OpenMS
FLASHDeconvAlgorithm Member List

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

appendDecoyPeakGroups_(DeconvolvedSpectrum &deconvolved_spectrum, const MSSpectrum &spec, int scan_number, const PeakGroup &precursor_pg)FLASHDeconvAlgorithmprivate
check_defaults_DefaultParamHandlerprotected
CMD enum valueProgressLogger
collectSurveyScans_(const std::vector< DeconvolvedSpectrum > &deconvolved_spectra, int b_scan_number, int a_scan_number, uint ms_level) constFLASHDeconvAlgorithmprivate
current_logger_ProgressLoggermutableprotected
current_max_ms_level_FLASHDeconvAlgorithmprivate
current_min_ms_level_FLASHDeconvAlgorithmprivate
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
determineTolerance_(const MSExperiment &map, const Param &sd_param, const FLASHHelperClasses::PrecalculatedAveragine &avg, uint ms_level)FLASHDeconvAlgorithmprivate
endProgress(UInt64 bytes_processed=0) constProgressLogger
error_name_DefaultParamHandlerprotected
filterLowPeaks_(MSExperiment &map)FLASHDeconvAlgorithmprivatestatic
findBestPrecursorPeakGroup_(const std::vector< DeconvolvedSpectrum > &survey_scans, double start_mz, double end_mz) constFLASHDeconvAlgorithmprivate
findPrecursorPeakGroupsFormIdaLog_(const MSExperiment &map, Size index, double start_mz, double end_mz)FLASHDeconvAlgorithmprivate
findPrecursorPeakGroupsForMSnSpectra_(const MSExperiment &map, const std::vector< DeconvolvedSpectrum > &deconvolved_spectra, uint ms_level)FLASHDeconvAlgorithmprivate
findPrecursorScanNumber_(const MSExperiment &map, Size index, uint ms_level) constFLASHDeconvAlgorithmprivate
findScanNumberBounds_(const MSExperiment &map, Size index, uint ms_level) constFLASHDeconvAlgorithmprivate
FLASHDeconvAlgorithm()FLASHDeconvAlgorithm
FLASHDeconvAlgorithm(const FLASHDeconvAlgorithm &)=defaultFLASHDeconvAlgorithm
FLASHDeconvAlgorithm(FLASHDeconvAlgorithm &&other) noexcept=defaultFLASHDeconvAlgorithm
forced_ms_level_FLASHDeconvAlgorithmprivate
getAveragine()FLASHDeconvAlgorithm
getDecoyAveragine()FLASHDeconvAlgorithm
getDefaults() constDefaultParamHandler
getHistogram_(const std::vector< double > &data, double min_range, double max_range, double bin_size)FLASHDeconvAlgorithmprivatestatic
getIsolationWindowMzRange_(const MSSpectrum &spec) constFLASHDeconvAlgorithmprivate
getLogType() constProgressLogger
getName() constDefaultParamHandler
getNoiseDecoyWeight() constFLASHDeconvAlgorithminline
getParameters() constDefaultParamHandler
getScanNumber(const MSExperiment &map, Size index)FLASHDeconvAlgorithmstatic
getSubsections() constDefaultParamHandler
getTolerances() constFLASHDeconvAlgorithm
GUI enum valueProgressLogger
ida_log_file_FLASHDeconvAlgorithmprivate
isolation_window_size_FLASHDeconvAlgorithmprivate
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
max_ms_level_FLASHDeconvAlgorithmprivate
merge_spec_FLASHDeconvAlgorithmprivate
mergeSpectra_(MSExperiment &map, uint ms_level)FLASHDeconvAlgorithmprivate
min_cos_FLASHDeconvAlgorithmprivate
native_id_precursor_peak_group_map_FLASHDeconvAlgorithmprivate
nextProgress() constProgressLogger
noise_decoy_weight_FLASHDeconvAlgorithmprivate
NONE enum valueProgressLogger
operator=(const FLASHDeconvAlgorithm &fd)=defaultFLASHDeconvAlgorithm
operator=(FLASHDeconvAlgorithm &&fd)=defaultFLASHDeconvAlgorithm
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs)DefaultParamHandler
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)ProgressLogger
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
precursor_map_for_ida_FLASHDeconvAlgorithmprivate
precursor_MS1_window_FLASHDeconvAlgorithmprivate
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
recursion_depth_ProgressLoggerprotectedstatic
report_decoy_FLASHDeconvAlgorithmprivate
run(MSExperiment &map, std::vector< DeconvolvedSpectrum > &deconvolved_spectra, std::vector< FLASHHelperClasses::MassFeature > &deconvolved_feature)FLASHDeconvAlgorithm
runFeatureFinding_(std::vector< DeconvolvedSpectrum > &deconvolved_spectra, std::vector< FLASHHelperClasses::MassFeature > &deconvolved_features)FLASHDeconvAlgorithmprivate
runSpectralDeconvolution_(MSExperiment &map, std::vector< DeconvolvedSpectrum > &deconvolved_spectra)FLASHDeconvAlgorithmprivate
sd_FLASHDeconvAlgorithmprivate
sd_noise_decoy_FLASHDeconvAlgorithmprivate
sd_signal_decoy_FLASHDeconvAlgorithmprivate
setLogger(ProgressLoggerImpl *logger)ProgressLogger
setLogType(LogType type) constProgressLogger
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setProgress(SignedSize value) constProgressLogger
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
subsections_DefaultParamHandlerprotected
tols_FLASHDeconvAlgorithmprivate
type_ProgressLoggermutableprotected
updateMembers_() overrideFLASHDeconvAlgorithmprotectedvirtual
updateMSLevels_(MSExperiment &map)FLASHDeconvAlgorithmprivate
updatePrecursorQScores_(std::vector< DeconvolvedSpectrum > &deconvolved_spectra, int ms_level)FLASHDeconvAlgorithmprivatestatic
use_RNA_averagine_FLASHDeconvAlgorithmprivate
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~FLASHDeconvAlgorithm() override=defaultFLASHDeconvAlgorithm
~ProgressLogger()ProgressLoggervirtual