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OpenMS
2.5.0
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Go to the documentation of this file.
103 void readExperiment(
MSExperiment & exp,
bool meta_only =
false)
const;
112 void readSpectra(std::vector<MSSpectrum> & exp,
const std::vector<int> & indices,
bool meta_only =
false)
const;
121 void readChromatograms(std::vector<MSChromatogram> & exp,
const std::vector<int> & indices,
bool meta_only =
false)
const;
128 Size getNrSpectra()
const;
135 Size getNrChromatograms()
const;
145 void setConfig(
bool write_full_meta,
bool use_lossy_compression,
double linear_abs_mass_acc,
int sql_batch_size = 500)
147 write_full_meta_ = write_full_meta;
148 use_lossy_compression_ = use_lossy_compression;
149 linear_abs_mass_acc_ = linear_abs_mass_acc;
150 sql_batch_size_ = sql_batch_size;
161 std::vector<size_t> getSpectraIndicesbyRT(
double RT,
double deltaRT,
const std::vector<int> & indices)
const;
165 void populateChromatogramsWithData_(sqlite3 *db, std::vector<MSChromatogram>& chromatograms)
const;
167 void populateChromatogramsWithData_(sqlite3 *db, std::vector<MSChromatogram>& chromatograms,
const std::vector<int> & indices)
const;
169 void populateSpectraWithData_(sqlite3 *db, std::vector<MSSpectrum>& spectra)
const;
171 void populateSpectraWithData_(sqlite3 *db, std::vector<MSSpectrum>& spectra,
const std::vector<int> & indices)
const;
173 void prepareChroms_(sqlite3 *db, std::vector<MSChromatogram>& chromatograms,
const std::vector<int> & indices = {})
const;
175 void prepareSpectra_(sqlite3 *db, std::vector<MSSpectrum>& spectra,
const std::vector<int> & indices = {})
const;
193 void writeExperiment(
const MSExperiment & exp);
211 void writeSpectra(
const std::vector<MSSpectrum>& spectra);
218 void writeChromatograms(
const std::vector<MSChromatogram>& chroms);
228 void writeRunLevelInformation(
const MSExperiment & exp,
bool write_full_meta,
int run_id);
232 void createIndices_();
Base class for TOPP applications.
Definition: TOPPBase.h:144
String filename_
Definition: MzMLSqliteHandler.h:235
void reserveSpaceChromatograms(Size s)
Sqlite handler for storing spectra and chromatograms in sqMass format.
Definition: MzMLSqliteHandler.h:77
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:58
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static String removeExtension(const String &file)
double linear_abs_mass_acc_
Definition: MzMLSqliteHandler.h:250
void reserveSpaceSpectra(Size s)
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void addSpectrum(const MSSpectrum &spectrum)
adds a spectrum to the list
const std::vector< MSChromatogram > & getChromatograms() const
returns the chromatogram list
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
Int run_id_
Definition: MzMLSqliteHandler.h:247
void setConfig(bool write_full_meta, bool use_lossy_compression, double linear_abs_mass_acc, int sql_batch_size=500)
Set file configuration.
Definition: MzMLSqliteHandler.h:145
Int spec_id_
Definition: MzMLSqliteHandler.h:245
QString toQString() const
Conversion to Qt QString.
Int chrom_id_
Definition: MzMLSqliteHandler.h:246
double write_full_meta_
Definition: MzMLSqliteHandler.h:251
void addChromatogram(const MSChromatogram &chromatogram)
adds a chromatogram to the list
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
bool use_lossy_compression_
Definition: MzMLSqliteHandler.h:249
const std::vector< MSSpectrum > & getSpectra() const
returns the spectrum list
int sql_batch_size_
Definition: MzMLSqliteHandler.h:252
Data filtering or extraction.
Definition: DataProcessing.h:71