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OpenMS
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This is the complete list of members for OpenSwathWorkflowSonar, including all inherited members.
| addChromatograms(OpenSwath::ChromatogramPtr base_chrom, OpenSwath::ChromatogramPtr newchrom) | OpenSwathWorkflowSonar | |
| CMD enum value | ProgressLogger | |
| computeSonarWindows_(const std::vector< OpenSwath::SwathMap > &swath_maps, double &sonar_winsize, double &sonar_start, double &sonar_end, int &sonar_total_win) | OpenSwathWorkflowSonar | |
| copyBatchTransitions_(const std::vector< OpenSwath::LightCompound > &used_compounds, const std::vector< OpenSwath::LightTransition > &all_transitions, std::vector< OpenSwath::LightTransition > &output) | OpenSwathWorkflow | protected |
| current_logger_ | ProgressLogger | mutableprotected |
| endProgress(UInt64 bytes_processed=0) const | ProgressLogger | |
| getLogType() const | ProgressLogger | |
| GUI enum value | ProgressLogger | |
| last_invoke_ | ProgressLogger | mutableprotected |
| LogType enum name | ProgressLogger | |
| MRMTransitionGroupType typedef | OpenSwathWorkflow | private |
| ms1_map_ | OpenSwathWorkflowBase | protected |
| MS1Extraction_(const OpenSwath::SpectrumAccessPtr &ms1_map, const std::vector< OpenSwath::SwathMap > &swath_maps, std::vector< MSChromatogram > &ms1_chromatograms, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool ms1_only=false, int ms1_isotopes=0) | OpenSwathWorkflowBase | protected |
| nextProgress() const | ProgressLogger | |
| NONE enum value | ProgressLogger | |
| OpenSwathWorkflow(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop) | OpenSwathWorkflow | inline |
| OpenSwathWorkflowBase() | OpenSwathWorkflowBase | inlineprotected |
| OpenSwathWorkflowBase(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop) | OpenSwathWorkflowBase | inlineprotected |
| OpenSwathWorkflowSonar(bool use_ms1_traces) | OpenSwathWorkflowSonar | inlineexplicit |
| operator=(const ProgressLogger &other) | ProgressLogger | |
| pasef_ | OpenSwathWorkflowBase | protected |
| performExtraction(const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription &rt_trafo, const ChromExtractParams &chromatogram_extraction_params, const ChromExtractParams &ms1_chromatogram_extraction_params, const Param &feature_finder_param, const OpenSwath::LightTargetedExperiment &assay_library, FeatureMap &result_featureFile, bool store_features_in_featureFile, OpenSwathTSVWriter &result_tsv, OpenSwathOSWWriter &result_osw, Interfaces::IMSDataConsumer *result_chromatograms, int batchSize, int ms1_isotopes, bool load_into_memory) | OpenSwathWorkflow | |
| performExtractionSonar(const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription &trafo, const ChromExtractParams &cp, const ChromExtractParams &cp_ms1, const Param &feature_finder_param, const OpenSwath::LightTargetedExperiment &transition_exp, FeatureMap &out_featureFile, bool store_features, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, Interfaces::IMSDataConsumer *chromConsumer, int batchSize, bool load_into_memory) | OpenSwathWorkflowSonar | |
| performSonarExtraction_(const std::vector< OpenSwath::SwathMap > &used_maps, const std::vector< ChromatogramExtractor::ExtractionCoordinates > &coordinates, std::vector< OpenSwath::ChromatogramPtr > &chrom_list, const ChromExtractParams &cp) | OpenSwathWorkflowSonar | |
| prepareExtractionCoordinates_(std::vector< OpenSwath::ChromatogramPtr > &chrom_list, std::vector< ChromatogramExtractorAlgorithm::ExtractionCoordinates > &coordinates, const OpenSwath::LightTargetedExperiment &transition_exp_used, const TransformationDescription &trafo_inverse, const ChromExtractParams &cp, const bool ms1=false, const int ms1_isotopes=-1) const | OpenSwathWorkflowBase | protected |
| prm_ | OpenSwathWorkflowBase | protected |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| scoreAllChromatograms_(const std::vector< OpenMS::MSChromatogram > &ms2_chromatograms, const std::vector< OpenMS::MSChromatogram > &ms1_chromatograms, const std::vector< OpenSwath::SwathMap > &swath_maps, const OpenSwath::LightTargetedExperiment &transition_exp, const Param &feature_finder_param, const TransformationDescription &trafo, const double rt_extraction_window, FeatureMap &output, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, int nr_ms1_isotopes=0, bool ms1only=false) const | OpenSwathWorkflow | protected |
| selectCompoundsForBatch_(const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t batch_idx) | OpenSwathWorkflow | protected |
| setLogger(ProgressLoggerImpl *logger) | ProgressLogger | |
| setLogType(LogType type) const | ProgressLogger | |
| setProgress(SignedSize value) const | ProgressLogger | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| threads_outer_loop_ | OpenSwathWorkflowBase | protected |
| TransitionType typedef | OpenSwathWorkflow | private |
| type_ | ProgressLogger | mutableprotected |
| use_ms1_ion_mobility_ | OpenSwathWorkflowBase | protected |
| use_ms1_traces_ | OpenSwathWorkflowBase | protected |
| writeOutFeaturesAndChroms_(std::vector< OpenMS::MSChromatogram > &chromatograms, std::vector< MSChromatogram > &ms1_chromatograms, const FeatureMap &featureFile, FeatureMap &out_featureFile, bool store_features, Interfaces::IMSDataConsumer *chromConsumer) | OpenSwathWorkflow | protected |
| ~ProgressLogger() | ProgressLogger | virtual |
1.9.1 
