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OpenSwathWorkflow Member List

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

computeBinnedCoverage(const std::pair< double, double > &rtRange, const std::vector< std::pair< double, double > > &pairs, int nrBins, int minPeptidesPerBin, int minBinsFilled)OpenSwathWorkflowinlineprivate
copyBatchTransitions_(const std::vector< OpenSwath::LightCompound > &used_compounds, const std::vector< OpenSwath::LightTransition > &all_transitions, std::vector< OpenSwath::LightTransition > &output)OpenSwathWorkflowinlineprivate
ms1_map_OpenSwathWorkflowprivate
OpenSwathWorkflow(bool use_ms1_traces)OpenSwathWorkflowinlineexplicit
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, bool load_into_memory)OpenSwathWorkflowinline
performRTNormalization(const OpenMS::TargetedExperiment &irt_transitions, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const String &mz_correction_function, 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) constOpenSwathWorkflowinlineprivate
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) constOpenSwathWorkflowinlineprivate
RTNormalization(TargetedExperiment transition_exp_, std::vector< OpenMS::MSChromatogram<> > chromatograms, double min_rsq, double min_coverage, Param feature_finder_param, const Param &irt_detection_param, std::vector< OpenSwath::SwathMap > &swath_maps, const String &mz_correction_function)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
selectCompoundsForBatch_(const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t j)OpenSwathWorkflowinlineprivate
simpleExtractChromatograms(const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenMS::TargetedExperiment &irt_transitions, std::vector< OpenMS::MSChromatogram<> > &chromatograms, const ChromExtractParams &cp)OpenSwathWorkflowinlineprivate
use_ms1_traces_OpenSwathWorkflowprivate

OpenMS / TOPP release 2.1.0 Documentation generated on Tue Jul 11 2017 14:38:46 using doxygen 1.8.13