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OpenSwathWorkflow Member List

This is the complete list of members for OpenSwathWorkflow, including all inherited members.

CMD enum valueProgressLogger
copyBatchTransitions_(const std::vector< OpenSwath::LightPeptide > &used_peptides, const std::vector< OpenSwath::LightTransition > &all_transitions, std::vector< OpenSwath::LightTransition > &output)OpenSwathWorkflowinlineprivate
current_logger_ProgressLoggermutableprotected
endProgress() const ProgressLogger
getLogType() const ProgressLogger
GUI enum valueProgressLogger
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
ms1_map_OpenSwathWorkflowprivate
NONE enum valueProgressLogger
OpenSwathWorkflow(bool use_ms1_traces)OpenSwathWorkflowinlineexplicit
operator=(const ProgressLogger &other)ProgressLogger
performExtraction(const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription trafo, const ChromExtractParams &cp, const Param &feature_finder_param, const OpenSwath::LightTargetedExperiment &transition_exp, FeatureMap &out_featureFile, bool store_features, OpenSwathTSVWriter &tsv_writer, Interfaces::IMSDataConsumer<> *chromConsumer, int batchSize)OpenSwathWorkflowinline
performRTNormalization(const OpenMS::TargetedExperiment &irt_transitions, const std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &feature_finder_param, const ChromExtractParams &cp_irt, Size debug_level)OpenSwathWorkflowinline
prepare_coordinates(std::vector< OpenSwath::ChromatogramPtr > &output_chromatograms, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, OpenSwath::LightTargetedExperiment &transition_exp_used, const double rt_extraction_window, const bool ms1) const OpenSwathWorkflowinlineprivate
prepare_coordinates_wrap(std::vector< OpenSwath::ChromatogramPtr > &chrom_list, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, OpenSwath::LightTargetedExperiment &transition_exp_used, const bool ms1, const TransformationDescription trafo_inverse, const ChromExtractParams &cp) const OpenSwathWorkflowinlineprivate
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
recursion_depth_ProgressLoggerprotectedstatic
RTNormalization(TargetedExperiment transition_exp_, std::vector< OpenMS::MSChromatogram<> > chromatograms, double min_rsq, double min_coverage, Param feature_finder_param)OpenSwathWorkflowinlineprivate
scoreAllChromatograms(const OpenSwath::SpectrumAccessPtr input, const OpenSwath::SpectrumAccessPtr swath_map, OpenSwath::LightTargetedExperiment &transition_exp, const Param &feature_finder_param, TransformationDescription trafo, const double rt_extraction_window, FeatureMap &output, OpenSwathTSVWriter &tsv_writer, std::map< std::string, OpenSwath::ChromatogramPtr > &ms1_chromatograms)OpenSwathWorkflowinlineprivate
selectChrom_(const MSChromatogram< ChromatogramPeak > &chromatogram_old, MSSpectrum< ChromatogramPeak > &chromatogram, double rt_extraction_window, double center_rt)OpenSwathWorkflowinlineprivate
selectPeptidesForBatch_(const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t j)OpenSwathWorkflowinlineprivate
setLogType(LogType type) const ProgressLogger
setProgress(SignedSize value) const ProgressLogger
simpleExtractChromatograms(const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenMS::TargetedExperiment &irt_transitions, std::vector< OpenMS::MSChromatogram<> > &chromatograms, const ChromExtractParams &cp)OpenSwathWorkflowinlineprivate
startProgress(SignedSize begin, SignedSize end, const String &label) const ProgressLogger
type_ProgressLoggermutableprotected
use_ms1_traces_OpenSwathWorkflowprivate
~ProgressLogger()ProgressLogger

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:41 using doxygen 1.8.9.1