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 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() const	ProgressLogger
getLogType() const	ProgressLogger
GUI enum value	ProgressLogger
last_invoke_	ProgressLogger	mutableprotected
LogType enum name	ProgressLogger
logTypeToFactoryName_(LogType type)	ProgressLogger	protectedstatic
ms1_map_	OpenSwathWorkflowBase	protected
MS1Extraction_(const std::vector< OpenSwath::SwathMap > &swath_maps, std::map< std::string, OpenSwath::ChromatogramPtr > &ms1_chromatograms, Interfaces::IMSDataConsumer *chromConsumer, const ChromExtractParams &cp, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo_inverse, bool load_into_memory, bool ms1only=false)	OpenSwathWorkflowBase	protected
nextProgress() const	ProgressLogger
NONE enum value	ProgressLogger
OpenSwathWorkflow(bool use_ms1_traces)	OpenSwathWorkflow	inlineexplicit
OpenSwathWorkflowBase(bool use_ms1_traces)	OpenSwathWorkflowBase	inlineexplicitprotected
OpenSwathWorkflowSonar(bool use_ms1_traces)	OpenSwathWorkflowSonar	inlineexplicit
operator=(const ProgressLogger &other)	ProgressLogger
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, OpenSwathOSWWriter &osw_writer, Interfaces::IMSDataConsumer *chromConsumer, int batchSize, bool load_into_memory)	OpenSwathWorkflow
performExtractionSonar(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, 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 bool ms1, const TransformationDescription trafo_inverse, const ChromExtractParams &cp) const	OpenSwathWorkflowBase	protected
ProgressLogger()	ProgressLogger
ProgressLogger(const ProgressLogger &other)	ProgressLogger
recursion_depth_	ProgressLogger	protectedstatic
scoreAllChromatograms(const OpenSwath::SpectrumAccessPtr input, const std::map< std::string, OpenSwath::ChromatogramPtr > &ms1_chromatograms, const std::vector< OpenSwath::SwathMap > &swath_maps, OpenSwath::LightTargetedExperiment &transition_exp, const Param &feature_finder_param, TransformationDescription trafo, const double rt_extraction_window, FeatureMap &output, OpenSwathTSVWriter &tsv_writer, OpenSwathOSWWriter &osw_writer, bool ms1only=false)	OpenSwathWorkflow	protected
selectCompoundsForBatch_(const OpenSwath::LightTargetedExperiment &transition_exp_used_all, OpenSwath::LightTargetedExperiment &transition_exp_used, int batch_size, size_t j)	OpenSwathWorkflow	protected
setLogType(LogType type) const	ProgressLogger
setProgress(SignedSize value) const	ProgressLogger
startProgress(SignedSize begin, SignedSize end, const String &label) const	ProgressLogger
type_	ProgressLogger	mutableprotected
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