writeSpectra

Cython signature: void writeSpectra(libcpp_vector[MSSpectrum] spectra) Writes a set of spectra to disk
createTables()

Cython signature: void createTables() Create data tables for a new file

getNrChromatograms()

Cython signature: size_t getNrChromatograms() Returns the number of chromatograms in the file

getNrSpectra()

Cython signature: size_t getNrSpectra() Returns number of spectra in the file, reutrns the number of spectra

getRunID()

Cython signature: uint64_t getRunID() Extract the RUN ID from the sqMass file

getSpectraIndicesbyRT()

Cython signature: libcpp_vector[size_t] getSpectraIndicesbyRT(double RT, double deltaRT, libcpp_vector[int] indices)

Parameters

  • RT – The retention time

  • deltaRT – Tolerance window around RT (if less or equal than zero, only the first spectrum after RT is returned)

  • indices – Spectra to consider (if empty, all spectra are considered)

Returns

The indices of the spectra within RT +/- deltaRT

readChromatograms()

Cython signature: void readChromatograms(libcpp_vector[MSChromatogram] & exp, libcpp_vector[int] indices, bool meta_only)

Parameters

  • exp – The result data structure

  • indices – A list of indices restricting the resulting spectra only to those specified here

  • meta_only – Only read the meta data

readExperiment()

Cython signature: void readExperiment(MSExperiment & exp, bool meta_only)

Parameters

  • exp – The result data structure

  • meta_only – Only read the meta data

readSpectra()

Cython signature: void readSpectra(libcpp_vector[MSSpectrum] & exp, libcpp_vector[int] indices, bool meta_only)

Parameters

  • exp – The result data structure

  • indices – A list of indices restricting the resulting spectra only to those specified here

  • meta_only – Only read the meta data

setConfig()

Cython signature: void setConfig(bool write_full_meta, bool use_lossy_compression, double linear_abs_mass_acc)

Parameters

  • write_full_meta – Whether to write a complete mzML meta data structure into the RUN_EXTRA field (allows complete recovery of the input file)

  • use_lossy_compression – Whether to use lossy compression (ms numpress)

  • linear_abs_mass_acc – Accepted loss in mass accuracy (absolute m/z, in Th)

writeChromatograms()

Cython signature: void writeChromatograms(libcpp_vector[MSChromatogram] chroms) Writes a set of chromatograms to disk

writeExperiment()

Cython signature: void writeExperiment(MSExperiment exp) Write an MSExperiment to disk

writeRunLevelInformation()

Cython signature: void writeRunLevelInformation(MSExperiment exp, bool write_full_meta)

Parameters

  • exp – The result data structure

  • meta_only – Only read the meta data

writeSpectra()

Cython signature: void writeSpectra(libcpp_vector[MSSpectrum] spectra) Writes a set of spectra to disk