| OpenMS 2.5.0

OpenSwathWorkflow Member List

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

CMD enum value | ProgressLogger |
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 | mutable protected
endProgress() const | ProgressLogger |
getLogType() const | ProgressLogger |
GUI enum value | ProgressLogger |
last_invoke_ | ProgressLogger | mutable protected
LogType enum name | ProgressLogger |
logTypeToFactoryName_(LogType type) | ProgressLogger | protected static
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, Interfaces::IMSDataConsumer *chromConsumer, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool ms1only=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, int threads_outer_loop) | OpenSwathWorkflow | inline
OpenSwathWorkflowBase() | OpenSwathWorkflowBase | inline protected
OpenSwathWorkflowBase(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, int threads_outer_loop) | OpenSwathWorkflowBase | inline protected
operator=(const ProgressLogger &other) | ProgressLogger |
performExtraction(const std::vector< OpenSwath::SwathMap > &swath_maps, const TransformationDescription 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 |
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 | protected static
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, 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
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 | mutable protected
use_ms1_ion_mobility_ | OpenSwathWorkflowBase | protected
use_ms1_traces_ | OpenSwathWorkflowBase | protected
writeOutFeaturesAndChroms_(std::vector< OpenMS::MSChromatogram > &chromatograms, const FeatureMap &featureFile, FeatureMap &out_featureFile, bool store_features, Interfaces::IMSDataConsumer *chromConsumer) | OpenSwathWorkflow | protected
~ProgressLogger() | ProgressLogger |