computeBinnedCoverage(const std::pair< double, double > &rtRange, const std::vector< std::pair< double, double > > &pairs, int nrBins, int minPeptidesPerBin, int minBinsFilled) | OpenSwathWorkflow | inlineprivate |
copyBatchTransitions_(const std::vector< OpenSwath::LightCompound > &used_compounds, const std::vector< OpenSwath::LightTransition > &all_transitions, std::vector< OpenSwath::LightTransition > &output) | OpenSwathWorkflow | inlineprivate |
ms1_map_ | OpenSwathWorkflow | private |
OpenSwathWorkflow(bool use_ms1_traces) | OpenSwathWorkflow | inlineexplicit |
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) | OpenSwathWorkflow | inline |
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) | OpenSwathWorkflow | inline |
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 | OpenSwathWorkflow | inlineprivate |
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 | OpenSwathWorkflow | inlineprivate |
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) | OpenSwathWorkflow | inlineprivate |
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) | OpenSwathWorkflow | inlineprivate |
selectChrom_(const MSChromatogram< ChromatogramPeak > &chromatogram_old, MSSpectrum< ChromatogramPeak > &chromatogram, double rt_extraction_window, double center_rt) | OpenSwathWorkflow | inlineprivate |
selectCompoundsForBatch_(const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t j) | OpenSwathWorkflow | inlineprivate |
simpleExtractChromatograms(const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenMS::TargetedExperiment &irt_transitions, std::vector< OpenMS::MSChromatogram<> > &chromatograms, const ChromExtractParams &cp) | OpenSwathWorkflow | inlineprivate |
use_ms1_traces_ | OpenSwathWorkflow | private |