OpenMS
OpenSwathWorkflowSonar Member List

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

addChromatograms(OpenSwath::ChromatogramPtr base_chrom, OpenSwath::ChromatogramPtr newchrom)OpenSwathWorkflowSonar
CMD enum valueProgressLogger
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)OpenSwathWorkflowprotected
current_logger_ProgressLoggermutableprotected
endProgress() constProgressLogger
getLogType() constProgressLogger
GUI enum valueProgressLogger
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
MRMTransitionGroupType typedefOpenSwathWorkflowprivate
ms1_map_OpenSwathWorkflowBaseprotected
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 ms1only=false, int ms1_isotopes=0)OpenSwathWorkflowBaseprotected
nextProgress() constProgressLogger
NONE enum valueProgressLogger
OpenSwathWorkflow(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop)OpenSwathWorkflowinline
OpenSwathWorkflowBase()OpenSwathWorkflowBaseinlineprotected
OpenSwathWorkflowBase(bool use_ms1_traces, bool use_ms1_ion_mobility, bool prm, bool pasef, int threads_outer_loop)OpenSwathWorkflowBaseinlineprotected
OpenSwathWorkflowSonar(bool use_ms1_traces)OpenSwathWorkflowSonarinlineexplicit
operator=(const ProgressLogger &other)ProgressLogger
pasef_OpenSwathWorkflowBaseprotected
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
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) constOpenSwathWorkflowBaseprotected
prm_OpenSwathWorkflowBaseprotected
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
recursion_depth_ProgressLoggerprotectedstatic
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) constOpenSwathWorkflowprotected
selectCompoundsForBatch_(const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t batch_idx)OpenSwathWorkflowprotected
setLogType(LogType type) constProgressLogger
setProgress(SignedSize value) constProgressLogger
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
threads_outer_loop_OpenSwathWorkflowBaseprotected
TransitionType typedefOpenSwathWorkflowprivate
type_ProgressLoggermutableprotected
use_ms1_ion_mobility_OpenSwathWorkflowBaseprotected
use_ms1_traces_OpenSwathWorkflowBaseprotected
writeOutFeaturesAndChroms_(std::vector< OpenMS::MSChromatogram > &chromatograms, std::vector< MSChromatogram > &ms1_chromatograms, const FeatureMap &featureFile, FeatureMap &out_featureFile, bool store_features, Interfaces::IMSDataConsumer *chromConsumer)OpenSwathWorkflowprotected
~ProgressLogger()ProgressLoggervirtual