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OpenMS
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This is the complete list of members for CalibrationWorkflow, including all inherited members.
| applyEstimatedWindows_(const CalibrationResult &result, ChromExtractParams &cp, ChromExtractParams &cp_ms1, bool pasef, bool use_ms1_im) const | CalibrationWorkflow | private |
| applyWindow_(const char *label, double estimate, double &dst_param, double user_value, bool applicable=true, bool commit=true) const | CalibrationWorkflow | private |
| auto_irt_enabled_ | CalibrationWorkflow | private |
| auto_irt_irt_bins_ | CalibrationWorkflow | private |
| auto_irt_irt_bins_nonlinear_ | CalibrationWorkflow | private |
| auto_irt_irt_peptides_per_bin_ | CalibrationWorkflow | private |
| auto_irt_irt_peptides_per_bin_nonlinear_ | CalibrationWorkflow | private |
| auto_irt_irt_seed_ | CalibrationWorkflow | private |
| auto_irt_linear_top_fraction_ | CalibrationWorkflow | private |
| auto_irt_nonlinear_top_fraction_ | CalibrationWorkflow | private |
| CalibrationWorkflow() | CalibrationWorkflow | |
| check_defaults_ | DefaultParamHandler | protected |
| CMD enum value | ProgressLogger | |
| current_logger_ | ProgressLogger | mutableprotected |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| determineIrtStrategy(const OpenSwath::LightTargetedExperiment &full_transition_exp, size_t num_runs=1) const | CalibrationWorkflow | |
| doDataNormalization_(const OpenSwath::LightTargetedExperiment &targeted_exp, const std::vector< OpenMS::MSChromatogram > &chromatograms, TransformationDescription &im_trafo, std::vector< OpenSwath::SwathMap > &swath_maps, double min_rsq, double min_coverage, const Param &default_ffparam, const Param &irt_detection_param, const Param &calibration_param, const bool pasef) | CalibrationWorkflow | |
| endProgress(UInt64 bytes_processed=0) const | ProgressLogger | |
| error_name_ | DefaultParamHandler | protected |
| estimated_im_window_ | CalibrationWorkflow | private |
| estimated_ms1_im_window_ | CalibrationWorkflow | private |
| estimated_ms1_mz_window_ | CalibrationWorkflow | private |
| estimated_mz_window_ | CalibrationWorkflow | private |
| getDefaults() const | DefaultParamHandler | |
| getEstimatedImWindow() const | CalibrationWorkflow | inline |
| getEstimatedMs1ImWindow() const | CalibrationWorkflow | inline |
| getEstimatedMs1MzWindow() const | CalibrationWorkflow | inline |
| getEstimatedMzWindow() const | CalibrationWorkflow | inline |
| getLogType() const | ProgressLogger | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| GUI enum value | ProgressLogger | |
| isValidWindow_(double v, double min_positive=1e-9) const noexcept | CalibrationWorkflow | inlineprivate |
| last_invoke_ | ProgressLogger | mutableprotected |
| linear_irt_file_ | CalibrationWorkflow | private |
| linear_irt_files_list_ | CalibrationWorkflow | private |
| linear_outlier_detection_ | CalibrationWorkflow | private |
| loadIrtExperimentFromFile_(const String &irt_file_path, const String &label) const | CalibrationWorkflow | |
| LogType enum name | ProgressLogger | |
| min_coverage_ | CalibrationWorkflow | private |
| min_rsq_ | CalibrationWorkflow | private |
| nextProgress() const | ProgressLogger | |
| NONE enum value | ProgressLogger | |
| nonlinear_irt_file_ | CalibrationWorkflow | private |
| nonlinear_irt_files_list_ | CalibrationWorkflow | private |
| nonlinear_outlier_detection_ | CalibrationWorkflow | private |
| OpenMS::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| performCalibration(std::vector< OpenSwath::SwathMap > &swath_maps, OpenSwath::LightTargetedExperiment &transition_exp, ChromExtractParams &cp, ChromExtractParams &cp_ms1, const IrtExperiments &irt_experiments, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const Param &calibration_param, const Param &mrm_mapping_param, bool pasef=false, bool load_into_memory=false, const String &irt_trafo_out="", const String &irt_mzml_out="", Size debug_level=0) | CalibrationWorkflow | |
| performLinearCalibration_(std::vector< OpenSwath::SwathMap > &swath_maps, const IrtExperiments &irt_experiments, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const Param &calibration_param, const Param &mrm_mapping_param, bool pasef, bool load_into_memory, const String &irt_trafo_out, const String &irt_mzml_out, Size debug_level) | CalibrationWorkflow | private |
| performLinearThenNonlinearCalibration_(std::vector< OpenSwath::SwathMap > &swath_maps, const IrtExperiments &irt_experiments, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const Param &calibration_param, const Param &mrm_mapping_param, bool pasef, bool load_into_memory, const String &irt_trafo_out, const String &irt_mzml_out, Size debug_level) | CalibrationWorkflow | private |
| performRTNormalization(const OpenSwath::LightTargetedExperiment &irt_transitions, std::vector< OpenSwath::SwathMap > &swath_maps, TransformationDescription &im_trafo, double min_rsq, double min_coverage, const Param &feature_finder_param, const ChromExtractParams &cp_irt, const Param &irt_detection_param, const Param &calibration_param, const Param &mrm_mapping_param, const String &irt_mzml_out, Size debug_level, bool pasef=false, bool load_into_memory=false) | CalibrationWorkflow | |
| prepareIrtExperiments(IrtStrategy strategy, const OpenSwath::LightTargetedExperiment &full_transition_exp, const std::vector< String > &priority_peptides, size_t run_index=0, const IrtExperiments *cached_irts=nullptr) | CalibrationWorkflow | |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| rt_estimation_padding_factor_ | CalibrationWorkflow | private |
| setLogger(ProgressLoggerImpl *logger) | ProgressLogger | |
| setLogType(LogType type) const | ProgressLogger | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProgress(SignedSize value) const | ProgressLogger | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| subsections_ | DefaultParamHandler | protected |
| type_ | ProgressLogger | mutableprotected |
| updateMembers_() override | CalibrationWorkflow | privatevirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| windows_estimate_im_ | CalibrationWorkflow | private |
| windows_estimate_mz_ | CalibrationWorkflow | private |
| windows_estimate_rt_ | CalibrationWorkflow | private |
| windows_rt_percentile_ | CalibrationWorkflow | private |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") | DefaultParamHandler | static |
| ~CalibrationWorkflow() override | CalibrationWorkflow | |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~ProgressLogger() | ProgressLogger | virtual |
1.9.8 